Highly Diverse Shrub Willows (Salix L.) Share Highly Similar Plastomes

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.

Ancient DNA extraction methods for herbarium specimens: When is it worth the effort?

“…For the six Salix samples, between 5.6% and 11.7% of the reads mapped to the respective references, and it was possible to recover complete plastomes for all samples. This mapping percentage is within the range reported in a recent study of Salix plastomes based on non‐archival, silica‐dried fresh material, for which the percentage of mapped reads varied between 3.1% and 23.5% (Wagner et al, 2021 ). For Xanthium , 0.1–3.1% of reads mapped to the reference, and only 21–83% of the plastome could be recovered.…”

Pervasive Phylogenomic Incongruence Underlies Evolutionary Relationships in Eyebrights (Euphrasia, Orobanchaceae)

“…In addition to challenges with the retention of multiple nrDNA copies, there is also ample evidence consistent with incomplete lineage sorting, with individuals with multiple samples combining variation greatly predating speciation, including variants across the tetraploid clade which was previously estimated to be 7.3 million years old ( Gussarova et al, 2008 ). Regardless of the evolutionary processes shaping variation, these results highlight that an “extended barcode” ( Coissac et al, 2016 ) based on plastid and nrDNA from genome skimming will fail to identify species in Euphrasia , as well as a range of other complex groups like willows ( Wagner et al, 2021 ). Here, researchers should instead look to sample the nuclear genome, using methods such as whole-genome resequencing or sequence capture with target enrichment probes ( Johnson et al, 2019 ).…”

“…Gene tree discordance is a pervasive feature of plant phylogenies, with numerous studies revealing diverse and conflicting topologies among loci within a genome ( Stull et al, 2020 ; Rose et al, 2021 ; Wagner et al, 2021 ). While discordance is frequently seen as a barrier to species tree reconstruction and an impediment to taxonomic and systematic research, characterizing discordance can provide major insights into evolutionary processes.…”

“…For example, discordance at deep phylogenetic scales can be indicative of hybridization that has promoted major species radiations ( Marques et al, 2019 ), while discordance at shallow phylogenetic scales can reveal contemporary population processes, such as the balance between drift, gene flow, and selection in the maintenance of genetic variation ( Lee-Yaw et al, 2019 ). Phylogenetic discordance is likely to be most prevalent in certain plant groups, particularly those characterized by hybridization, polyploidy, and/or recent (often postglacial) speciation ( Squirrell et al, 2002 ; Wagner et al, 2021 ). This includes taxonomically complex plant groups ( sensu Ennos et al, 2005 ), such as sedges ( Carex ), willows ( Salix ), and Epipactis orchids, where discrete species are often hard to define.…”

Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids

“…The widely used plastid markers or whole plastomes in plant phylogenies are mostly maternally inherited and hence cannot reflect reticulate relationships. Moreover, plastomes are often too conservative and would not provide sufficient resolution in phylogenetic analyses of less diverged lineages, as they occur in recently formed hybrids or neopolyploids [192]. Combinations of plastid and biparentally inherited nuclear markers, however, often reveal conflicting phylogenetic signals as a first indicator of reticulate relationships.…”