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

Abstract

Forest trees can increase our understanding of how evolutionary processes drive the genomic landscape and understand speciation due to the majority of forest trees being distributed widely and able to adapt to different climates and environments. Populus davidiana and Populus tremula are among the most geographically widespread and ecologically important tree species in Northern Hemisphere. Whole-genome resequencing data of 41 individuals of P. davidiana and P. tremula throughout Eurasia was conducted, finding that genetic differentiation was evident between the two species, the F ST values between P. davidiana and P. tremula was 0.3625. The ancestors of the two aspen diverged into P. davidiana and P. tremula species approximately 3.60 million years ago (Mya), which was in accordance with the rapid uplift of Qinghai-Tibet Plateau (QTP) around the Miocene/Pliocene boundary. The two species experienced a considerable long-term bottleneck after divergence, with population expansion beginning approximately 20,000 years ago after the end of the last glacial maximum. Although the majority of regions of genomic differentiation between the two species can be explained by neutral evolutionary processes, some outlier regions have also been tested that are significantly influenced by natural selection. We found that the highly differentiated regions of the two species exhibited significant positive selection characteristics, and also identified long-term balancing selection in the poorly differentiated regions in both species. Our results provide strong support for a role of linked selection in generating the heterogeneous genomic landscape of differentiation between P. davidiana and P. tremula. These results provide the detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in P. davidiana and P. tremula.

Resilience of genetic diversity in forest trees over the Quaternary

“…Whole-genome sequencing combined with coalescence-based demographic methods allowed inferring the demographic history of forest trees and its timescale well beyond the LGM, up to millions of years. However, most studies so far address single species or focus on inferring the timing of divergence and the extent of gene flow between populations or closely related species [14][15][16][17][18] . Congruence between population history and glacial oscillations has been observed in some species 14,19 but has remained far from being conclusive in others 20,21 .…”

Molecular phylogeny of Populus (Salicaceae, Salicales) with focus on inter- and intrasectional relationships

“…Vicariance has thus played an important role in the divergence of these species in the section Populus (Du et al, 2015;Wang, 2016). Furthermore, genome re-sequencing data has been applied in the evolution and speciation study of these three closely related aspen species, and how the genomic landscape was built up during speciation was clearly deciphered (Wang et al, 2016a;Wang et al, 2016b;Hou & Li, 2020;. Divergence of some parapatric or sympatric distributed species of section Populus or species within genus Populus may be even more complicated, and the second contact can not be entirely excluded.…”