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.species-codesGuide to species codes in alignment files. All species are in the genus Penstemon. See our manuscript for accession informationfull-s80t15Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 15. A key to species codes is given in the separate file entitled species-codes.txt.full-s80t20Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 20. A key to species codes is given in the separate file entitled species-codes.txt.full-s80t30Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 30. A key to species codes is given in the separate file entitled species-codes.txt.full-s90t15Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 15. A key to species codes is given in the separate file entitled species-codes.txt.full-s90t20Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 20. A key to species codes is given in the separate file entitled species-codes.txt.full-s90t30Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 30. A key to species codes is given in the separate file entitled species-codes.txt.full-s95t15Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 95% and minimum taxa per locus = 15. A key to species codes is given in the separate file entitled species-codes.txt.full-s95t20Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 95% and minimum taxa per locus = 20. A key to species codes is given in the separate file entitled species-codes.txt.full-s95t30Aligned MSG-based data matrix for the full set of taxa, built under the following pyRAD parameters: similarity threshold = 95% and minimum taxa per locus = 30. A key to species codes is given in the separate file entitled species-codes.txt.CG-s80t4Aligned MSG-based data matrix for the set of taxa in the CG-clade, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 4. A key to species codes is given in the separate file entitled species-codes.txt.CG-s80t8Aligned MSG-based data matrix for the set of taxa in the CG-clade, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 8. A key to species codes is given in the separate file entitled species-codes.txt.CG-s90t4Aligned MSG-based data matrix for the set of taxa in the CG-clade, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 4. A key to species codes is given in the separate file entitled species-codes.txt.CG-s90t8Aligned MSG-based data matrix for the set of taxa in the CG-clade, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 8. A key to species codes is given in the separate file entitled species-codes.txt.HS-s80t4Aligned MSG-based data matrix for the set of taxa in the HS-clade, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 4. A key to species codes is given in the separate file entitled species-codes.txt.HS-s80t8Aligned MSG-based data matrix for the set of taxa in the HS-clade, built under the following pyRAD parameters: similarity threshold = 80% and minimum taxa per locus = 8. A key to species codes is given in the separate file entitled species-codes.txt.HS-s90t4Aligned MSG-based data matrix for the set of taxa in the HS-clade, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 4. A key to species codes is given in the separate file entitled species-codes.txt.HS-s90t8Aligned MSG-based data matrix for the set of taxa in the HS-clade, built under the following pyRAD parameters: similarity threshold = 90% and minimum taxa per locus = 8. A key to species codes is given in the separate file entitled species-codes.txt