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 [email protected] with any problems

Lozier_etal_BombusDataForDRYAD

Lozier_etal_BombusDataForDRYA

Population Genomics Data for Bombus bifarius color pattern divergence

double digest radseq and rnaseq files for samples across a color pattern and spatial transect for the widespread western North American bumble bee, Bombus bifarius. The included ZIP file contains raw sequence data as well as data files used for analysis

Distribution of haplotypes of 6 Nosema genomic loci

Count of Roche 454 pyrosequencing haplotypes (rows) of 6 Nosema genomic loci in 31 bumble bee samples (columns). See Table S4 for geographic origins of these bee samples. Allele frequency data are used to generate Da distances and neighbor joining tree

Nosema genomic loci information

Information of six genomic loci used to genotype Nosema from 31 bumbles from North America and Europe. The top BlastX hit of each locus matches a sequence from another Nosema species.

Distribution of representative SSUrRNA sequences in various insect samples

Table showing how many times each SSU rRNA representative sequence (rows) is found in each insect sample (columns). Samples were from GenBank, or sequenced with Sanger sequencing or pyrosequencing. Each sample name contains sample ID/GenBank accession no. followed by parasite identification and/or host species identification. See Table S3 for other information associated with each insect sample. See Fig. S4 for phylogenetic network with labeled nodes. Representative DNA sequences can be found in fasta format in the file ssurRNA_rep_sequences.fasta

Information on European bees screended for Nosema

Sample ID, species and collection sites of individual European bees. See european_localities.csv for locality detail

European bumble bee collection localities

European collection sites of bumble bees screened for Nosem

Fasta file containing representative sequences of six Nosema genomic loci

Fasta file containing representative sequences of six Nosema genomic loci. Frequency of haplotypes in sampled bees can be found in genomic_loci_counts.csv