The landscape of extreme genomic variation in the highly adaptable Atlantic killifish

dc.contributor.author Reid, Noah M.
dc.contributor.author Jackson, Craig E.
dc.contributor.author Gilbert, Don
dc.contributor.author Minx, Patrick
dc.contributor.author Montague, Michael J.
dc.contributor.author Hampton, Thomas H.
dc.contributor.author Helfrich, Lily W.
dc.contributor.author King, Benjamin L.
dc.contributor.author Nacci, Diane E.
dc.contributor.author Aluru, Neelakanteswar
dc.contributor.author Karchner, Sibel I.
dc.contributor.author Colbourne, John K.
dc.contributor.author Hahn, Mark E.
dc.contributor.author Shaw, Joseph R.
dc.contributor.author Oleksiak, Marjorie F.
dc.contributor.author Crawford, Douglas L.
dc.contributor.author Warren, Wesley C.
dc.contributor.author Whitehead, Andrew
dc.date.accessioned 2017-03-28T17:28:29Z
dc.date.available 2017-03-28T17:28:29Z
dc.date.issued 2017-03-01
dc.description © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023. en_US
dc.description.abstract Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments. en_US
dc.description.sponsorship This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.). en_US
dc.identifier.citation Genome Biology and Evolution 9 (2017): 659-676 en_US
dc.identifier.doi 10.1093/gbe/evx023
dc.identifier.uri https://hdl.handle.net/1912/8839
dc.language.iso en_US en_US
dc.publisher Oxford University Press en_US
dc.relation.uri https://doi.org/10.1093/gbe/evx023
dc.rights Attribution 4.0 International *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ *
dc.subject Population genomics en_US
dc.subject Genome sequence en_US
dc.subject Comparative genomics en_US
dc.subject Adaptation en_US
dc.subject Genetic diversity en_US
dc.title The landscape of extreme genomic variation in the highly adaptable Atlantic killifish en_US
dc.type Article en_US
dspace.entity.type Publication
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