Master thesis – Summer Project Suggestions5p/10p/20p/40p
Interested in molecular lab work? 1 Developing novel molecular markers for water beetles. Which gene contains most intraspecific variation? This project will devote most time to molecular lab work, developing successful protocols and markers for water beetles. Mitochondrial genes are popular to use because of easy amplification, but because they are all linked, they do not constitute indepependent evidence from each other. Multiple nuclear genes, preferably single-copy nuclear genes, are optimal to use in many circumstances in taxonomy and phylogenetics, however they can be more difficult to amplify. You will attempt to amplify several nuclear genes, try out different published primers, design new primers, troubleshoot and optimize recipes and cycling conditions. Skillful and meticulous lab work and careful documentation of recipes and protocols is essential. The genes that work in the end will be tested for information content within and between species in phylogenetic analyses.Contact: Johannes BergstenInterested in molecular lab work? 2Amplifying genes from degraded DNA of 19th and early 20th century irreplaceable specimens. It is easiest to work with newly collected and well preserved specimens when doing DNA work. However many species, critical for various phylogenetic or taxonomic projects might only be known from old specimens, collected in the 1800s or early 1900s. DNA from such specimens is degraded and will be more difficult to amplify. Genes often need to be amplified in shorter overlapping fragments, and recipes and cycling conditions for PCR´s need to be modified, more powerful (and expensive) Taq enzymes used etc. Extra care is also needed not to contaminate the sample with foreign DNA. Primer design of internal primers for short segments of genes will be necessary. This project will develop standards for DNA work with older specimens and deal with some specific group of diving beetles where amplification of older specimens is necessary.Contact: Johannes BergstenInterested in Phylogenetics/Systematics? Phylogeny and classification of Hydradephagan water beetles.(More than one project available here, working with different genera)Are the genera Uvarus and Hydroglyphus monophyletic? Is Suphrodytes nested in the genus Hydroporus? Phylogenetic analysis of the family Haliplidae.Defining species groups in the endemic genus Madaglymbus of Madagascar.Testing the phylogenetic placement of a new Madagascan genus of diving beetles.Testing the phylogenetic placement of a new Rhantus species from Russia.There are several projects available that deals with testing the phylogenetic placement, monophyly, or phylogenetic relationship of various species and genera. They share the methodology of first assembling the data for the phylogenetic analyses which involves molecular labwork; DNA extraction, PCR amplification of a number of genes and sequencing. This is followed by the use of different software for sequence chromatogram editing, assembling, sequence alignment and finally phylogenetic analyses, including dating trees. In some cases morphological data will also be assembled from the literature or de novo. Attention will be paid to rigorous phylogenetic analyses using different optimality criteria, branch support measures and dating algorithms. Contact: Johannes BergstenInterested in Phylogenetics and testing evolutionary scenarios? (2 projects) Species level phylogeny of the diving-beetle genus Graphoderus based on DNA and morphology. Species level phylogeny of the diving-beetle genus Dytiscus based on DNA and morphology.These are two projects with similar structure and methodology. Material is already available for the most part. Additional lab work will be needed to some degree: PCR amplification, sequencing, mostly from already extracted DNA but some new extractions will be necessary. You will also do some morphological work, scoring characters and quantifying some structures. Analyses: DNA sequence alignment, Bayesian phylogenetic analyses with partitioned models, dating. Both genera include peculiar modifications of female elytra that together with adhesive suction cups on male tarsi have been interpreted in a sexual conflict scenario of sexual selection. You will use the estimated phylogeny to optimize characters involved in this scenario. This will lead to an improved understanding of how, when and in what order have characters evolved and are they correlated over evolutionary time. Contact: Johannes BergstenInterested in Taxonomy? 1 Describing and delineating Madagascan diving beetles:Do molecular and morphological data delimit the same species units? (More than one project available here, working with different genera)This project will work with water beetles from Madagascar, a poorly known fauna where about 20% of collected species represents new, undescribed, species for science. You will get familiar with methods, formats and tests for describing new species, including morphometrics, illustration and photo techniques, DNA sequence analysis for delimiting species, etc. You will also do practical molecular lab work to extract DNA from beetles, use PCR to amplify certain genes, and proceed to sequencing. Focus will be on describing species and test if molecular and morphological data coincide or conflict. You will be using advanced methods for modeling withinspecies coalescent patterns and Yule speciation models.Contact: Johannes BergstenInterested in Taxonomy? 2 Is “Agabus guttatus" more than one species in Sweden?DNA sequences has indicated that up to three different species hide under the name Agabus guttatus. In the United Kingdom all three potential species seem to co-occur, but only one of them has been found in Sweden. However the species has not been thoroughly sampled but is only based on a handful of sequenced specimens. This project will involve some fieldwork and sampling of Agabus guttatus from several localities in Sweden, north to south. Agabus guttatus is rather widespread and occurs in cold creeks or springs. Sampled specimens as well as previously collected specimens in the museum and in private collections, will be extracted in the molecular lab for DNA. You will do PCR on first a standard mitochondrial gene, and if more than one form is found, a couple of additional genes will be sequenced for some chosen specimens. You will also work with morphological characters that can potentially separate the species. Contact: Johannes BergstenInterested in work with Morphology? In search of morphological characters to separate two sisterspecies under the name Haliplus lineatocollis. DNA analyses have indicated that the widespread European species Haliplus lineatocollis is in fact two sister species. However, how the morphological variation looks like in the two species have not been quantified and which characters are reliable to distinguish them from one another is not clear. This project will work with quantifying morphological variation, both external morphology and genital structures that will be slidemounted and imaged. Geometric morphometric techniques and the TPS software package will be used to statistically analyze shape variation in male genitalia. An identification key will be produced for the new species. The work requires a stable hand and patience for genital dissections of beetles a few millimeters long.Contact: Johannes BergstenInterested in Ecology? Community phylogenetics of European diving beetlesIn this project you will test the following question: are local communities of diving beetles randomly drawn from the regional species pool with regards to their evolutionary relatedness? This is an emerging field where community ecologists are starting to use phylogenies to test for clustered, overdispersed or random patterns of local communities and from that draw conclusions of what ecological processes are important. For example an overdispersed community indicates that competitive exclusion is an important factor, excluding coexistence of closely related and ecologically similar species. In contrast a clustered community indicates environmental filtering of conserved traits important for that particular habitat. Finally, a random pattern is in agreement with Hubbell´s neutral theory of species equivalence. This project will use available dna sequence data to build phylogenetic trees and use the software PHYLOCOM to test for relatedness patterns of local communities. Important morphological traits might also be measured and coanalysed.Contact: Johannes Bergsten Interested in Genetics? Inheritance pattern of multiple male forms of darkling beetles.This project will deal with breeding darkling beetles in the lab, doing crosses of various male forms with females to elucidate the inheritance pattern and gene system involved in coding for the male forms. These male forms have previously been described as different species, but initial breeding experiments have shown that they arise within one and the same breeding population, and the male forms play different roles during sexual selection at mating. You will try with classical crossing estimate first if a single gene locus or multiple loci are involved, and if a single locus if there is a dominant or recessive allel.Contact: Johannes Bergsten Interested in Island Biogeography? Testing the frequency and timing of Madagascan colonization events of Dytiscinae diving beetles.Madagascar is often seen as an island where evolution did magic with the resident fauna in long isolation. But in fact most endemic species of the island originate from Cenozoic colonization events long after Madagascar was separated and isolated, often by crossing the Mozambique Channel, flying, drifting or rafting. Dytiscinae diving beetles are no exception, many are good flyers, and they seem to have repeatedly colonized Madagascar. This project will do phylogenetic analyses of the subfamily including both Madagascan and non-madagascan species. This will include some complementary molecular lab work although most data is already available. From the tree you will estimate how many times, independent of each other, Madagascar has been colonized. Special focus will be on algorithms for dating the tree to put absolute ages on the events and estimate error margins. You will see if colonization was spread out or especially frequent during some time period and compare with studies on other groups. Contact: Johannes Bergsten
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 Can DNA be sequenced from old museum material like these late 1900 th century specimens?
 Male front foot with suckers of Graphoderus zonatus verrucifer
 How many species?
 Haliplus lineatocollis photo taken from a variable-pressure scanning electron microscope
 Eretes sticticus, an extremely good flier that has colconized many islands including Madagascar
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