Altitudinal gradients in mountain regions are short-range clines of environmental parameters like temperature or radiation. Common garden experiments of populations from different altitudes have been used for a long time to study local adaptation. Modern genomics allows the investigation of footprints of selection at very high resolution. I will provide an overview of current methods and provide examples from the adaptation to high altitude of the wild plant Arabidopsis thaliana to the high Alps in Europe and maize landraces in Peru. In Arabidopsis thaliana, we investigated genomic and phenotypic signatures of adaptation to altitude in populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of individuals from each population. High-altitude populations showed a lower nucleotide diversity and negative Tajima’s D values and were more closely related to each other than to low-altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low- and high-altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low- and high-altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes known to be involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress to frost tolerance strongly suggest that the main determinant of local adaptation at high altitudes reflects the highly variable microclimate. Multigenerational reciprocal common garden experiments also suggest a strong epigenetic effect that may contribute to fitness via a home site advantage. A similar pattern of latitudinal differentiation was observed in the analysis of nearly 2000 genebank accessions of low and highland maize from Peru (0 to 3900 m altitude). They show a strong genetic and phenotypic differentiation that results from local adaptation, and FST-based outlier tests indicate genomic regions that likely were targets of differential selection. Taken together, the results provide strong evidence for local adaptation of plants along altitudinal gradients, and also show further avenues for the investigation of this diversity using genetic approaches to identify the functional basis of local adaptation.
All organisms live in environments that vary through time and space. Such environmental change has a dramatic impact on the evolutionary dynamics of populations and promotes adaptive evolution to local environments. For organisms with limited dispersal or rapid generation time relative to the pace of environmental change, local adaptation to variable environments is predicted to be common. Seasonal changes in climate coupled with inter-annual variability and anthropogenic changes over decadal scales is a potent driver of adaptive evolution. Is adaptive evolution to climate variability predictable at a genetic level? Are polymorphisms that promote adaptive evolution to short-term fluctuations in climate likely to persist in populations, potentially enabling species to adapt to long term changes in climate? To address these questions, I will present our recent theoretical investigations and empirical assessment of rapid and cyclic adaptation over seasonal time scales in the fruit fly, Drosophila melanogaster. Our theoretical models predict that polymorphisms underlying adaptation to seasonally fluctuating environments could plausibly cycle in frequency repeatedly over multiple years and can persist in populations for long periods of time. Using pooled estimates of allele frequencies from 20 paired spring-fall samples collected in North America and Europe, we show that seasonally selected polymorphisms can vary predictably among populations and that they tend to persist in the species for long periods of time. I will relate our work to the general topic of adaptation to anthropogenic climate change across taxa by discussing the importance of understanding the relationship between the pace of environmental change and an organism’s life-history.