Glacial refuge areas are expected to harbor a large fraction of the intraspecific biodiversity of the temperate biota. To test this hypothesis, we studied chloroplast DNA variation in 22 widespread European trees and shrubs sampled in the same forests. Most species had genetically divergent populations in Mediterranean regions, especially those with low seed dispersal abilities. However, the genetically most diverse populations were not located in the south but at intermediate latitudes, a likely consequence of the admixture of divergent lineages colonizing the continent from separate refugia.

Rapid climate change jeopardizes tree populations by shifting current climate zones. To avoid extinction, tree populations must tolerate, adapt, or migrate. Here we investigate geographic patterns of genetic variation in valley oak, Quercus lobata Née, to assess how underlying genetic structure of populations might influence this species' ability to survive climate change. First, to understand how genetic lineages shape spatial genetic patterns, we examine historical patterns of colonization. Second, we examine the correlation between multivariate nuclear genetic variation and climatic variation. Third, to illustrate how geographic genetic variation could interact with regional patterns of 21st Century climate change, we produce region-specific bioclimatic distributions of valley oak using Maximum Entropy (MAXENT) models based on downscaled historical (1971-2000) and future (2070-2100) climate grids. Future climatologies are based on a moderate-high (A2) carbon emission scenario and two different global climate models. Chloroplast markers indicate historical range-wide connectivity via colonization, especially in the north. Multivariate nuclear genotypes show a strong association with climate variation that provides opportunity for local adaptation to the conditions within their climatic envelope. Comparison of regional current and projected patterns of climate suitability indicates that valley oaks grow in distinctly different climate conditions in different parts of their range. Our models predict widely different regional outcomes from local displacement of a few kilometres to hundreds of kilometres. We conclude that the relative importance of migration, adaptation, and tolerance are likely to vary widely for populations among regions, and that late 21st Century conditions could lead to regional extinctions.

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change.KEYWORDS climate adaptation; environmental associations; genetic lineages; single nucleotide polymorphisms; fitness estimates P AST and present climate changes are major drivers of species displacements and range-size variation (Hughes 2000;Franks and Hoffmann 2012). Current predictions indicate that the impact of climate change will intensify over the next 20-100 years (Loarie et al. 2009;Bellard et al. 2012), with concomitant phenotypic and genetic effects on wild populations (Gamache and Payette 2004;Franks and Hoffmann 2012;Alberto et al. 2013a). The capability of species to respond to such alterations will rely on phenotypic plasticity, potential for in situ adaptation, and/or migration to more suitable habitats (Aitken et al. 2008). While phenotypic plasticity and migration might be insufficient to cope with these changes (Mclachlan et al. 2005;Malcom et al. 2011;Zhu et al. 2011), successful in situ adaptation will depend on the amount of standing genetic variation and the rate at which new alleles arise, are maintained, and/or get to fixation within populations (Hancock et al. 2011). Thus, our ability to detect present adaptive polymorphisms and to integrate them in predictive models of future maladaptation might be decisive to ensure the persistence of natural p...

Animals are the principal vectors of dispersal for a large number of plant species. Unfortunately it is not easy to discern their movement patterns or the fate of their dispersed seeds. Many animals transport seeds by consuming them and then, some time later, defecating them. Others gather seeds and then store them for later consumption. Both circumstances lead to a set of seeds that have been dispersed in a clumped pattern, which offers a unique opportunity to assess seed movements. We introduce a novel approach that uses maternally inherited seed tissue to quantify the genetic structure of dispersed seed pools. This direct approach measures the genetic variability within and among seed pools, and estimates the scale of seed movement, without requiring a highly polymorphic battery of markers or the location and genotypes of all possible seed parents. We demonstrate this approach with the specific case of seed transport of valley oak (Quercus lobata) acorns by acorn woodpeckers (Melanerpes formicivorus). These territorial birds store acorns in drilled holes in the bark of trees, called granaries. We sampled stored acorns from different granaries, extracted DNA from the maternally inherited pericarp, and then assessed individuals for three microsatellite markers. We found extremely high genetic structure among granaries, a low number of effective seed donors per granary, and restricted seed movement. A maternity analysis performed on the same sample with seven microsatellites confirms acorn transport is limited to approximately 100-m radius. Our findings provide insight into the foraging and seed-dispersal behaviour of acorn woodpeckers, with an approach that can be widely extended to other systems.

This study combines neutrality tests and environmental correlations to identify nonneutral patterns of evolution in candidate genes related to drought stress in two closely related Mediterranean conifers, Pinus pinaster Ait. and P. halepensis Mill. Based on previous studies, we selected twelve amplicons covering six candidate genes that were sequenced in a large sample spanning the full range of these two species. Neutrality tests relatively robust to demography (DHEW compound test and maximum likelihood multilocus Hudson-Kreitman-Aguadé test) were used to detect selection events at different temporal scales. Environmental associations between variation at candidate genes and climatic variables were also examined. These combined approaches detected distinct genes that may be targeted by selection, most of them specific to only one of the two conifers, despite their recent divergence (<10 Ma). An exception was 4-coumarate: CoA ligase, a gene involved in the production of various important secondary products that appeared to play a role in local adaptation processes of both pines. Another remarkable result was that all significant environmental correlations involved temperature indices, highlighting the importance of this climatic factor as a selective driver on Mediterranean pines. The ability to detect natural selection at the DNA sequence level depends on the nature and the strength of the selection events, on the timescale at which they occurred, and on the sensitivity of the methods to other evolutionary forces that can mimic selection (e.g., demography and population structure). Using complementary approaches can help to capture different aspects of the evolutionary processes that govern molecular variation at both intra-and interspecific levels.