Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing

 

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Title Lozier_Bimp-Bpen-RADtags_MolEcol_Dryad_120813
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Description ######## 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!
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When using this data, please cite the original publication:

Lozier JD (2014) Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing. Molecular Ecology 23(4): 788–801. http://dx.doi.org/10.1111/mec.12636

Additionally, please cite the Dryad data package:

Lozier JD (2014) Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.12j05
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