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

<p>Polyploids represent a new frontier in species discovery among embryophytes. Within mosses, polyploid discovery is challenged by low morphological complexity. The rapid expansion of sub-genome sequencing approaches in addition to computational approaches to identifying whole genome duplication using allelic variation among nuclear markers has allowed for increased polyploid discovery among mosses. We confirm the intergeneric hybrid nature of <em>E. hungaricus</em>, and the allopolyploid origin of <em>P. eurystomum </em>and of one population of <em>P. collenchymatum</em>. We also reveal that hybridization gave rise to <em>P. immersum, </em>as well as to yet unrecognized lineages sharing the phenotype of <em>P. pyriforme</em>,<em> P. sphaericum</em> and <em>P. collenchymatum. </em>Our findings and methods demonstrate the utility of a novel approach to allele phasing and subgenome assignment, called homologizer, when working with polyploid genomes, and its value in identifying progenitor species using target capture data.</p>