Frequent allopolyploidy with distant progenitors in the moss genera Physcomitrium and Entosthodon (Funariaceae) identified via subgenome phasing of targeted nuclear genes

Abstract

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 of one population of P. collenchymatum. We also reveal that hybridization gave rise to P. immersum, as well as to yet unrecognized lineages sharing the phenotype of P. Pyriforme, and P. 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.

Phylogenomics resolves the rediscovered Himalayan endemic Brachymeniopsis gymnostoma (Bryophyta, Funariaceae), as a species of Entosthodon, prompting also the transfer of Clavitheca poeltii

“…Of the total of 1,747,626 reads, 61.6% mapped to one of the target genes. HybPiper produced a contig for all 809 nuclear genes, none of which produced warnings about potential paralogs, potentially indicative of allopolyploidy (see Patel & al., in press). A subset of 648 genes was used to infer the phylogenetic position of Shevock & Ma 52863 by adding sequences of this sample to existing alignments from (Medina & al., 2019).…”

“…S2) and phenetic analyses of morphological traits (Fife, 1985). Furthermore, the nuclear loci lack any signal of extensive heterozygosity indicative of a hybrid origin, as seen in other Funariaceae (McDaniel & al., 2010; Beike & al., 2014; Patel & al., in press). Thus, Brachymeniopsis gymnostoma , based on Shevock & Ma is a non‐hybrid species that should be transferred to Entosthodon , and consequently the generic name Brachymeniopsis (Brotherus, 1929) should be considered a synonym of Entosthodon (Schwägrichen, 1823), given that the latter is the earliest name for the clade that holds the generic type E. attenuatus , which is the accepted name for the original type E. templetonii (Sm.)…”

“…(2022) argued that the transoceanic disjunction may be indicative of a phylogenetic divergence and that pending the discovery and study of additional populations, the two species should conservatively be retained. Furthermore, recent studies in the Funariaceae (Medina & al., 2018, 2019; Patel & al., in press) have highlighted that current morphological species concepts in Physcomitrium did not reflect phylogenetic structure and diversity, as the P. pyriforme (Hedw.) Brid.…”

“…Brid. harbors at least three lineages, including two allopolyploids of distinct progenitor species (Patel & al., in press). So far only one species with an immersed capsule appears to be of hybrid origin, namely P. immersum Sull.…”

“…So far only one species with an immersed capsule appears to be of hybrid origin, namely P. immersum Sull. (Medina & al., 2019; Patel & al., in press).…”