• Paraphyly of the genus Boehmeria (Urticaceae): a response to Liang et al. ‘Relationships among Chinese Boehmeria species and the evolution of various clade’

      Monro, Alexandre; Dodsworth, Steven; Fu, Long‑Fei; Friis, Ib; Wilmot-Dear, Christine M.; Maurin, Olivier; Royal Botanic Gardens, Kew; University of Bedfordshire; Chinese Academy of Sciences; Natural History Museum of Denmark (Springer, 2020-12-19)
      Boehmeria, as currently circumscribed, comprises 52 species and has a pantropical distribution. Liang et al. propose a sectional classification of Boehmeria based on the phylogenetic analysis of SNP data for 20 species and an additional 10 subspecific taxa of these at the rank of variety or form. They restrict their sampling to species documented in China. We found many shortcomings in the sampling and analyses which we feel have resulted in a misleading phylogeny for the genus and the economically important fibre-plant, Boehmeria nivea. By sampling only Chinese species of this genus for their in-group and using a single distantly related outgroup, Liang et al. have failed to capture the diversity of the genus and so erroneously concluded that it forms a monophyletic group. Previous published research clearly demonstrates that Boehmeria is paraphyletic and polyphyletic, comprising at least four monophyletic groupings most closely related to several genera within the Boehmerieae. For these reasons, the sections that Liang et al. (Ind Crops Prod 148:112092, 2020. https://doi.org/10.1016/j.indcrop.2020.112092) propose for Boehmeria are not effective tools for its classification. The important fibre-plant, Boehmeria nivea, should therefore not be considered as part of the genus Boehmeria for the purposes of crop breeding, but as sister to Archiboehmeria. Breeding programmes for ramie should therefore focus on populations and germplasm of Archiboehmeria atrata. We conclude that poor taxon sampling, overlooking relevant molecular and taxonomic literature, internal conflict within their SNP data and the overinterpretation of low support values has resulted in the erroneous conclusion that Boehmeria represents a monophyletic or ‘natural’ genus.
    • Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data

      Pérez-Escobar, Oscar Alejandro; Bogarin, Diego; Schley, Rowan; Bateman, Richard M.; Gerlach, Günter; Harpke, Dörte; Brassac, Jonathan; Fernández-Mazuecos, Mario; Dodsworth, Steven; Hagsater, Eric; et al. (Elsevier, 2019-11-14)
      Poor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family.