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Kim KW, Jackson BC, Zhang H, Toews DPL, Taylor SA, Greig EI, Lovette IJ, Liu MM, Davison A, Griffith SC, Zeng K, Burke T. Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird. Nat Commun 2019; 10:1852. [PMID: 31015412 PMCID: PMC6478913 DOI: 10.1038/s41467-019-09806-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 03/22/2019] [Indexed: 11/09/2022] Open
Abstract
Colour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.
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Affiliation(s)
- Kang-Wook Kim
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Benjamin C Jackson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hanyuan Zhang
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - David P L Toews
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853, USA.,Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Scott A Taylor
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853, USA.,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Emma I Greig
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY, 14853, USA
| | - Mengning M Liu
- School of Biology, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
| | - Angus Davison
- School of Biology, University of Nottingham, University Park, NG7 2RD, Nottingham, UK
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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Toomey MB, Marques CI, Andrade P, Araújo PM, Sabatino S, Gazda MA, Afonso S, Lopes RJ, Corbo JC, Carneiro M. A non-coding region near Follistatin controls head colour polymorphism in the Gouldian finch. Proc Biol Sci 2018; 285:20181788. [PMID: 30282656 PMCID: PMC6191701 DOI: 10.1098/rspb.2018.1788] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
Discrete colour morphs coexisting within a single population are common in nature. In a broad range of organisms, sympatric colour morphs often display major differences in other traits, including morphology, physiology or behaviour. Despite the repeated occurrence of this phenomenon, our understanding of the genetics that underlie multi-trait differences and the factors that promote the long-term maintenance of phenotypic variability within a freely interbreeding population are incomplete. Here, we investigated the genetic basis of red and black head colour in the Gouldian finch (Erythrura gouldiae), a classic polymorphic system in which naturally occurring colour morphs also display differences in aggressivity and reproductive success. We show that the candidate locus is a small (approx. 70 kb) non-coding region mapping to the Z chromosome near the Follistatin (FST) gene. Unlike recent findings in other systems where phenotypic morphs are explained by large inversions containing hundreds of genes (so-called supergenes), we did not identify any structural rearrangements between the two haplotypes using linked-read sequencing technology. Nucleotide divergence between the red and black alleles was high when compared to the remainder of the Z chromosome, consistent with their maintenance as balanced polymorphisms over several million years. Our results illustrate how pleiotropic phenotypes can arise from simple genetic variation, probably regulatory in nature.
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Affiliation(s)
- Matthew B Toomey
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Cristiana I Marques
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Pedro Andrade
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Pedro M Araújo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Centro de Ciências do Mar e do Ambiente, Departamento de Ciências da Vida, Universidade de Coimbra, 3004-517 Coimbra, Portugal
| | - Stephen Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Małgorzata A Gazda
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Ricardo J Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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