The rusty patched bumble bee (Bombus affinis), shown here in Cherokee Regional Park in St. Paul, Minnesota, is one of nine bee species listed as endangered by the U.S. Fish and Wildlife Service, and the species only remains in a small proportion of its original range. A research team led by John Mola, Ph.D., at Colorado State University sampled rusty patched bumble bees throughout their range and examined the allele frequencies in their genomes. They found that the species occurs in three distinct clusters in the midwestern U.S., that these clusters are genetically differentiated, and that they have small population sizes. They conclude that the remaining colonies are fragile and that entomologists should be cautious about management procedures that could be disruptive to colony health. (Photo courtesy of Tamara Smith, U.S. Fish and Wildlife Service)

By John P. Roche, Ph.D.

Numerous bee species are declining in the U.S. due to pesticides, pathogens, habitat loss, and climate change. Bees are important because they pollinate 80 percent of flowering plants, including $15 billion worth of agricultural products in the U.S. each year. Genetic factors have strong effects on the viability of bee populations, so bee conservation can be strengthened by data on population genetics.

John Mola, Ph.D., assistant professor of forest and rangeland stewardship at Colorado State University, and colleagues have studied the population genetics of rusty patched bumble bees (Bombus affinis) with the goal of informing management efforts for this endangered species. They report their findings in a study published last week in the Journal of Insect Science.

Rusty patched bumble bees used to be widespread in the northeastern and midwestern U.S., but they are now gone from 7090 percent of their historical range. They are one of nine bee species classified as endangered by the U.S. Fish and Wildlife Service (USFWS).

Mola and colleagues pursued two main questions in their study: One, what is the broad population structure of rusty patched bumble bees? And, two, what are patterns of population genetic diversity and differentiation across the range of the species? The team included researchers from Colorado State University, the University of Minnesota, the University of Wisconsin, the Minnesota Zoo, the USFWS, Ohio State University, the Wisconsin Department of Natural Resources, and the USDA Agricultural Research Service, as well as two independent ecological research consultants. (For more about the project, see Rusty-patched bumblebees struggle for survival found in its genes, from the CSU Warner College of Natural Resources.)

To examine the genetic makeup of the rusty patched bumble bee populations, in 2020 and 2021 the team collected samples from the final leg segment (or tarsus) of sampled bees. They collected a total of 498 bee samples, of which, after selecting for samples that met certain screening criteria, they had 470 samples to use in the study. They extracted DNA from the samples and amplified the DNA using polymerase chain reaction (PCR). They focused on sections of DNA with repeating sequences of base pairs called microsatellite markers to examine genetic differentiation across the species range. With these genetic data, the team calculated, for each population, the genetic diversity of the samples, the degree to which individuals in populations had different alleles at the same locus (called heterozygosity), the degree of inbreeding, and the proportion of males that were diploid (males that carried two sets of DNA instead of one). Bees have a haplodiploid reproduction system in which females queens and workers are diploid (having two sets of chromosomes) and reproductive drone males are normally haploid (having one set of chromosomes).

The rusty patched bumble bee (Bombus affinis), one of nine endangered bee species in the U.S., occurs in three genetically distinct clusters in the Midwest and Appalachia, a new study shows. But low levels of genetic diversity between colonies and other underlying genetic factors suggest their populations remain fragile, researchers say. Here, study coauthor Michelle Boone, Ph.D., a graduate student at the University of Minnesota during the study and now a project manager for the U.S. National Park Service Inventory and Monitoring Division, takes genetic samples from a rusty patched bumble bee. (Photo courtesy of Tamara Smith, U.S. Fish and Wildlife Service)

The rusty patched bumble bee (Bombus affinis), one of nine endangered bee species in the U.S., occurs in three genetically distinct clusters in the Midwest and Appalachia, a new study shows. But low levels of genetic diversity between colonies and other underlying genetic factors suggest their populations remain fragile, researchers say. Here, study coauthor Michelle Boone, Ph.D., a graduate student at the University of Minnesota during the study and now a project manager for the U.S. National Park Service Inventory and Monitoring Division, takes genetic samples from a rusty patched bumble bee. (Photo courtesy of Tamara Smith, U.S. Fish and Wildlife Service)

Mola and colleagues found support for the presence of three distinct genetic clusters of rusty patched bumble bees in the U.S.: a northwestern cluster in Minnesota; a large central cluster in Wisconsin, Illinois, and Iowa; and an Appalachian cluster in West Virginia and Virginia. The clusters were isolated geographically and had small population sizes. The investigators found differences in allelic richness and in the degree of inbreeding among clusters. These clusters were found to be genetically differentiated, but it is not yet known if this differentiation was caused by the decrease in numbers in these populations or if it existed prior to the population decline.

The researchers also observed that, of 115 males sampled, 18 (~15 percent) were diploid. The presence of diploid males in bumble bee colonies suggests inbreeding. The presence of diploid males is unhealthy for bee colonies because bee populations depend on haploid males for reproduction.

The amount of genetic differentiation among the three clusters, as determined by a measure of genetic variation called the pairwise fixation index, was fairly low. This suggests that there may still be considerable gene flow among the subpopulations.

Population problems in Bombus affinis observed in the study include the presence of inbreeding and low levels of heterozygosity. Also, rusty patched bumble bee populations are so small that random environmental or genetic fluctuations could lead to local extinction of remaining colonies.

The results of this study advance our knowledge of the population genetics of rusty patched bumble bee populations. But determining the degree and significance of population size and genetic variability in a bumble bee population is complex.

One cannot just simply count the number of individuals and be confident that means there is a large and robust population, Mola says. Instead, we can use the term genetic health to suggest that the underlying genetics of the population are either in line, or not, with a population that is resilient to processes causing random perturbations. In our study, we find that the low number of genetically distinct colonies we observeas opposed to counts of individual workersand the levels of male diploidy we observei.e., inbreedingsuggest that even though counts of individual workers at a site may be high, the underlying genetics suggest those populations may be at risk.

Genetic information can help wildlife managers identify genetics-based management units in nature, help them evaluate the risk/benefit ratios of performing introductions of bees to endangered populations, and help them design optimal interventions within the limits of their budgets. Management activities aimed at bolstering declining bee populations include reintroducing individuals of a species to locales where the species formerly lived and introducing captive-reared males or females to threatened populations.

Mola and colleagues suggest that the three separate clusters of Bombus affinis may have different management needs and that entomologists should be careful about activities that could disrupt the fragile remaining colonies, including moving males or females among populations. One potential management measure they do suggest is increasing the connectivity of habitats to increase gene flow among populations.

There are limitations in being able to compare across different bumble bee studies. Different studies can collect samples in different manners, can select different genetic loci for comparison, and can score alleles in different ways, all of which make comparisons difficult. But advances in the field depend on cooperation across multiple research groups and organizations. Doing this type of work inherently requires collaboration among a large team, Mola says. The species is not necessarily easy to find, and not everyone has the appropriate training and permits to take genetic material, so no one team can do a large-scale study on their own. So, continuing the culture of data sharing, generosity, and collegiality that currently characterizes the bee-conservation community is extremely important for the success of future research and conservation efforts.

Next research steps that the team suggests include collecting comparative data on the proportion of diploid males in populations that are declining versus populations that are stable. They also suggest collecting data on similar bumble bee species that live in similar habitats.

Summing up their findings, Mola says, The results suggest that even in some of the locations that we might think of as current-day strongholds for the species, it still has a much lower number of genetically distinct colonies compared to other stable species. So, we cannot rest easy, even in these areas where we see the species year-to-year with reliability.

The decline of the rusty patched bumble bee has been precipitous. But some signs are encouraging, including considerable apparent gene flow among populations. With ongoing research and carefully planned management, we can hope that populations of the species can become more genetically robustand eventually more abundant.

John P. Roche, Ph.D., is an author, biologist, and science writer with a Ph.D. and postdoctoral fellowship in the biological sciences and a dedication to making rigorous science clear and accessible. He authors books and articles, and prepares materials for universities, scientific societies, and publishers. Professional experience includes serving as a scientist and scientific writer at Indiana University, Boston College, and the UMass Chan Medical School; serving as a visiting professor at four tier-one schools; and developing concept-based science curricula for universities and publishers.

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Genetic Analysis Guides Conservation of Endangered Bumble Bee - Entomology Today