New pre-print on Arctic charr parallel evolution

Parallel evolution by non-parallel routes is a major fascination of mine. Here we have a pre-print submitted (and ms in the appropriate pipelines) about how such parallel evolution can happen, overcoming non-parallel backgrounds. The transcriptome!

This is the outcome of a major group effort, including two PhD theses and many many years' worth of sampling ...

Preprint at https://www.biorxiv.org/content/early/2018/02/14/265272.article-info

Abstract: 
Quantifying the extent to which evolution is predictable is critical to understanding biodiversity origins and its responses to future environmental challenges1,2. Replicate, or parallel, phenotypic evolution has been found in classic examples such as anole lizards, stickleback fishes, salmonid fishes, and cichlid fishes3-8 and reflects similar adaptive outcomes. However it is not well understood if, how, and at what rate ecologically relevant phenotypic evolution can overcome the heterogeneous genetic backgrounds that are pervasive in natural populations. To test evolutionary predictability in a Holarctic ‘natural experiment’, we used genome-informed single nucleotide polymorphism data, transcriptome-wide gene expression comparisons, and eco-morphology analysis within and across lakes and evolutionary lineages of a freshwater salmonid fish, Arctic charr (Salvelinus alpinus). We found significant parallel evolution in replicate specialist ‘ecotypes’ for adaptive morphological traits associated with foraging. This predictability overcomes pervasive population-specific variation caused by complex demographic histories, differing genomic divergence in response to selection, and non-parallel genetic associations with ecotype. Remarkably the functional molecular bases to ecotypes, inferred from gene expression and biological pathways, were extensively and significantly shared across ecotype replicates. Our findings suggest that parallel evolution by non-parallel evolutionary routes is possible when the regulatory molecular phenotype compensates for divergent histories.    


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NEW PAPER: Genomics of head and body shape parallelism in Arctic charr

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Published today as free open access in Molecular Ecology :  Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs Sam Fenton, Arne Jacobs, Colin Bean, Colin Adams & Kathryn Elmer The appearance of repeated phenotypes across replicates in similar environments have been described as examples of parallel evolution. However, the genomic bases of these similar phenotypes is rarely elucidated and so whether the same genomic pathways are used to achieve these similar phenotypes across replicates is rarely known. Here we used the repeated divergence of benthivorous-planktivorous ecomorph pairs of Arctic charr to investigate the genomic underpinnings of head and body shape morphology across replicates. We found that only a small number of associated SNPs for each phenotype were shared across all four ecomorph pairs we investigated with selection on associated SNPs varying considerably across replicates. Overall, these results suggest that the genomic underpinnings ...
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