LANDSCAPE GENOMICS OFPOPULUS TRICHOCARPA: THE ROLE OF HYBRIDIZATION, LIMITED GENE FLOW, AND NATURAL SELECTION IN SHAPING PATTERNS OF POPULATION STRUCTURE

Abstract

Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera, (2) isolation by distance (IBD), and (3) natural selection. Introgression was detected only at the margins of the species' distribution. IBD was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia (BC). We identified a large number of FST outliers. Gene Ontology analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, whereas in southern BC heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci.

Population genomics of the eastern cottonwood (Populus deltoides)

“…A better understanding of the genetic regulation of adaptation is fundamental for the development of adequate management and conservation strategies under a changing climate (Porth et al., 2015). In recent years, population genomics has been used to study tree populations, identifying genes under selection involved in local adaptation (Evans et al., 2014; Geraldes et al., 2014; Holliday et al., 2016; Zhou et al., 2014). The great advantage of population genomics studies over smaller‐scale population genetics studies is that the former allow identifying and correcting for genomewide demographic effects, increasing the power to detect locus‐specific effects (Stinchcombe & Hoekstra, 2008).…”

“…This population structure pattern agrees with the landscape over which P. deltoides is naturally distributed and is consistent with a scenario of isolation by distance. In P. trichocarpa , isolation by distance was identified as a main driver of population structure (Geraldes et al., 2014; Zhou et al., 2014). The eastern and western subpopulations are separated by a known phylogeographic barrier, the Appalachian Mountain discontinuity (Soltis, Morris, McLachlan, Manos, & Soltis, 2006).…”

“…To be able to perform this analysis, the 168 samples with known sampling location were grouped into 50 smaller populations based on similar latitude, longitude, and altitude, following the strategy used by Geraldes et al. (2014) (Table S1). The variance–covariance matrix, Ω, was estimated using 3,667 genic LD pruned SNPs ( r 2  ≤ 0.2) with no missing data.…”

“…The Populus trichocarpa genome, the first tree to be sequenced (Tuskan et al., 2006), created numerous opportunities for pioneering genomic studies in tree species. Several genomewide association, transcriptome, and population genomics studies have been reported for P. trichocarpa , contributing to the current knowledge about the species regulation of complex traits (McKown, Klápště, et al., 2014; Porth et al., 2013a, 2013b), extent of linkage disequilibrium (LD) and effective population size (Slavov et al., 2012; Zhou, Bawa, & Holliday, 2014), population structure (Geraldes et al., 2014; Slavov et al., 2012; Zhou et al., 2014), genetic diversity (Evans et al., 2014; Zhou et al., 2014), demographic history (Zhou et al., 2014), adaptation (Evans et al., 2014; Geraldes et al., 2014; Holliday, Zhou, Bawa, Zhang, & Oubida, 2016; Porth et al., 2015; Zhou et al., 2014), and sex determination (Geraldes et al., 2015). Studies in other poplar species (Stölting et al., 2013, 2015; Wang, Street, Scofield, & Ingvarsson, 2016a, 2016b) have significantly lagged behind.…”

“…In existing studies, high levels of genetic diversity and limited population structure have been observed. Genetic structure is mainly driven by interspecific hybridization, isolation by distance, and natural selection (Evans et al., 2014; Geraldes et al., 2014; Slavov et al., 2012; Stölting et al., 2015; Wang et al., 2016b; Zhou et al., 2014). Adaptation has been shown to have a complex genetic architecture (Evans et al., 2014; Holliday et al., 2016; McKown, Guy, et al., 2014; McKown, Klápště, et al., 2014; Porth et al., 2015) and to be a driver of divergent evolution between species (Wang et al., 2016b).…”