Hybridization in Birds-of-Paradise, genomic implications and evolutionary advantages

Project overview

Project period: 2023-2027

Participating units from the museum: Department of Bioinformatics and Genetics

The purpose of this project is to explore the evolutionary significance of introgressive hybridization in a lek-mating study system where male traits are expected to evolve under strong sexual selection. More explicitly, we will investigate the impact hybridization has on structural genome evolution and in re-shuffling genetic variation across species in such a system by applying comparative genomics methods on genomes obtained largely from historical museum specimens.

Project description

This proposal has two principal aims; 1) to study the evolutionary significance of introgression in evolutionary radiations where lek-mating behaviors contribute to particularly strong sexual selection in male traits, and 2) to study to what degree repeated introgression may impede genomic structural changes. To study this we will generate new high-quality genomes and re-sequence data for particularly interesting groups and individuals and create “pan-genomes” at species level, genus level and for the two major groups of Birds-of-Paradise (the core Birds-of-Paradise that include lekking species with male elaborated plumage ornamentation and their sister group that contain crow-like, monomorphic birds with simple mating systems).

This will enable us to conduct comparative studies of genome evolution at various depths among the Birds-of-Paradise as well as with clades outside Birds-of-Paradise from which data are already available. The genomes of hundreds of additional Birds-of-Paradise museum skins will also be re-sequenced for two purposes. The first is to sequence population data of hybrids from two hybridizing complex, which will enable us to correlate genomic variation with plumage variation and pinpoint genomic regions that may be important for introgression of genetic regions involved in phenotypic selection. The second purpose is to sequence additional putative intergeneric backcrosses as that will enable us to compare the location of introgressed tracks across different hybrid combinations, which will provide information as to what extent introgression and recombination patterns are conserved across the Birds-of-Paradise.

Financiers

• Swedish Research Council (https://www.vr.se/english.html)
• Carl Tryggers Stiftelse (https://www.carltryggersstiftelse.se/ )
• Olle Engkvists Stiftelse (https://engkviststiftelserna.se/)

Selected publications

• IRESTEDT, M., JONSSON, K. A., FJELDSA, J., CHRISTIDIS, L. & ERICSON, P. G. P. 2009. An unexpectedly long history of sexual selection in birds-of-paradise. Bmc Evolutionary Biology, 9. https://doi.org/10.1186/1471-2148-9-235
• IRESTEDT, M., THÖRN, F., MÜLLER, I. A., JØNSSON, K. A., ERICSON, P. G. P. & BLOM, M. P. K. 2022. A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins. Molecular Ecology Resources, 22, 2672-2684. https://doi.org/10.1111/1755-0998.13660
• PEONA, V., BLOM, M. P. K., XU, L. H., BURRI, R., SULLIVAN, S., BUNIKIS, I., LIACHKO, I., HARYOKO, T., JONSSON, K. A., ZHOU, Q., IRESTEDT, M. & SUH, A. 2021a. Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise. Molecular Ecology Resources, 21, 263-286. https://doi.org/10.1111/1755-0998.13252
• PEONA, V., KUTSCHERA, V. E., BLOM, M. P. K., IRESTEDT, M. & SUH, A. 2023. Satellite DNA evolution in Corvoidea inferred from short and long reads. Molecular Ecology, 32, 1288-1305. https://doi.org/10.1111/mec.16484
• PEONA, V., PALACIOS-GIMENEZ, O. M., BLOMMAERT, J., LIU, J., HARYOKO, T., JONSSON, K. A., IRESTEDT, M., ZHOU, Q., JERN, P. & SUH, A. 2021b. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philosophical Transactions of the Royal Society B-Biological Sciences, 376. https://doi.org/10.1098/rstb.2020.0186
• PROST, S., ARMSTRONG, E. E., NYLANDER, J., THOMAS, G. W. C., SUH, A., PETERSEN, B., DALEN, L., BENZ, B. W., BLOM, M. P. K., PALKOPOULOU, E., ERICSON, P. G. P. & IRESTEDT, M. 2019. Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise. Gigascience, 8. https://doi.org/10.1093/gigascience/giz003
• XU, L. H., AUER, G., PEONA, V., SUH, A., DENG, Y., FENG, S. H., ZHANG, G. J., BLOM, M. P. K., CHRISTIDIS, L., PROST, S., IRESTEDT, M. & ZHOU, Q. 2019. Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. Nature Ecology & Evolution, 3, 834-844. https://doi.org/10.1038/s41559-019-0850-1
• XU, L. H., IRESTEDT, M. & ZHOU, Q. 2020. Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds. Genes, 11. https://doi.org/10.3390/genes11111267