Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

Abstract

Increasing our understanding of how evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, genome‐wide patterns of within‐ and between‐ species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole‐genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories and investigate patterns of diversity and divergence within and between species. Using Populus trichocarpa as an outgroup species, we further infer the genealogical relationships and estimate the extent of ancient introgression among the three aspen species (Populus tremula, Populus davidiana and Populus tremuloides) throughout the genome. Our results show substantial variation in these patterns along the genomes with this variation being strongly predicted by local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long‐term balancing selection have also been crucial components in shaping patterns of genome‐wide variation during the speciation process.

Genomic insights into speciation history and local adaptation of an alpine aspen in the Qinghai–Tibet Plateau and adjacent highlands

“…Although these two species diverged nearly 1 million years ago, reproductive isolations are incomplete between them, possibly because of the large population size and long generation time of Populus species (Wang et al, 2020a, 2020b). This would have resulted in the occurrence of hybrids in the contacting region of the two species in the eastern QTP.…”

“…Both species belong to sect. Populus of the genus Populus L. (Salicaceae), which contains approximately seven species with widespread distribution throughout the Northern Hemisphere (Zhang et al, 2018; Wang et al, 2020a, 2020b). Aspens are commonly recognized as “keystone species” in boreal and temperate forests and usually play a pioneer role following forest disturbance (Edenius et al, 2011; Berrill et al, 2017; Zheng et al, 2017; Fan et al, 2018; Rogers et al, 2020).…”

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species

“…Extensive heterogeneity in the extent of admixture across genomes has been reported in multiple studies of closely related species, including trees (Wang et al 2020), insects (Martin et al 2019, Valencia-Motoya et al 2020 and cichlid fish (Gante et al 2016, Svardel et al 2020. Tracts of the southern O. korogwe genome with extensive evidence for hybridization (e.g.…”

Population Genomics Reveals Demographic History and Genomic Differentiation of Populus davidiana and Populus tremula

“…Under the process of positive selection, although genetic diversity was reduced, interspecific differentiation increased. Earlier speciation of Populus studies have revealed that apart from background selection, recent positive selection and long-term balancing selection have also been crucial components in shaping patterns of genome-wide variation during the Populus speciation process (Wang et al, 2020). However, since it is difficult to accurately estimate the variation in these highly differentiated regions exhibiting low genetic diversity, more caution is required in interpreting the functional characteristics of the overrepresented genes identified here.…”