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Modularity of genes involved in local adaptation to climate despite physical linkage

View ORCID ProfileKatie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn A. Hodgins
doi: https://doi.org/10.1101/202481
Katie E. Lotterhos
1Department of Marine and Environmental Sciences, Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA 01908
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  • ORCID record for Katie E. Lotterhos
  • For correspondence: k.lotterhos@neu.edu
Sam Yeaman
2Department of Biological Sciences, University of Calgary, AB, T2N1N4
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Jon Degner
3Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC V6T 1Z4 Canada
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Sally Aitken
3Department of Forest and Conservation Sciences, Faculty of Forestry, Vancouver, BC V6T 1Z4 Canada
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Kathryn A. Hodgins
4School of Biological Sciences, Monash University, Wellington Rd, Clayton VIC 3800
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Abstract

Background Physical linkage among genes shaped by different sources of selection is a fundamental aspect of genetic architecture. Theory predicts that evolution in complex environments selects for modular genetic architectures and high recombination rates among loci shaped by different sources of selection. However, limited data exist to test these predictions because the field lacks consensus for how to control for intercorrelated environmental variables. Here, we introduce a co-association network analysis, which clusters loci based on differing environmental associations, and use it to study the genetic architecture of local adaptation to climate in lodgepole pine (Pinus contorta).

Results We identified many modules of genes associated with distinct environments (aridity, freezing, geography), and discovered low recombination rates among some candidate genes in different modules. We observed limited evidence for environmental pleiotropic effects on distinct aspects of climate. We also found limited correspondence between the modularity of co-association networks and gene regulatory networks. We compared co-association networks to associations with principal components, and found the latter can lead to misinterpretation. Finally, we used simulations to illustrate the benefits and caveats of co-association networks.

Conclusions Co-association networks provided a useful framework for studying modularity. Our results supported the prediction that evolution to complex environments selects for modular genetic architectures, but some of our results went against the prediction that selection would increase recombination among loci experiencing different sources of selection. These results give new insight into evolutionary debates about the extent of modularity and pleiotropy in the evolution of genetic architectures.

  • List of abbreviations

    LD
    Linkage disequilibrium
    PC
    Principal components
    SNP
    single nucleotide polymorphism
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    Posted January 26, 2018.
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    Modularity of genes involved in local adaptation to climate despite physical linkage
    Katie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn A. Hodgins
    bioRxiv 202481; doi: https://doi.org/10.1101/202481
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    Modularity of genes involved in local adaptation to climate despite physical linkage
    Katie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken, Kathryn A. Hodgins
    bioRxiv 202481; doi: https://doi.org/10.1101/202481

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