DOI: 10.5061/dryad.12j05
title: Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing

description: Genetic variation is of key importance for a species’ evolutionary
 potential, and its estimation is a major component of conservation
 studies. New DNA sequencing technologies have enabled the analysis of
 large portions of the genome in nonmodel species, promising highly
 accurate estimates of such population genetic parameters. Restriction
 site-associated DNA sequencing (RADseq) is used to analyse thousands of
 variants in the bumble bee species Bombus impatiens, which is common, and
 Bombus pensylvanicus, which is in decline. Previous microsatellite-based
 analyses have shown that gene diversity is lower in the declining B.
 pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear
 much more similar in the two species. Both species exhibit allele
 frequencies consistent with historical population expansions. Differences
 in diversity observed at microsatellites thus do not appear to have arisen
 from long-term differences in population size and are either recent in
 origin or may result from mutational processes. Additional research is
 needed to explain these discrepancies and to investigate the best ways to
 integrate next-generation sequencing data and more traditional molecular
 markers in studies of genetic diversity.
description: Lozier_Bimp-Bpen-RADtags_MolEcol_Dryad_120813######## Description of files for Lozier et al. "Revisiting comparisons of genetic diversity in stable and declining species: Assessing genome-wide polymorphism in North American bumble bees using RAD sequencing" for Mol. Ecol. ######## Files contained in "Lozier_Bimp-Bpen-RADtags_MolEcol_Dryad_120813.zip" ######## imp_bamfiles: bam formatted alignment files for each individual used in the paper for B. impatiens, indexed by samtools; note file names correspond with county and state listed in the main paper, and headers contain the actual specimen ID number. imp_radreferencegenome: fasta file (and fai index) for the B. impatiens "RAD reference" genome used for aligning RAD tag reads. pen_bamfiles: bam formatted alignment files for each individual used in the paper for B. pensylvanicus, indexed by samtools; note file names correspond with county and state listed in the main paper, and headers contain the actual specimen ID number. pen_radreferencegenome: fasta file (and fai index) for the B. impatiens "RAD reference" genome used for aligning RAD tag reads. ######## The variant call formatted files (VCF 4.1) that are used for "Filter Set 1" in the paper. The files named: Bombus_imp_stringentRAD_DP_HWEfiltered.vcf Bombus_pen_stringentRAD_DP_HWEfiltered.vcf contain sample names as referred to in @PG in the headers of the .bam files (specimen IDs) that were used in actual analyses in the paper. The files named: Lozier_Bombus_imp_Finalvcf.vcf Lozier_Bombus_pen_Finalvcf.vcf contain sample names renamed to State/County format for easier interpretation, but should otherwise be identical. These can readily be further filtered by other criteria using software such as vcftools, or are small enough to be manipulated by excel if so desired.######## Also included is an excel file "ANGSD_ThetaPi_Bpen_Bimp_LozierBombusRADtags_DRYAD.xls" This file contains per-site estimates of Theta_pi (or nucleotide diversity) from ANGSD, sorted by Chromosome (RADref) and position. ######## please contact jlozier@as.ua.edu with any problems!