Data from: Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon

Premise of the study: Evolutionary radiations provide opportunities to
examine large-scale patterns in diversification and character evolution,
yet are often recalcitrant to phylogenetic resolution due to rapid
speciation events. The plant genus Penstemon has been difficult to resolve
using Sanger sequence-based markers, leading to the hypothesis that it
represents a recent North American radiation. The present study
demonstrates the utility of multiplexed shotgun genotyping (MSG), a style
of Restriction site-associated DNA sequencing (RADseq), to infer
phylogenetic relationships within a subset of species in this genus and
provide insight into evolutionary patterns. Methods: We sampled genomic
DNA, primarily from herbarium material, and subjected it to MSG library
preparation and Illumina sequencing. The resultant sequencing reads were
clustered into homologous loci, aligned, and concatenated into data
matrices that differed according to clustering similarity and amount of
missing data. We performed phylogenetic analyses on these matrices using
maximum likelihood (RAxML) and a species tree approach (SVDquartets). Key
results: MSG data provide a highly resolved estimate of species
relationships within Penstemon. While most species relationships were
highly supported, the position of certain taxa remains ambiguous,
suggesting that increased taxonomic sampling or additional methodologies
may be required. The data confirm that evolutionary shifts from
hymenopteran- to hummingbird-adapted flowers have occurred independently
many times. Conclusions: This study demonstrates that phylogenomic
approaches yielding thousands of variable sites can greatly improve
species-level resolution of recent and rapid radiations. Similar to other
studies, we found that less conservative similarity and missing data
thresholds resulted in more highly supported topologies.