DOI: 10.5061/dryad.83fb8
title: Data from: A test of the invasive pathogen hypothesis of bumble bee decline in North America

description: Emergent fungal diseases are critical factors in global biodiversity
 declines. The fungal pathogen Nosema bombi was recently found to be
 widespread in declining species of North American bumble bees (Bombus),
 with circumstantial evidence suggesting an exotic introduction from
 Europe. This interpretation has been hampered by a lack of knowledge of
 global genetic variation, geographic origin, and changing prevalence
 patterns of N. bombi in declining North American populations. Thus, the
 temporal and spatial emergence of N. bombi and its potential role in
 bumble bee decline remain speculative. We analyze Nosema prevalence and
 genetic variation in the United States and Europe from 1980, before an
 alleged introduction in the early 1990s, to 2011, extracting Nosema DNA
 from Bombus natural history collection specimens from across this time
 period. Nosema bombi prevalence increased significantly from low
 detectable frequency in the 1980s to significantly higher frequency in the
 mid- to late-1990s, corresponding to a period of reported massive
 infectious outbreak of N. bombi in commercial bumble bee rearing stocks in
 North America. Despite the increased frequency, we find no conclusive
 evidence of an exotic N. bombi origin based on genetic analysis of global
 Nosema populations; the widespread Nosema strain found currently in
 declining United States bumble bees was present in the United States
 before commercial colony trade. Notably, the US N. bombi is not detectably
 different from that found predominantly throughout Western Europe, with
 both regions characterized by low genetic diversity compared with high
 levels of diversity found in Asia, where commercial bee breeding
 activities are low or nonexistent.
description: Information of each
 museum bumble bee specimen screened for NosemaTable showing details of
 bees screened for Nosema. Details include specimen ID of bees, institution
 of origin, notes written on museum label associated with each bee,
 collection date, geographic origin of bee and number of times a bee was
 screened for Nosema using PCR.museum_bee_specimens_details.csvDistribution of representative SSUrRNA sequences in various insect samplesTable 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.ssurRNA_counts.csvAlignment of representative SSU rRNA sequences (fasta format)Fasta file of representative SSU rRNA sequences. See file ssurRNA_counts.csv for information on which insect hosts these ssu rRNA sequences are associated with.ssurRNA_rep_sequences.fastaNosema genomic loci informationInformation 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..nosema_genomic_loci_details.csvDistribution of haplotypes of 6 Nosema genomic lociCount 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.genomic_loci_counts.csvFasta file containing representative sequences of six Nosema genomic lociFasta file containing representative sequences of six Nosema genomic loci. Frequency of haplotypes in sampled bees can be found in genomic_loci_counts.csv.6loci.fastaEuropean bumble bee collection localitiesEuropean collection sites of bumble bees screened for Nosemaeuropean_localities.csvInformation on European bees screended for NosemaSample ID, species and collection sites of individual European bees. See european_localities.csv for locality detailseuropean_bee_infection.csv