Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study.

Colin R Mahony,Ian R Maclachlan,Sally N Aitken,Tongli Wang,Jeremy B Yoder,Brandon M Lind

doi:10.1111/eva.12871

Colin R Mahony, Ian R Maclachlan + Show 4 more

Open Access

https://doi.org/10.1111/eva.12871

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Abstract

We evaluate genomic data, relative to phenotypic and climatic data, as a basis for assisted gene flow and genetic conservation. Using a seedling common garden trial of 281 lodgepole pine (Pinus contorta) populations from across western Canada, we compare genomic data to phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and spatial scale of local adaptation in this species. We find that phenotype‐associated loci are equivalent or slightly superior to climate data for describing local adaptation in seedling traits, but that climate data are superior to genomic data that have not been selected for phenotypic associations. We also find agreement between the climate variables associated with genomic variation and with 20‐year heights from a long‐term provenance trial, suggesting that genomic data may be a viable option for identifying climatic drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with the experimental traits occur at broad spatial scales, suggesting that standing variation of adaptive alleles for this and similar species does not require management at scales finer than those indicated by phenotypic data. This study demonstrates that genomic data are most useful when paired with phenotypic data, but can also fill some of the traditional roles of phenotypic data in management of species for which phenotypic trials are not feasible.

Highlights

The impact of climate change is undeniable and evident in forests of western NorthAmerica
What is the relative value of genomic data vs. climatic and geographic data in explaining locally adaptive phenotypic variation? We address this by comparing the proportion of variance in four seedling traits that can be explained by geographic, climatic, and several types of genomic data including a full SNP array, a large set of neutral markers, and loci inferred from both genotype-phenotype associations and genotype-environment associations
We examine the congruence of genomic vs. phenotypic data in guiding climatic variable selection by contrasting the proportion of variance of individual climate variables that is explained by climate-associated genomic loci, seedling common garden phenotypes, and long-term provenance trial phenotypes

Summary

Introduction

The impact of climate change is undeniable and evident in forests of western NorthAmerica. The impact of climate change is undeniable and evident in forests of western North. There is mounting evidence that changes in climate are disrupting local adaptation in plants (Mcgraw et al 2015; Wilczek et al 2019), with impacts to productivity of commercial tree species (Rehfeldt et al 1999; Leites et al 2012) and conservation of vulnerable species (Parmesan 2006). Forest managers are seeking guidance on which source populations to use for planting, as the long-practiced ‘local is best’ strategy no longer matches trees with the climates to which they are adapted (Aitken and Bemmels 2016). In the past two decades, detailed climate data has been used to extend phenotypic inferences of local adaptation across managed landscapes (Sork et al 2013; Wadgymar et al 2017)

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