Do We Need to Identify Adaptive Genetic Variation When Prioritizing Populations for Conservation?

Abstract

When prioritizing populations for conservation of a given species, it is unclear whether the distribution of standing genetic variation can be used as a suitable proxy for the distribution of useful adaptive genetic variation. We tested whether using genome-wide and putatively adaptive genetic variation give similar prioritization results. We identified adaptive loci via their association with either environmental factors or phenotypic traits using two genomic data sets: yellow warblers (Setophaga petechia) across North America and lodgepole pines (Pinus contorta) in western Canada. We measured pairwise differentiation among populations using a principal components analysis and used a phylogenetic approach (NeighborNet networks) coupled with a measure of evolutionary distinctiveness (Shapley value) to attribute a priority rank to each population. Overall, we found that prioritization rankings using adaptive variation alone were not significantly divergent from rankings based on genome-wide genetic variation. Our testing framework might be of immediate use to conservation practitioners collecting next-generation sequencing data, and we call for further investigation in other species. Our results suggest that we may not need to pursue the contingent step of identifying adaptive variation in species of concern before prioritizing populations, i.e. a naive approach of using genome-wide genetic variation might be a suitable proxy for identifying local adaptation.

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Data availability

R code and data for this study are available at https://github.com/philippeff/PopulationPrioritization.

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Acknowledgements

We would like to thank Rachael Bay, who made her SNP data set available, and all the authors of the two data sets included in this study. Thanks to members of the Crawford Lab at SFU and presenters at the CSEE symposium on conservation genomics (CSEE meeting 2019) for comments on this project. The authors were supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) through doctoral scholarships to PFF (CGS-D) and JL (PGS-D) and Discovery and Accelerator Grants to AØM.

Funding

The authors were supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) through doctoral scholarships to PFF (CGS-D) and JL (PGS-D) and Discovery and Accelerator Grants to AØM.

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AØM conceived the project; PFF designed the project; PFF and JL collected the data, performed the analyses and wrote the first draft; all authors contributed to the final version of the manuscript.

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Correspondence to Philippe Fernandez-Fournier or Jayme M. M. Lewthwaite.

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Fernandez-Fournier, P., Lewthwaite, J.M.M. & Mooers, A.Ø. Do We Need to Identify Adaptive Genetic Variation When Prioritizing Populations for Conservation?. Conserv Genet 22, 205–216 (2021). https://doi.org/10.1007/s10592-020-01327-w

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Keywords

  • Population prioritization
  • Conservation genomics
  • GWAS
  • Adaptive genetic variation
  • Genetic distinctiveness
  • NeighborNet