Levels and patterns of nucleotide variability and population differentiation in Populus: insights from transcriptome resequencing and SNP genotyping

Levels and patterns of nucleotide variability are shaped by demography and natural selection. In this study we use NGS data from developing xylem transcriptome of 20 natural accessions of Populus trichocarpa to ask: (i) what is the overall level of nucleotide polymorphism in genic regions, (ii) how much variation is there in levels of polymorphism among genes, and (iii) how much variation is there among different site classes. We generated similar data for two other species of Populus (P. balsamifera, 3 natural accessions, and P. tremula, 4 natural accessions) and compare levels of nucleotide polymorphism and divergence among species for different classes of sites to estimate the strength of selection across species in coding and regulatory regions (UTRs). Finally, we genotyped over 28K SNPs in a large population sample of P. trichocarpa to investigate patterns of population differentiation and local adaptation in this species. Genotyping of this same SNP set in a small sample of P. balsamifera allowed us to ask whether interspecific gene flow contributes to levels of population differentiation and local adaptation.