title: Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).
abstract: The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females. 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. 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.
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Sangeet
authors.initials: S
authors.lastname: Lamichhaney
authors.affiliation: BGI-Shenzhen, Shenzhen, China.|State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
authors.forename: Guangyi
authors.initials: G
authors.lastname: Fan
authors.affiliation: Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Widemo
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Ulrika
authors.initials: U
authors.lastname: Gunnarsson
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.|Institute National de la Recherche Agronomique, AgroParisTech, Génetique Animale et Biologie Intégrative, Jouy-en-Josas, France.
authors.forename: Doreen Schwochow
authors.initials: DS
authors.lastname: Thalmann
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden.
authors.forename: Marc P
authors.initials: MP
authors.lastname: Hoeppner
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Susanne
authors.initials: S
authors.lastname: Kerje
authors.affiliation: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Ulla
authors.initials: U
authors.lastname: Gustafson
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Shi
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: He
authors.initials: H
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xinming
authors.initials: X
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Leihuan
authors.initials: L
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Jiahao
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Enjing
authors.initials: E
authors.lastname: Liang
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
authors.forename: Simon Ming-Yuen
authors.initials: SM
authors.lastname: Lee
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.
authors.forename: Jacob
authors.initials: J
authors.lastname: Höglund
authors.affiliation: BGI-Shenzhen, Shenzhen, China.
authors.forename: Xin
authors.identifier: http://orcid.org/0000-0003-3256-2940
authors.initials: X
authors.lastname: Liu
authors.affiliation: Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.|Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.|Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA.
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D001717:Birds / Q000235:genetics* / Q000502:physiology; D002875:Chromosomes; D005260:Female; D005828:Genetics, Population; D016678:Genome; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012098:Reproduction / Q000235:genetics*; D012726:Sexual Behavior, Animal / Q000502:physiology*