Phylogeny Reconstruction and Hybrid Analysis of Populus (Salicaceae) Based on Nucleotide Sequences of Multiple Single-Copy Nuclear Genes and Plastid Fragments

Abstract

Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.

Phylogenetic and Taxonomic Status Analyses of the Abaso Section from Multiple Nuclear Genes and Plastid Fragments Reveal New Insights into the North America Origin of Populus (Salicaceae)

“…With a large combined data set of 23 single-copy nuclear DNA and 34 ptDNA fragments, we reconstructed phylogenies of Populus ( Figures 1 and 2 , respectively). All species of Populus clustered together as a well-supported clade separated from the outgroup species that was consistent with previous studies which supported the monophyletic nature of Populus (Hamzeh et al, 2006; Wang et al, 2014). However, the taxonomic status of P. mexicana has been disputed in previous phylogenetic studies (Eckenwalder, 1996a; Cervera et al, 2005), and the exact systematic position remains unclear.…”

“…All the single-copy nuclear fragments were used in Du et al (2014) except LX17 locus and LX20 locus, which were designed based on the genome sequence of P. trichocarpa T.& G. in this study. Twenty-two of the ptDNA fragments (beginning with YLT) were used in Wang et al (2015), and the remaining 12 fragments were used in Wang et al (2014). All primers used in this study are listed in Supplementary Table S2.…”

“…According to a recent classification, the genus Populus is classified into 29 species in six sections (Abaso, Aigeiros, Leucoides, Populus, Tacamahaca, and Turanga) that are delineated by the occurrence of major hybridization barriers (Eckenwalder, 1996a). The phylogenetic analyses of the genus Populus have been performed using DNA sequences from both nuclear (nrDNA) and chloroplast (ptDNA) genomes (Leskinen and Alström-Rapaport, 1999; Azuma et al, 2000; Wang et al, 2014), and these analyses strongly suggest that Populus is a monophyletic group. However, these previous studies only focused on the five sections of the genus that excluded species of the section Abaso.…”

Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

“…However, when comparing the sequence variations for all five species belonging to the section Populus for only two gene regions (TB1 and KNOX, data not shown), all five species are nearly equally variable. Thus, it is assumed that the evolutionary difference between the species of the section Populus and P. trichocarpa is much higher than between P. trichocarpa and the other sections (e.g., Zhang et al (2017), Wang et al (2014) [20,33]). Interestingly, P. maximowiczii and P. deltoides differ much more from P. trichocarpa with regard to the nuclear genome than the cp genome.…”

The complete chloroplast genome of Cathay Poplar:Poplus cathayanaRehder

“…The chloroplast of angiosperm, mainly maternal inherited, now extensively used to investigate reticulate relationship among species. Comparative phylogenetic analysis based on nuclear DNA and cpDNA sequences has been used to detect recent hybridization (Hamzeh & Dayanandan 2004;Wang et al 2014). Feng et al (2013) tested five chloroplast barcodes among 21 Populus species from western China, but still failed to discriminate several groups of species, especially from sympatric or parapatric areas.…”