Abstract
Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome–environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.
Highlights
In the context of contemporary climate change, a major goal in evolutionary ecology is to understand and predict the ability of a given species to persist in presence of novel climate conditions (Bay et al, 2017)
These results suggest the presence of contrasted climates, even at a short geographical distance, among the locations inhabited by A. thaliana in the Midi-Pyrénées region
In agreement with previous studies reporting that global effects of the demographic evolutionary forces in A. thaliana should be limited at a small geographical scale (Nordborg et al, 2005; Platt et al, 2010), we observed that genomic variation among the 168 natural populations is weakly correlated to geographic variation
Summary
In the context of contemporary climate change, a major goal in evolutionary ecology is to understand and predict the ability of a given species to persist in presence of novel climate conditions (Bay et al, 2017). Species can migrate to track current climate spatial shifts. This response can, be limited for (i) long-distance dispersal organisms because of the presence of multiple anthropogenic barriers (Ewers and Didham, 2006), and (ii) organisms with restricted dispersal as for example sessile plants lacking dispersal mechanism or disperser reward (Wang et al, 2016). Organisms can rapidly acclimate to novel climate conditions via phenotypic plasticity, defined as the ability of a given genotype to produce different phenotypes when exposed to different environmental conditions (Fusco and Minelli, 2010). One of the main limits concerns the unreliability of environmental cues, leading to non-adaptive or mal-adaptive plastic responses (van Kleunen and Fischer, 2005). In the context of climate change, such unreliable cues can correspond to extreme climate events that fall outside the range of the climate conditions encountered by natural populations over their history (Orlowsky and Seneviratne, 2012)
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