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Variation in gene expression patterns across a conifer hybrid zone highlights the architecture of adaptive evolution under novel selective pressures
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  • Mitra Menon,
  • Jared Swenson,
  • Ehren Moler,
  • Kristen Waring,
  • Amy Whipple,
  • Andrew Eckert
Mitra Menon
University of California Davis

Corresponding Author:[email protected]

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Jared Swenson
Northern Arizona University
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Ehren Moler
California State Polytechnic University Pomona
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Kristen Waring
Northern Arizona University College of Engineering Forestry and Natural Sciences
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Amy Whipple
Northern Arizona University
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Andrew Eckert
Virginia Commonwealth University
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Natural plant populations often exhibit marked differences in gene expression patterns that can reflect heterogeneity in selective pressures. Analyzing gene expression as a quantitative trait provides a unique opportunity to evaluate the underlying genomic basis of a plethora of traits and their interactions in driving adaptive evolution. We investigated patterns and processes driving expression differentiation under conditions mimicking future climates by combining common garden experiments with transcriptome-wide datasets obtained from hybrid populations of Pinus strobiformis and P. flexilis. We found strong signals of genotype-environment interactions (GEI) at the individual transcript and the co-expression module levels suggesting a marked influence of drought related variables on adaptive evolution. Overall, survival was positively associated with P. flexilis ancestry, but it exhibited an environment-specific pattern. Co-expression modules exhibiting strong associations with survival and genomic ancestry were representative of similar functional categories across both gardens. Using network topology measures, putatively adaptive garden-specific expression traits were pleiotropic and belonged to modules exhibiting high population differentiation yet low preservation across gardens. Overall, our study suggests the presence of substantial genetic variation underlying univariate and multivariate traits in novel climates that may enable populations of long-lived forest trees to respond to rapid shifts in climatic conditions in early seedling stages when mortality tends to be the highest. Our finding of pleiotropic trait architectures underlying adaptive traits, however, implies rapid adaptive responses to changing selection pressures depend on whether trait covariances align with the direction of change in selection pressures.
26 Oct 2023Submitted to Molecular Ecology
30 Oct 2023Assigned to Editor
30 Oct 2023Submission Checks Completed
30 Oct 2023Review(s) Completed, Editorial Evaluation Pending
07 Nov 2023Reviewer(s) Assigned