After a strenuous year fighting a lawsuit against the company she co-founded, Tinder co-founder Whitney Wolfe Herd joined Russian entrepreneur and Badoo founder Andrey Andreev to launch Bumble....

This is a dataset of locations and population genetic information based on microsatellite analysis of rusty patched bumble bee (Bombus affinis). Data were collected over the course of two years (2020 and 2021), and genetic analysis took place in 2022.

EXCEL spreadsheet of demographic model of a bumblebee population

Bumble bees (Bombus) are vitally important pollinators of wild plants and agricultural crops worldwide. Fragmentary observations, however, have suggested population declines in several North American species. Despite rising concern over these observations in the United States, highlighted in a recent National Academy of Sciences report, a national assessment of the geographic scope and possible causal factors of bumble bee decline is lacking. Here, we report results of a 3-y interdisciplinary study of changing distributions, population genetic structure, and levels of pathogen infection in bumble bee populations across the United States. We compare current and historical distributions of eight species, compiling a database of >73,000 museum records for comparison with data from intensive nationwide surveys of >16,000 specimens. We show that the relative abundances of four species have declined by up to 96% and that their surveyed geographic ranges have contracted by 23–87%, some within the last 20 y. We also show that declining populations have significantly higher infection levels of the microsporidian pathogen Nosema bombi and lower genetic diversity compared with co-occurring populations of the stable (nondeclining) species. Higher pathogen prevalence and reduced genetic diversity are, thus, realistic predictors of these alarming patterns of decline in North America, although cause and effect remain uncertain. Bumble bees (Bombus) are integral wild pollinators within native plant communities throughout temperate ecosystems, and recent domestication has boosted their economic importance in crop pollination to a level surpassed only by the honey bee. Their robust size, long tongues, and buzz-pollination behavior (high-frequency buzzing to release pollen from flowers) significantly increase the efficiency of pollen transfer in multibillion dollar crops such as tomatoes and berries. Disturbing reports of bumble bee population declines in Europe have recently spilled over into North America, fueling environmental and economic concerns of global decline. However, the evidence for large-scale range reductions across North America is lacking. Many reports of decline are unpublished, and the few published studies are limited to independent local surveys in northern California/southern Oregon, Ontario, Canada, and Illinois. Furthermore, causal factors leading to the alleged decline of bumble bee populations in North America remain speculative. One compelling but untested hypothesis for the cause of decline in the United States entails the spread of a putatively introduced pathogen, Nosema bombi, which is an obligate intracellular microsporidian parasite found commonly in bumble bees throughout Europe but largely unstudied in North America. Pathogenic effects of N. bombi may vary depending on the host species and reproductive caste and include reductions in colony growth and individual life span and fitness. Population genetic factors could also play a role in Bombus population decline. For instance, small effective population sizes and reduced gene flow among fragmented habitats can result in losses of genetic diversity with negative consequences, and the detrimental impacts of these genetic factors can be especially intensified in bees. Population genetic studies of Bombus are rare worldwide. A single study in the United States identified lower genetic diversity and elevated genetic differentiation (FST) among Illinois populations of the putatively declining B. pensylvanicus relative to those of a codistributed stable species. Similar patterns have been observed in comparative studies of some European species, but most investigations have been geographically restricted and based on limited sampling within and among populations. Although the investigations to date have provided important information on the increasing rarity of some bumble bee species in local populations, the different survey protocols and limited geographic scope of these studies cannot fully capture the general patterns necessary to evaluate the underlying processes or overall gravity of declines. Furthermore, valid tests of the N. bombi hypothesis and its risk to populations across North America call for data on its geographic distribution and infection prevalence among species. Likewise, testing the general importance of population genetic factors in bumble bee decline requires genetic comparisons derived from sampling of multiple stable and declining populations on a large geographic scale. From such range-wide comparisons, we provide incontrovertible evidence that multiple Bombus species have experienced sharp population declines at the national level. We also show that declining populations are associated with both high N. bombi infection levels and low genetic diversity. This data was used in the paper "Patterns of widespread decline in North American bumble bees" published in the Proceedings of the National Academy of United States of America. For more information about this dataset contact: Sydney A. Cameron: scameron@life.illinois.edu James Strange: James.Strange@ars.usda.gov Resources in this dataset:Resource Title: Data from: Patterns of Widespread Decline in North American Bumble Bees (Data Dictionary). File Name: meta.xmlResource Description: This is an XML data dictionary for Data from: Patterns of Widespread Decline in North American Bumble Bees.Resource Title: Patterns of Widespread Decline in North American Bumble Bees (DWC Archive). File Name: occurrence.csvResource Description: File modified to remove fields with no recorded values.Resource Title: Patterns of Widespread Decline in North American Bumble Bees (DWC Archive). File Name: dwca-usda-ars-patternsofwidespreaddecline-bumblebees-v1.1.zipResource Description: Data from: Patterns of Widespread Decline in North American Bumble Bees -- this is a Darwin Core Archive file. The Darwin Core Archive is a zip file that contains three documents.

The occurrence data is stored in the occurrence.txt file. The metadata that describes the columns of this document is called meta.xml. This document is also the data dictionary for this dataset. The metadata that describes the dataset, including author and contact information for this dataset is called eml.xml.

Find the data files at https://bison.usgs.gov/ipt/resource?r=usda-ars-patternsofwidespreaddecline-bumblebees

Data and code repository for Soroye et al. 2020. (DOI: 10.1126/science.aax8591)Gridded environmental observations and R scripts used to process data and generate all results from study.The bumblebee dataset has been previously used in Kerr et al 2015, and contains data assembled from a variety of sources including (Polce et al 2018, Rasmont et al 2015, Potts et al 2015, and Williams et al 2014), and other sources listed in the complete acknowledgement below. This data is provided in accordance with the Research Standards and data policies of Science, to allow any researchers to reproduce or extend the analysis. Researchers wishing to use these data for novel applications or questions should first seek permission from the original data providers (see complete acknowledgement below for a list).J. T. Kerr, A. Pindar, P. Galpern, L. Packer, S. G. Potts, S. M. Roberts, P. Rasmont, O. Schweiger, S. R. Colla, L. L. Richardson, D. L. Wagner, L. F. Gall, D. S. Sikes, A. Pantoja, Climate change impacts on bumblebees converge across continents. Science 349, 177–180 (2015). doi:10.1126/science.aaa7031C. Polce, J. Maes, X. Rotllan-Puig, D. Michez, L. Castro, B. Cederberg, L. Dvorak, Ú.Fitzpatrick, F. Francis, J. Neumayer, A. Manino, J. Paukkunen, T. Pawlikowski, S. Roberts, J. Straka, P. Rasmont, Distribution of bumblebees across europe. One Ecosyst. 3, e28143 (2018). doi:10.3897/oneeco.3.e28143S. G. Potts, J. C. Biesmeijer, R. Bommarco, A. Felicioli, M. Fischer, P. Jokinen, D. Kleijn,A.-M. Klein, W. E. Kunin, P. Neumann, L. D. Penev, T. Petanidou, P. Rasmont, S. P. M. Roberts, H. G. Smith, P. B. Sørensen, I. Steffan-Dewenter, B. E. Vaissière, M. Vilà, A. Vujić, M. Woyciechowski, M. Zobel, J. Settele, O. Schweiger, Developing European conservation and mitigation tools for pollination services: Approaches of the STEP (Status and Trends of European Pollinators) project. J. Apic. Res. 50, 152–164 (2015). doi:10.3896/IBRA.1.50.2.07P. H. Williams, R. W. Thorp, L. L. Richardson, S. R. Colla, Bumble Bees of North America:An Identification Guide (Princeton Univ. Press, 2014).P. Rasmont, M. Franzen, T. Lecocq, A. Harpke, S. Roberts, K. Biesmeijer, L. Castro, B.Cederberg, L. Dvorak, U. Fitzpatrick, Y. Gonseth, E. Haubruge, G. Mahe, A. Manino, D. Michez, J. Neumayer, F. Odegaard, J. Paukkunen, T. Pawlikowski, S. Potts, M. Reemer,J. Settele, J. Straka, O. Schweiger, Climatic Risk and Distribution Atlas of European Bumblebees. BioRisk 10, 1–236 (2015). doi:10.3897/biorisk.10.4749The authors would like to thank all contributors to the bumble bee dataset, and the tireless hours of those who helped put it together, especially Alana Pindar, Paul Galpern, Laurence Packer, Simon G. Potts, Stuart M. Roberts, Pierre Rasmont, Oliver Schweiger, Sheila R. Colla, Leif L. Richardson, David L. Wagner, Lawrence F. Gall, Derek S. Sikes, and Alberto Pantoja. We are grateful to data contributors from North America: Bee Biology and Systematics Lab, USDA-ARS, Utah State University; John Ascher, National University of Singapore and American Museum of Natural History, New York, USA; Doug Yanega, University of California, Riverside (NSF-DBI #0956388 and #0956340), California, USA; Illinois Natural History Survey, Illinois, USA; Packer Lab Research Collection, York University, Canada; Canadian National Collection, Agriculture and Agri-Food Canada; Canada; Peabody Museum, Yale University; Sam Droege, USGS Patuxent Wildlife Research Center, USA; Boulder Museum of Natural History, University of Colorado, Colorado, USA. From Europe: Status and Trends of European Pollinators (STEP) Collaborative Project (grant 244090, www.STEP-project.net); Bees, Wasps and Ants Recording Society; BDFGM Banque de Données Fauniques (P. Rasmont & E. Haubruge); BWARS (UK, S.P.M. Roberts); SSIC (Sweden, B. Cederberg); Austria (J. Neumayer); EISN (Netherland, M. Reemer); CSCF (Suisse, Y. Gonseth); Poland (T. Pawlikowski); NBDC (Eire, U. FitzPatrick); FMNH (Finland, J. Paukkunen); Czech Republic (J. Straka, L. Dvorak); France (G. Mahé); NSIC (Norway, F. Odegaard); UK (S.P.M. Roberts); Italy (A. Manino); Spain (L. Castro) Global Biodiversity Information Facility (GBIF), http://gbif.org for records from North America and Europe.

Variation in bumble bee color patterns is well-documented within and between species. Identifying the genetic mechanisms underlying such variation may be useful in revealing evolutionary forces shaping rapid phenotypic diversification. The widespread North American species Bombus bifarius exhibits regional variation in abdominal color forms, ranging from red-banded to black-banded phenotypes and including geographically and phenotypically intermediate forms. Identifying genomic regions linked to this variation has been complicated by strong, near species level, genome-wide differentiation between red- and black-banded forms. Here, we instead focus on the closely related black-banded and intermediate forms that both belong to the subspecies B. bifarius nearcticus. We analyze an RNA sequencing (RNAseq) data set and identify a cluster of single nucleotide polymorphisms (SNPs) within one gene, Xanthine dehydrogenase/oxidase-like, that exhibit highly unusual differentiation compared to the rest of the sequenced genome. Homologs of this gene contribute to pigmentation in other insects, and results thus represent a strong candidate for investigating the genetic basis of pigment variation in B. bifarius and other bumble bee mimicry complexes.

Please see the published manuscript for full data collection details.

Please refer to the publication Rahman et al. 2021; "A combined RAD-Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris" published in Scientific Reports for detailed methods. This data repository contains following files:

1. Final SNP dataset from publicly available wildtype B. terrestris sequencing data (1.NCBI22filtered.recode.vcf) Please refer to the methods section "SNP comparison to other bumble bees and Hymenoptera"

2. Final SNP dataset from in-house RAD-Seq B. terrestris sequencing data (2.populations.snps.vcf) Please refer to the methods section "Analysis of RAD-Seq Dataset"

3. Final SNP dataset from in-house WGS B. terrestris sequencing data (3.BterGWASSNPonlymissingrm75QC.recode.vcf) Please refer to the methods section "Analysis of whole-genome resequencing dataset"

4. Population/Phenotype Assignment file for RAD-Seq Samples (4.RAD_pheno.txt)&nbs...

TripDurationsDefaultResults of the Bumble-BEEHAVE simulation described in 1. Individual level comparisonColony_Validation_1_250Results of the Bumble-BEEHAVE simulations presented in 2. Colony level comparison (runs 1 - 250)Colony_Validation_251_7500Results of the Bumble-BEEHAVE simulations presented in 2. Colony level comparison (runs 251 - 7500)Population_ValidationResults of the Bumble-BEEHAVE simulations presented in 3. Population level comparisonSingleHabitatPatchResults of the Bumble-BEEHAVE simulation described in 4. Model applications: Setting/Output 1Baron_500initialQueensResults of the Bumble-BEEHAVE simulation described in 4. Model applications: Setting/Output 2 with 500 initial queenBaron_7500initialQueensResults of the Bumble-BEEHAVE simulation described in 4. Model applications: Setting/Output 2 with 7500 initial queens

AbstractThe pollination services provided by bees are essential for supporting natural and agricultural ecosystems. However, bee population declines have been documented across the world. Many of the factors known to undermine bee health (e.g., poor nutrition) can decrease immunocompetence and, thereby, increase bees’ susceptibility to diseases. Given the myriad of stressors that can exacerbate disease in wild bee populations, assessments of the relative impact of landscape habitat conditions on bee pathogen prevalence are needed to effectively conserve pollinator populations. Herein, we assess how landscape-level conditions, including various metrics of floral/nesting resources, insecticides, weather, and honey bee (Apis mellifera) abundance, drive variation in wild bumble bee (Bombus impatiens) pathogen loads. Specifically, we screened 890 bumble bee workers from varied habitats in Pennsylvania, USA for three pathogens (deformed wing virus, black queen cell virus, and Vairimorpha (= N...