DOI: 10.5061/dryad.qh8sh
title: Data from: Sequence capture of ultraconserved elements from bird museum specimens

description: New DNA sequencing technologies are allowing researchers to explore the
 genomes of the millions of natural history specimens collected prior to
 the molecular era. Yet, we know little about how well specific
 next-generation sequencing (NGS) techniques work with the degraded DNA
 typically extracted from museum specimens. Here, we use one type of NGS
 approach, sequence capture of ultraconserved elements (UCEs), to collect
 data from bird museum specimens as old as 120 years. We targeted 5060 UCE
 loci in 27 western scrub-jays (Aphelocoma californica) representing three
 evolutionary lineages that could be species, and we collected an average
 of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs).
 Despite older specimens producing fewer and shorter loci in general, we
 collected thousands of markers from even the oldest specimens. More
 sequencing reads per individual helped to boost the number of UCE loci we
 recovered from older specimens, but more sequencing was not as successful
 at increasing the length of loci. We detected contamination in some
 samples and determined that contamination was more prevalent in older
 samples that were subject to less sequencing. For the phylogeny generated
 from concatenated UCE loci, contamination led to incorrect placement of
 some individuals. In contrast, a species tree constructed from SNPs called
 within UCE loci correctly placed individuals into three monophyletic
 groups, perhaps because of the stricter analytical procedures used for SNP
 calling. This study and other recent studies on the genomics of museum
 specimens have profound implications for natural history collections,
 where millions of older specimens should now be considered genomic
 resources.
description: trinity-assemblies-for-dryad.tar.gzRaw reads assembled de novo into contigs using trinity (trinityrnaseq_r2013-02-25).toepad-taxa.confThe taxon-names configuration file for creating UCE data sets for use with the get_match_counts.py (https://github.com/faircloth-lab/phyluce).toepad-taxa-COMPLETE.tar.gzUntrimmed and trimmed Nexus files, PHYLIP concatenated alignment, and RAxML input/output for the 100% complete data matrix.toepad-taxa-COMPLETE-RAxML_bipartitions.FINAL.treNewick-formatted tre file for the 100% complete concatenated matrix.toepad-taxa-INCOMPLETE.tar.gzUntrimmed and trimmed Nexus files, PHYLIP concatenated alignment, RAxML input/output for the incomplete data matrix. Includes directory of coverage computations for all UCE loci as well as loci in 75% complete data matrix.toepad-taxa-INCOMPLETE-RAxML_bipartitions.FINALNewick-formatted tre file for the 75% complete concatenated matrix.wesj-103135-reference-sequence.tar.gzQuasi-reference sequence and sequences indexes for LACM-103135. Used for SNP-calling.wesj-toepads-realigned.bam.placeholderMerged BAM file that we realigned around indels using GATK. Contains alignment information for all individuals across which we called SNPs using GATK.wesj-toepads-realigned.bamwesj-toepads-rawSNPS-Q30.vcf.gzRaw SNP calls output by GATK (i.e., not filtered using VariantFiltration).wesj-toepads-inDels-Q30.vcf.gzInDel calls using for VariantFiltration in GATK.wesj-toepads-Q30-QD2-LOW-STRICT.vcf.gzFiltered raw SNP data (i.e., these have been put through VariantFiltration).Q30-QD2-MISS_0.75.recode.vcf.gzFiltered SNPs that have undergone VariantFiltration and also selection for presence in 75% of individuals genotypes. SNPs in this file have further been filtered for the presence of informative sites.Q30-QD2-MISS_0.75.recode.snapp.nexus.gzFiltered SNPs that have undergone VariantFiltration and also selection for presence in 75% of individuals genotypes. SNPs in this file have further been filtered for the presence of informative sites. SNPs in this file have been re-formatted for SNAPP, and this file contains data for individuals USNM-144749 and MLZ-59834, which we removed from the data set prior to analysis.Structure_infile_SNPS_jays.txt.gzFiltered SNPs that have undergone VariantFiltration and also selection for presence in 75% of individuals genotypes. SNPs in this file have further been filtered for the presence of informative sites. Finally, SNPs in this file have been re-formatted for STRUCTURE.SNAPP_analysis.tar.gzInput files prepared for SNAPP and output files generated by SNAPP. The WESJ_SNAPP_TIPS_ed.xml input file created for SNAPP *does not* contain data for individuals USNM-144749 and MLZ-59834, which we removed from the data set prior to analysis.Structure_Results_SNPs_jays.tar.gzOutput files generated by STRUCTURE.toepad-taxa.ProcessingSteps.DRYAD.txtProcessing steps we used for analysis of these data.SRA-locations.txtLocations of raw sequence read files in the NCBI SRA.