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Replicated DNA methylation differences between stick insect ecotypes
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  • Clarissa de Carvalho,
  • Jon Slate,
  • Romain Villoutreix,
  • Víctor Soria-Carrasco,
  • Rüdiger Riesch,
  • Jeff Feder,
  • Zachariah Gompert,
  • Patrik Nosil
Clarissa de Carvalho
The University of Sheffield

Corresponding Author:[email protected]

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Jon Slate
University of Sheffield
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Romain Villoutreix
Centre d'Ecologie Fonctionnelle et Evolutive
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Víctor Soria-Carrasco
John Innes Centre
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Rüdiger Riesch
Royal Holloway University of London
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Jeff Feder
U. Notre Dame
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Zachariah Gompert
Utah State University
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Patrik Nosil
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Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. To being to address this issue requires high-resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e., ecotypes). By integrating results from sequencing of whole transcriptomes, genomes, and methylomes, we investigate whether environmental, host, and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in CpG context. We report an overall genome-wide methylation level for T. cristinae of ~14%, being enriched in gene bodies and impoverished in repetitive elements. Genome-wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host-plant effects. Using methylome-environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation with genetic relatedness and the ecologically-important variable of host plant suggest a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test if methylation has a heritable component and the extent to which it responds to experimental manipulation in field and laboratory studies.
13 Jun 2023Submitted to Molecular Ecology
16 Jun 2023Submission Checks Completed
16 Jun 2023Assigned to Editor
16 Jun 2023Review(s) Completed, Editorial Evaluation Pending
22 Jun 2023Reviewer(s) Assigned
04 Aug 2023Editorial Decision: Revise Minor
11 Sep 20231st Revision Received
13 Sep 2023Submission Checks Completed
13 Sep 2023Assigned to Editor
13 Sep 2023Review(s) Completed, Editorial Evaluation Pending
25 Sep 2023Editorial Decision: Accept