DOI: 10.5061/dryad.16pj5
title: Data from: Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae)

description: Premise of the study: The ability to conduct species delimitation and
 phylogeny reconstruction with genomic data sets obtained exclusively from
 herbarium specimens would rapidly enhance our knowledge of large,
 taxonomically contentious plant genera. In this study, the utility of
 genotyping by sequencing is assessed in the notoriously difficult genus
 Solidago (Asteraceae) by attempting to obtain an informative
 single-nucleotide polymorphism data set from a set of specimens collected
 between 1970 and 2010. Methods: Reduced representation libraries were
 prepared and Illumina-sequenced from 95 Solidago herbarium specimen DNAs,
 and resulting reads were processed with the nonreference Universal
 Network-Enabled Analysis Kit (UNEAK) pipeline. Multidimensional clustering
 was used to assess the correspondence between genetic groups and
 morphologically defined species. Results: Library construction and
 sequencing were successful in 93 of 95 samples. The UNEAK pipeline
 identified 8470 single-nucleotide polymorphisms, and a filtered data set
 was analyzed for each of three Solidago subsections. Although results
 varied, clustering identified genomic groups that often corresponded to
 currently recognized species or groups of closely related species.
 Discussion: These results suggest that genotyping by sequencing is broadly
 applicable to DNAs obtained from herbarium specimens. The data obtained
 and their biological signal suggest that pairing genomics with large-scale
 herbarium sampling is a promising strategy in species-rich plant groups.
description: barcode
 keyfileThis file associates
 sequencing barcodes with samples.Solidago_keyfile.txtSolidago_TASSEL_optionsThis file details variable options used during the TASSEL alignment and SNP calling pipeline.Junceae_30percent_hapmap.hmpHapmap file for Solidago subsection Junceae filtered for SNPs present in at least 30% of samples.Junceae_70percent_hapmap.hmpHapmap file for Solidago subsection Junceae filtered for SNPs present in at least 70% of samples.Squarrosae_30percent_hapmap.hmpHapmap file for Solidago subsection Squarrosae filtered for SNPs present in at least 30% of samples.Squarrosae_70percent_hapmap.hmpHapmap file for Solidago subsection Squarrosae filtered for SNPs present in at least 70% of samples.Triplinerviae_30percent_hapmap.hmpHapmap file for Solidago subsection Triplinerviae filtered for SNPs present in at least 30% of samples.Triplinerviae_70percent_hapmap.hmpHapmap file for Solidago subsection Triplinerviae filtered for SNPs present in at least 70% of samples.FastqToTagCountPluginFastqToTagCountPlugin XML fileFastqToTBTPluginFastqToTBTPlugin XML fileGBSHapMapFiltersPlugin.chr1.snpmergedGBSHapMapFiltersPlugin.chr1.snpmerged XML fileMergeDuplicateSNP_vcf_Plugin.chr1MergeDuplicateSNP_vcf_Plugin.chr1 XML fileMergeMultipleTagCountPluginMergeMultipleTagCountPlugin XML fileMergeDuplicateSNPsPlugin.chr1MergeDuplicateSNPsPlugin.chr1 XML fileMergeTagsByTaxaFilesPluginMergeTagsByTaxaFilesPlugin XML fileTagCountToFastqPluginTagCountToFastqPlugin XML fileTagsToSNPByAlignmentPlugin.chr1TagsToSNPByAlignmentPlugin.chr1 XML filetbt2vcfPlugin.chr1tbt2vcfPlugin.chr1 XML fileUExportTagPairPluginUExportTagPairPlugin XML fileUTagCountToTagPairPluginUTagCountToTagPairPlugin XML file