Range-wide genetic analysis of an endangered bumble bee (Bombus affinis, Hymenoptera: Apidae) reveals population structure, isolation by distance, and low colony abundance.

Declines in bumble bee species range and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumble bee (Bombus affinis) is the first federally listed bumble bee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted a site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range-wide male diploidy rate of ~15%. Our results suggest the Appalachians represent a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for B. affinis compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies, suggesting that B. affinis has undergone a recent decline and exhibit substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where B. affinis is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and help set clear recovery targets for this and other threatened bumble bee species.

Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator.

The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a federally listed endangered species. Due to habitat loss and large declines in population size, B. affinis is facing imminent extinction unless human intervention and recovery efforts are implemented. To better understand B. affinis biology and population genetic and genomic landscapes, we sequenced and assembled the B. affinis genome from a single haploid male. Whole genome HiFi sequencing on PacBio coupled with HiC sequencing resulted in a complete and highly contiguous contig assembly that was scaffolded into a chromosomal context, resolving 18 chromosomes distributed across the 365.1 Mb assembly. All material for both HiFi and HiC sequencing was derived from a single abdominal tissue segment from the single male. These assembly results, coupled with the minimal amount of tissue destructively sampled, demonstrate methods for generating contiguous and complete genomic resources for a rare and endangered species with limited material available and highlight the importance of sample preservation. Precise methods and applications of these methods are presented for potential applications in other species with similar limitations in specimen availability and curation considerations.

Addressing Detection Uncertainty in Bombus affinis (Hymenoptera: Apidae) Surveys Can Improve Inferences Made From Monitoring.

The U.S. Fish and Wildlife Service developed national guidelines to track species recovery of the endangered rusty patched bumble bee [Bombus affinis Cresson (Hymenoptera: Apidae)] and to investigate changes in species occupancy across space and time. As with other native bee monitoring efforts, managers have specifically acknowledged the need to address species detection uncertainty and determine the sampling effort required to infer species absence within sites. We used single-season, single-species occupancy models fit to field data collected in four states to estimate imperfect detection of B. affinis and to determine the survey effort required to achieve high confidence of species detection. Our analysis revealed a precipitous, seasonal, decline in B. affinis detection probability throughout the July through September sampling window in 2021. We estimated that six, 30-min surveys conducted in early July are required to achieve a 95% cumulative detection probability, whereas >10 surveys would be required in early August to achieve the same level of confidence. Our analysis also showed B. affinis was less likely to be detected during hot and humid days and at patches of reduced habitat quality. Bombus affinis was frequently observed on Monarda fistulosa (Lamiales: Lamiaceae), followed by [Pycnanthemum virginianum Rob. and Fernald (Lamiales: Lamiaceae)], Eutrochium maculatum Lamont (Asterales: Asteraceae), and Veronicastrum virginicum Farw. (Lamiales: Plantaginaceae). Although our research is focused on B. affinis, it is relevant for monitoring other bumble bees of conservation concern, such as B. occidentalis Greene (Hymenoptera: Apidae) and B. terricola Kirby (Hymenoptera: Apidae) for which monitoring efforts have been recently initiated and occupancy is a variable of conservation interest.