Selective Sweeps and Polygenic Adaptation Drive Local Adaptation along Moisture and Temperature Gradients in Natural Populations of Coast Redwood and Giant Sequoia.

Amanda R De La Torre,Manoj K Sekhwal,David B Neale

doi:10.3390/genes12111826

Amanda R De La Torre, Manoj K Sekhwal + Show 1 more

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https://doi.org/10.3390/genes12111826

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Abstract

Dissecting the genomic basis of local adaptation is a major goal in evolutionary biology and conservation science. Rapid changes in the climate pose significant challenges to the survival of natural populations, and the genomic basis of long-generation plant species is still poorly understood. Here, we investigated genome-wide climate adaptation in giant sequoia and coast redwood, two iconic and ecologically important tree species. We used a combination of univariate and multivariate genotype–environment association methods and a selective sweep analysis using non-overlapping sliding windows. We identified genomic regions of potential adaptive importance, showing strong associations to moisture variables and mean annual temperature. Our results found a complex architecture of climate adaptation in the species, with genomic regions showing signatures of selective sweeps, polygenic adaptation, or a combination of both, suggesting recent or ongoing climate adaptation along moisture and temperature gradients in giant sequoia and coast redwood. The results of this study provide a first step toward identifying genomic regions of adaptive significance in the species and will provide information to guide management and conservation strategies that seek to maximize adaptive potential in the face of climate change.

Highlights

The objectives of this research were to dissect the genomic basis of local adaptation to climate in natural populations of giant sequoia and coast redwood by (i) locating genomic regions showing signals of natural selection that might provide information about the mode of adaptation, (ii) identifying the main environmental variables driving adaptation in the species, and (iii) understanding the main biological functions of genes associated with environmental variation
While recent genome-wide environmental association studies in conifer species have consistently reported polygenic adaptation [19,30,31,32,33], our study suggests a more complex genomic architecture in coast redwood and giant sequoia, with regions of the genomes undergoing polygenic adaptation, other regions with sweep-like signatures, and a smaller third group of genomic regions showing signatures of both polygenic adaptation and selective sweeps
In our study on coast redwood, we found that 79% of the scaffolds showing signatures of selective sweeps were associated with regions identified by multivariate redundancy analysis (RDA)

Summary

Introduction

Understanding the genomic architecture of local adaptation is of great biological interest and paramount to predicting species’ responses to present and future changes in the climate. Recent improvements in sequencing methods and genotyping approaches have allowed the detection of signatures of recent or ongoing positive selection from their molecular signature on neutral polymorphism in species genomes [2,3,4]. While most of this knowledge comes from model and domesticated species, the genomic architecture of local adaptation in natural populations of long-lived non-model species remains understudied [5]

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