A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy
dc.contributor.author | Paris, JR | |
dc.contributor.author | Whiting, JR | |
dc.contributor.author | Daniel, MJ | |
dc.contributor.author | Ferrer Obiol, J | |
dc.contributor.author | Parsons, PJ | |
dc.contributor.author | van der Zee, MJ | |
dc.contributor.author | Wheat, CW | |
dc.contributor.author | Hughes, KA | |
dc.contributor.author | Fraser, BA | |
dc.date.accessioned | 2022-03-21T15:55:31Z | |
dc.date.issued | 2022-03-09 | |
dc.date.updated | 2022-03-21T14:59:32Z | |
dc.description.abstract | Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis. | en_GB |
dc.description.sponsorship | Natural Environment Research Council (NERC) | en_GB |
dc.description.sponsorship | European Research Council (ERC) | en_GB |
dc.description.sponsorship | National Science Foundation (NSF) | en_GB |
dc.format.extent | 1233- | |
dc.identifier.citation | Vol. 13, article 1233 | en_GB |
dc.identifier.doi | https://doi.org/10.1038/s41467-022-28895-4 | |
dc.identifier.grantnumber | NE/P013074/1 | en_GB |
dc.identifier.grantnumber | 58382 | en_GB |
dc.identifier.grantnumber | ISO-1354775 | en_GB |
dc.identifier.grantnumber | DEB-1740466 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/129115 | |
dc.identifier | ORCID: 0000-0001-5905-9056 (Fraser, Bonnie A) | |
dc.language.iso | en | en_GB |
dc.publisher | Nature Research | en_GB |
dc.relation.url | https://github.com/josieparis/guppy-colour-polymorphism | en_GB |
dc.relation.url | https://doi.org/10.5281/zenodo.5036659 | en_GB |
dc.relation.url | https://doi.org/10.5281/zenodo.5940510 | en_GB |
dc.relation.url | https://github.com/josieparis/gatk-snp-calling | en_GB |
dc.relation.url | https://doi.org/10.5281/zenodo.5903522 | en_GB |
dc.relation.url | https://github.com/JimWhiting91/genotype_plot | en_GB |
dc.relation.url | https://doi.org/10.5281/zenodo.5913504 | en_GB |
dc.rights | © Crown 2022. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. | en_GB |
dc.title | A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2022-03-21T15:55:31Z | |
dc.identifier.issn | 2041-1723 | |
exeter.article-number | 1233 | |
dc.description | This is the final version. Available on open access from Nature Research via the DOI in this record | en_GB |
dc.description | Data availability; The DNA sequencing data generated in this study have been deposited in the European Nucleotide Archive (ENA) under the Study Accession PRJEB36506 with the following codes: SAMEA6512722-SAMEA6512725 (Pool-seq Iso-Y data); SAMEA8750557-SAMEA8750565 (whole-genome sequencing data for Paria); SAMEA8795870-SAMEA8795872 (long-read pacbio data for Iso-Y6). The DNA sequencing data generated for Upper Marianne individuals have been deposited in the ENA under the Study Accession PRJEB10680 under the accession codes: SAMEA3649957-SAMEA3649973. The male guppy reference genome can be accessed at the ENA under the Accession GCA_904066995. The female guppy reference genome can be accessed at the ENA under Accession GCA_000633615.2. Source data are provided with this paper at https://github.com/josieparis/guppy-colour-polymorphism; https://doi.org/10.5281/zenodo.5036659. Recombination data were provided through personal communication with permission of the authors. | en_GB |
dc.description | Code availability: All code, scripts and additional data related to analysis are available on GitHub (https://github.com/josieparis/guppy-colour-polymorphism; https://doi.org/10.5281/zenodo.5940510), (https://github.com/josieparis/gatk-snp-calling; https://doi.org/10.5281/zenodo.5903522) and (https://github.com/JimWhiting91/genotype_plot; https://doi.org/10.5281/zenodo.5913504). | en_GB |
dc.identifier.eissn | 2041-1723 | |
dc.identifier.journal | Nature Communications | en_GB |
dc.relation.ispartof | Nature Communications, 13(1) | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2022-02-16 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2022-03-09 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2022-03-21T15:52:51Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2022-03-21T15:55:48Z | |
refterms.panel | A | en_GB |
refterms.dateFirstOnline | 2022-03-09 |
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Except where otherwise noted, this item's licence is described as © Crown 2022. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.