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.