Three new taxa of the genus Populus originated from hybrid speciation between sect. Leucoides and sect. Tacamahaca

Extensive research has confirmed that hybrid speciation exists widely, yet how it occurs remains unclear. The Qinghai-Tibet Plateau (QTP) is an evolutionary center for Populus and an ideal place to study evolution. We identified 23 known and 7 new taxa of Populus through a systematic investigation on the plateau. We introduce three new taxa, P. gonggaensis, P. butuoensis, and P. dafengensis. They have unique morphological characteristics and a narrow geographical distribution. We resequenced the whole genome of 150 individuals from typical populations of 30 taxa and constructed the phylogenetic tree of Populus in the region with 2.28 million SNPs. The three new taxa, together with P. wilsonii and P. lasiocarpa, constituted the base clade, and each formed an independent terminal clade. Further analysis of genetic structure, gene flow, hybridization, and historical effective population size proved that they were all intersectional hybrid species originating from the distant hybridization between sect. Leucoides and sect. Tacamahaca in the Middle Pleistocene. Therefore, taxonomically, it is appropriate to regard them as three new species of sect. Leucoides. Moreover, we found that three new taxa were endowed heterosis, no matter from the results of field investigation or homogenous garden experiments, they all had better adaptability than their parents, and most of the positive selected genes responded to stress. The study provides comprehensive evidence for the hybrid speciation of Populus and proposes three new taxa. It also presents a novel and comprehensive method for studying the phylogeny of Populus.