Structural genomic changes underlie alternative reproductive strategies in the ruff ( Philomachus pugnax )

• Published in: Nature Genetics
• Main Authors: Lamichhaney, Sangeet, Fan, Guangyi, Widemo, Fredrik, Gunnarsson, Ulrika, Thalmann, Doreen Schwochow, Hoeppner, Marc P., Kerje, Susanne, Gustafson, Ulla, Shi, Chengcheng, Zhang, He, Chen, Wenbin, Liang, Xinming, Huang, Leihuan, Wang, Jiahao, Liang, Enjing, Wu, Qiong, Lee, Simon Ming-Yuen, Xu, Xun, Höglund, Jacob, Liu, Xin, Andersson, Leif
• Other Authors: Department of Medical Biochemistry and Microbiology, Uppsala University, Beijing Genomics Institute Shenzhen (BGI), University of Macau (UMac), Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences (SLU), Institut National de la Recherche Agronomique (INRA), Department of Animal Bredding and Genetics, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Bioinformatics Infrastructure for Life Sciences (BILS), University of Gothenburg (GU), Department of Ecology and Genetics Uppsala (EBC), Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Knut and Alice Wallenberg foundation; National Basic Research Program of China (973 Program) 2013CB835204, Shenzhen municipal government of China (DRC-SZ) 843, Key Laboratory of Genomics; Chinese Ministry of Agriculture; Platform of Whole Genome-Based Molecular Breeding; ShenZhen Engineering Laboratory for Genomics-Assisted Animal Breeding; Swedish Research Council 1989-2546, 1992-2685, 2013-5418, 2001-6005, 80576801, 70374401, Uppsala University and Hospital; Science for Life Laboratory
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2016
• Subjects: Dna-sequencing data; Zonotrichia-albicollis; Social-behavior; Polymorphism; Mimicry; Complex; Identification; Association; Phenotypes; [SDV]Life Sciences [q-bio]; Philomachus pugnax; Ruff
• Online Access: https://hal.inrae.fr/hal-02641550; https://doi.org/10.1038/ng.3430

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.