Phylogenomics resolves the Himalayan endemic Brachymeniopsis gymnostoma (Bryophyta, Funariaceae), rediscovered after almost a century, as a species of Entosthodon

Traits of the spore-bearing generation have historically provided the basis for systematic concepts across the phylogenetic spectrum and depth of mosses. Whether taxa characterized by a simple sporophytic architecture are closely related or emerged from independent reduction is often ambiguous. Phylogenomic inferences in the Funariaceae, which hold the model taxon Physcomitrium patens, revealed that several such shifts in sporophyte complexity occurred, mostly within the Entosthodon-Physcomitrium complex. Here, we report the rediscovery, nearly 100 years after its description, of the Chinese endemic and monospecific genus Brachymeniopsis, which is characterized by, among other traits, its short sporophytes lacking the sporangial peristome teeth controlling spore dispersal. Phylogenomic inferences reveal that its sole species, B. gymnostoma arose within the clade of Entosthodon sensu stricto, a genus with typically long-exerted capsules. We therefore propose to transfer B. gymnostoma to ..., Targeted DNA sequencing of nuclear loci was carried out using similar protocols to (Medina et al., 2019). We extracted DNA from gametophyte tissue of a sample of Brachymeniopsis herbarium specimen Zhang 9430 (conn) using the modified CTAB/chloroform method (Doyle and Doyle, 1987). We prepared an Illumina library for high-throughput sequencing using NEB-Next Ultra II DNA with fragmentase in 1/2 volumes. We performed target enrichment on 809 nuclear protein-coding genes (Medina et al., 2019) and included the sample with 95 other enriched libraries libraries (but no Entosthodon to avoid contamination) on an Illumina MiSeq 2x300 paired end sequencing. We extracted the 809 protein-coding genes plus flanking regions \"supercontigs\" with HybPiper v 1.3.1 (Johnson et al., 2016). This Dryad repository contains the alignments, gene trees, and species trees with the Medina et al., (2019) samples plus Zhang 9430.,