https://doi.org/10.5061/dryad.9w0vt4bnr

This dataset includes FASTA files of multiple sequence alignments of 352 low-copy nuclear loci, as well as summary tables of the output of these analyses.

Description of the data and file structure

Accession names match supplementary data provided in the Zenodo repository: https://zenodo.org/records/7832162

Table 1: Results of HybPhaser Analysis
Key to column headers:

• Sample Number - Accession number from NCBI Sequence Read Archive
• Voucher - Collector surname and collection number
• Country - Country where voucher was collected
• Taxon - species name
• bp - Total base pair count
• allele_divergence - % sequence divergence calculated by HybPhaser
• locus_heterozygosity - Percentage of loci with heterozygosity scores above threshold
• loci with >0.5% SNPs - Percentage of loci with >0.5% SNPs
• loci with >1% SNPs - Percentage of loci with >1% SNPs
• loci with >2% SNPs - Percentage of loci with >2% SNPs
• NumReads - Total number of reads obtained from sample
• ReadsMapped - Total number of reads mapped to target
• PctOnTarget - Percentage of total reads mapped to target
• GenesWithSeqs - Number of loci with sequences

Table 2: Results of HybPhaser Read Assignment
Key to column headers:

• sample - Sample code of phased sample
• bp - Total base pair count
• bpoftarget - Total length of recovered sequence, relative to target sample (percentage)
• paralogs_all - Total number of paralogous loci recovered
• paralogs_each - Number of paralogous copies recovered
• nloci - Total number of loci recovered
• allele_divergence - % sequence divergence calculated by HybPhaser
• locus_heterozygosity - Percentage of loci with heterozygosity scores above threshold
• loci with >0.5% SNPs - Percentage of loci with >0.5% SNPs
• loci with >1% SNPs - Percentage of loci with >1% SNPs
• loci with >2% SNPs - Percentage of loci with >2% SNPs
• Remaining columns - proportion of total reads mapped to all possible references using BWA

Sharing/Access information

Additional data available at the following Zenodo repository:

• https://zenodo.org/records/7832162