Data from: Rapid allopolyploid radiation of moonwort ferns (Botrychium ; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions

Polyploidy is a major speciation process in vascular plants, and is
postulated to be particularly important in shaping the diversity of extant
ferns. However, limitations in the availability of bi-parental markers for
ferns have greatly limited phylogenetic investigation of polyploidy in
this group. With a large number of allopolyploid species, the genus
Botrychium is a classic example in ferns where recurrent polyploidy is
postulated to have driven frequent speciation events. Here, we use PacBio
sequencing and the PURC bioinformatics pipeline to capture all homeologous
or allelic copies of four long (∼1kb) low-copy nuclear regions from a
sample of 45 specimens (25 diploids and 20 polyploids) representing 37
Botrychium taxa, and three outgroups. This sample includes most currently
recognized Botrychium species in Europe and North America, and the
majority of our specimens were genotyped with co-dominant nuclear
allozymes to ensure species identification. We analyzed the sequence data
using maximum likelihood (ML) and Bayesian inference (BI)
concatenated-data (“gene tree”) approaches to explore the relationships
among Botrychium species. Finally, we estimated divergence times among
Botrychium lineages and inferred the multi-labeled polyploid species tree
showing the origins of the polyploid taxa, and their relationships to each
other and to their diploid progenitors. We found strong support for the
monophyly of the major lineages within Botrychium and identified most of
the parental donors of the polyploids; these results largely corroborate
earlier morphological and allozyme-based investigations. Each polyploid
had at least two distinct homeologs, indicating that all sampled
polyploids are likely allopolyploids (rather than autopolyploids). Our
divergence-time analyses revealed that these allopolyploid lineages
originated recently—within the last two million years—and thus that the
genus has undergone a recent radiation, correlated with multiple
independent allopolyploidizations across the phylogeny. Also, we found
strong parental biases in the formation of allopolyploids, with individual
diploid species participating multiple times as either the maternal or
paternal donor (but not both). Finally, we discuss the role of polyploidy
in the evolutionary history of Botrychium and the interspecific
reproductive barriers possibly involved in these parental biases.