Genome Resequencing in an Ecologically and Economically Important Forest Tree, Populus trichocarpa: Selection and Demographic History

Temperate zone forest trees exhibit large ranges spanning wide environmental gradients, and many populations exhibit patterns of local adaptation.  Often shaping entire ecosystems, trees provide fuel, fibre, and ecosystem services with global importance.  Here, we report the high-coverage, whole-genome sequencing of 544 genomes of Populus trichocarpa, a dominant riparian tree of the west coast of North America. We identified nearly 18 million single nucleotide polymorphisms across approximately 345 million bp of the nuclear genome that was accessible. Patterns of polymorphism throughout the species’ range are consistent with demographic history models including strong ancestral bottlenecks and recent population divergence. There was also evidence of rapid growth in the center of the range and rapid decline of populations at the southern range margin after the last glacial maximum. We used three fundamentally different tests to scan the genome for recent positive and divergent selection (F_ST, iHS, and SPA). We identified 70 genomic regions that exhibit patterns consistent with recent positive selection, which also show stronger associations with phenological and growth traits than expected by chance. Putative regions under selection are overrepresented in functional annotations related to callose biosynthesis and metabolism, regulation of transcription, metal transport and binding, photoperiodic pathway genes, and dormancy cycle genes. Our results indicate that climate has been an agent of recent demographic changes and natural selection.  This study is of basic importance for the understanding of recent and future climate change, and provides genomic resources necessary for the domestication of an ecologically and economically important forest tree.