Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)

Abstract

The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution. The Phyllostachys, Shibataea, and Arundinaria clades defined from plastid phylogeny, were not supported as monophyletic group. However, the RAD-seq phylogeny largely agreed with the morphology-based taxonomy, with two clades having leptomorph rhizomes strongly supported as monophyletic group. We also explored two approaches, BWA-GATK (a mapping system) and Stacks (a grouping system), for differences in SNP calling and phylogeny inference. For the same level of missing data, the BWA-GATK pipeline produced much more SNPs in comparison with Stacks. Phylogenetic analyses of the largest data matrices from both pipelines, using concatenation and coalescent methods provided similar tree topologies, despite the presence of missing data. Our study demonstrates the utility of RAD-seq data for elucidating phylogenetic relationships between genera and higher taxonomic levels in this important but phylogenetically challenging group.

Phylogenomics, biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation

“…2, 3), demonstrating the power of RAD-seq data that contain thousands of loci across the genome in phylogenetic studies. Much better-resolved and more strongly supported phylogenies from analyses of RAD-seq data, compared with previous phylogenies based on only a few genes, have also been reported in other studies (Wang et al, 2017;Deng et al, 2018;Du et al, 2020). Although RAD-seq data were generally considered appropriate for phylogenomic studies of young lineages of recent divergence due to concerns regarding allelic dropout, this study and others (Leaché & Oaks, 2017;Du et al, 2020;Zhou et al, 2020) have shown that RAD-seq data generated from careful preparation of DNA libraries are also valuable for phylogenomic studies of lineages with divergence dated back to the late Cretaceous or early Paleogene.…”

Phylogenetic reconstruction of Ficus subg. Synoecia and its allies (Moraceae), with implications on the origin of the climbing habit

“…At the genus level, the nuclear phylogeny of Ficus is more in accordance with the classic subdivision (Bruun‐Lund & al., 2017). This phenomenon was also reported in Cyperaceae, Rosaceae, and Poaceae (Massatti & al., 2016; Xiang & al., 2016; Wang & al., 2017). These observations imply that the nuclear phylogeny of Ficus may be a suitable model for the investigation of evolutionary history.…”

Schizostachyum dakrongense (Poaceae, Bambusoideae), a new species from Dakrong Nature Reserve, Vietnam

“…These results implied that the nuclear genome and the plastid genome may have different evolutionary trajectories (Zhang et al 2012;Yang et al 2013). The most recent study based on phylogenetic analyses with RAD-seq data identified eight major lineages in Arundinarieae with strong support, which conflicts with earlier studies (Wang et al 2017).…”