Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data

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ID: 330774
2026
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Abstract
Successful implementation of evolutionary programs to rescue climatically threatened species requires identification of adaptive variation. Although many genotype-environment association methods have been successful in identifying adaptive variation, current approaches can be improved in two important aspects. First, most existing methods do not account for genotype uncertainty in widely available low-coverage whole-genome sequencing data. Researchers often restrict analysis to loci for which genotypes can be inferred reliably or call the most probable genotype, allowing the use of genotype-based methods. However, discarding data and false genotype calls increase the uncertainty in estimates of genetic variation and can introduce systematic biases. Second, most methods use phenomenological approaches, such as logistic regression, to partition estimated variation into adaptive and non-adaptive components. Consequently, current approaches may fail to account for evolutionary processes, such as migration-selection balance. Structured migration between climatically disparate locations can produce deviations from a smooth S-shape response curve, which can be difficult to accommodate using generalized linear models. To overcome these challenges, we developed a method that accounts for genotype uncertainty in sequencing data and propagates this uncertainty to inform the parameters of an evolutionary model. A key feature of this model is that it describes mechanistically how genetic variation arises from joint interactions between local adaptation, structured migration, mutation, and drift. Our synthetic simulation tests reveal that accounting for genotype uncertainty and structured migration substantially reduces false negatives. We also applied our approach to analyze data on North American rosy-finches (3.7 million SNPs), a high-alpine, climatically threatened clade of bird species.
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openalex_W7215041781 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Nikunj Goel, Christen M. Bossu, Seorim Yi, Timothy M. Brown, Erica C. N. Robertson, Peri E. Bolton, Ben J. Vernasco, Reza Goljani Amirkhiz, Erika S. Zavaleta, Kristen Ruegg, Mevin B. Hooten
Journal molecular biology and evolution
Year 2026
DOI
10.1093/molbev/msag255
URL
https://doi.org/10.1093/molbev/msag255
Keywords Keywords not found

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