Abstract
Plastome phylogenomics is used in a broad range of studies where single markers do not bear enough information. Phylogenetic reconstruction in the genus Salix is difficult due to the lack of informative characters and reticulate evolution. Here, we use a genome skimming approach to reconstruct 41 complete plastomes of 32 Eurasian and North American Salix species representing different lineages, different ploidy levels, and separate geographic regions. We combined our plastomes with published data from Genbank to build a comprehensive phylogeny of 61 samples (50 species) using RAxML (Randomized Axelerated Maximum Likelihood). Additionally, haplotype networks for two observed subclades were calculated, and 72 genes were tested to be under selection. The results revealed a highly conserved structure of the observed plastomes. Within the genus, we observed a variation of 1.68%, most of which separated subg. Salix from the subgeneric Chamaetia/Vetrix clade. Our data generally confirm previous plastid phylogenies, however, within Chamaetia/Vetrix phylogenetic results represented neither taxonomical classifications nor geographical regions. Non-coding DNA regions were responsible for most of the observed variation within subclades and 5.6% of the analyzed genes showed signals of diversifying selection. A comparison of nuclear restriction site associated DNA (RAD) sequencing and plastome data on a subset of 10 species showed discrepancies in topology and resolution. We assume that a combination of (i) a very low mutation rate due to efficient mechanisms preventing mutagenesis, (ii) reticulate evolution, including ancient and ongoing hybridization, and (iii) homoplasy has shaped plastome evolution in willows.
Highlights
Plastid markers are frequently used in plant phylogenetics because they possess several advantages over nuclear markers (Taberlet et al, 1991; Gitzendanner et al, 2018)
Length variation was due to one large insertion at the margin of the inverted repeat (IRb) that was observed in 21 samples, two large indels (>200 bp) in S. triandra and species of subg
Even complete plastome data are unsuitable for phylogenetic reconstruction, DNA barcoding, and analyses of biogeographical history in shrub willows
Summary
Plastid markers are frequently used in plant phylogenetics because they possess several advantages over nuclear markers (Taberlet et al, 1991; Gitzendanner et al, 2018). They are haploid but occur in high copy number, which simplifies the sequencing process. The availability of various plastid markers with different levels of molecular evolution combined with the conserved structure of the plastome makes them a popular choice for molecular systematic studies on different levels of divergence (Shaw et al, 2005, 2007; Wicke and Schneeweiss, 2015). In combination with nuclear markers, this makes plastomes useful for the analysis of introgression, hybridization, and polyploidy. The dispersion of maternally inherited genomes occurs at shorter geographic distances than for nuclear genomes. The consequence of a reduced gene dispersal and high genetic drift in organelle genomes
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