Low‐copy nuclear data confirm rampant allopolyploidy in the Cystopteridaceae (Polypodiales)

Abstract

Here we present the first nuclear phylogeny for Cystopteridaceae (Polypodiales), using the single‐copy locus gapCp “short”. This phylogeny corroborates broad results from plastid data in demonstrating strong support for the monophyly of the family's three genera—Cystopteris, Acystopteris, and Gymnocarpium—and of the major groups within Cystopteris (C. montana, the sudetica and bulbifera clades, and the C. fragilis complex). In addition, it confirms the rampant hybridization (allopolyploidy) that has long been suspected within both Cystopteris and Gymnocarpium. In some cases, these data provide the first DNA‐sequence‐based evidence for previous hypotheses of polyploid species origins (such as the cosmopolitan G. dryopteris being an allotetraploid derivative of the diploids G. appalachianum and G. disjunctum). Most of the allopolyploids, however, have no formal taxonomic names. This pattern is particularly strong within the C. fragilis complex, where our results imply that the eight included accessions of “C. fragilis” represent at least six distinct allopolyploid taxa.

Next‐generation polyploid phylogenetics: rapid resolution of hybrid polyploid complexes using PacBio single‐molecule sequencing

“…Our inferred multilabeled Cystopteridaceae ‘species tree’ is generally consistent with earlier gene trees of the family, including those inferred from plastid (Rothfels et al ., , ; Wei & Zhang, ) and single‐locus nuclear data (Rothfels et al ., ): Acystopteris and Cystopteris are sister genera; Gymnocarpium is sister to the rest of the family; Cystopteris comprises the Cystopteris montana clade, Cystopteris sudetica clade, Cystopteris bulbifera clade, and the C. fragilis complex; C. montana is sister to the rest of the genus; and Cystopteris protrusa is sister to the rest of the C. fragilis complex (Fig. a).…”

“…b–e). Rampant allopolyploidy in Cystopteridaceae has been inferred before with single‐locus data (Rothfels et al ., , ), but our study is the first to do so with multiple nuclear loci while accounting for incomplete lineage sorting. Novel inferences from our analyses include: tetraploid G. oyamense is relatively distantly related to our diploid G. oyamense accession, suggesting at least one undiscovered (or extinct) diploid species within G. oyamense ; there is extensive reticulation within Acystopteris , a clade thought to include only three species (our data suggest that there are at least three distinct extant tetraploids and at least two extant diploids, plus at least two unsampled diploid lineages; Fig.…”

“…Our third evaluation was to compare the results of our Purc allele inferences with the sequences obtained from the classic cloning and Sanger‐sequencing approach. To do so, we created a combined alignment ( Muscle and AliView ; Edgar, ; Larsson, ) of GAP sequences from our Purc ‐based species network inference (see the next section) and our earlier Sanger‐based studies (Rothfels et al ., , ) for those accessions that were shared across the two data sets. From this combined alignment we then inferred a maximum parsimony tree in Paup v.4.0a147 (Swofford, ), to visualize the similarities and differences between the Purc and Sanger‐based inferences.…”

Distributions of vascular plants in the Czech Republic. Part 7

“…Gymnocarpium dryopteris (Fig. 52) Gymnocarpium dryopteris is an allotetraploid species whose assumed diploid parents are G. appalachianum and G. disjunctum (Pryer & Haufler 1993, Rothfels et al 2014. It is widely distributed in the temperate zones in the Northern Hemisphere, including Europe (except the southernmost parts but including Iceland), western, central and eastern Siberia, the Russian Far East, eastern China and North America including Greenland.…”

Genetic and genomic aspects of hybridization in ferns

“…More recently, systematists have adopted the sequencing and phylogenetic analysis of biparentally‐inherited, low copy nuclear genes to resolve progenitor‐hybrid relationships in fern reticulate complexes (e.g., Ceratopteris : Adjie et al, ; Myriopteris [= Cheilanthes ]: Grusz et al, ; Crepidomanes : Nitta et al, ; Gaga : Li et al, ; Pteris : Chao et al, ; Jaruwattanaphan et al, ; Asplenium : Shepard et al, ; Dyer et al, ; Chang et al, ; Schneider et al, ; Cryptogramma : Metzgar et al, ; Dryopteris : Lee & Park, ; Hori et al, ; Polypodium : Sigel et al, ; Cystopteridaceae: Rothfels et al, ). Unlike isozymes, low copy nuclear genes reveal changes in the genotype at the nucleotide level, although it is often difficult to discern whether nucleotide differences represent alleles that are unique to an allopolyploid taxon, reflect unsampled diversity within the progenitor species, or are the result of polymerase chain reaction (PCR) error.…”