Abstract
Populus not only has significant economic and ecological values, but also serves as a model tree that is widely used in the basic research of tree growth, physiology, and genetics. However, high levels of morphological variation and extensive interspecific hybridization of Populus pose an obstacle for taxonomy, and also to the understanding of phylogenetic interspecific relationships and biogeographical history. In this study, a total of 103 accessions representing almost all the wild species of Populus were collected and whole-genome re-sequenced to examine the phylogenetic relationships and biogeography history. On the basis of 12,916,788 nuclear single nucleotide polymorphisms (SNPs), we reconstructed backbone phylogenies using concatenate and coalescent methods, we highly disentangled the species relationships of Populus, and several problematic taxa were treated as species complexes. Furthermore, the phylogeny of the chloroplast genome showed extensive discordance with the trees from the nuclear genome data, and due to extensive chloroplast capture and hybridization of Populus species, plastomes could not accurately evaluate interspecies relationships. Ancient gene flow between clades and some hybridization events were also identified by ABBA–BABA analysis. The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus, and subsequent long dispersal and migration across land bridges were contributed to the modern range of Populus. The diversification of Populus mainly occurred in East Asia in recent 15 Ma, possibly promoted by the uplift of the Tibetan Plateau. This study provided comprehensive evidence on the phylogeny of Populus and proposed a four-subgeneric classification and a new status, subgenus Abaso. Meanwhile, ancestral distribution reconstruction with nuclear data advanced the understanding of the biogeographic history of Populus.
Highlights
Populus, collectively known as poplar, aspen, cottonwood, or “Yang Shu” in Chinese, is widely distributed from subtropical to boreal forests in the northern hemisphere, primarily in temperate forests (Ding, 1995; Eckenwalder, 1996)
We assembled 103 complete chloroplast genomes, which had a common typical quadripartite structure, containing a large single-copy (LSC) region and a small single-copy (SSC) region separated by two inverted repeat (IR)
The deep phylogenetic relationships of Populus species were well resolved based on nuclear genomic phylogeny
Summary
Collectively known as poplar, aspen, cottonwood, or “Yang Shu” in Chinese, is widely distributed from subtropical to boreal forests in the northern hemisphere, primarily in temperate forests (Ding, 1995; Eckenwalder, 1996). Owing to its excellent features, poplars have been planted in many parts of the world and have become a highly promising crop option. They are widely used in windbreaks, protective stands to prevent soil erosion, and in row or gallery plantings to stabilize the banks of streams and canals, and show impressive productivity for desirable wood products (Stettler et al, 1996). Poplar is recognized as an excellent model tree for the study of genetics, tree growth, and its underlying physiology for its fast growth rate, easy vegetative propagation, and relatively small genome (Stettler et al, 1996; Bradshaw et al, 2000; Cronk, 2005). A clear understanding of the evolutionary history of Populus will provide an important foundation for biological studies and genetic breeding programs
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