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Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage

View ORCID ProfileKatie E. Lotterhos, Kathryn A. Hodgins, Sam Yeaman, Jon Degner, Sally Aitken
doi: https://doi.org/10.1101/202481
Katie E. Lotterhos
1Department of Marine and Environmental Sciences, Northeastern Marine Science Center, Nahant Rd, Nahant, MA 01908
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  • For correspondence: k.lotterhos@neu.edu
Kathryn A. Hodgins
2School of Biological Sciences, Monash University, Wellington Rd, Clayton VIC 3800
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Sam Yeaman
3Department of Biological Sciences, University of Calgary, AB, T2N1N4
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Jon Degner
4Department of Forest and Conservation Sciences, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
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Sally Aitken
4Department of Forest and Conservation Sciences, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada
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Abstract

Physical proximity among alleles shaped by different sources of selection is a fundamental aspect of genetic architectures critical for predicting their evolution. Theory predicts that evolution in complex environments should select for modular genetic architectures with limited pleiotropy among modules. However, limited data exist to test this hypothesis because the field lacks consensus for how to control for intercorrelated climate variables. We aim to characterize the genetic architecture of adaptation to climate, including the modularity of the architecture (number of distinct climate factors), overlap among modules, and physical linkage among loci. We introduce a co-association network analysis, which parses loci into groups based on differing environmental associations, and use it to study the genetic architecture of local adaptation to climate in lodgepole pine (Pinus contorta). We identified several non-overlapping modules of genes associated with environmental factors (aridity, freezing, geography), which supports the hypothesis of modular environmental pleiotropy. Notably, we found moderate physical linkage among some candidate loci in different modules, which may facilitate or hinder adaptation depending on the multivariate trajectory of climate change. Moreover, we show that associations with environmental principal components would have missed candidates and resulted in a limited interpretation regarding the selective environment. Finally, simulations revealed that the propensity of co-association modules to arise under neutrality increased with demographic complexity, but also that true causal loci are more highly-connected within the module, which may be useful for prioritizing candidates.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 13, 2017.
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Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage
Katie E. Lotterhos, Kathryn A. Hodgins, Sam Yeaman, Jon Degner, Sally Aitken
bioRxiv 202481; doi: https://doi.org/10.1101/202481
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Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage
Katie E. Lotterhos, Kathryn A. Hodgins, Sam Yeaman, Jon Degner, Sally Aitken
bioRxiv 202481; doi: https://doi.org/10.1101/202481

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