Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps

Abstract

Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST-based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.

Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

“…Overall, we genotyped 180 individuals of A. halleri from nine natural populations using 20 microsatellite markers, which is above the average number of microsatellites typically used in population and conservation genetic studies [49]. We compared them to a pooled whole-genome re-sequencing approach (Pool-Seq; [50, 51]) and tested whether estimates of genetic variation derived from microsatellite polymorphisms are valid and useful proxies of genome-wide genetic variation and differentiation. Specifically, we tested whether estimates from both marker types were correlated (relative comparison) and had similar absolute values (absolute comparison).…”

Common garden experiments in the genomic era: new perspectives and opportunities

“…Despite the advantages of common garden experiments, the study of local adaptation in non-model species during the past decade has been strongly driven by the study of genetic markers in natural populations (Luikart et al, 2003). Typically, evolutionary biologists go to natural populations, sample tissue from the individuals and genotype them with high-throughput methods and then proceed with a genome scan analysis of selection (see, for example, Eckert et al, 2010;Bourret et al, 2013;Fischer et al, 2013). Although this method can be quite powerful, it has some limitations (for example, false positives, no information on the adaptive phenotype).…”

Population Genomics for Understanding Adaptation in Wild Plant Species

“…There is good evidence for local adaptation in A. lyrata from transplant experiments (e.g., 92), and initial population genomics analyses have suggested footprints of selection and climate associations in A. halleri (38). The A. lyrata reference genome (63) was used to identify candidate loci for adaptation to serpentine soils in this species (148) and for genetic adaptation to genome doubling in the close relative A. arenosa (59,161).…”