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Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
BGI Shenzhen, Shenzhen, Peoples R China.;Univ Macau, Inst Chinese Med Sci, State Key Lab Qual Res Chinese Med, Taipa, Peoples R China..
Swedish Univ Agr Sci, Dept Wildlife Fish & Environm Studies, S-90183 Umea, Sweden..
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
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2016 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 1, 84-+ p.Article in journal (Refereed) PublishedText
Abstract [en]

The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females(1-4). This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles(5,6). Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.

Place, publisher, year, edition, pages
2016. Vol. 48, no 1, 84-+ p.
National Category
URN: urn:nbn:se:uu:diva-274919DOI: 10.1038/ng.3430ISI: 000367255300018PubMedID: 26569123OAI: oai:DiVA.org:uu-274919DiVA: diva2:898151
Knut and Alice Wallenberg FoundationSwedish Research Council, 1989-2546Swedish Research Council, 1992-2685Swedish Research Council, 2013-5418Swedish Research Council, 2001-6005Swedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-01-27 Created: 2016-01-26 Last updated: 2016-04-12Bibliographically approved
In thesis
1. The genetic basis for adaptation in natural populations
Open this publication in new window or tab >>The genetic basis for adaptation in natural populations
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations.

Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci.

The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry.

This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. 60 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1192
Adaptive evolution, Atlantic herring, ecological adaptation, seasonal reproduction, TSHR, Darwin’s finches, natural selection, beak, ALX1, HMGA2, ruff, lek, inversion, HSD17B2, MC1R
National Category
Genetics and Breeding
urn:nbn:se:uu:diva-279969 (URN)978-91-554-9502-2 (ISBN)
Public defence
2016-04-29, B41, BMC, Husargätan 3, Uppsala, 13:15 (English)
Available from: 2016-04-06 Created: 2016-03-06 Last updated: 2016-04-12

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Lamichhaney, SangeetGunnarsson, UlrikaHöppner, Marc P.Kerje, SusanneHöglund, JacobAndersson, Leif
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