Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish

C.J. Brauer, P.J. Unmack, L.B. Beheregaray

    Research output: Contribution to journalArticle

    7 Citations (Scopus)

    Abstract

    Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray–Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species’ spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.

    Original languageEnglish
    Pages (from-to)6841-6856
    Number of pages16
    JournalMolecular Ecology
    Volume26
    Issue number24
    DOIs
    Publication statusPublished - 2017

    Fingerprint

    transcriptomics
    gene expression
    Fishes
    Gene Expression
    fish
    Population
    RNA Sequence Analysis
    genetic variation
    RNA
    phylogenetics
    sequence analysis
    isolated population
    phenotypic plasticity
    divergent evolution
    Water Quality
    phylogeny
    dry environmental conditions
    plasticity
    population size
    Population Density

    Cite this

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    abstract = "Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in nonmodel species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray–Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g., dry/hot lowland; wet/cold upland) and represent opposite ends of the species’ spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an anova-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed that variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.",
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    Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish. / Brauer, C.J.; Unmack, P.J.; Beheregaray, L.B.

    In: Molecular Ecology, Vol. 26, No. 24, 2017, p. 6841-6856.

    Research output: Contribution to journalArticle

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