Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.

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...