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1. New reference genome assembly for the declining American Bumble Bee, Bombus pensylvanicus

   https://doi.org/10.1093/g3journal/jkaf181  

   Lozier, Jeffrey D; Schweizer, Rena M; Sim, Sheina B; Koch, Jonathan_Berenguer Uhuad; Branstetter, Michael G; Benavides, Ligia R; Geib, Scott M; Evans, Jay D (August 2025, G3: Genes, Genomes, Genetics)

   Vogel, K (Ed.)

   Abstract We present the first chromosome-level genome assembly for Bombus pensylvanicus, a historically widespread native pollinator species that was distributed across eastern North America but has subsequently undergone declines in range area and local relative abundance. This species has been of significant interest as a model for understanding both patterns and possible causes of bumble bee decline in the region, including the role of genetic variation. Here we present a chromosome-level reference genome assembled using Pacific Biosciences singe-molecule HiFi sequences and Hi-C data and annotated using evidence derived from RNA sequencing of multiple tissue types. The B. pensylvanicus genome has a total length of ∼352.6 Mb and was assembled into a total of 224 scaffolds, with 19 primary pseudomolecules representing putative chromosomes and an N50 = 14.872 Mb. Annotation with the Eukaryotic Genome Annotation Pipeline—External (EGAPx) identified 11,411 genes (10,263 protein coding), and BUSCO analysis of 5,991 Hymenoptera-specific BUSCO groups indicated a completeness for the proteins of 99.0% (98.6% single-copy, 0.5% duplicated) and for the genome of 98.5% (98.2% single-copy, 0.3% duplicated). We present synteny analyses with other recently assembled Bombus genomes representing different subgenera and examine the distribution of repetitive regions of the genome relative to the distribution of genes and noncoding RNAs. 

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2. Chromosome-scale genome assembly of the hunt bumble bee, Bombus huntii Greene, 1860, a species of agricultural interest

   https://doi.org/10.1093/g3journal/jkae160  

   Koch, Jonathan_Berenguer Uhuad; Sim, Sheina B; Scheffler, Brian; Lozier, Jeffrey D; Geib, Scott M (July 2024, G3: Genes, Genomes, Genetics)

   Vogel, K (Ed.)

   Abstract The Hunt bumble bee, Bombus huntii, is a widely distributed pollinator in western North America. The species produces large colony sizes in captive rearing conditions, experiences low parasite and pathogen loads, and has been demonstrated to be an effective pollinator of tomatoes grown in controlled environment agriculture systems. These desirable traits have galvanized producer efforts to develop commercial Bombus huntii colonies for growers to deliver pollination services to crops. To better understand Bombus huntii biology and support population genetic studies and breeding decisions, we sequenced and assembled the Bombus huntii genome from a single haploid male. High-fidelity sequencing of the entire genome using PacBio, along with HiC sequencing, led to a comprehensive contig assembly of high continuity. This assembly was further organized into a chromosomal arrangement, successfully identifying 18 chromosomes spread across the 317.4 Mb assembly with a BUSCO score indicating 97.6% completeness. Synteny analysis demonstrates shared chromosome number (n = 18) with Bombus terrestris, a species belonging to a different subgenus, matching the expectation that presence of 18 haploid chromosomes is an ancestral trait at least between the subgenera Pyrobombus and Bombus sensu stricto. In conclusion, the assembly outcome, alongside the minimal tissue sampled destructively, showcases efficient techniques for producing a comprehensive, highly contiguous genome. 

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3. Whole Genome Sequencing Reveals the Structure of Environment-Associated Divergence in a Broadly Distributed Montane Bumble Bee, Bombus vancouverensis

   https://doi.org/10.1093/isd/ixac025  

   Heraghty, Sam D; Rahman, Sarthok Rasique; Jackson, Jason M; Lozier, Jeffrey D (September 2022, Insect Systematics and Diversity)

   Ware, Jessica (Ed.)

   Abstract Broadly distributed species experience divergent abiotic conditions across their ranges that may drive local adaptation. Montane systems where populations are distributed across both latitudinal and elevational gradients are especially likely to produce local adaptation due to spatial variation in multiple abiotic factors, including temperature, oxygen availability, and air density. We use whole-genome resequencing to evaluate the landscape genomics of Bombus vancouverensis Cresson (Hymenoptera: Apidae), a common montane bumble bee that is distributed throughout the western part of North America. Combined statistical approaches revealed several large windows of outlier SNPs with unusual levels of differentiation across the region and indicated that isothermality and elevation were the environmental features most strongly associated with these variants. Genes found within these regions had diverse biological functions, but included neuromuscular function, ion homeostasis, oxidative stress, and hypoxia that could be associated with tolerance of temperature, desiccation, or high elevation conditions. The whole-genome sequencing approach revealed outliers occurred in genome regions with elevated linkage disequilibrium, elevated mean FST, and low intrapopulation nucleotide diversity. Other kinds of structural variations were not widely associated with environmental predictors but did broadly match geographic separation. Results are consistent with other studies suggesting that regions of low recombination may harbor adaptive variation in bumble bees within as well as between species and refine our understanding of candidate genes that could be further investigated as possible targets of selection across the B. vancouverensis range. 

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4. The diversity, evolution, and development of setal morphologies in bumble bees (Hymenoptera: Apidae: Bombus spp.)

   https://doi.org/10.7717/peerj.14555  

   Hines, Heather M.; Kilpatrick, Shelby Kerrin; Mikó, István; Snellings, Daniel; López-Uribe, Margarita M.; Tian, Li (January 2022, PeerJ)

   Bumble bees are characterized by their thick setal pile that imparts aposematic color patterns often used for species-level identification. Like all bees, the single-celled setae of bumble bees are branched, an innovation thought important for pollen collection. To date no studies have quantified the types of setal morphologies and their distribution on these bees, information that can facilitate understanding of their adaptive ecological function. This study defines several major setal morphotypes in the common eastern bumble bee Bombus impatiens Cresson, revealing these setal types differ by location across the body. The positions of these types of setae are similar across individuals, castes, and sexes within species. We analyzed the distribution of the two most common setal types (plumose and spinulate) across the body dorsum of half of the described bumble bee species. This revealed consistently high density of plumose (long-branched) setae across bumble bees on the head and mesosoma, but considerable variation in the amount of metasomal plumosity. Variation on the metasoma shows strong phylogenetic signal at subgeneric and smaller group levels, making it a useful trait for species delimitation research, and plumosity has increased from early Bombus ancestors. The distribution of these setal types suggests these setae may serve several functions, including pollen-collecting and thermoregulatory roles, and probable mechanosensory functions. This study further examines how and when setae of the pile develop, evidence for mechanosensory function, and the timing of pigmentation as a foundation for future genetic and developmental research in these bees. 

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5. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

   https://doi.org/10.1111/mec.17125  

   Heraghty, Sam D.; Jackson, Jason M.; Lozier, Jeffrey D. (September 2023, Molecular Ecology)

   Abstract Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii , a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change. 

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