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The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments
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  • Emily Tetrault,
  • John Swenson,
  • Ben Aaronson,
  • Chelsea Marcho,
  • Craig Albertson
Emily Tetrault
University of Massachusetts Amherst
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John Swenson
University of Massachusetts Amherst
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Ben Aaronson
University of Massachusetts Amherst
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Chelsea Marcho
University of Massachusetts Amherst
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Craig Albertson
University of Massachusetts

Corresponding Author:rcraigalbertson@gmail.com

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Adaptive phenotypes are shaped by a combination of genetic and environmental forces, and while the literature is rich with studies focusing on either genetics or environment contributions, those that consider both are rare. Here we utilize the cichlid oral jaw apparatus to fill this knowledge-gap. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when reared in the pelagic versus benthic environment. Further, these data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible in either the pelagic (n=15) or the benthic environment (n=11), as well as loci where differences were robust to foraging environment (n=13). All in all, these data provide novel insights into the epigenetic, genetic, and cellular bases of species- and environment-specific bone shapes, as well as the evolution of phenotypic plasticity in this iconic model system.
30 Nov 2022Submitted to Molecular Ecology
02 Dec 2022Assigned to Editor
02 Dec 2022Submission Checks Completed
02 Dec 2022Review(s) Completed, Editorial Evaluation Pending
11 Dec 2022Reviewer(s) Assigned
20 Feb 2023Editorial Decision: Revise Minor