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Irestedt, M., Batalha-Filho, H., Roselaar, C.S., Christidis, L. & Ericson, P.G.P. (in press) Contrasting phylogeographic signatures in two Australo-Papuan bowerbird species complexes (Aves: Ailuroedus). Zoologica Scripta.
The Australo-Papuan catbird genus Ailuroedus has a complex distribution and a contested taxonomy. Here we integrate phylogenetic analysis of DNA data and morphology to study the group's biogeography and to re-examine its taxonomy. We couple phylogeographic and abiotic data to examine differences between the major groups defined in our phylogenetic analysis. Our results are consistent with Ailuroedus catbirds being divided into two species complexes, one distributed in humid forests in the lowlands on New Guinea and another in comparably drier and colder forests mainly in mid-mountains on New Guinea and Australia. Vicariant events during the Pliocene are surmised to have been the major force in shaping the contemporary phylogeographical signature of this genus. Several previously suggested vicariant events, such as fragmentation of xeric forests in Australia and the uplift of the central mountain range on New Guinea, are reinforced as important Pliocene barriers for tropical forest taxa in this region. Interaction between Pleistocene climatic fluctuations and differences in habitat requirements may explain a higher and more recent population structures in the mid-mountain catbird complex and the lack of representatives from the lowland clade in the comparably drier Australia. Phylogeographical patterns in both catbird complexes, respectively, both comply and deviate from other lowland and mid-mountain taxa in the region. This highlights that taxon-specific properties, such as their historical spatial and ecological distributions, capacity to disperse and tolerance to habitat changes, affect the phylogeographical histories of organisms. Within both species complexes the genetic differentiation between several geographically isolated populations was found to exceed those commonly observed for avian sister species. As these genetically distinct taxa also were found to be morphological diagnosable we suggest a revised classification of the genus Ailuroedus, where we recognize three species within the lowland complex and seven species within the mid-mountain complex.

Li, X., Dong, F., Lei, F., Alström, P., Zhang, R., Ödeen, A., Fjeldså, J., Ericson, P.G.P., Zou F. & Yang, X. (in press). Shaped by uneven Pleistocene climate: mitochondrial phylogeographic pattern and population history of White Wagtail Motacilla alba (Aves: Passeriformes). Journal of Avian Biology.
We studied the phylogeography and population history of the White Wagtail Motacilla alba, which has a vast breeding range, covering areas with different Pleistocene climatic histories. The mitochondrial NADH dehydrogenase subunit II gene (ND2) and Control Region (CR) were analyzed for 273 individuals from 45 localities. Our data comprised all nine subspecies of White Wagtail. Four primary clades were inferred (M, N, SW and SE), with indications of M. grandis being nested within M. alba. The oldest split was between two haplotypes from the endemic Moroccan M. a. subpersonata (clade M) and the others, at 0.63–0.96 Mya; other divergences were at 0.31–0.38 Mya. The entire differentiation falls within the part of the Pleistocene characterized by Milankovitch cycles of large amplitudes and durations. Clade N was distributed across the northern Palearctic; clade SW in southwestern Asia plus the British Isles and was predicted by Ecological niche models (ENMs) to occur also in Central and South Europe; and clade SE was distributed in Central and East Asia. The deep divergence within M. a. subpersonata may reflect retention of ancestral haplotypes. Regional differences in historical climates have had different impacts on different populations: clade N expanded after the last glacial maximum (LGM), whereas milder Pleistocene climate of East Asia allowed clade SE a longer expansion time (since MIS 5); clade SW expanded over a similarly long time as clade SE, which is untypical for European species. ENMs supported these conclusions in that the northern part of the Eurasian continent was unsuitable during the LGM, whereas southern parts remained suitable. The recent divergences and poor structure in the mitochondrial tree contrasts strongly with the pronounced, well defined phenotypical differentiation, indicating extremely fast plumage divergence.

Sangster, G., Roselaar, C.S., Irestedt, M. & Ericson, P.G.P. 2016. Sillem’s Mountain Finch Leucosticte sillemi is a valid species of rosefinch (Fringillidae). Ibis, 184, pp. 184-189.
Sillem’s Mountain Finch Leucosticte sillemi was described in 1992 on the basis of an adult and an immature specimen collected in western Tibet in September 1929 but its taxonomic validity and phylogenetic position have been unclear. Based on phylogenetic analysis of mitochondrial DNA from the holotype, we show that L. sillemi is not a colour morph of L. brandti but represents a valid, overlooked species of rosefinch (Carpodacus) that has secondarily acquired a pale plumage convergent on that of Leucosticte. Sillem’s Mountain Finch is one of the least known species of birds and represents the only known species of rosefinch of which the males have lost all reddish plumage colouration. This species and its sister taxon, the Tibetan Rosefinch C. roborowskii, are likely the world’s highest-altitude sister-species pair of birds.

Alström, P., Jönsson, K.A., Fjeldså, J., Ödeen, A., Ericson, P.G.P. & Irestedt, M. 2015. Dramatic niche shifts and morphological change in two insular bird species. Royal Society Open Science, 2:140364.
Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has diverged mainly in plumage, which may be the result of selection for improved camouflage in its new arboreal niche, while selection pressures for other morphological changes have probably been weak owing to preadaptations for the novel niche. By contrast, we suggest that Amaurocichla's niche change has led to divergence in both structure and plumage.

Fuchs, J., Ericson, P.G.P., Bonillo, C., Couloux, A. & Pasquet, E. 2015. The complex phylogeography of the Indo‐Malayan Alophoixus bulbuls with the description of a putative new ring species complex. Molecular Ecology, 24, pp. 5460-5474.
The Indo-Malayan bioregion provided some of the most spectacular discoveries of new vertebrate species (e.g. saola, khanyou, bare-faced bulbul) over the last 25 years. Yet, very little is known about the processes that led to the current biodiversity in this region. We reconstructed the phylogeographic history of a group of closely related passerines, the Alophoixus bulbuls. These birds are continuously distributed in Indo-Malaya around the Thailand lowlands such their distribution resembles a ring. Our analyses revealed a single colonization event of the mainland from the Sundaland with sequential divergence of taxa from South West to North East characterized by significant gene flow between parapatric taxa, and reduced or ancient gene flow involving the two taxa at the extremities of the ring. We detected evidence of population expansion in two subspecies, including one that was involved in the closing of the ring. Hence, our analyses indicate that the diversification pattern of Alophoixus bulbuls fits a broken ring species model in which some lineages have been isolated from each other for some time before coming into secondary contact after population expansion. To our knowledge, the Alophoixus bulbuls represent the first case of a putative broken ring species complex in Indo-Malaya. We also discuss the implications of our results on our understanding of the biogeography in Indo-Malaya.

Qu, YH, Fu, J., Han, N., Zhao, H., Gao, B., Tian, S., Cheng, Y., Song, G., Ericson, P.G.P., Wang, D., Quan, Q., Jiang, Z., Li, R., Lei, F. & Zhang, Y. 2015. Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas. Scientific Reports 5: 14256.
Species that undertake altitudinal migrations are exposed to a considerable seasonal variation in oxygen levels and temperature. How they cope with this was studied in a population of grea tit (Parus major) that breeds at high elevations and winters at lower elevations in the eastern Himalayas. Comparison of population genomics of high altitudinal great tits and those living inlowlands revealed an accelerated genetic selection for carbohydrate energy metabolism (amino sugar, nucleotide sugar metabolism and insulin signaling pathways) and hypoxia response (PI3K-akt,mTOR and MAPK signaling pathways) in the high altitudinal population. The PI3K-akt, mTOR and MAPK pathways modulate the hypoxia-inducible factors, HIF-1α and VEGF protein expression thusindirectly regulate hypoxia induced angiogenesis, erythropoiesis and vasodilatation. The strategies observed in high altitudinal great tits differ from those described in a closely related species onthe Tibetan Plateau, the sedentary ground tit (Parus humilis). This species has enhanced selectio in lipid-specific metabolic pathways and hypoxia-inducible factor pathway (HIF-1). Comparative population genomics also revealed selection for larger body size in high altitudinal great tits.

Qu, Y., Song, G.,Gao, B., Quan, Q., Ericson, P.G.P. & Lei, F. 2015. The influence of geological events on the endemism of East Asian birds studied through comparative phylogeography. Journal of Biogeography, 42, pp. 177-192.
East Asia is known for its exceptionally high biological diversity and endemism. Various geological and climatic events during the Pliocene and Pleistocene have been invoked to explain this high endemism, and these processes have had different impacts on different organisms. Herein, we investigate the relative role of these historical processes in the genetic evidence for endemism of intraspecific lineages of two East Asian species: the grey-cheeked fulvetta (Alcippe morrisonia) and the red-headed tree babbler (Stachyridopsis ruficeps). We studied the genetic structure based on mitochondrial and nuclear DNA and evaluated the phylogeographical lineages using coalescent species tree approaches. The influences of different historical processes on diversification among phylogeographical lineages were analysed using coalescent models. We tested correlations between ecological divergence and phylogeographical splits. The genetic structure analysis and species tree estimation revealed three deeply divergent lineages within both species. One lineage is endemic to the mountains of Southwest China and the other to Taiwan. Coalescent simulations suggested that lineage diversification mostly occurred during the late Pliocene. Within this time frame, uplift of the mountains of Southwest China and formation of the island of Taiwan are geological events consistent with the geographical isolation and ecological niche divergence of these phylogeographical lineages. Our results suggest that the main driver of avian endemism in East Asia was the formation of new montane and island habitats following the uplift of the mountains of Southwest China and formation of the island of Taiwan in the Pliocene. However, the populations in the two regions were affected differently by the climatic oscillations during the Pleistocene. The mountains of Southwest China were climatically stable during glaciations, allowing populations to persist throughout the Pleistocene and maintain their genetic uniqueness. In contrast, glaciations resulted in lowered sea levels, allowing dispersal between the island of Taiwan and mainland China,  thus obscuring the genetic endemism of the Taiwanese populations. 

Batalha-Filho, H., Pessoa, R.O., Fabre, P.-H., Fjeldså, J., Irestedt, M., Ericson, P.G.P., Silveira, L.F. & Miyaki, C.Y. (in press) Phylogeny and historical biogeography of gnateaters (Passeriformes, Conopophagidae) in the South America forests. Molecular Phylogenetics and Evolution.We inferred the phylogenetic relationships, divergence time and biogeography of Conopophagidae (gnateaters) based on sequence data of mitochondrial genes (ND2, ND3 and cytb) and nuclear introns (TGFB2 and G3PDH) from 45 tissue samples (43 Conopophaga and 2 Pittasoma) representing all currently recognized species of the family and the majority of subspecies. Phylogenetic relationships were estimated by maximum likelihood and Bayesian inference. Divergence time estimates were obtained based on a Bayesian relaxed clock model. These chronograms were used to calculate diversification rates and reconstruct ancestral areas of the genus Conopophaga. The phylogenetic analyses support the reciprocal monophyly of the two genera, Conopophaga and Pittasoma. All species were monophyletic with the exception of C. lineata, as C. lineata cearae did not cluster with the other two C. lineata subspecies. Divergence time estimates for Conopophagidae uggested that diversification took place during the Neogene, and that the diversification rate within Conopophaga clade was highest in the late Miocene, followed by a slower diversification rate, suggesting a diversity-dependent pattern. Our analyses of the diversification of family Conopophagidae provided a scenario for evolution in Terra Firme forest across tropical South America. The spatiotemporal pattern suggests that Conopophaga originated in the Brazilian Shield and that a complex sequence of events possibly related to the Andean uplift and infilling of former sedimentation basins and erosion cycles shaped the current distribution and diversity of this genus.

Ericson, P.G.P., Klopfstein, S., Irestedt, M., Nguyen, J.M.T. & Nylander, J.A.A. 2014. Dating the diversification of the major lineages of Passeriformes (Aves). BMC Evolutionary Biology, 14:8.
The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% of all living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the late Cretaceous. However, previous molecular dating studies have relied heavily on the geological split between New Zealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thus be circular in their argument.
This study provides a time-scale for the evolution of the major clades of passerines using seven nuclear markers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealand split from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretations of the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that the diversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration for the New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals and leads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genes analyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines, which can be used as secondary calibration points in future molecular studies.
Our analysis, which takes recent paleontological and geological findings into account, provides the best estimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporal framework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, and adds to the growing support for a Cretaceous origin of Passeriformes.

Price, T.D., Hooper, D.M., Buchanan, C.D., Johansson, U.S., Tietze, D.T., Alström, P., Olsson, U., Ghosh-Harihar, M., Ishtiaq, F., Gupta, S.K., Martens, J., Harr, B., Singh, P. & Dhananjai Mohan, D. 2014. Niche filling slows the diversification of Himalayan songbirds. Nature, 509, pp. 222-225.
Speciation generally involves a three-step process - range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.

Qu, Y., Ericson, P.G.P., Quan, Q., Song, G., Zhang, R., Gao, B. & Lei, F. 2014. Long-term isolation and stability explain high genetic diversity in the Eastern Himalaya. Molecular Ecology, 23, pp. 705-720.
China’s Southwest Mountainous Region in Eastern Himalaya is a “biodiversity hotspot” of global interest for conservation. Yet little is known about what has driven this unique diversity. The dramatic topography of the Southwest Mountainous Region resulting from the tectonic uplift during the late Pliocene leads to dramatic ecological stratification, which creates physical barriers to migration and isolates organisms into different subregions and mountain systems. This agrees with the observation that the phylogeographic patterns found in four species of birds (Alcippe morrisonia, Stachyridopsis ruficeps, Parus monticolus and Aegithalos concinnus) distributed in this region are characterized by deep splits between lineages that coalesce between 0.8 and 2.1 Mya. Unlike other regions at this latitude, the Southwest Mountainous Region was largely unaffected by the Pleistocene glaciations. Genetically isolated populations of these birds could thus be maintained throughout the Pleistocene in these rather stable montane environments. In comparison, we found radically different phylogeographic patterns in populations of the same four species distributed in the adjacent lowland, the Central China region. This region has a distinctly different geological history with dramatic, climate-induced shifts in vegetation during the Pleistocene. Here we found a considerably less geographic structure in the genetic variation and a much younger coalescence time (0.3-0.9 Mya). We also found evidence of genetic bottlenecks during the glacial periods and gene flow during the interglacial expansions. We conclude that the high genetic diversity in the Southwest Mountainous Region results from a long-term in situ diversification within these evolutionary isolated and environment stable montane habitats.

Batalha-Filho, H., Irestedt, M., Fjeldså, J., Ericson, P.G.P., Silveira, L.F. & Miyaki, C.Y. 2013. Molecular systematics and evolution of the Synallaxis ruficapilla complex (Aves: Furnariidae) in the Atlantic Forest. Molecular Phylogenetics and Evolution, 67, pp. 86-94.
The Neotropical Synallaxis ruficapilla complex is endemic to the Atlantic Forest and is comprised of three species: S. ruficapilla, whitneyi, and S. infuscata. This group is closely related to the Synallaxis moesta complex that occurs in the Andes, Tepuis, and Guianan shield. Here we used mitochondrial and nuclear gene sequences to infer the phylogeny and the time of diversification of the S. ruficapilla and S. moesta complexes. We also included samples of an undescribed population of Synallaxis that resembles other populations of the S. ruficapilla complex. Our results showed that different geographical lineages within the S. ruficapilla complex are reciprocally monophyletic, but the northern form (S. infuscata) grouped with an Andean taxon. This suggests that at least two lineages of this group independently colonized the Atlantic Forest. Specimens of the undescribed population formed a monophyletic clade with deep divergence. Estimated diversification dates were within the late Pliocene to Pleistocene (2.75 - 0.16 million of years ago). This suggests that at this time there was a higher connectivity between habitats in the rugged landscapes of the circum-Amazonian bioregions. The observed Pleistocene diversification within the Atlantic Forest is congruent in space and time with studies of other co-distributed organisms, and may be associated with climate changes and tectonic activity during this period.

Bristol, R.M., Fabre, P.-H., Irestedt, M., Jønsson, K.A., Shah, N.J., Tatayah, V., Warren, B.H. & Groombridge, J.J. 2013. Molecular phylogeny of the Indian Ocean Terpsiphone paradise flycatchers: undetected evolutionary diversity revealed amongst island populations. Molecular Phylogenetics and Evolution, 67, pp. 336-347.
We construct a molecular phylogeny of Terpsiphone flycatchers of the Indian Ocean and use this to investigatetheir evolutionary relationships. A total of 4.4 kb of mitochondrial (cyt-b, ND3, ND2, control region) and nuclear (G3PDH, MC1R) sequence data were obtained from all species, sub-species and island population of the region. Colonisation of the western Indian Ocean has been within the last two million years and greatly postdates the formation of the older islands of the region. A minimum of two independent continent-island colonisation events must have taken place in order to explain the current distribution and phylogenetic placement of Terpsiphone in this region. While five well-diverged Indian Ocean clades are detected, th relationship between them is unclear. Short intermodal branches are indicative of rapid range expansion across the region, masking exact routes and chronology of colonisation The Indian Ocean Terpsiphone taxa fall into five well supported clades, two of which (the Seychelles paradise flycatcher and the Mascarene paradise flycatcher) correspond with currently recognised species whilst a further three (within the Madagascar paradise flycatcher) are not entirely predicted by taxonomy and are neither consistent with distance-based nor island age-based models of colonisation. We identify the four non-Mascarene clades as Evolutionarily Significant Units (ESUs), while the Mascaren paradise flycatcher contains two ESUs corresponding to the Mauritius and Réunion subspecies. All six ESUs are sufficiently diverged to be worthy of management as if they were separate species. This phylogenetic reconstruction highlights the importance of sub-specific molecular phylogenetic reconstructions in complex island archipelago settings in clarifying phylogenetic history and ESUs that may otherwise be overlooked and inadvertently lost. Our phylogenetic reconstruction has identified hidden ockets of evolutionary distinctiveness, which provide a valuable platform upon which to re-evaluate investment of conservation resources within the Terpsiphone flycatchers of the Indian Ocean.

Fuchs, J., Pons, J.-M., Liu, L., Ericson, P.G.P., Couloux, A. & Pasquet, E. 2013. A multi-locus phylogeny suggests an ancient hybridization event between Campephilus and melanerpine woodpeckers (Aves: Picidae). Molecular Phylogenetics and Evolution, 67, pp. 578-588.
The ever increasing number of analysed loci in phylogenetics has not only allowed resolution of some parts of the Tree of Life but has also highlighted parts of the tree where incongruent signals among loci were detected. Previous molecular studies suggested conflicting relationships for the New World genus Campephilus, being either associated to the Megapicini or Dendropocini. Yet, the limited number of analysed loci and the use of the concatenation approach to reconstruct the phylogeny prevented the disentanglement of lineage sorting and introgression as causal explanation of this topological conflict. We sequenced four mitochondrial, nine autosomal and three Z-linked loci and used a Bayesian method that incorporates population level processes into the phylogenetic framework to understand which process (lineage sorting of genetic polymorphism or hybridization/introgression) best explains this conflict. Our analyses revealed that the autosomal FGB intron-7 and to a lesser extent the Z-linked loci have a different phylogenetic history from the mitochondrial loci and some other nuclear loci we analysed. We suggest that this conflicting pattern is the result of introgression consecutive to a hybridization event at the time when members of the Campephilus and melanerpine (Melanerpes and Sphyrapicus) lineages colonized the New World. The case of Campephilus highlights that the mitochondrial genome does not always carry the ‘wrong´ phylogenetic signal after a past hybridization event. Indeed, we here emphasise that the signature of such event can also be detected in the nuclear genome. With the ongoing increase in the number of loci analysed in phylogenetic studies, it is very likely that further cases will be discovered. Our current results indicate that 1) the genus Campephilus is related to the Asian genera Blythipicus, Chrysocolaptes and Reinwardtipicus, in accordance with morphological data and 2) that the nuclear genome of Campephilus is likely the mixture of two unrelated lineages. Yet, further work with a denser sampling of loci is necessary to evaluate the extant of the Sphyrapicus/Melanerpes lineage nuclear genome that introgressed into the Campephilus genome.

Irestedt, M., Fabre, P.-H., Batalha-Filho, H., Jønsson, K.A., Cees S. Roselaar, C.S., Sangster, G. & Ericson, P.G.P. 2013. The spatio-temporal colonization and diversification across the Indo-Pacific by a “great speciator” (Aves, Erythropitta erythrogaster). Proceedings of the Royal Society of London Ser. B., 280 (1759).
The Indo-Pacific region has arguably been the most important area for the formulation of theories about biogeography and speciation, but modern studies of the tempo,mode and magnitude of diversification across this region are scarce. We study the biogeographic history and characterize levels of diversification in the wide-ranging passerine bird Erythropitta erythrogaster using molecular, phylogeographic nd population genetics methods, as well as morphometric and plumage analyses. Our results suggest that E. erythrogaster colonized the Indo-Pacific during the Pleistocene in an eastward direction following a stepping tone pathway, and that sea-level fluctuations during the Pleistocene only locally may have promoted gene flow. A molecular species delimitation test suggests that several allopatric island populations of E. erythrogaster may be regarded as species. Most of these putative new species are further characterized y diagnostic differences in plumage. Our study reconfirms the E. erythrogaster complex as a ‘great speciator’: it represents a complex of up to 17 allopatrically distributed, reciprocally monophyletic and/or morphologically diagnosable species that originated during the Pleistocene. Our results support the view that observed latitudinal gradients of genetic divergence among avian sister species may have been affected by incomplete knowledge of taxonomic limits in tropical bird species.

Johansson, U.S., Ekman, J., Bowie, R.C.K., Halvarsson, P., Ohlson, J.I., Price, T.D. & Ericson, P.G.P. 2013. A complete multilocus species phylogeny of the tits and chickadees (Aves: Paridae). Molecular Phylogenetics and Evolution, 69, pp. 852-860.
The avian family Paridae (tits and chickadees) contains c. 55 species distributed in the Palearctic, Nearctic, Afrotropic and Indomalaya. The group includes some of the most well-known and extensively studied avian species, and the evolutionary history, in particular the post-glacial colonization of the northern latitudes, has been comparably well-studied for several species. Yet a comprehensive phylogeny of the whole clade is lacking. Here, we present the first complete species phylogeny for the group based on sequence data from two nuclear introns and one mitochondrial gene for 67 taxa of Paridae. Our results strongly support the inclusion of the Fire-capped Tit (Cephalopyrus flammiceps), currently placed in the Remizidae, as the basalmost member of the Paridae. The Yellow-browed Tit (Sylviparus modestus) and the Sultan Tit (Melanochlora sultanea) constitute the next two sequential branches whereas the remaining tits falls into two large clades, one of which contains the seed hoarding and nest excavating species. The indicated clades within these two groups are largely congruent with recent classifications, but several unforeseen relationships are indicated, such as non-monophyly of the Sombre Tit (Poecile lugubris) and the Marsh Tit (Poecile palustris), as well as non-monophyly of both the African grey and the African black tits. Further, our results support a close relationship between the White-fronted Tit (Parus semilarvatus) and the varied Tit (Poecile varius) as well as a close relationship between the White-naped Tit (Parus nuchalis) and the Yellow-cheecked and Black-lored tits (Parus spilonotus and P. xanthogenys). We propose a new classification that is in accordance with this phylogeny.

Ohlson, J.I., Fjeldså, J. & Ericson, P.G.P. 2013. Molecular phylogeny of the manakins (Aves: Passeriformes: Pipridae), with a new classification and the description of a new genus. Molecular Phylogenetics and Evolution, 69, pp. 796-804.
The phylogenetic relationships within the manakin family (Pipridae) were investigated with sequence data from three nuclear introns and one mitochondrial protein-coding gene. This study confirms a sister group relationship between Neopelminae and Piprinae. We also find support for dividing the Piprinae into two principal clades: Ilicurini and Piprini. The genera Pipra and Chloropipo are found to be polyphyletic. Chloropipo species are placed in three different clades, including two species in an unresolved position alongside Ilicurini and Piprini. We propose a new classification of the family, where the most important modifications include recognizing the genus Ceratopipra for five species formerly placed in Pipra and the erection of a new genus for Chloropipo holochlora.

Ohlson, J.I., Irestedt, M., Ericson, P.G.P. & Fjeldså, J. 2013. Phylogeny and classification of the New World suboscines (Aves, Passeriformes). Zootaxa, 3613, pp. 1-35.
Here we present a phylogenetic hypothesis for the New World suboscine radiation, based on a dataset comprising of 219 terminal taxa and five nuclear molecular markers (ca. 6300 bp). We also estimate ages of the main clades in this radiation. This study corroborates many of the recent insights into the phylogenetic relationships of New World suboscines. It further clarifies a number of cases for which previous studies have been inconclusive, such as the relationships of Conopophagidae, Melanopareiidae and Tityridae. We find a remarkable difference in age of the initial divergence events in Furnariida and Tyrannida. The deepest branches in Furnariida are of Eocene age, whereas the extant lineages of Tyrannida have their origin in the Oligocene. Approximately half of the New World suboscine species are harboured in 5 large clades that started to diversify around the Mid Miocene Climatic Optimum (16-12 Mya). Based on our phylogenetic results we propose a revised classification of the New World suboscines. We also erect new family or subfamily level taxa for four small and isolated clades: Berlepschiinae, Pipritidae, Tachurididae and Muscigrallinae.

Olsson, U., Irestedt, M., Sangster, G., Ericson, P.G.P. & Alström, P. 2013. Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera. Molecular Phylogenetics and Evolution, 66, pp. 790-799.
The avian taxon Cisticolidae includes c. 110 species which are distributed throughout the tropical and subtropical parts of the Old World. We estimated the phylogeny of 47 species representing all genera assumed to be part of Cisticolidae based on sequence data from two mitochondrial and two nuclear markers, in total 3495 bp. Bayesian inference and maximum likelihood analyses resulted in a generally well-supported phylogeny which clarified the position of several previously poorly known taxa. The placement of Drymocichla, Malcorus, Micromacronus, Oreophilais, Phragmacia, Phyllolais, Poliolais and Urorhipis in Cisticolidae is corroborated, whereas Rhopophilus and Scotocerca are removed from Cisticolidae. Urorhipis and Heliolais are placed in the genus Prinia whereas Prinia burnesii is shown to be part of Timaliidae, and is placed in the genus Laticilla. Although not recovered by all single loci independently, four major clades were identified within Cisticolidae, and one of these is here described as a new taxon (Neomixinae).

Qu, Y., Zhao, H.-W., Han, N., Zhou, G., Song, G., Gao, B., Tian, S., Zhang, J., Zhang, R., Meng, X., Zhang, Y., Zhang, Y., Zhu, Y., Wang, W., Lambert, D., Ericson, P.G.P., Yeung, C., Zhu, H., Jiang, Z., Li, R. & Lei, F. 2013. The genome of a jay-like tit reveals insights into its adaption to Tibetan plateau. Nature Communications, 4:2071.
The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological imilarities. Here we present the ground tit’s genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and t diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving enes in hypoxia response and skeletal development. There results indicated that ground tit evolves basic strategies and ‘tit-to-jay’ change for coping with the life in an extreme environment.

Aliabadian, M., Kaboli, M., Förschler. M.I., Nijman, V., Chamani, A., Tillier, A., Prodon, R., Pasquet, E., Ericson, P.G.P. & Zuccon, D. 2012. Convergent evolution of morphological and ecological traits in the open-habitat chat complex (Aves, Muscicapidae: Saxicolinae). Molecular Phylogenetics and Evolution, 65, pp. 35-45.
Open-habitat chats (genera Myrmecocichla, Cercomela, Oenanthe and relative) are a morphologically and ecologically cohesive group of genera with unclear phylogenetic relationships. They are distributed mostly in open, arid and/or rocky habitats of Africa and Eurasia. Here, we present the most comprehensive molecular phylogenetic analysis of this group to date, with a complete taxon sampling at the species level. The analysis, based on a multilocus dataset including three mitochondrial and three nuclear loci, allows us to elucidate the phylogenetic relationships and test the traditional generic limits. All genera are non-monophyletic, suggesting extensive convergence on similar plumage patterns in unrelated species. While the colour pattern appear to be a poor predictor of the phylogenetic relationships, some of the ecological and behavioural traits agree relatively well with the major clades. Following our results, we also propose a revised generic classification for the whole group.

Ericson, P.G.P. 2012. Evolution of terrestrial birds in three continents: biogeography and parallel radiations. Journal of Biogeography, 39, pp. 813-824.
The aim was to reconstruct the biogeographical history of a large clade of mainly terrestrially adapted birds (coraciiform and piciform birds, owls, diurnal raptors, New World vultures, trogons, mousebirds, cuckoo-rollers, seriemas, parrots and passerines) to test the hypothesis of its Gondwanan origin. The phylogenetic tree used in the analysis was a family-level tree estimated from previously published nuclear DNA sequence data. Each family for which a thorough and taxonomically well-sampled phylogenetic analysis exists was subject to an initial dispersal—vicariance analysis in order to reconstruct ancestral areas for its two most basal lineages. Both basal lineages were then used to represent the family in the subsequent reconstruction of ancestral distributions for the entire radiation.
    The analysis showed that three reciprocally monophyletic groups of terrestrial birds have diversified in the Gondwanan land areas Australia,South America and Africa, respectively. Although each of these three groups originally also may have included other groups, the only survivors today from the Australian radiation are the passerines and parrots, while the falcon and seriemas have survived from the South American radiation. The group of survivors from the African radiation is considerably more taxonomically diverse and includes all coraciiform and piciform birds, owls, diurnal raptors (except falcons), New World vultures, trogons, mousebirds and cuckoo-rollers. The outlined evolutionary scenario with three geographically isolated clades of terrestrial birds is consistent with the available estimates of Late Cretaceous to early Palaeogene datings of these radiations. The diversifications and ecological adaptations within each of the three groups most likely took place in isolation on the different continents. Many cases of convergently evolved adaptations may be revealed through the increased understanding of the phylogenetic relationships of terrestrial birds.

Fabre, P.-H., Irestedt, M., Fjeldså, J., Bristol, R., Groombridge, J.J., Irham, M. & Jønsson, K.A. 2012. Dynamic colonization exchanges between continents and islands drive diversification in paradise-flycatchers (Tersiphone, Monarchidae). Journal of Biogeography, 39, pp. 1900-1918.
We use parametric biogeographical reconstruction based on an extensive DNA sequence dataset to characterize the spatio-temporal pattern of colonization of the Old World monarch flycatchers (Monarchidae). We then use this framework to examine the role of dispersal and colonization in their evolutionary diversification and to compare plumages between island and continental Tersiphone species.
   We generate a DNA sequence dataset of 2300 bp comprising one nuclear and three mitochondrial markers for 89% (17/19) of the Old World Monarchidae species and 70% of the Tersiphone subspecies. By applying maximum likelihood and Bayesian phylogenetic methods and implementing a Bayesian molecular clock to provide a temporal framework, we reveal the evolutionary history of the group. Furthermore, we employ both Lagrange and Bayes-Lagrange analyses to assess ancestral areas at each node of the phylogeny. By combining the ancestral area reconstruction with information on plumage traits we are able to compare patterns of plumage evolution on islands and continents.
   We provide the first comprehensive molecular phylogenetic reconstruction for the Old World Monarchidae. Our phylogenetic results reveal a relatively recent diversification associated with several dispersal events within this group. Moreover, ancestral area analyses reveal an Asian origin of the Indian Ocean and African clades. Ancestral state reconstruction analyses of plumage characters provide an interpretation of the plumage differentiation on islands and continents. Ancestral plumage traits are inferred to be close to those of the Asian paradise-flycatcher (Tersiphone paradisi), and island species display a high degree of plumage autapomorphy compared with continental species.
  Tersiphone paradisi is polyphyletic and comprises populations that have retained the ancestral plumage of the widespread Tersiphone genus. The genus appears to have colonized south-west Asia, the Indian Ocean and Africa from eastern Asia. The phylogeny and divergence time estimates indicate multiple simultaneous colonizations of the western Old World by Tersiphone. These results reinforce a hypothesis of range expansions of a Tersiphone paradisi-like ancestor into eastern Asia and the western Old World.

Fuchs, J., Irestedt, M., Fjeldså, J., Couloux, A., Pasquet, E. & Bowie, R.C.K. 2012. Molecular phylogeny of African bush-shrikes and allies: tracing the biogeographic history of an explosive radiation of corvoid birds. Molecular Phylogenetics and Evolution, 64, pp. 93-105.
The Malaconotidea (e.g., butcherbirds, bush-shrikes, batises, vangas) represent an Old World assemblage of corvoid passerines that encompass many different foraging techniques (e.g., typical flycatchers, flycatcher-shrikes, canopy creepers, undergrowth skulkers). At present, relationships among the primary Malaconotidea clades are poorly resolved, a result that could either be attributed to a rapid accumulation of lineages over a short period of time (hard polytomy) or to an insufficient amount of data having been brought to bear on the problem (soft polytomy). Our objective was to resolve the phylogenetic relationships and biogeographic history of the Malaconotidea using DNA sequences gathered from 10 loci with different evolutionary properties. Given the range of substitution rates of molecular markers we sequenced (mitochondrial, sex-linked, autosomal), we also sought to explore the effect of altering the branch-length prior in Bayesian tree estimation analyses. We found that changing the branch-length priors had no major effect on topology, but clearly improved mixing of the chains for some loci. Our phylogenetic analyses clarified the relationships of several genera (e.g., Pityriasis, Machaerirhynchus) and provide for the first time strong support for a sister-group relationship between core platysteirids and core vangids. Our biogeographic reconstruction somewhat unexpectedly suggests that the large African radiation of malaconotids originated after a single over-water dispersal from Australasia around 45-33.7 mya, shedding new light on the origins of the Afrotropical avifauna.

Jønsson, K.A., Fabre, P.-H., Fritz, S.A., Etienne, R.S., Ricklefs, R.E., Jørgensen, T.B., Fjeldså, J., Rahbek, C., Ericson, P.G.P., Woogg, F., Pasquet, E. & Irestedt, M. 2012. Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas. Proceedings of the National Academy of Sciences, 109, pp. 6620-6625.
Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is notwell-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, butpoorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 million y ago. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation) - or even larger (size variation) - as that of other better known avian adaptive radiations, including the much younger Galapagos Darwin´s finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.

Jønsson, K.A.  Fabre, P.-H., & Irestedt, M. 2012. Brains, tools, innovation and biogeography in crows and ravens. BMC Evolutionary Biology, 12: 72.
Crows and ravens (Passeriformes: Corvus) are large-brained birds with enhanced cognitive abilities relative to other birds. They are among the few non-hominid organisms on Earth to be considered intelligent and well-known examples exist of several crow species having evolved innovative strategies and even use of tools in their search for food. The 40 Corvus species have also been successful dispersers and are distributed on most continents and in remote archipelagos.
This study presents the first molecular phylogeny including all species and a number of subspecies within the genus Corvus. We date the phylogeny and determine ancestral areas to investigate historical biogeographical patterns of the crows. Additionally, we use data on brain size and a large database on innovative behaviour and tool use to test whether brain size (i) explains innovative behaviour and success in applying tools when foraging and (ii) has some correlative role in the success of colonization of islands. Our results demonstrate that crows originated in the Palaearctic in the Miocene from where they dispersed to North America and the Caribbean, Africa and Australasia. We find that relative brain size alone does not explain tool use, innovative feeding strategies and dispersal success within crows.
Our study supports monophyly of the genus Corvus and further demonstrates the direction and timing of colonization from the area of origin in the Palaearctic to other continents and archipelagos. The Caribbean was probably colonized from North America, although some North American ancestor may have gone extinct, and the Pacific was colonized multiple times from Asia and Australia. We did not find a correlation between relative brain size, tool use, innovative feeding strategies and dispersal success. Hence, we propose that all crows and ravens have relatively large brains compared to other birds and thus the potential to be innovative if conditions and circumstances are right.

Moltesen, M., Irestedt, M., Fjeldså, J., Ericson, P.G.P. & Jønsson, K.A. 2012. Molecular phylogeny of Chloropseidae and Irenidae - Cryptic species and biogeography. Molecular Phylogenetics and Evolution, 65, pp. 903-914.
Chloropseidae (Leafbirds) and Irenidae (Fairy-bluebirds) are colourful Oriental birds, which have been placed as a deep (old) branch in the radiation of passeroid songbirds. We present a densely sampled molecular phylogeny of the two families based on two nuclear introns (GAPDH and ODC) and two mitochondrial genes (ND3 and cyt-b) largely stemming from old museum specimens. Our results show that several subspecies within both Chloropseidae and Irenidae are genetically distinct and separated in the Miocene some 10-11 Million years ago (Mya), indicating a substantial underestimation of species numbers within the two families. Based on our molecular findings, plumage distinctiveness and contemporary distributions we propose that several subspecies be recognised at the species level. Furthermore, we use the molecular data to examine biogeographical patterns of the two families in the light of historical geological re-arrangements in the region. The results indicate that the Philippines were colonised in the Pliocene and that colonisation probably progressed via the Sulu islands from Borneo and not via Palawan, which was first colonised in the Pleistocene.  

Ohlson, J.I., Irestedt, M., Fjeldså, J. & Ericson, P.G.P. 2012. Nuclear DNA from a 180-year-old study skin reveals the phylogenetic position of the Kinglet Calyptura Calyptura cristata(Passeriformes: Tyrannides). Ibis, 154, pp. 533-541.
The Kinglet Calyptura Calyptura cristata is one of the most enigmatic bird species in South America. It is known only from specimens collected in the 19th century and from a few recent observations. The knowledge of its biology is scanty and its systematic position is highly obscure. Traditionally, Calyptura was placed in the Cotingidae, but associated with genera that are now known to fall outside Cotingidae. In an attempt to clarify its phylogenetic position, sequence data for four nuclear markers was obtained from a 180 years old museum study skin of Calyptura, and incorporated into a comprehensive dataset of Tyrant Flycatchers, Cotingas, Manakins and allies. Our analyses show that Calyptura is most closely related to Platyrinchus and Neopipo and these three genera constitute a deep branch in the clade containing Rhynchocyclidae (Tody-tyrants and Flatbills) and Tyrannidae (typical Tyrant Flycatchers). The Calyptura specimen is among the oldest avian museum specimens from which a substantial amount of nuclear DNA sequence data have been obtained, further highlighting the immense value of museum collections for DNA-based phylogenetic studies.

Zhang, R.Y., Song, G., Qu, Y.H., Alström, P., Ramos, R., Xing, X.Y., Ericson, P.G.P., Fjeldså, J. Wang, H.T., Yang, X.J., Kristin, A., Shestopalov, A.M., Choe, J.C. & Lei, F.M. (in press) Comparative phylogeography of two widespread magpies: Importance of habitat preference and breeding behavior on genetic structure in China. Molecular Phylogenetics and Evolution, 65, pp. 562-672.
Historical geological events and climatic changes are believed to have played important roles in shaping the current distribution of species. However, sympatric species may have responded in different ways to such climatic fluctuations. Here we compared genetic structures of two corvid species, the Azure-winged Magpie Cyanopica cyanus and the Eurasian Magpie Pica pica, both widespread but with different habitat dependence and some aspects of breeding behavior. Three mitochondrial genes and two nuclear introns were used to examine their co-distributed populations in East China and the Iberian Peninsula. Both species showed deep divergences between these two regions that were dated to the late Pliocene/ early Pleistocene. In the East Chinese clade of C. cyanus, populations were subdivided between Northeast China and Central China, probably since the early to mid-Pleistocene, and the Central subclade showed a significant pattern of isolation by distance. In contrast, no genetic structure was found in the East China populations of P. pica. We suggest that the different patterns in the two species are at least partly explained by ecological differences between them, especially in habitat preference and breeding behavior. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations.

Zuccon, D. & Ericson, P.G.P. 2012. Molecular and morphological evidences place the extinct New Zealand endemic Turnagra capensis in the Oriolidae. Molecular Phylogenetics and Evolution, 62, pp. 414-426.
The affinities of Piopio Turnagra capensis, an extinct New Zealand passerine, remain poorly known. It has been included into or associated with several bird families (Calleatidae, Cracticidae, Pachycephalidae, Ptilonorhynchidae, Turdidae), often on tenuous grounds. We reassessed Turnagra phylogenetic relationships using nuclear and mitochondrial sequences and a set of morphological and behavioural traits. Molecular and phenotypic characters strongly suggest a novel hypothesis, congruently placing Turnagra in Oriolidae, a highly dispersive corvoid family distributed from the Austro-Papuan landmass to Eurasia andAfrica , but missing from the Pacific islands. We show also that the published molecular support to link Turnagra with Ptilonorhynchidae was biased by the use of incorrect genetic data and weak analyses.

Zuccon, D., Prŷs-Jones, R., Rasmussen, P.C.& Ericson, P.G.P. 2012. The phylogenetic relationships and generic limits of finches (Fringillidae). Molecular Phylogenetics and Evolution, 62, pp. 581-596.
The phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers  are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Following our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.

Alström, P., Fregin, S., Norman, J.A., Ericson, P.G.P., Christidis, L. & Olsson, U. 2011.Multilocus analysis of a taxonomically densely sampled dataset reveal extensive non-monophyly in the avian family Locustellidae. Molecular Phylogenetics and Evolution, 58, pp. 513-526.
The phylogeny of most of the species in the avian passerine family Locustellidae is inferred using a Bayesian species tree approach (Bayesian Estimation of Species Trees, BEST), as well as a traditional Bayesian gene tree method (MrBayes), based on a dataset comprising one mitochondrial and four nuclear loci. The trees inferred by the different methods agree fairly well in topology, although in a few cases there are marked differences. Some of these discrepancies might be due to convergence problems for BEST (despite up to 1 000 000 000 iterations). The phylogeny strongly disagrees with the current taxonomy at the generic level, and we propose a revised classification that recognizes four instead of seven genera. These results emphasize the well known but still often neglected problem of basing classifications on non-cladistic evaluations of morphological characters. An analysis of an extended mitochondrial dataset with multiple individuals from most species, including many subspecies, suggest that several taxa presently treated as subspecies or as monotypic species as well as a few taxa recognized as separate species are in need of further taxonomic work.

Alström, P., Höhna, S., Gelang, M., Ericson, P.G.P. & Olsson, U. 2011. Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset. BMC Evolutionary Biology 2011, 11: 352.
The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.
    There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).
    The molecular phylogeny presented here is strongly inconsistent with the traditional, morphologybased classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the wellknown but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.

Alström, P., Saitoh, T., Williams, D., Nishiumi, I., Shigeta, Y., Ueda, K., Irestedt, M., Björklund, M. & Olsson, U. 2011. The Arctic Warbler Phylloscopus borealis - three anciently separated cryptic species revealed. Ibis, 153, pp. 395-410.
The Arctic Warbler Phylloscopus borealis breeds across the northern Palaearctic and northwestern-most Nearctic, from northern Scandinavia to Alaska, extending south to southern Japan, and winters in Southeast Asia, the Philippines and Indonesia. Several subspecies have been described based on subtle morphological characteristics, although the taxonomy varies considerably among different authors. A recent study (T. Saitoh et al. (2010) BMC Evol. Biol. 10: 35) identified three main mitochondrial DNA clades, corresponding to: (1) continental Eurasia and Alaska, (2) south Kamchatka, Sakhalin and northeast Hokkaido, and (3) most of Japan (Honshu, Shikoku, Kyushu). These three clades were estimated to have diverged during the late Pliocene to early Pleistocene (border at c. 2.6 million years ago). Differences in morphometrics have also been reported among members of the three clades (T. Saitoh et al. (2008) Ornithol. Sci. 7: 135—142). Here we analyse songs and calls from throughout the range of the Arctic Warbler, and conclude that these differ markedly and consistently among the populations representing the three mitochondrial clades. Kurile populations, for which no sequence data are available, are shown to belong to the second clade. To determine the correct application of available scientific names, mitochondrial DNA was sequenced from three name-bearing type specimens collected on migration or in the winter quarters. Based on the congruent variation in mitochondrial DNA, morphology and vocalizations, we propose that three species be recognized: Arctic Warbler Phylloscopus borealis (sensu stricto) (continental Eurasia and Alaska), Kamchatka Leaf Warbler Phylloscopus examinandus (Kamchatka (at least the southern part), Sakhalin, Hokkaido and Kurile Islands), and Japanese Leaf Warbler Phylloscopus xanthodryas (Japan except Hokkaido).

Christidis, L., Irestedt, M., Rowe, D., Boles, W.E. & Norman, J.A. 2011. Mitochondrial and nuclear DNA phylogenies reveal a complex evolutionary history in the Australasian robins (Passeriformes: Petroicidae). Molecular Phylogenetics and Evolution, 61, pp. 726-738.
The Australasian robins (Petroicidae) comprise a relatively homogeneous group of small to medium-sized insectivorous birds. Their center of diversity is Australia and New Guinea (40 species) but seven species have managed to colonize geographically distant islands such as Tanimbar, New Britain, New Zealand, New Caledonia, Norfolk Island, Vanuatu, Solomon Islands, Fiji and Samoa. To resolve the evolutionary relationships within the Petroicidae, we here present the results of a phylogenetic analysis of sequence data from two mitochondrial genes (ND2, CO1) and one nuclear intron (b-Fibrinogen intron 5) for all 14 genera and 40 of the 46 currently recognized species. All phylogenetic analyses identified six primary lineages, treated here as subfamilies, within the Petroicidae: (1) Eopsaltriinae comprising Eopsaltria (excluding E. flaviventris), Tregellasia, Peneothello, Melanodryas, Poecilodryas and Heteromyias; (2) Drymodinae comprising Drymodes; (3) Microecinae comprising Microeca, Monachella and Eopsaltria flaviventris; (4) Petroicinae comprising Petroica and Eugerygone; (5) Pachycephalopsinae comprising Pachycephalopsis; and (6) Amalocichlinae comprising Amalocichla. The genera Eopsaltria, Microeca, Peneothello and Poecilodryas were found to be paraphyletic. Based on assessments of phylogenetic branching patterns and/or DNA divergence it also was apparent that Eopsaltria australis, Tregellasia leucops, Melanodryas cucullata, Heteromyias albispecularis, Drymodes supercilious and Microeca flavigaster may each comprise more than one species. The Petroicidae display a complex biogeographical history involving repeated radiations both within, and across Australia and New Guinea. It appears that dispersal into smaller islands such as New Britain, Tanimbar and the South Pacific has only been undertaken by species with a ‘‘flycatcher´´ body form.

Irestedt, M., Gelang, M., Sangster, G., Olsson, U., Ericson, P.G.P. & Alström, P. 2011. Neumann's Warbler Hemitesia neumanni (Sylvioidea) may be a relic of a Paleotropic Miocene avifauna. Ibis, 153, pp. 78-86.
We present molecular evidence that Neumann´s Warbler Hemitesia neumanni is deeply nested within the Cettiidae. The species´ distribution in the Albertine Rift of East Africa is intriguing, as the family Cettiidae is principally an Asian radiation. This disjunct distribution could be a result of colonization of Africa by long-distance dispersal, or the Cettiidae may at some point in the past have had a much larger geographical distribution that also covered parts of Africa.
   Neumann´s Warbler Hemitesia neumanni is a small passerine of uncertain affinities that has a restricted distribution in mountain forests in the Albertine Rift, East Africa. The short tail, relatively large head with a prominent whitish supercilium, black stripe through the eye, black lateral crown-stripe and a dark greenish grey central crown-stripe make it a very distinctive species. It is mostly found on or close to the ground (Barlein et al. 2006). Rothschild (1908)originally described Neumann´s Warbler as Sylvietta neumanni. However, except for its short tail, it shows no particular resemblance to the genus Sylvietta (crombecs) and Rothschild´s decision to place it within this genus was probably influenced by a shared African distribution. Several external morphological differences between Neumann´s Warbler and the genus Sylvietta, and the observation that Neumann´s Warbler has many morphological features in common with the Asian warbler genus Tesia, led Chapin (1948) to place Neumann´s Warbler in the monotypic genus Hemitesia, in which it has been retained in subsequent classifications (e.g. Watson et al. 1986. Sibley & Monroe 1990, Barlein et al. 2006).
   The combination of being a restricted-range species in Africa and having a potentially close relationship with Asian warblers makes an investigation of the affinities of Neumann´s Warbler interesting, as it may improve the understanding of the timing, frequency and direction of historical avifaunal exchanges between Africa and Asia. In this study, we examine the phylogenetic relationships of Neumann´s Warbler and estimate divergence times for a diverse taxon sampling of Asian and African warblers by analysing nuclear and mitochondrial DNA sequences.

Johansson, U.S., Pasquet, E. & Irestedt M. 2011. The New Zealand thrush: An extinct oriole. PLoS ONE, 6(9), e24317.
The New Zealand Thrush, or Piopio, is an extinct passerine that was endemic to New Zealand. It has often been placed in its own family (Turnagridae), unresolved relative to other passerines, but affinities with thrushes, Australaian magpies, manucodes, whistlers, birds-of-paradise and bowerbirds has been suggested based on morphological data. An affinity with the bowerbirds was also indicated in an early molecular study, but low statistical support make this association uncertain. In this study we use sequence data from three nuclear introns to examine the phylogenetic relationships of the piopios. All three genes independently indicate an oriole (Oriolidae) affinity of the piopios, and the monophyly of the typical orioles (Oriolus), figbirds (Sphecotheres), and the piopios is strongly supported in the Bayesian analysis of the concatenated data set (posterior probability = 1.0). The exact placement of the piopios within Oriolidae is, however, more uncertain but in the combined analysis and in two of the gene trees the piopios are placed basal to the typical orioles while the third gene suggest a sister relationship with the figbirds. This is the first time an oriole affinity has been proposed for the piopios. Divergence time estimates for the orioles suggest that the clade originated ca 20 million years ago, and based on these estimates it is evident that the piopios must have arrived on New Zealand by dispersal across the Tasman Sea and not as a result of vicariance when New Zealand separated from Gondwana in the late Cretaceous.

Jønsson, K.A., Irestedt, M., Bowie, R.C.K., Christidis, L. & Fjeldså, J. 2011. Systematics and biogeography of Indo-Pacific ground-doves. Molecular Phylogenetics and Evolution, 59, pp. 538-543.
Ground-doves represent an insular bird radiation distributed across the Indo-Pacific. The radiation comprises sixteen extant species, two species believed to be extinct and six species known to be extinct. In the present study, we present a molecular phylogeny for all sixteen extant species, based on two mitochondrial markers. We demonstrate that the Gallicolumba as currently circumscribed is not monophyletic and recommend reinstalling the name Alopecoenas for a monophyletic radiation comprising ten extant species, distributed in New Guinea, the Lesser Sundas and Oceania. Gallicolumba remains the name for six species confined to New Guinea the Philippines and Sulawesi. Although our phylogenetic analyses fail to support a single origin for the remaining Gallicolumba species, we suspect that the addition of nuclear sequence data may alter this result.
    Because a number of ground-dove taxa have gone extinct, it is difficult to assess  biogeographical patterns. However, the Alopecoenas clade has clearly colonized many remote oceanic islands rather recently, with several significant water crossings. The Gallicolumba radiation(s), on the other hand, is significantly older and it is possible that diversification  within that group may in part have been shaped by plate tectonics and corresponding re-arrangements of land masses within the Philippine and Sulawesi region.

Pasko, L.,  Ericson, P.G.P. & Elzanowski, A. 2011 Phylogenetic utility and evolution of indels: a study in neognathous birds. Molecular Phylogenetics and Evolution, 61, pp. 760-771.
Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the rerieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.

Alström, P., Davidson, P., Duckworth, J.W., Eames, J.C., Le, T.T., Nguyen, C., Olsson, U., Robson, C. & Timmins, R. 2010. Description of a new species of Phylloscopus warbler from Vietnam and Laos. Ibis, 152, pp. 145-168.
A new species of Phylloscopus warbler, which we name Phylloscopus calciatilis Limestone Leaf Warbler, is described from central and northern Vietnam and central and northern Laos; it probably also breeds in southernmost China. In morphology, the new species is very similar to Sulphur-breasted Warbler Phylloscopus ricketti, but it is smaller with a proportionately larger bill and rounder wing. Its song and calls are diagnostic. Based on mitochondrial and nuclear DNA, the new species is most closely related to P. ricketti and Yellow-vented Warbler Phylloscopus cantator, and it is inferred to be sister to the latter. The mitochondrial divergences between these three species are at the low end of the variation found in other species of Phylloscopus and Seicercus warblers, but greater than in other taxa generally treated as subspecies. Possible introgressive hybridization between the new species and P. ricketti is discussed, but more data are needed to establish whether it does occur and, if it does, to what extent. The new species appears to have a restricted breeding range in limestone karst environments, where it is locally common and therefore not under any immediate threat. In view of the recognition of the new species, all previous records of P. ricketti sensu lato need to be re-evaluated.

Drovetski, S.V., Zink, R.M., Ericson, P.G.P. & Fadeev, I.V. 2010. A multilocus study of pine grosbeak phylogeography supports the pattern of greater intercontinental divergence in Holarctic boreal forest birds than in birds inhabiting other high-latitude habitats. Journal of Biogeography, 37, pp. 696-706.
Boreal forest bird species appear to be divided into lineages endemic to each northern continent, in contrast to Holarctic species living in open habitats. For example, the three-toed woodpecker (Picoides tridactylus) and the winter wren (Troglodytes troglodytes) have divergent Nearctic and Palaearctic mitochondrial DNA clades. Furthermore, in these species, the next closest relative of the Nearctic/Palaearctic sister lineages is the Nearctic clade, suggesting that the Palaearctic may have been colonized from the Nearctic. The aim of this study is to test this pattern of intercontinental divergence and colonization in another Holarctic boreal forest resident — the pine grosbeak (Pinicola enucleator).
  We sequenced the mitochondrial ND2 gene and Z-specific intron 9 of the ACO1 gene for 74 pine grosbeaks collected across the Holarctic. The sequences were used to reconstruct the phylogeographical history of this species using maximum likelihood analysis.
  We discovered two distinct mitochondrial and Z-specific lineages in the Nearctic and one in the Palaearctic. The two Nearctic mtDNA lineages, one in the northern boreal forest and one in south-western mountain forest, were more closely related to each other than either was to the Palaearctic clade. Two Nearctic Z-chromosome clades were sympatric in the boreal and south-western mountain forests. Unlike the topology of the mtDNA tree, the relationship among the Z-chromosome clades was the same as in the three-toed woodpecker and winter wren [Nearctic (Nearctic, Palaearctic)]. The Palaearctic Z-chromosome clade had much lower genetic diversity and a single-peak mismatch distribution with a mean < 25% of that for either Nearctic region, both of which had ragged mismatch distributions.
  Our data suggest that, similar to the other boreal forest species, the pine grosbeak has divergent lineages in each northern continent and could have colonized the Palaearctic from the Nearctic. Compared with many Holarctic birds inhabiting open habitats, boreal forest species appear to be more differentiated, possibly because the boreal forests of the Nearctic and Palaearctic have been isolated since the Pliocene (3.5 Ma).

Ericson, P.G.P., Olson, S.L., Irestedt, M., Alvarenga, H. & Fjeldså, J. 2010. Circumscription of a monophyletic family for the tapaculos (Aves: Rhinocryptidae): Psiloramphus in and Melanopareia out. Journal of Ornithology, 151, pp. 337-345.
The tapaculos (Rhinocryptidae) are tracheophone, suboscine birds restricted to South and Central America. Most tapaculos share a number of internal and external characteristics that have been used to define the family taxonomically. The genera Melanopareia and Psiloramphus do not fully fit this pattern and have caused considerable dispute among taxonomists since they were first described. In this paper we delimit the systematic boundaries of the tapaculos and assess their generic relationships by an analysis of molecular sequence data. The results show that while Psiloramphus is nested well within the Rhinocryptidae, Melanopareia falls far outside that clade. A new family is erected for Melanopareia.

Fjeldså, J., Irestedt, M., Ericson, P.G.P. & Zuccon, D. 2010. The Cinnamon Ibon Hypocryptadius cinnamomeus is a forest canopy sparrow. Ibis, 152, pp. 747-760.
The Cinnamon Ibon inhabits the canopy of cloud-forest of Mindanao Island in the Philippines, and has until now been classified as an aberrant member of the Zosteropidae (white-eyes). We assessed the systematic position of this enigmatic species using DNA sequence data (two mitochondrial markers, two nuclear introns and two nuclear exons) and broad taxon sampling. The species was robustly placed among the granivorous passeroid clades, as a basal branch in the family of true sparrows, Passeridae. Morphological data lend further support, as the Cinnamon Ibon shows similar specialization of the skull as other granivorous passeroids. The species´ restricted distribution in the montane cloud-forest of the island of Mindanao, which is of oceanic origin, is difficult to explain without assuming an over-water dispersal event.

Johnsen, A., Rindal, E., Ericson, P.G.P., Zuccon, D., Kerr, K.C.R., Stoeckle, M.Y. & Lifjeld, J.T. 2010. DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species. Journal of Ornithology 151, pp. 565-578.
Birds are a taxonomically well-described group of animals, yet DNA barcoding, i.e. the molecular characterization of species using a standardised genetic marker, has revealed unexpected patterns of genetic divergences among North American birds. We performed a comprehensive COI (cytochrome c oxidase subunit I) barcode survey of 296 species of Scandinavian birds, and compared genetic divergences among 78 trans-Atlantic species whose breeding ranges include both Scandinavia and North America. Ninety-four percent of the Scandinavian species showed unique barcode clusters; the remaining six percent had overlapping barcodes with one or more congeneric species, which may reflect incomplete lineage sorting or a single gene pool. Four species showed large intra-specific divergences within Scandinavia, despite no apparent morphological differentiation or indications of reproductive isolation. These cases may reflect admixture of previously isolated lineages, and may thus warrant more comprehensive phylogeographic analyses. Nineteen (24%) of 78 trans-Atlantic species exhibited divergent genetic clusters which correspond with regional subspecies. Three of these trans-Atlantic divergences were paraphyletic. Our study demonstrates the effectiveness of COI barcodes for identifying Scandinavian birds and highlights taxa for taxonomic review. The standardised DNA barcoding approach amplified the power of our regional studies by enabling independently obtained data sets to be merged together with the established avian barcode library.

Jønsson, K.A., Bowie, R.C.K., Moyle, R.G., Irestedt, M., Christidis, L., Norman, J.A. & Fjeldså, J. 2010. Phylogeny and biogeography of Oriolidae (Aves: Passeriformes). Ecography, 33, pp. 232-241.
Understanding oscine passerine dispersal patterns out of their Australian area of origin is hampered by a paucity of robust phylogenies. We constructed a molecular phylogeny of the oscine family, Oriolidae, which is distributed from Australia through to the Old World. We used the phylogeny to assess direction and timing of dispersal and whether dispersal can be linked with the well-documented movements of geological terranes in the Indonesian Archipelago. We sampled 29 of 33 species of Oriolidae from fresh tissue and from toe pads from museum specimens, and examined two nuclear introns and two mitochondrial genes. Model-based phylogenetic analyses yielded strong support for clades that generally mirrored classical systematics. Biogeographical analyses and divergence time estimates demonstrated that the family originated in the Australo-Papuan region from where it dispersed first to Asia and then onwards to Africa and the Philippines before back-colonising Asia and the Indonesian archipelago. Thus, contrary to several other avian families in the region, Oriolidae represents a sequential dispersal pattern from Australia to Africa via Asia. However, it is noteworthy that the Pacific islands and archipelagos remain uncolonised and that members inhabiting Wallacea are recent colonisers suggesting that Oriolidae are poorly adapted to island life.

Jønsson, K.A., Irestedt, M., Ericson, P.G.P. & Fjeldså, J. 2010. A molecular phylogeny of minivets (Passeriformes: Campephagidae: Pericrocotus): implications for biogeography and convergent plumage evolution. Zoologica Scripta, 39, pp. 1-8.
Minivets are conspicuous and mostly intensely colourful birds inhabiting wooded environments in tropical and subtropical South and Southeast Asia and temperate East Asia. We present a robust phylogeny of the group based on nuclear and mitochondrial DNA data including all 12 recognized species and also many subspecies representing disjunct populations in the Oriental mainland and in Indonesia. The study indicates that minivets radiated within mainland Asia and dispersed to the Indonesian archipelago. We also demonstrate that in accordance with studies on other bird groups, plumage characters are highly plastic and that the diversity of plumage patterns and colouration represents an example of convergent evolution.

Müller, J., Scheyer, T.M., Head, J.J., Barrett, P.M., Werneburg, I., Ericson, P.G.P., Pol, D. & Sánchez-Villagra, M.R. 2010. Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes. Proceedings of the National Academy of Sciences of the United States of America, 107, pp. 2118-2123.
The development of distinct regions in the amniote vertebral column results from somite formation and Hox gene expression, with the adult morphology displaying remarkable variation among lineages. Mammalian regionalization is reportedly very conservative or even constrained, but there has been no study investigating vertebral count variation across Amniota as a whole, undermining attempts to understand the phylogenetic, ecological, and developmental factors affecting vertebral column variation. Here, we show that the mammalian (synapsid) and reptilian lineages show early in their evolutionary histories clear divergences in axial developmental plasticity, in terms of both regionalization and meristic change, with basal synapsids sharing the conserved axial configuration of crown mammals, and basal reptiles demonstrating the plasticity of extant taxa. We conducted a comprehensive survey of presacral vertebral counts across 436 recent and extinct amniote taxa. Vertebral counts were mapped onto a generalized amniote phylogeny as well as individual ingroup trees, and ancestral states were reconstructed by using squared-changeparsimony.We also calculated the relationship between presacral and cervical numbers to infer the relative influence of homeotic effects and meristic changes and found no correlation between somitogenesis and Hox-mediated regionalization. Although conservatism in presacral numbers characterized early synapsid lineages, in some cases reptiles and synapsids exhibit the same developmental innovations in response to similar selective pressures. Conversely, increases in body mass are not coupled with meristic or homeotic changes, but mostly occur in concert with postembryonic somatic growth. Our study highlights the importance of fossils in large-scale investigations of evolutionary developmental processes.

Olsson, U., Alström, P., Svensson, L., Aliabadian, M. & Sundberg, P. 2010. The Lanius excubitor (Aves, Passeriformes) conundrum — taxonomic dilemma when molecular and non-molecular data tell different stories. Molecular Phylogenetics and Evolution, 55, pp. 347-357.
The phylogeny of 18 taxa in the Lanius excubitor complex, and the related species L. sphenocercus, L. ludovicianus and L. somalicus, was estimated based on the mitochondrial cytochrome b gene and the non-coding D-loop (in total ~1.3 kb). According to the mitochondrial gene tree, Lanius excubitor s.l. is non-monophyletic, with some of its subspecies being more closely related to L. sphenocercus, L. ludovicianus, and L. somalicus. Also the division of the L. excubitor complex into a northern (L. excubitor) and a southern (L. meridionalis) species, as has been proposed based on morphological and ecological similarity and geographical distributions, is not compatible with the mitochondrial tree. Overall, genetic divergences among the ingroup taxa are small, indicating a recent radiation. A tree based on the nuclear ornithine decarboxylase (ODC) introns 6-7 is unresolved with respect to the ingroup, but provides strong support for a clade containing the Lanius excubitor complex, L. sphenocercus, L. ludovicianus and L. somalicus. We discuss the incongruence between the current taxonomy and the mitochondrial gene tree, and conclude that based on the latter the Lanius excubitor complex may be treated as at least six species, L. borealis, L. elegans, L. excubitor, L. lahtora, L. meridionalis, and L. uncinatus, but that other taxonomic treatments are also possible. However, uncertainty regarding to which extent the mitochondrial gene tree reflects the species phylogeny prevents us from recommending taxonomic change without further investigation. This study highlights the possible danger of relying on a single molecular marker, such as mitochondrial DNA, in taxonomic revisions and phylogenetic inference.

Sangster, G., Alström, P., Forsmark, E. & Olsson, U. 2010. Multi-locus phylogenetic analysis of Old World chats and flycatchers reveals extensive paraphyly at family, subfamily and genus level (Aves: Muscicapidae). Molecular Phylogenetics and Evolution, 57, pp. 380-392.
The chats and flycatchers (Muscicapidae) represent an assemblage of 275 species in 48 genera. Defining natural groups within this assemblage has been challenging because of its high diversity and a paucity of phylogenetically informative morphological characters. We assessed the phylogenetic relationships of 124 species and 34 genera of Muscicapidae, and 20 species of Turdidae, using molecular sequence data from one mitochondrial gene and three nuclear loci, in total 3240 bp. Bayesian and maximum likelihood analyses yielded a well-resolved tree in which nearly all basal nodes were strongly supported. The traditionally defined Muscicapidae, Muscicapinae and Saxicolinae were paraphyletic. Four major clades are recognized in Muscicapidae: Muscicapinae, Niltavinae (new family-group name), Erithacinae and Saxicolinae. Interesting relationships recovered by this analysis include: (i) a clade comprising the ‘blue´ flycatcher genera Niltava, Cyornis, Cyanoptila and Eumyias and some species of Rhinomyias; (ii) the position of Erithacus rubecula in a clade of otherwise exclusively African species; (iii) a close relationship between the shortwing Heinrichia calligyna and the flycatcher Rhinomyias insignis; (iv) a sister-relationship between forktails Enicurus and whistling thrushes Myophonus; and (v) a sister relationship of Ficedula and the ‘chats´ Monticola, Phoenicurus, Saxicola and Oenanthe. A high number of traditionally defined genera was found to be paraphyletic or polyphyletic.

Zuccon, D. & Ericson, P.G.P. 2010. The Monticola Rock-Thrushes: Phylogeny and biogeography revisited. Molecular Phylogenetics and Evolution, 55, pp. 901-910.
We investigated the phylogenetic relationships within the Monticola rock-thrushes, an open-habitat genus inhabiting a large part of the Old World. Our results support one Oriental clade and one clade including African, Malagasy and Eurasian taxa. The biogeographic reconstruction obtained with the dispersal-vicariance analysis suggested Southern Africa plus Palearctic as the Monticola ancestral area. Our phylogenetic hypothesis suggests also some taxonomic changes. The polytypic Monticola solitarius includes two reciprocally monophyletic clades that should be recognized as full species, M. solitarius s.s. and M. philippensis. With the exclusion of the south-western population, M. imerinus, all other Malagasy rock-thrush populations should be merged in the monotypic, albeit polymorphic, M. sharpei. The genus Thamnolaea is shown to be non-monophyletic, with T. semirufa being part of the Monticola radiation, while T. cinnamomeiventris is related to other chat species inhabiting open-habitats. We demonstrate that a previous phylogenetic hypothesis for the rock-thrushes was flawed by the inclusion of contaminated sequences obtained from study-skins and we suggest some working guidelines to improve the reliability of the sequences obtained from old or degraded DNA.

Zuccon, D. & Ericson, P.G.P. 2010. A multi-gene phylogeny disentangles the chat flycatcher complex (Aves: Muscicapidae). Zoologica Scripta, 39, pp. 213-224.
We reconstructed the first well-sampled phylogenetic hypothesis in the chat-flycatcher complex combining nuclear and mitochondrial sequences. The dichotomy between chats-terrestrial feeders and flycatchers-aerial feeders does not reflect monophyletic groups. The flycatching behaviour and morphological adaptations to aerial feeding (short tarsi, broad bill, rictal bristles) evolved independently from chat ancestors in three different lineages. The genera Alethe, Brachypteryx, and Myiophonus are nested within the Muscicapidae radiation and their morphological and behavioural similarities with the true thrushes Turdidae are presumably the result of convergence. The postulated close relationships among Erithacus, Luscinia and Tarsiger cannot be confirmed. Erithacus is part of the African forest robin assemblage (Cichladusa, Cossypha, Pogonocichla, Pseudalethe, Sheppardia, Stiphrornis), while Luscinia and Tarsiger belong to a large, mainly Asian radiation. Enicurus belongs to the same Asian clade and it does not deserve the recognition as a distinct subfamily or tribe. We found good support also for an assemblage of chats adapted to arid habitats (Monticola, Oenanthe, Thamnolaea, Myrmecocichla, Pentholaea, Cercomela, Saxicola, Campicoloides, Pinarochroa) and a redstart clade (Phoenicurus, Chaimarrornis and Rhyacornis). Five genera (Muscicapa, Copsychus, Thamnolaea, Luscinia and Ficedula) are polyphyletic and in need of taxonomic revision.

Fjeldså, J. & Irestedt, M. 2009. Diversification of the South American avifauna: patterns and implications for conservation in the Andes. Annals of the Missouri Botanical Garden, 96, 398-409.
By combining distributions and phylogenies for large groups of birds, it is now possible to disentangle the relative roles of contemporary ecology and history in explaining the distribution of biodiversity on earth. In South America, avian lineages, which represent radiations during the warm parts of the Tertiary, are best represented in the tropical lowlands and Andean forelands. During the upper Tertiary, diversification was most intense in the tropical Andes region, with recruitment back into the tropical lowlands and into South America´s open biomes. Within the tropical Andes, endemism (mean inverse range size) and mean branch length (number of phylogenetic nodes on lineages) increase from the foothills up to the tree line and then decline again in the barren highlands, suggesting that the tree-line zone plays a special role in the diversification process. The resulting endemism is locally aggregated, often with marked peaks in areas immediately adjacent to ancient population centers. Thus, the process of evolution of new species is linked with local factors that, over a shorter time perspective, were also favorable for people. If we want to maintain the process of diversification, it becomes essential to supplement the traditional approach of preserving biodiversity in wilderness areas with few people with efforts to support sustainable development in populated areas.

Fregin, S., Haase, M., Olsson, U. & Alström, P. 2009. Multi-locus phylogeny of the family Acrocephalidae (Aves: Passeriformes) — The traditional taxonomy overthrown. Molecular Phylogenetics and Evolution, 52, pp. 866-878.
We present the first study of the warbler family Acrocephalidae based on one mitochondrial and three nuclear DNA loci, in total 2900 bp, including most or all of the species in three (Acrocephalus, Hippolais and Chloropeta) of the four genera and one species in the fourth genus (Nesillas) in this family. All three genera were suggested to be non-monophyletic, although the non-monophyly of Acrocephalus is not fully convincingly demonstrated. Six major clades were found, which agreed largely with the results from two earlier mitochondrial studies, and for which the names Hippolais, Iduna, Acrocephalus, Calamocichla, Notiocichla and Calamodus have been used. However, the results also revealed some new constellations, due to better resolution of deeper nodes and the inclusion of more taxa. The taxonomic implications are discussed.

Gelang, M. Cibois, A., Pasquet, E., Olsson, U., Alström, P. & Ericson, P.G.P. 2009. Phylogeny of babblers (Aves, Passeriformes): major lineages, family limits and classification. Zoologica Scripta, 38, pp 225-236.
Babblers, family Timaliidae, have long been subject to debate on systematic position, family limits and internal taxonomy. In this study, we use five molecular regions to estimate the relationships among a large proportion of genera traditionally placed in Timaliidae. We find good support for five main clades within this radiation, and propose a new classification, dividing the babblers into the families Sylviidae and Timaliidae. Within the latter family, four subfamilies are recognized: Zosteropinae, Timaliinae, Pellorneinae and Leiothrichinae. Several taxa, previously not studied with molecular data, are phylogenetically placed within Sylviidae or Timaliidae. This is, however, not the case for the genus Pnoepyga, for which we propose the family name Pnoepygidae fam. n.

Irestedt, M., Fjeldså, J., Dalén, L. & Ericson, P.G.P. 2009. Convergent evolution, habitat shifts and variable diversification rates in the ovenbird-woodcreeper family (Furnariidae). BMC Evolutionary Biology, 9:268.
The Neotropical ovenbird-woodcreeper family (Furnariidae) is an avian group characterized by exceptionally diverse ecomorphological adaptations. For instance, members of the family are known to construct nests of a remarkable variety. This offers a unique opportunity to examine whether changes in nest design, accompanied by expansions into new habitats, facilitates diversification. We present a multi-gene phylogeny and age estimates for the ovenbird-woodcreeper family and use these results to estimate the degree of convergent evolution in both phenotype and habitat utilisation. Furthermore, we discuss whether variation in species richness among ovenbird clades could be explained by differences in clade-specific diversification rates, and whether these rates differ among lineages with different nesting habits. In addition, the systematic positions of some enigmatic ovenbird taxa and the postulated monophyly of some species-rich genera are evaluated.
  The phylogenetic results reveal new examples of convergent evolution and show that ovenbirds have independently colonized open habitats at least six times. The calculated age estimates suggest that the ovenbird-woodcreeper family started to diverge at ca 33 Mya, and that the timing of habitat shifts into open environments may be correlated with the aridification of South America during the last 15 My. The results also show that observed large differences in species richness among clades can be explained by a substantial variation in net diversification rates. The synallaxines, which generally are adapted to dry habitats and build exposed vegetative nests, had the highest diversification rate of all major furnariid clades.
  Several key features may have played an important role for the radiation and evolution of convergent phenotypes in the ovenbird-woodcreeper family. Our results suggest that changes in nest building strategy and adaptation to novel habitats may have played an important role in a diversification that included multiple radiations into more open and bushy environments. The synallaxines were found to have had a particularly high diversification rate, which may be explained by their ability to build exposed vegetative nests and thus to expand into a variety of novel habitats that emerged during a period of cooling and aridification in South America.

Irestedt, M., Jønsson, K.A., Fjeldså, J., Christidis, L. & Ericson, P.G.P. 2009. An unexpectedly long history of sexual evolution in birds-of-paradise. BMC Evolutionary Biology 2009, 9:235.
The birds-of-paradise (Paradisaeidae) form one of the most prominent avian examples of sexual selection and show a complex biogeographical distribution. The family has accordingly been used as a case-study in several significant evolutionary and biogeographical syntheses. As a robust phylogeny of the birds-of-paradise has been lacking, these hypotheses have been tentative and difficult to assess. Here we present a well supported species phylogeny with divergence time estimates of the birds-of-paradise. We use this to assess if the rates of the evolution of sexually selected traits and speciation have been excessively high within the birds-of-paradise, as well as to re-interpret biogeographical patterns in the group.
  The phylogenetic results confirm some traditionally recognized relationships but also suggest novel ones. Furthermore, we find that species pairs are geographically more closely linked than previously assumed. The divergence time estimates suggest that speciation within the birds-of-paradise mainly took place during the Miocene and the Pliocene, and that several polygynous and morphologically homogeneous genera are several million years old. Diversification rates further suggest that the speciation rate within birds-of-paradise is comparable to that of the enitre core Corvoidea.
  The estimated ages of morphologically homogeneous and polygynous genera within the birds-of-paradise suggest that there is no need to postulate a particularly rapid evolution of sexually selected morphological traits. The calculated divergence rates further suggest that the speciation rate in birds-of-paradise has not been excessively high. Thus the idea that sexual selection could generate high speciation rates and rapid changes in sexual ornamentations is not supported by our birds-of-paradise data. Potentially, hybridization and long generation times in polygynous male birds-of-paradise have constrained morphological diversification and speciation, but external ecological factors on New Guinea may also have allowed the birds-of-paradise to develop and maintain magnificent male plumages. We further propose that the restricted but geographically complex distributions of birds-of-paradise species may be a consequence of the promiscuous breeding system.

Miller, W. Drautz, D.I., Janecka, J.E., Leskc, A.M., Ratan, A., Tomsho, L.P., Packard, M., Zhang, Y., McClellan, L.R., Qi, J., Zhao, F., Gilbert, M.T.P., Dalén L., Arsuaga, J.L., Ericson, P.G.P., Huson, D.H., Helgen, K.M., Murphy, W.J., Götherström, A., Schuster, S.C. 2009. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Research, 19, pp. 213-220.
We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine´s phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine´s basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first highfidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples´ heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wildcaptured individual and one born in captivity. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

Norman, J.A., Ericson, P.G.P., Jønsson, K.A., Fjeldså, J. & Christidis, L. 2009. A multigene phylogeny reveals novel relationships for aberrant genera of Australo-Papuan core Corvoidea and polyphyly of the Pachycephalidae and Psophodidae (Aves: Passeriformes). Molecular Evolution and Phylogenetics, 52, pp. 488-497.
A range of molecular data sets have identified the Australo-Papuan region as the center of diversification for the oscine passerines. Although the core Corvoidea is the largest and most diverse assemblage within the Australo-Papuan region, its composition and intergeneric relationships are relatively poorly understood. In order to provide better clarity on these issues we obtained DNAsequence data from the nuclear gene regions RAG-1 and myoglobin intron II, and the mitochondrial cytochrome b gene for 36 species of core Corvoidea representing the major lineages from Australo-Papua and including many of the aberrant genera. Bayesian and likelihood analysis of single gene and combined trees indicated that myoglobin intron II provided the best resolution relative to RAG-1 and cytochrome b. Machaerirhynchus (generally considered to be allied to the Monarchidae) and Rhagologus, (Pachycephalidae) were both strongly linked with the Artamidae (Gymnorhina, Artamus, Peltops). The highly enigmatic Ifrita was found to be part of an assemblage that included the Monarchidae and Paradisaedae. The Rhipiduridae, Dicuridae and Corcoracidae were also linked to this assemblage. There was no support for a monophyletic Pachycephalidae, which instead was broken up into several smaller clades. One of these included Pachycephala, Colluricincla, parts of Pitohui and arguably Falcunculus. Another clade comprised Oreoica and Aleadryas to which Pitohui cristatus has also been linked. The Psophodidae was found to be polyphyletic; Ptilorrhoa and Cinclosoma formed a clade but Psophodes was not part of and it and was not closely allied to any of the genera examined. The phylogenetic insights gained from this study are discussed in a biogeographic context. 

Ohlson, J. I., Fjeldså, J. & Ericson, P.G.P. 2009. A new genus for three species of tyrant flycatchers (Passeriformes: Tyrannidae), formerly placed in Myiophobus. Zootaxa, 2290, pp. 36-40.
A new genus, Nephelomyias, is erected for three species of Andean tyrant flycatchers (Aves: Passeriformes: Tyrannidae) traditionally placed in the genus Myiophobus. An extensive study based on molecular data has shown that they form a well supported clade that is not closely related to other Myiophobus species. Instead, they form a small independent lineage in Tyrannidae, together with Pyrrhomyias, Hirundinea and Myiotriccus.

Sangster, G. 2009. Acoustic differences between the scoters Melanitta nigra nigra and M. n. americana. Wilson J. Ornithol., 121, 696-702.
Scoter vocalizations may play a role in pair formation and pair bonding. I compared the courtship calls of male Black Scoters (Melanitta nigra nigra and M. n. americana) using published and archived recordings. Courtship calls of the two subspecies differed diagnosably in duration. In contrast, recordings from different localities within the ranges of each taxon showed no diagnosable differentiation. This finding represents the first indication that these taxa differ in characters other than bill morphology and supports recent proposals to treat M. n. americana as a distinct species (M. americana). In contrast to courtship displays, vocal displays of ducks have never been used for the assessment of species limits in Anatidae. My results indicate that vocalizations are a potentially useful additional character in the species-level taxonomy of ducks.

Sangster, G. 2009. Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation. Proc. R. Soc. London Ser. B. 276: 3185-3191.
The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation´. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950—2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress´.

Sangster, G., van den Berg, A.B., van Loon, A.J. & Roselaar, C.S. 2009. Dutch avifaunal list: taxonomic changes in 2004-2008. Ardea, 97: 373-381.
This is the third update on the taxonomy of species and higher taxa on the Dutch List since Voous (1977). It summarizes decisions made by the Commissie Systematiek Nederlandse Avifauna (CSNA) between Jan 2004 and Dec 2008. Changes in this report fall into five categories: (1) the sequence within and among some groups is changed to reflect their phylogenetic relationships (flamingos and grebes, eagles, shanks, gulls, terns, swallows and tits); (2) 20 scientific names are changed due to generic revisions (Aquila pennata, A. fasciata, Chroicocephalus genei, C. philadelphia, C. ridibundus, Hydrocoloeus minutus, Onychoprion anaethetus, Sternula albifrons, Hydroprogne caspia, Megaceryle alcyon, Cecropis daurica, Geokichla sibirica, Cyanistes caeruleus, Lophophanes cristatus, Periparus ater, Poecile montanus, P. palustris, Pastor roseus, Agropsar sturninus, Melospiza melodia); (3) two scientific names replace others presently on the list due to the recognition of extralimital taxa as species (Turdus eunomus, T. atrogularis); (4) one species is added because of a split from a species already on the Dutch List (Sylvia subalpina); (5) two species become monotypic due to the recognition of an extralimital taxon as species (Tarsiger cyanurus, Oenanthe pleschanka).

Ödeen, A., Håstad, O. & Alström, P. 2009. Evolution of ultraviolet vision in shorebirds (Charadriiformes). Biology Letters.
Diurnal birds belong to one of two classes of colour vision. These are distinguished by the maximum absorbance wavelengths of the SWS1 visual pigment sensitive to violet (VS) and ultraviolet (UVS). Shifts between the classes have been rare events during avian evolution. Gulls (Laridae) are the only shorebirds (Charadriiformes) previously reported to have the UVS type of opsin, but too few species have been sampled to infer that gulls are unique among shorebirds or that Laridae is monomorphic for this trait. We have sequenced the SWS1 opsin gene in a broader sample of species. We confirm that cysteine in the key amino acid position 90, characteristic of the UVS class, has been conserved throughout gull evolution but also that the terns Anous minutus, A. tenuirostris and Gygis alba, and the skimmer Rynchops niger carry this trait. Terns, excluding Anous and Gygis, share the VS conferring serine in position 90 with other shorebirds but it is translated from a codon more similar to that found in UVS shorebirds. The most parsimonious interpretation of these findings, based on a molecular gene tree, is a single VS to UVS shift and a subsequent reversal in one lineage.

Alström, P., Olsson, U., Lei, F., Wang, H-t., Gao, W. & Sundberg, P. 2008.
Phylogeny and classification of the Old World Emberizini (Aves, Passeriformes). Molecular Phylogenetics and Evolution, 47, pp. 960-973.
The phylogeny of the avian genus Emberiza and the monotypic genera Latoucheornis, Melophus and Miliaria (collectively the Old World Emberizini), as well as representatives for the New World Emberizini, the circumpolar genera Calcarius and Plectrophenax and the four other generally recognized tribes in the subfamily Emberizinae was estimated based on the mitochondrial cytochrome b gene and introns 6—7 of the nuclear ornithine decarboxylase (ODC) gene. Our results support monophyly of the Old World Emberizini, but do not corroborate a sister relationship to the New World Emberizini. Calcarius and Plectrophenax  form a clade separated from the other Emberizini. This agrees with previous studies, and we recommend the use of the name Calcariini. Latoucheornis, Melophus and Miliaria are nested within Emberiza, and we therefore propose they be synonymized with Emberiza. Emberiza is divided into four main clades, whose relative positions are uncertain, although a sister relation between a clade with six African species and one comprising the rest of the species (30, all Palearctic) is most likely. Most clades agree with traditional, morphology-based, classifications. However, four sister relationships within Emberiza, three of which involve the previously recognized Latoucheornis, Melophus and Miliaria, are unpredicted, and reveal cases of strong morphological divergence. In contrast, the plumage similarity between adult male Emberiza (formerly Latoucheornis) siemsseni and the nominate subspecies of the New World Junco hyemalis is shown to be the result of parallel evolution. A further case of parallel plumage evolution, between African and Eurasian taxa, is pointed out. Two cases of discordance between  the mitochondrial and nuclear data with respect to branch lengths and genetic divergences are considered to be the result of introgressive hybridization.

Alström, P, Rasmussen, P.C., Olsson, U., & Sundberg, P. 2008. Species delimitation based on multiple criteria: the Spotted Bush Warbler Bradypterus thoracicus complex (Aves, Megaluridae). Zoological Journal of the Linnean Society, 154, pp. 291-307.
We demonstrate the importance of using multiple criteria in species delimitations, whatever the conceptual base for species delimitation. We do this by studying plumage, biometrics, egg coloration, song, mitochondrial DNA and habitat/altitudinal distribution in the Spotted Bush Warbler Bradypterus thoracicus (Blyth) complex, and by conducting playback experiments. Taxa that we suggest are best treated as separate species [B. thoracicus (Blyth), B. davidi (La Touche) and B. kashmirensis (Sushkin)] differ in most or all of these aspects, particularly in song and mitochondrial DNA, while those that we treat as subspecies (suschkini) or synonyms (przevalskii) differ slightly and only in morphology.

Ericson, P.G.P. 2008.
Current perspectives on the evolution of birds. Contributions to Zoology, 77, pp. 109-116.
The paper summarizes the current understanding of the evolution and diversification of birds. New insights into this field have mainly come from two fundamentally different, but complementary sources of information: the many newly discovered Mesozoic bird fossils and the wealth of genetic analyses of living birds at various taxonomic levels. The birds have evolved from theropod dinosaurs from which they can be defined by but a few morphological characters. The early evolutionary history of the group is characterized by the extinctions of many major clades by the end of the Cretaceous, and by several periods of rapid radiations and speciation. Recent years have seen a growing consensus about the higher-level relationships among living birds, at least as can be deduced from genetic data.

Fuchs, J., Ericson, P.G.P. & Pasquet, E. 2008. Mitochondrial phylogeographic structure of the White-browed Piculet (Sasia ochracea): cryptic genetic differentiation and endemism in Indochina. Journal of Biogeography, 35, pp. 565-575.
Our understanding of geographical patterns of gene flow between populations of birds in the Indo-Malayan faunal region is surprisingly poor compared to in other parts of the World. Nevertheless, a thorough knowledge of general patterns of phylogeographic structure is utterly important for conservation purposes. Species with poor dispersal capacities could serve as indicators of endemism and genetic isolation in the Indochinese subregion. From their morphology (tiny size, short tail, short and rounded wings), piculets of the genus Sasia are inferred to have poor dispersal capacities and we thus studied the pattern of genetic variation within this species. We sampled 43 individuals throughout the breeding range of Sasia ochracea. DNA was extracted from both fresh tissues (N=15) and toe pads from ancient museum skins (N=28). We amplified a 801 bp fragment of the mitochondrial ND2 gene to reconstruct the phylogeographic history of the White-Browed Piculet. The sequence data were analysed using Bayesian inference, statistical parsimony and population genetics methods (analysis of molecular variance, mismatch distribution). We estimated the amount of ongoing gene flow using the coalescent-based method implemented in Mdiv. The analysis of molecular variance indicated that the current taxonomy does not adequately reflect the amount of genetic variation within Sasia ochracea., as the wide majority of the genetic variation was nested within the nominal subspecies, which is distributed from Nepal to Cochinchina. BI analyses and haplotype network suggest the occurrence of five main lineages that strongly correlate with geography. Our coalescent-based analyses indicated very limited amount of ongoing gene flow between these five lineages. Our dating analyses suggest that the genetic structuring likely occurred during the last 400 kyrs. Our analyses revealed that Sasia ochracea is composed of at least five lineages: Southern Vietnam (South-Annam and Cochinchina), India and Nepal, Myanmar and India, Indochina, and probably Tenasserim. We strongly recommend that studies aiming to understand the phylogeographic structure within Indo-Malayan species sample these areas.

Fuchs, J., Pons, J.-M., Ericson, P.G.P., Bonillo, C., Couloux, A. & Pasquet, E. 2008. Molecular support for a rapid cladogenesis of the woodpecker clade Malarpicini, with further insights into the genus Picus (Piciformes: Picinae). Molecular Phylogenetics and Evolution, 48, pp. 34-46.
Despite the considerable advances in recent years of our understanding of the systematics and evolution of the woodpeckers (Aves: Picidae), many unresolved issues remain. For example, it has been shown that several of the currently recognized genera are non-monophyletic. One of these is Picus although it has been only moderately sampled so far. Being widely distributed in Eurasia and adapted to many different habitats the genus Picus serve as an interesting taxon for studies of biogeography and speciation, but these are hampered by our poor understanding of the systematics of the genus. In order to outline the internal systematic relationships of Picus we sequenced seven loci (four autosomal, one Z-linked and two mitochondrial) with different evolutionary dynamics for all but two species of Picus. Our results show that the species currently placed into the genus Picus fall into two subclades. We propose that the genus is split so that miniaceus Pennant 1769, flavinucha Gould 1834 and mentalis Temminck 1825 are placed in a separate genus, Chrysophlegma Gould, 1850, while the remaining species are retained in Picus. The inclusion in our study of representatives of all genera included in the tribe Malarpicini, a group of woodpeckers which has proven difficult to resolve in several previous molecular studies, also allowed us to determine the earliest divergences within this clade. The results suggest that the low level of basal resolution in Malarpicini is attributable to multiple cladogenetic events in a short period of time rather than insufficient character sampling. This conclusion is supported by the observation of nucleotide insertion-deletions that support mutually exclusive phylogenetic hypotheses in different gene trees. We attribute this pattern of incongruent indels, together with short internodes in the tree, to incomplete lineage sorting.

Gilbert, M.T.P., Drautz, D.I., Leskc, A.M., Ho, S.Y.W., Qi, J.,Ratan, A., Hsu, C.-H., Sher, A., Dalén L., Götherström, A., Tomsho, L.P., Rendulic, S., Packard, M., Campos, P.F., Kuznetsova, T., Shidlovskiy, F., Tikhonov, A., Willerslev, E., Iacumin, P., Buigues, B., Ericson, P.G.P., Germonpré, M., Kosintsev, P., Nikolaev, V., Nowak-Kemp, M.Knight, J.R., Irzyk, G.P., Perbost, C.S., Fredrikson, K.M., Harkins, T.T., Sheridan, S., Miller, W. & Schuster, S.C.  2008. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences, USA, 105, pp. 8327-8332.
We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, 1—2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the 14C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

Irestedt, M. & Ohlson, J.I. 2008. The division of the major songbird radiation into Passerida and “core Corvoidea“ (Aves: Passeriformes) - the species tree versus gene trees. Zoologica Scripta, 37, pp. 305-313.
The knowledge of evolutionary relationships among oscine songbirds has been largely improved in recent years by molecular phylogenetic studies. However, current knowledge is still largely based on sequence data from a limited number of loci. In this study we reevaluate relationships among basal lineages within the “core Corvoidea“ and Passerida radiations, by adding additional loci to previously published data. The trees obtained from the individual genes suggest incongruent topologies. Especially the positions of Callaeatidae (wattlebirds), Cnemophilidae (satinbirds) and Melanocharitidae (longbills and berrypeckers) vary among the trees, but RAG-1 is the only gene that unambiguously suggested a “core Corvoidea“ affinity for these taxa. Analyses of various combined data sets shows that the phylogenetic positions for Callaeatidae, Cnemophilidae and Melanocharitidae largely depend on which genes that have been combined. As the RAG-1 gene has contributed to a majority of the phylogenetic information in previous studies, it has deeply influenced previous molecular affinities of these taxa. Based on current data we found a reasonable support for a Passerida affinity of Callaeatidae and Cnemophilidae, contrary to previous molecular studies. The position of Melanocharitidae is more unstable but a basal position among Passerida is congruent with a deletion observed in the GAPDH loci. Molecular clock estimations conducted on the combined data sets were generally found to be similar, but for some divergences significant differences were found. These results illustrate the potential problem of phylogenies predominantly based on characters from one or a few loci, and exemplify the importance of well supported phylogenies before reasonable time estimates of passerine divergences could be achieved.

Johansson, U.S., Bowie, R.C.K. & Fjeldså, J. 2008. Phylogenetic relationships within Passerida (Aves: Passeriformes): a review and a new molecular phylogeny based on three nuclear intron markers. Molecular Phylogenetics and Evolution, 48, pp. 858-876.
The avian clade Passerida was first identified based on DNA-DNA hybridization data [C.G. Sibley and J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Monophyly of the Passerida, with the exception of a few taxa, has later been corroborated in several studies; however the basal phylogenetic relationships have remained poorly understood. In this paper we review the current knowledge of the phylogenetic relationships within Passerida and present a new phylogeny based on three nuclear introns (myoglobin intron 2, ornithine decarboxylase introns 6 and 7, as well as β-fibrinogen intron 5). Our findings corroborate recent molecular hypotheses, but also identify several hitherto unrecognized relationships.

Johansson, U.S., Bowie, R.C.K., Hackett, S.J. & Schulenberg, T.S. 2008. The phylogenetic affinities of Crossley's Babbler (Mystacornis crossleyi): adding a new niche to the vanga radiation of Madagascar. Biology Letters, 4, pp. 677-680.
Crossley´s Babbler (Mystacornis crossleyi) is a passerine endemic to Madagascar. Traditionally it has been classified as a babbler (Timaliidae), although affinities with warblers and vangas have been suggested. We investigated the phylogenetic affinities of Crossley´s Babbler using sequence data from two nuclear introns (myoglobin intron 2 and β-fibrinogen intron 5) and one mitochondrial gene (ND2). We present for the first time a molecular phylogeny that confidently places this enigmatic species within the vangas (Vangidae). The inclusion of Crossley´s Babbler within the vangas adds another foraging niche - gleaning small invertebrates from the ground - to this already large adaptive radiation of songbirds.

Jønsson, K.A., Irestedt, M., Fuchs, J., Ericson, P.G.P., Christidis, L., C.K.Bowie, R., Norman, J.A., Pasquet, E., Fjeldså, J. 2008. Explosive avian radiations and multi-directional dispersal across Wallacea: Evidence from the Campephagidae and other Crown Corvida (Aves). Molecular Phylogenetics and Evolution, 47, pp. 221-236.
The systematic relationships among avian families within Crown Corvida have been poorly studied so far and as such been of limited use for biogeographic interpretations. The group has its origin in Australia and is thought to have colonized Africa and the New World via Asia beginning some 35 Mya when terranes of Australian origin approached Asian landmasses. Recent detailed tectonic mapping of the origin of land masses in the region around Wallace´s line have revealed a particularly complex movement of terranes over the last 20-30 Myr. Thus the biogeographic dispersal pattern of Crown Corvida is a particularly exciting case for linking vicariance and dispersal events with Earth history. Here we examine phylogenetic affinities among 72 taxa covering a broad range of genera in the basal radiations within Crown Corvida with an emphasis on Campephagidae and Pachycephalidae. Bayesian analyses of nuclear DNA sequence data identified the family Campephagidae as monophyletic but the large genus Coracina is not. Within the family Pachycephalidae the genera Pachycephala and Colluricincla are paraphyletic with respect to each other. The resulting phylogeny suggests that patterns of dispersal across Wallace´s line are complex and began at least 25 Mya. We find evidence of explosive radiations and multi-directional dispersal within the last 10 My, and three independent long distance ocean dispersal events between Wallacea and Africa at 10-15 Mya. Furthermore, the study reveals that in the Campephagidae a complex series of dispersal events rather than vicariance is the most likely explanation for the current biogeographical pattern in the region.

Nylander, J.A.A., Olsson, U., Alström, P. & Sanmartín, I. 2008.
Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Systematic Biology, 57: pp. 257-268.
The phylogeny of the thrushes (Aves:Turdus) has been difficult to reconstruct due to short internal branches and lack of node support for certain parts of the tree. Reconstructing the biogeographic history of this group is further complicated by the fact that current implementations of biogeographic methods, such as  dispersal-vicariance analysis (DIVA; Ronquist, 1997), require a fully resolved tree. Here, we apply a Bayesian approach to dispersal-vicariance analysis that accounts for phylogenetic uncertainty and allows a more accurate analysis of the biogeographic history of lineages. Specifically, ancestral area reconstructions can be presented as marginal distributions, thus displaying the underlying topological uncertainty. Moreover, if there are multiple optimal solutions for a single node on a certain tree, integrating over the posterior distribution of trees often reveals a preference for a narrower set of solutions. We find that despite the uncertainty in tree topology, ancestral area reconstructions indicate that the Turdus clade originated in the eastern Palearctic during the Late Miocene. This was followed by a nearly dispersal to Afric afrom where a worldwide radiation took place. The uncertainty in tree topology and short branch lengths seems to indicate that this radiation took place within a limited time span during the Late Pliocene. The results support the role of Africa as a probable source area for intercontinental dispersals as suggested for other passerine groups, including basal diversification within the songbird tree.

Ohlson, J.I., Fjeldså, J. & Ericson, P.G.P. 2008. Tyrant flycatchers coming out in the open: phylogeny and ecological radiation of Tyrannidae (Aves, Passeriformes). Zoologica Scripta, 37, pp. 315-335.
Tyrant flycatchers constitute a substantial component of the land bird fauna in all South American habitats. Past interpretations of the morphological and ecological evolution in the group have been hampered by the lack of a wellresolved hypothesis of their phylogenetic interrelationships. Here, we present a well-resolved phylogeny based on DNA sequences from three nuclear introns for 128 taxa. Our results confirm much of the overall picture of Tyrannidae relationships, but also identify several novel relationships. The genera Onychorhynchus, Myiobius and Terenotriccus are placed outside Tyrannidae and may be more closely related to Tityridae. Tyrannidae consists of two main lineages. An expanded pipromorphine clade includes flatbills, tody-tyrants and antpipits but also Phylloscartes and Pogonotriccus. The spadebills, Neopipo and Tachuris are their closest relatives. The remainder of the tyrant flycatchers forms a well-supported clade, subdivided in two large subclades, which differ consistently in foraging behaviour, the perch-gleaning elaeniines and the sallying myiarchines, tyrannines and fluvicolines. A third clade is formed by the genera Myiotriccus, Pyrrhomyias, Hirundinea and three species currently placed in Myiophobus. Ancestral habitat reconstruction and divergence date estimation suggest that early divergence events in Tyrannida took place in a humid forest environment during the Oligocene. Large-scale diversification in open habitats is confined to the clade consisting of the elaeniines, myiarchines, tyrannines and fluvicolines. This radiation correlates in time to the expansion of semi-open and open habitats from the Mid-Miocene (ca 15 Mya) onwards. The pipromorphine, elaeniine and myiarchinetyrannine-fluvicoline clades each employ distinct foraging strategies (upward striking, perch-gleaning and sallying, respectively), but the degree of diversity in morphology and microhabitat exploitation is markedly different between these clades. While the pipromorphines and elaeniines each are remarkably homogenous in morphology and exploit a restricted range of microhabitats, the myiarchine-tyrannine-fluvicoline clade is more diverse in these respects. This greater ecological diversity, especially as manifested in their success in colonizing a wider spectrum of open habitats, appears to be connected to a greater adaptive flexibility of the search-and-sally foraging behaviour.

Zuccon, D., Pasquet, E. & Ericson, P.G.P. 2008. Phylogenetic relationships among Palearctic-Oriental starlings and mynas (genera Sturnus and Acridotheres: Sturnidae). Zoologica Scripta, 37, pp. 469-481.
We used nuclear and mitochondrial genes to generate a phylogenetic hypothesis for the Palearctic-Oriental starlings and mynas (genera Sturnus, Acridotheres, Leucopsar, Creatophora, and Fregilupus: Sturnidae). Our results indicate that the group underwent a rapid diversification in Asia since the late Miocene. A reassessment of the morphological and ecological characters used in previous taxonomic revisions shows that all characters are highly homoplasic. We suggest that the elevated morphological and ecological plasticity favoured the adaptation of starlings and mynas to the local environment, the exploitation of all niches and their successful radiation in southeast Asia. Under the current limits the genera Sturnus and Acridotheres are not monophyletic, and we propose a revised phylogenetic taxonomy for the entire clade. We confirm that the extinct Fregilupus varius is a starling and it colonised Réunion Island (Mascarenes) by transoceanic dispersal from Asia.

Alerstam, T., Rosén, M., Bäckman, J., Ericson, P.G.P. & Hellgren, O. 2007. Flight speeds among bird species: allometric and phylogenetic effects. PLoS Biology, 5 (8), e197.
Flight speed is expected to increase with mass and wing loading among flying animals and aircraft for fundamental aerodynamic reasons. Assuming geometrical and dynamical similarity, cruising flight speed is predicted to vary as (body mass)1/6 and (wing loading)1/2 among bird species. To test these scaling rules and the general importance of mass and wing loading for bird flight speeds, we used tracking radar to measure flapping flight speeds of individuals or flocks of migrating birds visually identified to species as well as their altitude and winds at the altitudes where the birds were flying. Equivalent airspeeds (airspeeds corrected to sea level air density, Ue) of 138 species, ranging 0.01—10 kg in mass, were analysed in relation to biometry and phylogeny. Scaling exponents in relation to mass and wing loading were significantly smaller than predicted (about 0.12 and 0.32, respectively, with similar results for analyses based on species and independent phylogenetic contrasts). These low scaling exponents may be the result of evolutionary restrictions on bird flight-speed range, counteracting too slow flight speeds among species with low wing loading and too fast speeds among species with high wing loading. This compression of speed range is partly attained through geometric differences, with aspect ratio showing a positive relationship with body mass and wing loading, but additional factors are required to fully explain the small scaling exponent of Ue in relation to wing loading. Furthermore, mass and wing loading accounted for only a limited proportion of the variation in Ue. Phylogeny was a powerful factor, in combination with wing loading, to account for the variation in Ue. These results demonstrate that functional flight adaptations and constraints associated with different evolutionary lineages have an important influence on cruising flapping flight speed that goes beyond the general aerodynamic scaling effects of mass and wing loading.

Alström, P., Olsson, U., Rasmussen, P.C., Yao, C.-T., Ericson, P.G.P. & Sundberg, P. 2007. Morphological, vocal and genetic divergence in the Cettia acanthizoides complex (Aves: Cettiidae). Zoological Journal of the Linnean Society, 149, pp. 437-452.
We used morphological, vocal and molecular (one mitochondrial and two nuclear loci) data to re-evaluate the taxonomic status of the taxa acanthizoides, concolor and brunnescens in the Cettia acanthizoides (J. Verreaux, 1871) complex. We conclude that all three are valid taxa, and that acanthizoides of China and concolor of Taiwan are best treated as conspecific, while brunnescens of the Himalayas is better considered a separate species. The degree of morphological, acoustic and genetic differentiation is variably congruent among all taxa; the recently separated acanthizoides and concolor differ slightly in plumage and structure but are indistinguishable in vocalisations, while the earlier diverged brunnescens and acanthizoides/concolor differ only slightly more in morphology but to a much greater degree in vocalisations. We stress the essential nature of taxonomic revisions as a prerequisite for biodiversity estimates required for conservation planning.

Fjeldså, J., Irestedt, M., Jønsson, K.A., Ohlson, J.I. & Ericson, P.G.P. 2007. Phylogeny of the ovenbird genus Upucerthia: a case of independent adaptations for terrestrial life. Zoologica Scripta, 36, pp. 133-141.
In view of the amount of adaptive radiation among ovenbirds, Furnariinae, the traditional taxonomy needs scrutiny. We used nuclear DNA data to study relationships of the genus Upucerthia. Five species belong in the Furnariini, as traditionally assumed. The other species represent two independent cases of specialization for terrestrial life, in response to formation of arid habitats in the southern Andes, within the paraphyletic assemblage of arboreal species referred to as Philydorini.

Fuchs, J., Ohlson, J.I., Ericson, P.G.P. & Pasquet, E. 2007. Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data. Zoologica Scripta, 36, pp. 11-25.
The woodpeckers (Piciformes: Picinae) comprise a widely distributed and species-rich clade of birds that is strongly associated with trees for feeding, nesting, or both. Because of this association, woodpeckers provide a useful model for evaluating the impact of climatic and tectonic events on the diversification of forest birds during the Tertiary. In order to resolve the biogeographical history of the woodpeckers, we have analysed sequences from two nuclear introns and one mitochondrial gene using likelihood and Bayesian approaches. Our analyses favour a tropical Eurasian origin; divergences between African, Indo-Malayan and New World clades with subsequent colonizations of Africa and the New World occurred synchronously during the Middle Miocene, a period corresponding to the expansion of the C4 grasses and the uplift of the Himalayan-Tibetan plateau. The taxonomic diversification of woodpeckers at this time may be attributed to the fragmentation of forests in response to the drier climate, which in turn prevented gene flow between tropical stocks in Africa, Indo-Malaya and the New World. Our estimates of colonization times of South America predate the closure of the Panama Isthmus and support the hypothesis of a short-lived, terrestrial corridor at the end of the Miocene, 5.7 Myr BP.

Gilbert, M.T.P., Tomsho, L.P., Rendulic, S., Packard, M., Drautz, D.I., Sher, A., Tikhonov, A., Dalén L., Kuznetsova, T., Kosintsev, P., Campos, P.F., Higham, T., Collins, M.J., Wilson, A.S., Shidlovskiy, F., Buigues, B., Ericson, P.G.P., Germonpré, M., Götherström, A., Iacumin, P., Nikolaev, V., Nowak-Kemp, M., Willerslev, E., Knight, J.R., Irzyk, G.P., Perbost, C.S., Fredrikson, K.M., Harkins, T.T., Sheridan, S., Miller, W. & Schuster, S.C. 2007. Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science, 317, pp. 1927-1930.
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

Johansson, U.S., Alström, P., Olsson, U., Ericson, P.G.P., Sundberg, P. & Price, T.D. 2007. Build-up of the Himalayan avifauna through immigration: a biogeographical analysis of the Phylloscopus and Seicercus warblers. Evolution, 61, pp. 324-333. The Himalayan mountain range is one of the most species rich areas in the world, harboring ~8% of the world´s bird species. In this study, we compare the relative importance of immigration versus in situ speciation to the build-up of the Himalayan avifauna, by evaluating the biogeographic history of the Phylloscopus/Seicercus warblers, a speciose clade that is well represented in Himalayan forests. We use a comprehensive, multigene phylogeny in conjunction with dispersal-vicariance analysis to discern patterns of speciation and dispersal within this clade. The results indicate that virtually no speciation has occurred within the Himalayas. Instead, several speciation events are attributed to dispersal into the Himalayas followed by vicariance between the Himalayas and China/Southeast Asia. Most, perhaps all, of these events appear to be pre-Pleistocene. The apparent lack of speciation within the Himalayas stands in contrast to the mountain driven Pleistocene speciation suggested for the Andes and the East African mountains.

Jønsson, K.A., Fjeldså, J., Ericson, P.G.P. & Irestedt, M. (in press) Systematic placement of the enigmatic Eupetes macrocercus and implications for the biogeography of a main songbird radiation, the Passerida. Biology Letters, 3, pp. 323-326.
Biogeographic connections between Australia and other continents are still poorly understood although the plate tectonics of the Indo-Pacific region is now well described. Eupetes macrocercus is an enigmatic taxon distributed in a small area on the Malay Peninsula and on Sumatra and Borneo. It has generally been associated with Ptilorrhoa in New Guinea to the other side of Wallace´s Line but a relationship with the West African Picathartes has also been suggested. Using three nuclear markers, we demonstrate that Eupetes is the sister taxon of the South African genus Chaetops, and their sister taxon in turn being Picathartes, with a divergence in the Eocene. Thus this clade is distributed in remote corners of Africa and Asia which makes the biogeographic history of these birds very intriguing. The most parsimonious explanation would be that they represent a relictual basal group in the Passerida clade established, after a long-distance dispersal from the Australo-Papuan region to Africa. Many earlier taxonomic arrangements may have been based on assumptions about relationships with similar-looking forms in the same, or adjacent, biogeographic regions, and revisions with molecular data may uncover such cases of neglect of ancient relictual patterns reflecting past connections between the continents.

Ohlson, J.I., Prum, R.O. & Ericson, P.G.P. 2007. A molecular phylogeny of the cotingas (Aves: Cotingidae). Molecular Phylogenetics and Evolution, 42, pp. 25-37.
The phylogenetic relationships of members of Cotingidae were investigated using >2100 bp of sequence data from two nuclear introns (myoglobin intron 2 and G3PDH intron 11) and one protein-coding mitochondrial gene (cytochrome b). Strong support was found for a monophyletic clade including 23 traditional cotingid genera, corresponding to the Cotingidae sensu Remsen et al. (2005) Neither Oxyruncus nor any of the genera in Tityrinae sensu Prum et al. (2000) are members of Cotingidae. Within Cotingidae a polytomy of four well-supported clades was recovered: 1) the fruiteaters Pipreola and Ampelioides; 2) the Ampelion group, including Phytotoma, 3) Rupicola and Phoenicircus, and 4) the 'core cotingas' consisting of the remainder of the Cotingas (e.g. fruitcrows, Cotinga, Procnias, Lipaugus and Carpodectes), with Snowornis in a basal position. The separation of Snowornis from Lipaugus (Prum et al. 2000) was strongly supported, as were the close relationships between Gymnoderus and Conioptilon, and between Tijuca and Lipaugus. However, basal relationships among 'core cotinga' clades were not resolved.

Alström, P., Ericson, P.G.P., Olsson, U. & Sundberg, P. 2006. Phylogeny and classification of the avian superfamily Sylvioidea, based on nuclear and mitochondrial sequence data. Molecular Phylogenetics and Evolution, 38, pp. 381-397.
Sylvioidea is one of the three superfamilies recognized within the largest avian radiation, the parvorder Passerida. In the present study, which is the first taxon-dense analysis of the Sylvioidea, we use sequence data from the nuclear myoglobin intron II and mitochondrial cytochrome b gene to investigate the interrelationships among the four "sylvioid" clades found by previous workers, as well as the relationships within the largest of these clades. The nuclear and mitochondrial loci estimate basically the same phylogeny, with minor differences in resolution. The trees based on myoglobin and the combined data, respectively, identify a strongly supported clade that includes the taxa previously allocated to Sylvioidea, except for Sitta (nuthatches), Certhia (treecreepers), Parus (tits), Remiz (penduline tits), Troglodytes and Campylorhynchus (wrens), Polioptila (gnatcatchers), and Regulus (crests/kinglets); this also comprises larks, which have previously been placed in the superfamily Passeroidea. We refer to this clade as Sylvioidea. This clade is further divided into 11 main, well supported clades, which we suggest form the basis for a revised classification. In addition, our data suggest several cases of non-monophyletic genera.

Dalsätt, J., Mörs, T. & Ericson, P.G.P. 2006. Fossil Birds from the Miocene and Pliocene of Hambach (NW Germany). Paleontographica A, 277, pp. 113-121.
The bird remains are described from the Middle Miocene (MN 5) and Late Pliocene (MN 16) local faunas Hambach 6C and Hambach 11/13 from the Lower Rhine Basin in Northwestern Germany. Although the birds are the rarest vertebrate class in both faunas, at least the Miocene Hambach 6C site has produced one remarkable finding: the Old World´s earliest record of anhingas. The northernmost occurrence of Anhinga pannonica, yet another “tropical" element in the Hambach fauna, is a further evidence for the Mid-Miocene climate optimum. The seven avian specimens identified from Hambach 6C belong to Anhingidae, Anatidae, Galliformes, and Rallidae. Extant representatives of these taxa occupy different environments: anhingas, ducks, geese and rails are all aquatic or semiaquatic species, while the galliforms occur in terrestrial habitats. Thus the birds fit well in differentiated coastal lowland habitats of an estuarine environment as they are documented by the palaeoecology of the other vertebrates, with the exception that there are no repesentatives of exclusively marine birds.
The Late Pliocene of Hambach 11 and Hambach 13 has provided only three bird fossils, which belong to Anatidae and Galliformes. The few bird remains, washed together in a freshwater channel with numerous bones and teeth of mostly smaller vertebrates, also exhibit a mixture of aquatic and terrestrial birds. As the other vertebrates do, they document that different habitates formed the lowland surroundings of the Pliocene Lower Rhine Basin.

Dalsätt, J., Zhou, Z., Zhang, Z. & Ericson, P.G.P. 2006. Food remains in Confuciusornis sanctus suggest a fish diet. Naturwissenschaften, 93, pp. 444-446.
Despite hundreds of excellent fossils of Confuciusornis, the most abundant group of birds in the Early Cretaceous, ‘Jehol Biota´ in China, there is yet no indication of the food choice of these birds. Here, we describe fish remains preserved in the alimentary system of a specimen of Confuciusornis sanctus from the Jiufotang Formation. This find is about five million years younger than all previously published confuciusornithid birds from the Yixian Formation. Although it is unknown how common fish was in the diet of Confuciusornis, the find does not support previous hypotheses that it fed on plants or grain.

Ekman, J. & Ericson, P.G.P. 2006. Out of Gondwanaland; the evolutionary history of cooperative breeding and social behaviour among crows, magpies, jays and allies. Proceedings of the Royal Society of London, 273, pp. 1117-1125.
Cooperative breeding is comparatively rare among birds on the mainly temperate and boreal Northern Hemisphere. Here we test if the distribution of breeding system reflects a response to latitude in a phylogenetic analysis using correlates with geographical range among the corvids (crows, jays, magpies and allied groups). The corvids trace their ancestry to the predominantly cooperative ‘Corvida´ branch of oscine passerines from the Australo-Papuan region on the ancient Gondwanaland supercontinent, but we could not confirm the ancestral state of the breeding system within the family, while family cohesion may be ancestral. Initial diversification among pair-breeding taxa that are basal in the corvid phylogeny represented by genera, such as Pyrrhocorax and Dendrocitta, indicates that the corvid family in its current form could have evolved from pair-breeding ancestors only after they had escaped the Australo-Papuan shield. Within the family, cooperative breeding (alloparental care/family cohesion) is strongly correlated to latitude and its predominance in species maintaining a southerly distribution indicates a secondary evolution of cooperative breeding in the lineage leading away from the basal corvids. Multiple transitions show plasticity in the breeding system, indicating a response to latitude rather than evolutionary inertia. The evolutionary background to the loss of cooperative breeding among species with a northerly distribution is complex and differs between species, indicating a response to a variety of selection forces. Family cohesion where the offspring provide alloparental care is a main route to cooperatively breeding groups among corvids. Some corvid species only lost alloparental care while maintaining coherent family groups. Other species lost family cohesion, and as a corollary they also lost the behaviour, where retained offspring provide alloparental care.

Ericson, P.G.P., Anderson, C.L., Britton, T., Elzanowski, A., Johansson, U.S., Källersjö, M., Ohlson, J.I., Parsons, T.J., Zuccon, D. & Mayr, G. 2006. Diversification of Neoaves: integration of molecular sequence data and fossils. Biology Letters, 2, pp. 543-547.
Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

Ericson, P.G.P., Zuccon, D., Ohlson, J.I., Johansson, U.S., Alvarenga, H. & Prum, R.O. 2006. Higher level phylogeny and morphological evolution of tyrant flycatchers, cotingas, manakins and their allies (Aves: Tyrannida). Molecular Phylogenetics and Evolution, 40, pp. 471-483.
Despite increased understanding of higher-level relationships in passerine birds in the last 15 years, the taxonomic boundaries and phylogenetic interrelationships of the major groups of the Tyrannida (including the cotingas, manakins, tityrines and tyrant flycatchers) remain unclear. Here we present an analysis of DNA sequence data obtained from two nuclear exons, three introns, and one mitochondrial gene for 26 genera of Tyrannida and 6 tracheophone outgroups. The analysis resulted in well-supported hypotheses about the earliest evolution within Tyrannida. The Cotingidae, Pipridae, Tityrinae (sensu Prum et al., 2000), Tyrannidae, and the tyrannid subfamiles Tyranninae and Pipromorphinae (sensu Sibley and Monroe, 1990) were all found to be reciprocally monophyletic (given the present taxon sampling). The Cotingidae and Pipridae form a clade that is the sister group to a well-supported clade including Oxyruncus, the Tityrinae, Piprites, and the Tyrannidae. Oxyruncus is the sister group to the Tityrinae, and Piprites is placed as the sister group to the Tyrannidae. The tyrannid sufamilies Tyranninae and Pipromorphinae are monophyletic sister taxa, but the relationships of Platyrinchus mystaceus to these two clades remains ambiguous. The presence of medial (=internal) cartilages in the syrinx is a synapomorphy for the Oxyruncus-Tityrinae-Piprites-Tyrannidae clade. Although morphological synapomorphies currently support the monophyly of both the Pipridae and the Cotingidae, convergences and/or reversals in morphological character states are common in Tyrannida. The relationship between Oxyruncus and the Tityrinae is congruent with additional syringeal synapomorphies and allozyme distance data. Accordingly, we propose the recognition the family Tityridae within the Tyrannida to include the genera Schiffornis, Laniisoma, Laniocera, Iodopleura, Xenopsaris, Pachyramphus, Tityra, and Oxyruncus.

Fuchs, J., Ohlson, J.I., Ericson, P.G.P. & Pasquet, E. 2006. Molecular phylogeny and biogeographic history of the piculets (Piciformes: Picumninae). Journal of Avian Biology, 37, pp. 487-496.
The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short-tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in Southeast Asia) while the second concerns Picumnus (one species in Southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the Southeast Asian representative of Picumnus in their own monotypic genera (Verreauxia and Vivia, respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and ß-fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo-Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myrs BP. This time corresponds to the beginning of the formation of the Northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, Southeast Asia and South America, respectively.

Irestedt, M., Fjeldså, J. & Ericson, P.G.P. 2006. Evolution of the ovenbird-woodcreeper assemblage (Aves: Furnariidae) - major shifts in nest architecture and adaptive radiation. Journal of Avian Biology, 37, pp. 260-272.
The Neotropical ovenbirds (Furnariidae) form an extraordinary morphologically and ecologically diverse passerine radiation, which includes many examples of species that are superficially similar to other passerine birds as a resulting from their adaptations to similar lifestyles. The ovenbirds further exhibits a truly remarkable variation in nest types, arguably approaching that found in the entire passerine clade. Herein we present a genus-level phylogeny of ovenbirds based on both mitochondrial and nuclear DNA including a more complete taxon sampling than in previous molecular studies of the group. The phylogenetic results are in good agreement with earlier molecular studies of ovenbirds, and supports the suggestion that Geositta and Sclerurus form the sister clade to both core-ovenbirds and woodcreepers. Within the core-ovenbirds several relationships that are incongruent with traditional classifications are suggested. Among other things, the philydorine ovenbirds are found to be non-monophyletic. The mapping of principal nesting strategies onto the molecular phylogeny suggests cavity nesting to be plesiomorphic within the ovenbird-woodcreeper radiation. It is also suggested that the shift from cavity nesting to building vegetative nests is likely to have happened at least three times during the evolution of the group. We suggest that the shifts in nest architecture within the furnariine and synallaxine ovenbirds have served as an ecological release that has facilitated diversification into new habitats and new morphological specializations.

Irestedt, M., Ohlson, J.I., Zuccon, D., Källersjö, M. & Ericson, P.G.P. 2006. Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes). Zoologica Scripta, 35, pp. 567-580.
Museum study skins represent an invaluable source for DNA to be used in phylogenetics, phylogeography and population genetics. This becomes evident just by comparing the number of study skins of birds housed in museums worldwide (ca 10 millions) with the corresponding number of tissue samples (probably fewer than 500,000). While the laboratory techniques used so far have primarily allowed PCR-based studies of mitochondrial genes from museum skins, we here present the first avian phylogeny based on a large number of nuclear sequences. The targeted fragment size and the properties of the primers are important factors to obtain good amplification results. In this study we routinely amplified fragments of approximately 350 bp nuclear DNA.  This advancement in methodology opens up a new avenue for the use of avian museum skins, as nuclear DNA is especially useful when studying ancient patterns of diversification. The phylogenetic hypothesis of the Old World suboscines (Eurylaimides) presented herein, strongly supports a monophyletic origin of the pittas (Pittidae). The phylogeny further suggests that pittas could be divided into three major groups that are in overall good agreement with external morphological variation found in this group. Broadbills (Eurylaimidae), as currently defined, is on the other hand found to be a paraphyletic family as both Sapayoa aenigma and the asities (Philepittidae) are nested among them. Based on the phylogenetic results we suggest a revised classification of the “Old World" suboscines (Eurylaimides).

Olsson, U., Alström, P., Gelang, M., Ericson, P.G.P. & Sundberg, P. 2006. Phylogeography of Indonesian and Sino-Himalayan region bush warblers (Cettia, Aves). Molecular Phylogenetics and Evolution, 41, pp. 556-565.
We present a hypothesis for the phylogeny and phylogeography of a group of bush warblers in the genus Cettia, based on parts of the mitochondrial cytochrome b gene and the nuclear myoglobin intron II (in all ~1.7 kb). Ancestral areas were reconstructed by dispersal-vicariance analysis and constrained Bayesian inference. The results suggest that the insular taxa in the C. vulcania group are most closely related to C. flavolivacea,  and originated from a dispersal by an ancestral population in the Himalayas towards the south, to the Sunda region. From this population, a second dispersal along a different route colonized China and northern Vietnam. Hence, the Chinese taxon intricata and Vietnamese oblita, currently allocated to Cettia flavolivacea, are more closely related to the vulcania group than to the other taxa in the flavolivacea group, and we propose that they be treated as conspecific with C. vulcania, restricting C. flavolivacea to Myanmar and the Himalayas.

Qu, Y.H., Ericson, P.G.P., Lei, F.M., Gebauer, A., Kaiser, M. & Helbig, A. 2006. Molecular phylogenetic relationship of snow finch complex (genera Montifringilla, Pyrgilauda, and Onychostruthus) from the Tibetan plateau. Molecular Phylogenetics and Evolution, 40, pp. 218-226.
The snow finch complex (Montifringilla, Pyrgilauda, and Onychostruthus) has its center of distribution on the Tibetan plateau, with six out of seven species in the genera occurring there. Phylogenetic relationships among these six species of three genera have been studied based on DNA sequence data obtained from the mitochondrial cytochrome b gene and the nuclear myoglobin gene. The results support monophyly of the snow finch complex group and three major evolutionary lineages are recognized. The first clade consists of ruficollis, blanfordi, and davidiana. These three taxa are sometimes placed in their own genus, Pyrgilauda, and the DNA data supports this. The three taxa nivalis, henrici, and adamsi have traditionally been placed in the genus Montifringilla, and they group together strongly in the present analysis. The results further suggest that nivalis and adamsi are more closely related to each other than are nivalis and henrici, despite that the latter two are often regarded as conspecific. The third distinct lineage within the snow finch complex consists of taczanowskii, which has been placed its own genus, Onychostruthus. This taxon has a basal position in the phylogenetic tree and is sister to all other snow finches. We estimated that taczanowskii split from the other taxa between 2 and 2.5 mya, i.e., about the time for the most recent uplift of the Tibetan plateau, “the Tibet movement", 3.6-1.7 mya. Cladogenesis within the Montifringilla and Pyrgilauda clades seems to be contemporary with the second phase of “Tibet movement" at 2.5 mya and the third phase at 1.7 mya and “Kunhuang movement" in 1.5-0.6 mya. The dramatic climatic and ecological changes following from the uplift of the Tibetan plateau, together with the cyclic contraction and expansion of suitable habitats during the Pleistocene, are probably the most important factors for the cladogenesis in snow finch complex.

Zuccon, D., Cibois, A., Pasquet, E. & Ericson, P.G.P. 2006. Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa. Molecular Phylogenetics and Evolution, 41, pp. 333-344.
We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu Sibley and Monroe, 1990). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starling: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data presents evidence for the role of climatic changes in shaping present day distribution of the group.

Olson, S.L., Irestedt, M., Ericson, P.G.P. & Fjeldså, J. 2005. Independent evolution of two Darwinian marsh-dwelling ovenbirds (Furnariidae: Limnornis, Limnoctites). Ornitologia Neotropical16, pp. 347-359.
The Curve-billed Reedhaunter (Limnornis curvirostris) and the Straight-billed Reedhaunter (Limnoctites rectirostris) are marsh-dwelling ovenbirds that were first collected by Charles Darwin in Uruguay. Each has a limited distribution in southernmost Brazil, Uruguay, and northern Argentina, within which the birds occupy very distinct habitats. Originally described as congeners because of overall similarity of plumage, the two species have been treated as close relatives through most of their history despite obvious structural differences. We analyzed DNA sequences from three different genes of these species, comparing them with a wide variety of other species of Furnariidae and several outgroup taxa. Limnoctites rectirostris belongs among the species traditionally placed in Cranioleuca, being most closely related to the marsh-dwelling Sulphur-throated Spinetail (C. sulphurifera) among the species we sampled. This is supported by vocalizations and nidification. Limnornis curvirostris forms a clade with the Wren-like Rushbird (Phleocryptes melanops), with the Sharp-tailed Streamcreeper (Lochmias nematura) as a rather distant sister-taxon. A close relationship between Limnornis and Phleocryptes is supported by the apparently unique nest architecture and blue-green egg color.

Ericson, P.G.P., Jansén, A.-L., Johansson, U.S. & Ekman, J. 2005. Inter-generic relationships of the crows, jays, magpies and allied groups (Aves: Corvidae) based on nucleotide sequence data. Journal of Avian Biology, 36, pp. 222-234.
Phylogenetic relationships were studied based on DNA sequences obtained from all recognized genera of the family Corvidae sensu stricto. The aligned data set consists 2589 bp obtained from one mitochondrial and two nuclear genes. Maximum parsimony, maximum-likelihood, and Bayesian inference analyses were used to estimate phylogenetic relationships. The analyses were done for each gene separately, as well as for all genes combined. An analysis of a taxonomically expanded data set of cytochrome b sequences was performed in order to infer the phylogenetic positions of six genera for which nuclear genes could not be obtained. Monophyly of the Corvidae is supported by all analyses, as well as by the occurrence of a deletion of 16 bp in the ß-fibrinogen intron in all ingroup taxa. Temnurus and Pyrrhocorax are placed as the sister group to all other corvids, while Cissa and Urocissa appear as the next clade inside them. Further up in the tree, two larger and well-supported clades of genera were recovered by the analyses. One has an entirely New World distribution (the New World jays), while the other includes mostly Eurasian (and one African) taxa. Outside these two major clades are Cyanopica and Perisoreus whose phylogenetic positions could not be determined by the present data. A biogeographic analysis of our data suggests that the Corvidae underwent an initial radiation in Southeast Asia. This is consistent with the observation that almost all basal clades in the phylogenetic tree consist of species adapted to tropical and subtropical forest habitats.

Fjeldså, J., Irestedt, M. & Ericson, P.G.P. 2005. Molecular data reveal some major adaptational shifts in the early evolution of the most diverse avian family, the Furnariidae. Journal of Ornithology, 146, pp. 1-13.
A robust phylogeny for the family Furnariidae (sensu lato) was obtained using long sequences of nuclear and mitochondrial DNA. Contrary to the widely accepted sistergroup relationship of ovenbirds (Furnariinae) and woodcreepers (Dendrocolaptinae), a basal clade is suggested for Sclerurus and Geositta, and Xenops, hitherto considered an aberrant ovenbird, is transferred to the woodcreeper lineage. The morphological variation is re-interpreted in view of this revised phylogenetic hypothesis. Presumably, the remarkable adaptive radiation in this family started as primitive, Sclerurus-likes forms, which used the tail as a prop during terrestrial feeding, lured up to seek food on tree-trunks. The two basal woodcreeper genera Xenops and Glyphorynchus show strong cranial specializations for hammering in wood, thus presenting a remarkable parallelism with the family Picidae, Xenops resembling a piculet, Glyphorynchus a tiny woodpecker. However, this specialization was lost in other woodcreepers, which show a more normal passerine skull, adapted for probing and prying in tree-trunk crevices and sallying for escaping insects. The ovenbirds developed a more flexible (rhynchokinetic) bill, well suited for retrieving prey hiding in dead-leaf clusters suspended in the vegetation, and in masses of epiphytes. Adaptations to live in open terrain are secondary.

Johansson, U.S. & Ericson, P.G.P. 2005. A re-evaluation of basal phylogenetic relationships within trogons (Aves: Trogonidae) based on nuclear DNA sequences. Journal of Zoological Systematics and Evolutionary Research, 43, pp. 166-173.
The avian clade Trogonidae (trogons) consists of approximately 40 species distributed pantropically in the Neotropical, Afrotropical and Indomalayan zoogeographical regions. In this study we evaluate the basal phylogenetic relationships within the trogons based on DNA sequences from three nuclear introns (myoglobin intron 2, beta-fibrinogen intron 7 and glyceraldehydes-3-phosphodehydrogenase [G3PDH] intron 11). In addition, previously published cytochrome b and 12S sequences were re-analyzed and combined with the nuclear data set. The analysis of the three nuclear genes combined suggests a sister group relationship between the Afrotropical (Apaloderma) and Indomalayan (Harpactes) clades, whereas the Neotropical taxa (Trogon, Pharomachrus, and Priotelus) form an unresolved polytomy basal to these two groups. In addition, two of the three individual gene trees also support a sister group relationship between the Afrotropical and Indomalayan trogons. This is at odds with previously published studies based on mitochondrial sequence data and DNA-DNA hybridization. The third nuclear intron (G3PDH), however, suggests that the Afrotropical trogons are basal relative the other trogons. This was also suggested by the mitochondrial data set, as well as the analysis of the combined nuclear and mitochondrial data. Both of these conflicting hypotheses are supported by high posterior probabilities. An insertion in beta-fibrinogen further supports a basal position of the Afrotropical clade. Analyses of the myoglobin intron with additional outgroups place the root differently and strongly support monophyly of each of the zoogeographical regions (including the Neotropics), and these three clades form a basal trichotomy. This suggests that that rooting is a serious problem in resolving basal phylogenetic relationships among the trogons.

Olsson, U., Alström, P., Ericson, P.G.P. & Sundberg, P. 2005. Non-monophyletic taxa and cryptic species - evidence from a molecular phylogeny of leaf-warblers (Phylloscopus, Aves). Molecular Phylogenetics and Evolution, 36, pp. 261-276.
The avian taxa Cryptigata and Acanthopneuste have been treated either as subgenera within Phylloscopus (leaf-warblers), or as a distinct genus and an informal group, respectively. The circumscriptions of these taxa have varied between authors. We estimated the phylogeny, based on the mitochondrial cytochrome b and 12S genes and the nuclear myoglobin intron II, of all except two of the species placed in the Cryptigata and Acanthopneuste groups, as well as two recently described species and representatives of all subgenera and major clades in Phylloscopus and Seicercus recognized by previous studies. Neither Cryptigata nor Acanthopneuste are found to be monophyletic. The polytypic species P. reguloides and P. davisoni show unexpectedly deep divergences between some of their respective subspecies, and the latter species is non-monophyletic. We propose that the former be split into three species and the latter into two species. Seicercus xanthoschistos is nested in a clade that includes only Phylloscopus, and we recommend that it be placed in Phylloscopus. The rate of morphological divergence varies considerably among the taxa in this study. Our results emphasize the importance of dense taxon sampling in intrageneric phylogenetic studies.

Qu, Y.H., Ericson, P.G.P., Lei, F.M. & Li, S. H. 2005. Post-glacial colonization of the Tibetan plateau inferred from the matrilineal genetic structure of the endemic red-necked snow finch, Pyrgilauda ruficollis. Molecular Ecology, 14, pp. 1767-1781.
Most phylogeographic studies of post-glacial colonization focus on high latitude locations in the northern hemisphere. Here, we studied the phylogeographic structure of the red-necked snow finch Pyrgilauda ruficollis, an endemic species of the Tibetan plateau. We analyzed 879 bp of the mitochondrial cytochrome b gene and 529 bp of the control region in 41 birds from four regional groups separated by mountain ranges. We detected 34 haplotypes, 31 of which occurred in a single individual and only three of which were shared among sampling sites within regional groups or among regional groups. Haplotype diversity was high (h=0.94); nucleotide diversity was low (ð=0.00415) and genetic differentiation was virtually non-existent. Analyses of mismatch distributions and geographically nested clades yielded results consistent with contiguous range expansion, and the expansion times were estimated as 0.07 to 0.19 mya. Our results suggest that P. ruficollis colonized the Tibetan plateau after the extensive glacial period (0.5 to 0.175 mya), expanding from the eastern margin towards the inner plateau. Thus, in contrast to many of the post-glacial phylogeographic structures known at high latitudes, this colonization occurred without matrilineal population structuring. This might be due to the short glacial cycles typical of the Tibetan plateau, adaptation of P. ruficollis to cold conditions, or refugia and colonized habitat being semi-continuous and thus promoting population mixing.

Irestedt, M., Fjeldså, J., Nylander, J.A.A. & Ericson, P.G.P. 2004. Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors. BMC Evolutionary Biology 2004 4:23.
The typical antbird (Thamnophilidae) forms a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set. The phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the Terenura antwrens, the wing-banded antbird (Myrmornis torquata), the spot-winged antshrike (Pygiptila stellaris) and the russet antshrike (Thamnistes anabatinus) are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the Herpsilochmus antwrens, while the second clade consists of most antwren genera, the Myrmeciza antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of Myrmotherula antwrens and Myrmeciza antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood. The phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and morphological adaptations to new habitats or food sources, and genera like Myrmeciza antbirds and the Myrmotherula antwrens obviously need taxonomic revisions. Although, Bayes factors seem promising for evaluating the relative contribution of components to an evolutionary model, the results suggests that even if strong evidence for a model allowing separate topology parameters is found, this might not mean strong evidence for separate gene phylogenies, as long as vital components of the substitution model are still missing.

Ericson, P.G.P. & Sjögren, H. 2004. Boken om göken. Bokförlaget Atlantis. 92 pp.
Redan aristoteles förundrades mycket över gökens levnadsvanor. Han visste att gökars ägg varierar i utseende beroende på hos vilka fosterföräldrar de ska läggas, men hur kunde gökhonan veta vilken värdart hon skulle besöka? Och varför tillät fosterföräldrarna att gökungen kastade deras ägg och ungar ur boet? Svaren på dessa och andra frågor om göken var länge lika fantasieggande som felaktiga. Först idag, genom nogsamt planerade experiment och DNA-analyser, kan gökens beteende ges sin förklaring. Författarna har gjort en beskrivande och avslöjande bok om gökens märkliga liv, alltifrån äggets vandring i äggledaren till den vuxna fågelns långa höstflyttning till Afrika. Boken är rikt illustrerad bl a med bilder som på ett helt nytt sätt tolkar och visar samspelet mellan gökens och värdarternas äggutseenden. Gökens snillrikt bedrägliga beteende visas även i en serie unika foton.

Ericson, P.G.P. & Tyrberg, T. 2004. The early history of the Swedish avifauna. A review of the subfossil record and early written sources. Kungl. Vitterhets Historie och Antikvitets Akademiens Handlingar, Antikvariska serien, 45, 349 pp.
Many animal and plant species recolonized Scandinavia as soon as suitable living conditions appeared after the last ice age. Other species have reached Scandinavia later, while several of the first immigrants have ceased to breed due to lack of suitable habitats and other factors. Changes of the composition of the Swedish avifauna during the 14,000 years since deglaciation began are analyzed herein based on archaeozoological data from bird remains recovered from more than 500 archaeological and natural deposits. For the post-Medieval period, up to ca AD 1800, the biogeographic analysis is based on written (but often unpublished) accounts. Although the subfossil record of birds is unevenly distributed in time and space, certain general patterns of the evolution and distribution of the Swedish avifauna can be observed. A large proportion of the species that inhabit Sweden today seemingly immigrated quite soon after the ice withdrew. The most important route of immigration was from the south and west, but later immigrants also followed northerly or easterly routes. The results also show that some species, traditionally regarded as very late immigrants (e.g., Mute Swan, Pochard and Partridge), have bred in Sweden for several thousand years. Other species, such as the White Stork and Black Stork, have no subfossil record and are suggested to have immigrated after the medieval period. The book contains a brief outline of the postglacial history of the Scandinavian fauna and flora, as well as a discussion about the characteristics of the archaeozoological source material. It also includes chapters on the history of domesticated birds and prehistoric falconry in Sweden.

Irestedt, M., Fjeldså, J. & Ericson, P.G.P. 2004. Phylogenetic relationships of woodcreepers (Aves: Dendrocolaptinae) - incongruence between molecular and morphological data. Journal of Avian Biology, 35, pp. 280-288.
The woodcreepers is a highly specialized lineage within the New World suboscine radiation. Most systematic studies of higher-level relationships of this group rely on morphological characters, and few studies utilizing molecular data exist. In this paper, we present a molecular phylogeny of the major lineages of woodcreepers (Aves: Dendrocolaptinae), based on nucleotide sequence data from a nuclear non-coding gene-region (myoglobin intron II) and a protein-coding mitochondrial gene (cytochrome b). A good topological agreement between the individual gene trees suggests that the resulting phylogeny reflects the true evolutionary history of woodcreepers well. However, the DNA-based phylogeny conflicts with the results of a parsimony analysis of morphological characters. The topological differences mainly concern the basal branches of the trees. The morphological data places the genus Drymornis in a basal position (mainly supported by characters in the hindlimb), while our data suggests it to be derived among woodcreepers. Unlike most other woodcreepers, Drymornis is ground-adapted, as are the ovenbirds, and the observed morphological similarities between Drymornis and the ovenbird outgroup may thus be explained from convergence or from reversal to an ancestral state. This observation raises the question of the use of characters associated with locomotion and feeding in phylogenetic reconstruction based on parsimony.

Mayr, G. & Ericson, P.G.P. 2004. Evidence for a sister group relationship between the Madagascan mesites (Mesitornithidae) and cuckoos (Cuculidae). Senckenbergiana biologica, 84, pp. 119-135.
The Madagascan Mesitornithidae (mesites or roatelos) are an enigmatic and poorly known group of small terrestrial birds. In this study their phylogenetic relationships are analyzed using a data set of 91 morphological characters and 29 extant avian taxa. Parsimony analysis of this data strongly supports monophyly of the taxon (Mesitornithidae + Cuculidae [cuckoos]) which has not been proposed before. Derived anatomical, parasitological, and behavioral characters are presented which support monophyly of this clade. Monophyly of the taxon (Mesitornithidae + Cuculidae) is also supported by a preliminary analysis of DNA sequences of two nuclear, protein-coding genes, RAG-1 and myoglobin intron II. In addition, sistergroup relationships of several other gruiform and non-gruiform taxa (Columbidae and Pteroclidae) are supported by derived morphological characters. Monophyly of a taxon including the remaining "Gruiformes" (i.e. excluding Mesitornithidae) is neither supported by morphological nor molecular analyses.

Storå, J. & Ericson, P.G.P. 2004. A prehistoric breeding population of harp seals (Phoca groenlandica) in the Baltic Sea. Marine Mammal Science, 20, pp. 115-133.
The pelagic and gregarious, low Arctic harp seal (Phoca groenlandica) is the most common seal species in most refuse faunas from coastal hunter-gatherer sites dating from the late Atlantic to the early Subboreal period (ca. 4000-2000 cal BC) in the Baltic Sea. Our main objective is to examine the migration contra breeding population hypotheses regarding the Baltic harp seals. Analyses of epiphyseal fusion data and osteometry of archaeological harp seal remains from 25 dwelling-sites suggest that a local breeding population established itself in the early Subboreal period. In the Middle Neolithic the rookery possibly was situated in the Baltic proper, south of Åland and west of Gotland. The mean adult size of the Baltic harp seals decreased, suggesting minimal genetic exchange with the north Atlantic Ocean population. Genetic drift, inter-specific competition, and over-hunting by humans are all factors likely to have contributed to the eventual extinction of harp seals in the Baltic Sea.

Zhang, F., Ericson, P.G.P. & Zhou, Z. 2004. Description of a new enantiornithine bird from the Early Cretaceous of Hebei, northern China. Canadian Journal of Earth Sciences, 41, pp. 1097-1107.
This paper describes a new enantiornithine fossil bird, Vescornis hebeiensis, nov. sp. from the Early Cretaceous of China. We refer Vescornis to the crown clade Euenantiornithes based on several characteristics observed in the thoracic girdle and wing. Vescornis also exhibits characteristics that separate it from other enantiornithine birds, such as the short alular phalanx, the vestigial manual claws, and the well-developed and long foot claws. These features suggest an adaptation towards an improved flight capability, while the ability of Vescornis to climb is reduced compared with many other enantiornithine birds.

Ericson, P.G.P., Envall, I., Irestedt, M. & Norman, J.A. 2003. Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data. BMC Evolutionary Biology 3:16.
Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria. Several novel phylogenetic relationships were recovered and strongly supported by the data, regardless of which method of analysis was employed. These include placing the gulls and allied groups as a sistergroup to the sandpiper-like birds, and not to the plover-like birds. The auks clearly belong to the clade with the gulls and allies, and are not basal to most other charadriiform birds as suggested in analyses of morphological data. Pluvialis, which has been supposed to belong to the plover family (Charadriidae), represents a basal branch that constitutes the sister taxon to a clade with plovers, oystercatchers and avocets. The thick-knees and sheathbills unexpectedly cluster together. The DNA sequence data contains a strong phylogenetic signal that results in a well-resolved phylogenetic tree with many strongly supported internodes. Taxonomically it is the most inclusive study of shorebird families that relies on nucleotide sequences. The presented phylogenetic hypothesis provides a solid framework for analyses of macroevolution of ecological, morphological and behavioural adaptations observed within the order Charadriiformes.

Ericson, P.G.P., Irestedt, M. & Johansson, U.S. 2003. Evolution, biogeography, and patterns of diversification in passerine birds. Journal of Avian Biology, 34, pp. 3-15.
This paper summarizes and discusses the many new insights into passerine evolution gained from an increased general interest in avian evolution among biologists, and particularly from the extensive use of DNA sequence data in phylogenetic reconstruction. The sister group relationship between the New Zealand rifleman and all other passerines, indicates the importance of the former southern supercontinent Gondwana in the earliest evolution of this group. Following the break-up of Gondwana, the ancestors of other major passerine groups became isolated in Australia (oscines), South America (New World suboscines), and, possibly, the then connected Kerguelen Plateau/ India/Madagascar tectonic plates (Old World suboscines). The oscines underwent a significant radiation in the Australo-Papuan region, and only a few oscine lineages have spread further than to the nearby Southeast Asia. A remarkable exception is the ancestor to the vast Passerida radiation, which now comprises 35% of all bird species. This group obviously benefitted greatly from the increased diversity in plant seed size and morphology during the Tertiary. The lyrebirds (and possibly scrub-birds) constitute the sister group to all other oscines, which renders "Corvida" (sensu Sibley and Ahlquist 1990) paraphyletic. Sequence data suggests that Passerida, the other clade of oscines postulated based on the results of DNA-DNA hybridizations, is monophyletic, and that the rockfowl and rock-jumpers are the most basal members of this clade. The suboscines in the Old World (Eurylamides) and the New World (Tyrannides), respectively, are sister groups. A provisional, working classification of the passerines is presented based on the increased understanding of the major patterns of passerine evolution.

Ericson, P.G.P. & Johansson, U.S. 2003. Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data. Molecular Phylogenetics and Evolution, 29, pp. 126-138.
Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved - only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated - these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.

Fjeldså, J., Zuccon, D., Irestedt, M., Johansson, U.S. & Ericson, P.G.P. 2003. Sapayoa aenigma: a New World representative of 'Old World suboscines'. Proceedings of the Royal Society of London Ser. B. (Suppl.), 270, pp. S238-S241.
Passerine birds are very plastic in their adaptations, which has made it difficult to define phylogenetic lineages and correctly allocate all species to these. Sapayoa aenigma, a member of the large group of New World flycatchers, has been difficult to place, and DNA-DNA hybridization experiments have indicated that it may have been misplaced. This is confirmed here, as base sequencing of two nuclear genes places it as a deep branch in the group of broadbills and pittas of the Old World tropics. The peculiar distribution of this lineage may be best explained in terms of a Gondwanic and Late Cretaceous origin of the passerine birds, as this particular lineage dispersed from the Antarctic landmass, reaching the Old World tropics via the drifting Indian plate, and South America via the West Antarctic Peninsula.

James, H.F., Ericson, P.G.P., Slikas, B., Lei, F.-M., Gill, F.B., & Olson, S.L. 2003. Pseudopodoces humilis, a misclassified terrestrial tit (Aves: Paridae) of the Tibetan Plateau: evolutionary consequences of shifting adaptive zones. Ibis, 145, pp. 185-202.
Pseudopodoces humilis (Hume's Ground Jay) is a small passerine bird that inhabits the high rocky steppes of the Tibetan (Qinghai-Xizang) Plateau. Although it was long classified as a small species of ground jay (Podoces), two previous anatomical studies cast doubt on its assignment to the Corvidae (crows and jays). We studied the evolutionary relationships of Pseudopodoces using three independent datasets drawn from comparative osteology, the nuclear c-myc gene, and the mitochondrial cytochrome b gene. All three datasets agree on the placement of Pseudopodoces in the family Paridae (tits and chickadees). The cytochrome b data further suggest that Pseudopodoces may be closest to the Great Tit (Parus major) species group. Pseudopodoces is the only species of Paridae whose distribution is limited to treeless terrain. Its evolutionary relationships were long obscured by adaptations to open habitat, including pale, cryptic plumage; a long, decurved bill for probing in crevices among rocks or in the ground; and long legs for terrestrial locomotion. Despite these accommodations to a novel adaptive zone, its evolutionary affinity with the Paridae is clearly expressed in comparative osteology and genetics, and is supported by its habit of nesting in cavities.

Johansson, U.S. & Ericson, P.G.P. 2003. Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960). Journal of Avian Biology, 34, pp. 185-197.
Woodpeckers, honeyguides, barbets, and toucans form a well-supported clade with approximately 355 species. This clade, commonly referred to as Pici, share with the South American clade Galbulae (puffbirds and jacamars) a zygodactyl foot with a unique arrangement of the deep flexor tendons (Gadow's Type VI). Based on these characters, Pici and Galbulae are often considered sister taxa, and have in traditional classification been placed in the order Piciformes. There are, however, a wealth of other morphological characters that contradicts this association, and indicates that Pici is closer related to the Passeriformes (passerines) than to Galbulae. Galbulae, in turn, is considered more closely related to the rollers and ground-rollers (Coracii). In this study, we evaluate these two hypotheses by using DNA sequence data from exons of the nuclear RAG-1 and c-myc genes, and an intron of the nuclear myoglobin gene, totally including 3400 basepairs of aligned sequences. The results indicate a sister group relationship between Pici and Galbulae, i.e. the monophyly of the Piciformes, and this association has high statistical support in terms of bootstrap values and posterior probabilities. This study also support several associations within the traditional order Coraciiformes, including a sister group relationship between Alcedinidae and a Todidae - Momotidae clade, with Meropidae placed basal relative these three taxa.

Mayr, G., Manegold, A. & Johansson, U.S. 2003. Monophyletic groups within "higher land birds" - comparison of morphological and molecular data. Journal of Zoological Systematics and Evolutionary Research, 41, pp. 233-248.
The relationships within the "higher land birds" and putatively related taxa are analyzed in a study using 89 morphological characters and DNA sequences of three nuclear, protein-coding genes, c-myc, RAG-1, and myoglobin intron II. Separate analyses of the different data sets and a "total evidence" analysis in which the data sets of the morphological and molecular analyses were combined are compared. All three analyses support the hitherto disputed sister group relationship between Pici (Ramphastidae, Indicatoridae, and Picidae) and Galbulae (Galbulidae and Bucconidae). Previously unrecognized osteological characters are presented which support this clade. Analysis of the morphological data and of the combined data set further supported monophyly of the taxon (Strigiformes + (Falconidae + Accipitridae)). Also supported by analyses of the morphological data and of the combined data set is a sister group relationship between Nyctibiidae and Caprimulgidae and between Apodidae/Hemiprocnidae and Trochilidae. The morphological data further support monophyly of the taxa (Upupidae + Bucerotidae) and (Aegothelidae + (Apodidae/Hemiprocnidae + Trochilidae)). Other placements in the three analyses received either no or only weak bootstrap support.

Hou, Lianhai & Ericson, P.G.P. 2002. A middle Eocene shorebird from China. Condor, 104, pp. 896-899.
We describe a new species of shorebird, tentatively referred to the family Charadriidae, from the Huadian Formation (Middle Eocene) in Jilin Province, China. In general morphology the specimen closely matches that of an extant charadriid, and corresponds in size to the Killdeer (Charadrius vociferus). If correctly identified this is the oldest record of the Charadriidae. The Middle Eocene paleoenvironment of the Huadian region is thought to have resembled a subtropical swamp.

Johansson, U.S., Irestedt, M., Parsons, T.J., & Ericson, P.G.P. Basal phylogenetic relationships within Tyrannoidea. 2002. Auk, 119, pp. 984-995.
The outlines of the phylogenetic relationships within the New World suboscine clade Tyrannoidea were investigated based on nucleotide sequence data from two nyclear genes (c-myc and RAG-1) and one mitochondrial gene (cytochrome b), totaling over 2400 basepairs. Representatives of the major tyrannoid lineages were sequenced, including Pachyramphus, Schiffornis, Tityra, and Oxyruncus. The data set with the three genes combined were analyzed both under the parsimony and maximum likelihood criteria, and under different character weighting schemes. The analyses resulted in similar topologies that differed only in poorly supported nodes. The three manakins Pipra, Manacus, and Chiroxiphia, included in this study were found to be monophyletic, whereas Schiffornis, sometimes also considered to be a manakin, did not group with the manakins, but occurred with Pachyramphus and Tityra in the clade Tityrinae. The two clades Pipromorphinae and Tyranninae are also strongly supported in this analysis and appear as sistergroups, thus supporting the monophyly of the tyrant flycatcher assemblage. Phytotoma was placed with the only cotingid species included in this analysis, whereas the position of Oxyruncus was unresolved.

Ericson, P.G.P., Christidis, L., Irestedt, M. & Norman, J.A. 2002. Systematic affinities of the lyrebirds (Passeriformes: Menura), with a novel classification of the major groups of passerine birds. Molecular Phylogenetics and Evolution, 25, pp. 53-62.
Phylogenetic relationships of the lyrebirds are investigated using DNA sequence data. The aligned data matrix consists of 4027 base pairs obtained from three nuclear genes (c-myc, RAG-1 and myoglobin intron II) and two mitochondrial genes (cytochrome b and ND2). Both maximum-likelihood and parsimony analyses show that the lyrebirds unambiguously belong to the oscine radiation, and that they are the sister taxon to all other oscines. The results do not support the suggestion based on DNA-DNA hybridization data (Sibley and Ahlquist, 1990) that the treecreepers and bowerbirds are part of the lyrebird clade. Nevertheless, treecreepers and bowerbirds are sister taxa to all other oscines (except the lyrebirds) and may constitute a monophyletic group, although bootstrap support values for this clade are low. A major disagreement between the present analysis and that based on DNA-DNA hybridization data is that the Corvida (sensu Sibley and Ahlquist, 1990) and Passerida are not reciprocally monophyletic, as we find the latter group be nested within the Corvida. Also, the superfamilies Meliphagoidea and Corvoidea sensu Sibley and Ahlquist (1990), are not recovered as monophyletic in the present study. Within the oscine radiation, all taxa belonging to the earliest splits are confined to the Australo-Papuan region. This suggests strongly that the origins and early radiation of the oscines occurred in the southern supercontinent Gondwana. A new classification of the major groups of passerines is presented following from the results presented in the present study, as well as those published recently on analyses of sequence data from the nuclear c-myc and RAG-1 genes (Irestedt et al., 2001; Ericson et al., 2002).

Irestedt, M., Fjeldså, J., Johansson, U.S. & Ericson, P.G.P. 2002. Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes). Molecular Phylogenetics and Evolution, 23, pp. 499-512.
Based on their highly specialized "tracheophone" syrinx, the avian families Furnariidae (ovenbirds), Dendrocolaptidae (woodcreepers), Formicariidae (ground antbirds), Thamnophilidae (typical antbirds), Rhinocryptidae (tapaculos) and Conopophagidae (gnateaters) have long been recognized to constitute a monophyletic group of suboscine passerines. However, the monophyly of these families have been contested, and their interrelationships are poorly understood, and this constrains the possibilities for interpreting adaptive tendencies in this very diverse group. In this study we present a higher-level phylogeny and classification for the tracheophone birds based on phylogenetic analyses of sequence data obtained from 32 ingroup taxa. Both mitochondrial (cytochrome b) and nuclear genes (c-myc, RAG-1 and myoglobin) have been sequenced, and more than 3000 bp were subjected to parsimony and maximum-likelihood analyses. The phylogenetic signals in the mitochondrial and nuclear genes were compared and found to be very similar. Although the results from the analysis of the combined dataset (all genes, but with transitions at third codon positions in the cytochrome b excluded) partly corroborate previous phylogenetic hypotheses, several novel arrangements were also suggested. Especially interesting is the result that the genus Melanopareia represents a basal branch within the tracheophone group, positioned in the phylogenetic tree well away from the typical tapaculos with which it has been supposed to group. Other novel results include the observation that the ground antbirds are paraphyletic, and that Sclerurus is the sister taxon to an ovenbird-woodcreeper clade. Patterns of generic richness within each clade suggest that the early differentiation of feeble-winged forest groups took place south of the Amazon Basin, while the more recent diversification was near the equator and (in tapaculos and ovenbirds) in the south of the continent.

Ericson, P.G.P., Christidis, L., Cooper, A., Irestedt, M., Jackson, J., Johansson, U.S. & Norman, J.A. 2002. A Gondwanan origin of passerine birds supported by DNA sequences of the endemic New Zealand wrens. Proceedings of the Royal Society of London. Ser. B., 269, pp. 235-241
Zoogeographic, palaeontological and biochemical data support a southern hemisphere origin for passerine birds, while accumulating molecular data suggests that most extant avian orders originated in the mid-late Cretaceous. We obtained DNA sequence data from the nuclear c-myc and RAG-1 genes of the major passerine groups and demonstrate that the endemic New Zealand wrens (Acanthisittidae) are the sister taxon to all other extant passerines, supporting a Gondwanan origin and early radiation of passerines. We hypothesise that the Acanthisittids were isolated when New Zealand split off from Gondwana ca. 82-85 Mya, suboscines in turn were derived from an ancestral lineage that inhabited western Gondwana, and that the ancestors of the oscines (songbirds) were subsequently isolated by the split of Australia from Antarctica. The later spread of passerines into the Northern Hemisphere reflects the northward migration of these former Gondwanan elements.

Ericson, P.G.P., Parsons, T.J. & Johansson, U.S. 2001. Morphological and molecular support for non-monophyly of the Galloanserae. In: (Gauthier, J. and Gall, L.F. eds.) New Perspectives on the Origin and Evolution of Birds: Proceedings of the International Symposium in Honor of John H. Ostrom.. New Haven: Peabody Museum of Natural History, Yale University. pp.157-168.
This paper discusses morphological and molecular data bearing on the earliest evolution of the Neornithes. Phylogenetic analyses of basal neornithine groups frequently result in poorly resolved trees, most likely caused by rapid branching events in the Cretaceous and early Tertiary. Although data that efficiently resolve the earliest history of modern birds are few, a consensus opinion about their basal phylogeny have emerged in recent years. Two major splits within Neornithes are postulated. The first occurs when the palaeognathous birds branch off from the rest (the Neognathae), and the second when the Anseriformes and Galliformes split from all other neognaths. Morphological data presented by Livezey (1997) supporting this second dichotomy are combined with additional data from Ericson (1997) and re-analysed. In addition a new data set consisting of nucleotide sequences from the nuclear, single-copy gene c-myc is analysed separately and in combination with the morphological data. Neither analyses support the suggested anseriform-galliform relationship. Instead, the Anseriformes group with the Ciconiiformes, Phoenicopteriformes and Charadriiformes, i.e. a clade of wading birds.

Irestedt, M., Johansson, U.S., Parsons, T.J. & Ericson, P.G.P. 2001. Phylogeny of major lineages of suboscines (Passeriformes) analysed by nuclear DNA sequence data. Journal of Avian Biology, 32, pp.15-25.
Phylogenetic relationships among major groups of passeriform birds were studied by analyses of nucleotide sequence data from two nuclear genes, c-myc and RAG-1. The results corroborated both the monophyly of the order Passeriformes, and the major dichotomy into oscine and suboscine passerines previously suggested based on syringeal morphology and DNA-DNA hybridizations. The representatives of the Old World suboscines (families Eurylaimidae, Philepittidae and Pittidae) formed a monophyletic clade but familial relationships within this group was not resolved. The New World suboscines clustered into two clades. The first contained Furnarius (Furnariidae), Lepidocolaptes (Dendrocolaptidae), Thamnophilus (Formicariidae), and Rhinocrypta (Rhinocryptidae). Previously, the monophyly of this group has been inferred from their possession of a unique, "tracheophone" syrinx, and from DNA-DNA hybridization data. Traditionally the Conopophagidae is included in this group but the results from nuclear DNA data does not indicate this. However, weak nodal supports in this part of the tree makes the phylogenetic inferences tentative. The second clade of New World suboscines includes Gubernetes and Muscivora (Tyrannidae), Phytotoma (Phytotomidae), Tityra (Cotingidae) and Pipra (Pipridae). This group of families have been considered monophyletic based on morphology (although ambiguously) and DNA-DNA hybridization. The sister group relationship of Tityra and Phytotoma supports the previously supposed cotingid affinity of Phytotoma. Nuclear DNA data also unambiguously group the lyrebirds Menura with the oscines. Overall, the presented results from the analysis of nuclear DNA agree well with morphology and DNA-DNA hybridization data. The precise age of the divergencies studied herein are unknown but many of them might date back to the early Tertiary. The general agreement between data from the nuclear DNA and other sources, along with the fact that neither of the studied genes showed sign of saturation, indicate the great potential of these two nuclear genes to resolve very old divergencies in birds.

Johansson, U.S., Parsons, T.J., Irestedt, M. & Ericson, P.G.P. 2001. Clades within the 'higher land birds', evaluated by nuclear DNA sequences. Journal of Zoological Systematics and Evolutionary Research, 39, pp. 37-51.
In this study we investigated the phylogenetic relationships within the "higher land birds" (Anomalogonatae) by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c-myc and RAG-1. Nuclear genes has not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of a synapomorphic insertion of four amino acids in the c-myc gene in all apodiform taxa. Monophyly were also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic with the New World barbets more closely related to the Ramphastidae than to the Old World barbets. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. In agreement with certain morphological and biochemical studies, The monophyly of the Coraciiformes and the Piciformes, respectively, could not be corroborated.

Ericson, P.G.P. 2000. Systematics, anatomy and paleoecology of the Paleogene family Presbyornithidae (Aves: Anseriformes). PaleoBios, 20, pp. 1-23.
Since the family Presbyornithidae was first described from the Eocene Green River Fm. of Utah, fossils referred to this genus have been collected from many Paleogene localities around the world. Fossils of this family are extraordinarily abundant and permit detailed studies of all parts of the skeleton. This paper describes the osteology of the Presbyornithidae based upon all material known from the New World. The family is revised and found to comprise four species placed in the two genera Presbyornis (three species) and Telmabates (one species). Presbyornis pervetus is by far the most common and widespread member of the family. The large size variation in the skeleton of P. pervetus is attributed to sexual dimorphism. Phylogenetic analyses of the Presbyornithidae have shown it to be a member of the order Anseriformes (ducks, geese, swans, and their allies). In addition to derived anseriform characters, the presbyornithid skeleton has many plesiomorphic features in common with other late Cretaceous and early Tertiary birds. Nearly all presbyornithids have been collected from lacustrine environments. Avian egg-shells associated with the fossils at certain localities suggest P. pervetus was a gregarious breeder along the shores of fresh water lakes. At several localities large numbers of presbyornithid fossils form mass-mortality layers in which the skeletons are disarticulated. Although the cause of death is unknown avian botulism or catastrophic volcanism may have contributed to the mass death of the birds.

Ericson, P.G.P. 1999. New material of Juncitarsus (Phoenicopteriformes), with a guide for differentiating that genus from the Presbyornithidae (Anseriformes). In: (Olson, S.L. Ed.) Avian Paleontology at the Close of the 20th Century: Proceedings of the 4th International Meeting of the Society of Avian Paleontology and Evolution, Washington, D.C., 4-7 June 1996. Smithsonian Contributions to Paleobiology, 89, pp. 245-251.
In many aspects, the postcranial skeleton of the early Tertiary Juncitarsus (Phoenicopteridae), is very similar to that of Presbyornis and Telmabates (Presbyornithidae). The phylogenetic positions of the two families, indicates that these similarities are due to the retention of morphologies possessed by their most recent ancestor. In this paper it is shown how finds of isolated skeletal elements of either genus can be correctly identified.

Ericson, P.G.P. 1997. Swedish records of the eastern Palearctic Hoopoe subspecies Upupa epops saturata. Bulletin of the British Ornithologist's Club, 117, pp. 19-26.
The occurrence of Hoopoes of the subspecies Upupa epops saturata in Sweden is documented by a quantitative analysis of the mantle and breast colours measured by a spectrometer. This subspecies is characterized by being very dark and inhabits the north-eastern parts of Palearctic. It has not previously been reported from Europe. Hoopoes of the subspecies U. e. saturata are typically observed in Sweden in the autumn and only a few spring finds, possibly of wintering individuals, exist.

Ericson, P.G.P. 1997. Systematic relationships of the Paleogene family Presbyornithidae (Aves: Anseriformes). Zoological Journal of the Linnean Society, 121, pp. 429-483.
The early Tertiary (Paleocene and Eocene) family Presbyornithidae is one of the most completely known group of fossil birds. Essentially all parts of the skeleton are represented in the fossil record, allowing a thorough analysis of the phylogenetic position of the family. 42 families of nonpasserine birds representing the orders Ciconiiformes, Anseriformes, Galliformes, Gruiformes and Charadriiformes, were included in a cladistic analysis of 71 skeletal characters. The previously suggested anseriform affinity of the Presbyornithidae was confirmed. Furthermore, the family proved to be closer to the Anatidae than to the Anhimidae or Anseranatidae. The many postcranial similarities with certain charadriiform birds as the Burhinidae, obviously are plesiomorphies. By this observation, a better understanding of character evolution in nonpasserine skeletal morphology is gained. The often suggested close relationship of anseriform and galliform birds is not confirmed by osteology. Instead, the Anseriformes and the Phoenicopteridae form a monophyletic clade that is the sister to the remaining ciconiiform birds. This result renders the Ciconiiformes sensu Wetmore (1960) polyphyletic.

Ericson, P.G.P. & Amarilla, L.A. 1997. First observations and new distributional data for birds in Paraguay. Bulletin of the British Ornithologist's Club, 117, pp. 60-67.

Ericson, P.G.P. & Hernández Carrasquilla F. 1997. Subspecific affinity of Prehistoric Baltic cormorants (Aves: Phalacrocoracidae). Ardea, 85, pp. 1-7.
Cormorants of the subspecies Phalacrocorax carbo sinensis breed in large numbers in the Baltic Sea. They migrate to the Mediterranean region to winter and are then replaced in the Baltic by wintering individuals of the Norwegian population of the nominate subspecies carbo. Cormorants bred in the Baltic during Prehistoric times too, but as evident from a comparison of skeletal measurements in present-day and Prehistoric Cormorants, these individuals belonged to the nominate subspecies carbo. The Swedish subfossil record of the Cormorants available for study, does not include any remains small enough to suggest the presence of sinensis. Precisely when the subspecies sinensis immigrated into the Baltic is unknown, but it must have occurred sometime between 1500 and 1800 AD.

Ericson, P.G.P., Tyrberg, T., Kjellberg, A.S., Jonsson, L. & Ullén, I. 1997. The earliest record of the House Sparrow (Passer domesticus) in northern Europe. Journal of Archaeological Science, 24, pp. 183-191.
Remains of the House Sparrow Passer domesticus recovered from a late Bronze Age (1200 - 800 BC) settlement in central Sweden are described. The House Sparrow is conspicuously rare in prehistoric Europe, and this record constitutes the earliest from the northern part. The find predates the introduction of Domestic Fowl Gallus gallus to Sweden, a species with which the House Sparrow has been assumed to be spread simultaneously. Instead, it is here suggested that House Sparrows most likely spread over Europe along with the Horse Equus caballus.

Eames, J. & Ericson, P.G.P. 1996. The Björkegren expeditions to French Indochina: A collection of birds from Vietnam and Cambodia. Natural History Bulletin of the Siam Society, 44, pp. 75-111.
Details are given of a collection of birds made during 1935 and 1938/39 in Cambodia and Vietnam by the Swedish ornithologist Bertil Björkegren. The collecting localities, together with dates and sex, are provided for all the specimens where available. In addition, notes made by Björkegren are included for selected species. Most notably, Björkegren collected the type and paratypes of the Grey-crowned Crocias Crocias langbianis. Most of the collection was made at Sa Pa in north-west Vietnam and in the western highlands in southern Vietnam. The collection is retained in the Swedish Museum of Natural History, Stockholm.

Ericson, P.G.P. 1996. The skeletal evidence for a sister-group relationship of anseriform and galliform birds - a critical evaluation. Journal of Avian Biology, 27, pp.195-202.
The osteological basis for the proposed close phylogenetical relationship of anseriform and galliform birds is evaluated and found to be very weak. Out of eleven postulated synapomorphies in cranial morphology (Cracraft 1988), three must be excluded since they express variation that is already covered by any of the other eleven characters. Another six of the postulated synapomorhies either cannot be verified to occur in most anseriforms and galliforms, or have a wide distribution outside this group. A re-analysis of the combined morphological and biochemical data set of Cracraft and Mindell (1989) with the questionable osteological characters excluded, does not corroborate an anseriform-galliform sister-group relationship, but leaves the Neognathae unresolved.