Data from: Utilizing RADseq data for phylogenetic analysis of challenging taxonomic groups: a case-study in Carex sect. Racemosae

PREMISE OF THE STUDY: Relationships among closely related and recently
diverged taxa can be especially difficult to resolve. Here we use both
Sanger sequencing and next-generation RADseq data sets to estimate
phylogenetic relationships among species of Carex section Racemosae
(Cyperaceae), a clade largely restricted to high latitudes and elevations.
Interest in relationships among these taxa derives from questions about
the species’ biogeographic histories and possible links between
diversification and Pleistocene glaciations. METHODS: A combination of
approaches and molecular markers were used to estimate relationships among
Carex species within sect. Racemosae and taxa from closely related
sections. Nuclear and chloroplast loci generated by Sanger sequencing were
analyzed with *BEAST, and SNP data from RADseq loci were analyzed as a
concatenated data set using maximum likelihood and as independent loci
using SVDquartets. KEY RESULTS: Sanger sequencing data sets resolved
relationships among taxa at intermediate phylogenetic depths (albeit with
low levels of support). Only the RADseq data resolved relationships with
strong support at all phylogenetic depths. Moreover, different methods and
data partitions of the RADseq data resulted in nearly identical
topologies. Carex sect. Racemosae is a strongly supported clade, although
a handful of species were found to group with closely related sections.
Herbarium specimens up to 35 yr old successfully produced informative
RADseq data. CONCLUSIONS: Despite the short read lengths of RADseq data,
they nevertheless resolved relationships that Sanger sequencing data did
not. Resolution of the phylogenetic relationships among recently and
rapidly diversifying taxa within sect. Racemosae clades suggest a role for
the Pleistocene glaciations in clade diversification.