The Landscape of Extreme Genomic Variation in the Highly Adaptable Atlantic Killifish

Noah M. Reid, Craig E. Jackson, Don Gilbert, Patrick Minx, Michael J. Montague, Thomas H. Hampton, Lily W. Helfrich, Benjamin L. King, Diane E. Nacci, Neel Aluru, Sibel I. Karchner, John Colbourne, Mark E. Hahn, Joseph R. Shaw, Marjorie F. Oleksiak, Douglas L. Crawford, Wesley C. Warren, Andrew Whitehead

Research output: Contribution to journalArticlepeer-review

22 Citations (Scopus)
138 Downloads (Pure)

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.
Original languageEnglish
Pages (from-to)659-676
JournalGenome Biology and Evolution
Volume9
Issue number3
DOIs
Publication statusPublished - 1 Mar 2017

Keywords

  • population genomics
  • genome sequence
  • comparative genomics
  • adaptation
  • genetic diversity

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