How population structure and nest membership shape pathogen patterns in bumble bees?
Data files
Oct 14, 2025 version files 569.46 KB
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data_table_bb_pop_patho.csv
564.75 KB
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README.md
4.71 KB
Abstract
Host density, genetic diversity, and social groups are key factors influencing pathogen transmission in wildlife populations, but their interactions remain poorly understood in insects. Islands can provide natural laboratories with distinct populations that vary in density and genetic diversity, whereby dense, genetically homogenous populations are expected to facilitate pathogen transmission. We used bumble bees to test these predictions, assessing the population structure of the two common species Bombus pascuorum and B. terrestris across island and mainland sites in the British Isles and France, and testing bees for five micro-parasitic and four viral pathogens. B. pascuorum formed distinct genetic clusters on islands, with varying levels of heterozygosity, and only the Isle of Arran clustered with mainland populations. B. terrestris populations were less structured, but populations on the Isle of Man and the Scilly Isles were genetically separated from other island and mainland populations while showing low heterozygosity. Colony density was similar between species and not linked to genetic diversity, but had a positive effect on the prevalence of some pathogens. Contrary to expectations, there was no protective effect of high genetic diversity, suggesting that generalist bumble bee pathogens could be more affected by host species diversity and density. Yet, within B. terrestris populations, we found that nestmates showed more similar pathogen profiles than unrelated individuals, suggesting that genetic similarity and high contact rates within nests affect pathogen prevalence in wild bees.
https://doi.org/10.5061/dryad.prr4xgxws
Description of the data and file structure
This file is the primary dataset utilized for the various analyses described in our article, "How population structure and sociality shape pathogen patterns in bumble bees". In this article, we investigate the population structure of two bumble bee species and link this structure to disease patterns. Microsatellite data were used to calculate genetic diversity in bee populations and in sibship reconstructions. Inferred nest membership then allowed us to estimate the bumble bee density using mark recapture models and to further look into the similarity in pathogen infections within and between nests.
Files and variables
File: data_table_bb_pop_patho.csv
Description: Individual genotype data (allele sizes) and pathogen prevalence for Bombus pascuorum and B. terrestris collected in seven island and four mainland populations in the British Isles and France in 2021 and 2022.
The csv file contains the following columns
Population: Population for collectionSite: Collection site within populationLat: Latitude collection siteLong: Longitude collection siteDate: Collection dateYear: Collection yearSpecies: Bumble bee species, P for Bombus pascuorum and T for B. terrestrisID: Bumble bee IDComment: Comment for samples that had to be excluded from parts of the analyses - empty field when sample was included in all analyses- Microsatellite alleles - showing alle size in bp, 0 indicates no amplification and NA indicates that the locus was not used in the analysis
- BL06 1: Locus BL06 allele 1
- BL06 2: Locus BL06 allele 2
- B118 1: Locus B118 allele 1, in B. pascuorum null allele and removed from analysis
- B118 2: Locus B118 allele 2, in B. pascuorum null allele and removed from analysis
- BL03 1: Locus BL03 allele 1
- BL03 2: Locus BL03 allele 2
- B96 1: Locus B96 allele 1
- B96 2: Locus B96 allele 2
- B126 1: Locus B126 allele 1
- B126 2: Locus B126 allele 2
- BL11 1: Locus BL11 allele 1
- BL11 2: Locus BL11 allele 2
- B119 1: Locus B119 allele 1, only used in B. terrestris, null allele in 2021 and removed from combined analysis
- B119 2: Locus B119 allele 2, only used in B. terrestris, null allele in 2021 and removed from combined analysis
- B131 1: Locus B131 allele 1, only used in B. pascuorum
- B131 2: Locus B131 allele 2, only used in B. pascuorum
- B10 1: Locus B10 allele 1, in B. pascuorum no good amplification in Ouessant samples and removed from combinedanalysis
- B10 2: Locus B10 allele 2, in B. pascuorum no good amplification in Ouessant samples and removed from combined analysis
- B100 1: Locus B100 allele 1, only used in B. terrestris
- B100 2: Locus B100 allele 2, only used in B. terrestris
- B121 1: Locus B121 allele 1, only used in B. pascuorum
- B121 2: Locus B121 allele 2, only used in B. pascuorum
- B124 1: Locus B124 allele 1, in B. pascuorum 2021 null allele and removed from combined analysis
- B124 2: Locus B124 allele 2, in B. pascuorum 2021 null allele and removed from combined analysis
- B11 1: Locus B11 allele 1
- B11 2: Locus B11 allele 2
- B132 1: Locus B132 allele 1
- B132 2: Locus B132 allele 2
- Nest: Nest assigned using sibship reconstruction in Colony - Nests are named by their collection size and then numbered
- Pathogen prevalence - presence/absence data from pathogen screening, NA indicates that a sample was not screened for pathogens, 0 indicated not PCR amplification (absence) and 1 positive PCR amplification (presence)
- A. bombi: Apicystis bombi prevalence: 0 indicates absence and 1 presence
- C. bombi: Crithidia bombi prevalence: 0 indicates absence and 1 presence
- SBPV: Slow bee paralysis virus prevalence: 0 indicates absence and 1 presence
- N. apis: Nosema apis prevalence: 0 indicates absence and 1 presence
- N. bombi: Nosema bombi prevalence: 0 indicates absence and 1 presence
- N. ceranae: Nosema ceranae prevalence: 0 indicates absence and 1 presence
- DWV-A: Deformed wing virus type A prevalence: 0 indicates absence and 1 presence
- DWV-B: Deformed wing virus type B prevalence: 0 indicates absence and 1 presence
- BQCV: Black queen cell virus prevalence: 0 indicates absence and 1 presence
Code/software
The csv file can be opened and analysed using, for instance:
- R
- Microsoft Excel
- Open office
- Mac numbers
216 Bombus pascuorum and 573 B. terrestris were collected from flowers from mid June to late August in 2021 across seven islands in the Irish Sea, the English Channel, and off the coast of Brittany in France, and four coastal sites in England and France in 2021. From late June to early August 2022, islands (except for the Scilly Isles) were sampled again using five sampling sites on large islands (Arran, Isle of Man, Guernsey, Belle-Ile) or collecting across the whole island on smaller islands (< 15 km2, Alderney and Ouessant). A total of 988 B. pascuorum and 1,163 B. terrestris were obtained in 2022.
DNA was extracted from bees using a single hind leg. Bees were genotyped at 12 loci, and fragments were run on a Thermo Fisher Scientific Genetic Analyzer 3130 Series. Alleles were scored in Geneious Prime® v2023.0.1. Sibship reconstruction was performed in COLONY v2.0.6,7, and population structure was assessed using DAPC (discriminant analysis of principal components) and the Bayesian clustering algorithm in Structure v2.3.4.
To study how population structure affects pathogen prevalence, we used island samples from 2022. We screened bumble bees for nine pathogens. Tissue from half bees (laterally bisected) was homogenized, and RNA was extracted and reverse transcribed to cDNA to test for RNA viruses and mRNA from parasite infections. PCR was used to screen for black queen cell virus (BQCV), deformed wing virus type A and B (DWV-A and DWV-B), slow bee paralysis virus (SBPV), Apicistis bombi, Crithidia bombi, Nosema apis, N. bombi, and N. ceranae.