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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 taxonPhyscomitrium patens, revealed that several such shifts in sporophyte complexity occurred, and mostly within theEntosthodon‐Physcomitriumcomplex. Here, we report the rediscovery of the monospecific, Himalayan endemic generaBrachymeniopsisandClavitheca, after nearly 100 years and 40 years since their respective descriptions. The genera are characterized by, among other traits, their short sporophytes lacking the sporangial peristome teeth controlling spore dispersal. Phylogenomic inferences reveal thatBrachymeniopsis gymnostomaarose within the clade ofEntosthodons.str., a genus with typically long‐exserted capsules. We therefore propose to transferB. gymnostomato the genusEntosthodon, asE. gymnostomuscomb. nov.Furthermore,Clavitheca poeltii, the sole species of the genus, is morphologically highly similar toE. gymnostomus, and should also be transferred toEntosthodon, but is retained as a distinct taxon,E. poeltiicomb. nov., until additional populations allow for testing the robustness of the observed divergence in costa and seta length between the Nepalese and Chinese populations.

 

Allopolyploids represent a new frontier in species discovery among embryophytes. Within mosses, allopolyploid discovery is challenged by low morphological complexity. The rapid expansion of sequencing approaches in addition to computational developments to identifying genome merger and whole-genome duplication using variation among nuclear loci representing homeologs has allowed for increased allopolyploid discovery among mosses. Here, we test a novel approach to phasing homeologs within loci and phasing loci across subgenomes, or subgenome assignment, called Homologizer, in the family Funariaceae. We confirm the intergeneric hybrid nature of Entosthodon hungaricus, and the allopolyploid origin of Physcomitrium eurystomum and one population of Physcomitrium collenchymatum. We also reveal that hybridization gave rise to Physcomitrium immersum, as well as to yet unrecognized lineages sharing the phenotype of Physcomitrium pyriforme and Physcomitrium sphaericum. Our findings demonstrate the utility of our approach when working with polyploid genomes, and its value in identifying progenitor species using target capture data.

 

Florschuetziella scaberrima (Broth.) Vitt, previously known only from the type material collected in 1915 from Yunnan, China, was rediscovered nearly a century later in 2005. The species is morphologically indistinguishable from the Mexican endemic F. steerei Vitt, but given the paucity of material the two are provisionally retained as distinct, allopatric species. Both species exhibit traits reminiscent of Leratia neocaledonica Broth. & Paris, a species endemic to New Caledonia. A shared ancestry with the other species currently accommodated in Leratia Broth. & Paris, i.e., L. exigua (Sull.) Goffinet and L. obtusifolia (Hook.) Goffinet, and the phylogenetically nested position of Florschuetziella Vitt within Leratia supports the merger of the two generic names, and hence the transfer of species of Florschuetziella, prompting the proposed new combinations Leratia steerei (Vitt) Goffinet, S.He & Shevock and Leratia scaberrima (Broth.) Goffinet, S.He & Shevock. 

Mosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO Viridiplantae odb10 dataset. The newly generated F. antipyretica genome is the third moss genome, and the second seedless aquatic plant genome, to be sequenced and assembled to date. 

In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.