Adaptation to Climate Across the Arabidopsis thaliana Genome

Abstract

Understanding the genetic bases and modes of adaptation to current climatic conditions is essential to accurately predict responses to future environmental change. We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino acid-changing variants were significantly enriched among the loci strongly correlated with climate, suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown together in a common environment. Our results provide a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.

Key questions in the genetics and genomics of eco-evolutionary dynamics

“…Interestingly, this evidence often comes from some of the same systems and traits that were discussed above, including Pitx1 in stickleback, lactose tolerance in some human populations (Tishkoff et al, 2007), diazinon resistance in blowflies (Hartley et al, 2006), acetylcholinesterase resistance in Drosophila (Karasov et al, 2010) and local adaptation in Arabidopsis (Hancock et al, 2011). These studies suggest that new mutations can be important even when populations contain lots of standing variation, although not necessarily for the same traits.…”

“…In short, genome scans typically implicate divergence in many genes; and yet these scans still remain biased against genes of small effect. Indeed, other approaches, such as reciprocal transplants and correlations with environmental variables, typically reveal many more loci under selection (Michel et al, 2010;Fournier-Level et al, 2011;Hancock et al, 2011).…”

Evolutionary and Ecological Responses to Anthropogenic Climate Change

“…Their analysis revealed five loci that were significantly associated with aridity gradients and putatively orthologous to Arabidopsis (Arabidopsis thaliana) genes that confer stress tolerance (Eckert et al, 2010a). Additionally, Hancock et al (2011) discovered a diverse series of genes and Gene Ontology categories with an excess of nonsynonymous changes that are correlated with climatic variables in Arabidopsis. Such genome-wide scans could identify candidate genes involved in climatic adaptation in other species, but they must be carefully validated experimentally (Hancock et al, 2011).…”

“…Additionally, Hancock et al (2011) discovered a diverse series of genes and Gene Ontology categories with an excess of nonsynonymous changes that are correlated with climatic variables in Arabidopsis. Such genome-wide scans could identify candidate genes involved in climatic adaptation in other species, but they must be carefully validated experimentally (Hancock et al, 2011).…”

“…For polygenic quantitative traits (Rockman, 2012), genomic approaches could be used to detect subtle changes at multiple loci of small effect (Hansen et al, 2012;Turchin et al, 2012). Continuing advancements in genomic technologies and bioinformatics will improve our understanding of climatic adaptation in model (Fournier-Level et al, 2011;Hancock et al, 2011) and nonmodel (Allendorf et al, 2010) organisms. For example, Eckert et al (2010a) investigated the genetic basis of climatic adaptation in loblolly pine (Pinus taeda) by evaluating associations between environmental clines and allelic variation at markers genome wide.…”