Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
dc.contributor.author | Whiting, JR | |
dc.contributor.author | Paris, JR | |
dc.contributor.author | van der Zee, MJ | |
dc.contributor.author | Parsons, PJ | |
dc.contributor.author | Weigel, D | |
dc.contributor.author | Fraser, BA | |
dc.date.accessioned | 2021-05-26T09:37:58Z | |
dc.date.issued | 2021-05-24 | |
dc.description.abstract | Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage. | en_GB |
dc.description.sponsorship | H2020 European Research Council | en_GB |
dc.description.sponsorship | Natural Environment Research Council | en_GB |
dc.identifier.citation | Vol. 17, No. 5, article e1009566 | en_GB |
dc.identifier.doi | 10.1371/journal.pgen.1009566 | |
dc.identifier.grantnumber | GUPPYCon 758382 | en_GB |
dc.identifier.grantnumber | NE/P013074/1 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/125835 | |
dc.language.iso | en | en_GB |
dc.publisher | Public Library of Science | en_GB |
dc.rights | Copyright: © 2021 Whiting et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | en_GB |
dc.title | Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2021-05-26T09:37:58Z | |
dc.identifier.issn | 1553-7390 | |
dc.description | This is the final version. Available from Public Library of Science via the DOI in this record. | en_GB |
dc.description | Data Availability: Raw sequencing reads are available on ENA: PRJEB43917 (Aripo, Madamas, Tacarigua) and PRJEB10680 (Guanapo and Oropouche). Final VCF data are available on FigShare, doi: 10.6084/m9.figshare.14315771. Other data and scripts used to analyse data are available on github: github.com/JimWhiting91/guppy_convergence. This repository is archived with Zenodo, doi: 10.5281/zenodo.4740381. | en_GB |
dc.identifier.eissn | 1553-7404 | |
dc.identifier.journal | PLOS Genetics | en_GB |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2021-04-27 | |
exeter.funder | ::European Commission | en_GB |
rioxxterms.version | VoR | en_GB |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2021-05-26T09:28:22Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2021-05-26T09:38:10Z | |
refterms.panel | A | en_GB |
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Except where otherwise noted, this item's licence is described as Copyright: © 2021 Whiting et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.