DOI: 10.5061/dryad.1q8p3
title: Data from: Multiplexed shotgun genotyping resolves species relationships within the North American genus Penstemon

description: 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.
description: 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.