TY - JOUR T1 - When local means local: Polygenic signatures of local adaptation within whitebark pine (<em>Pinus albicaulis</em> Engelm.) across the Lake Tahoe Basin, USA JF - bioRxiv DO - 10.1101/056317 SP - 056317 AU - Brandon M. Lind AU - Christopher J. Friedline AU - Jill L. Wegrzyn AU - Patricia E. Maloney AU - Detlev R. Vogler AU - David B. Neale AU - Andrew J. Eckert Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/05/31/056317.abstract N2 - For populations exhibiting high levels of gene flow, the genetic architecture of fitness-related traits is expected to be polygenic and underlain by many small-effect loci that covary across a network of linked genomic regions. For most coniferous taxa, studies describing this architecture have been limited to single-locus approaches, possibly leaving the vast majority of the underlying genetic architecture undescribed. Even so, molecular investigations rarely search for patterns indicative of an underlying polygenic basis, despite prior expectations for this signal. Here, using a polygenic perspective, we employ single and multilocus analyses of genome-wide data (n = 116,231 SNPs) to describe the genetic architecture of adaptation within whitebark pine (Pinus albicaulis Engelm.) across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069) there is strong evidence for polygenic adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we find little evidence for large-effect loci and that the frequencies of loci associated with 4/5 phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher covariance than random SNPs. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results provide replicative support for theoretical expectations and highlight advantages of a polygenic perspective, as unremarkable loci when viewed from a single-locus perspective are noteworthy when viewed through a polygenic lens, particularly when considering protective measures such as conservation guidelines and restoration strategies. ER -