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Abstract The apid subfamily Nomadinae is the oldest and most diverse clade of brood parasitic bees. Through the incorporation of data from a variety of sources, we generated the most detailed and taxonomically complete phylogeny of this group to date. Despite differing amounts of genetic data available for different species, the tree topology largely matched with expected relationships based on previous findings, with 95% of barcode-only taxa placed in taxonomically consistent positions and all tribes recovered as monophyletic. We further carried out divergence time estimation to investigate the evolutionary history of Nomadinae and place the phylogeny along the geological time scale, recovering an estimated age of 99 Ma for the group. Testing for the effect of barcode-only taxa on estimated dates indicated that ages for deep nodes were robust, though the inclusion of such taxa with limited sequence data tended to push shallower nodes towards older dates. Though this approach may not be appropriate for all applications, the potential for integration of cytochrome oxidase DNA barcode sequences with modern phylogenomic (ultraconserved element) sequence data is an encouraging indication that the wealth of previously published data available through sequence repositories retains the capacity to be informative to future phylogenetic studies. 

Abstract Host–microbe interactions underlie the development and fitness of many macroorganisms, including bees. Whereas many social bees benefit from vertically transmitted gut bacteria, current data suggests that solitary bees, which comprise the vast majority of species diversity within bees, lack a highly specialized gut microbiome. Here we examine the composition and abundance of bacteria and fungi throughout the complete life cycle of the ground-nesting solitary bee Anthophora bomboides standfordiana. In contrast to expectations, immature bee stages maintain a distinct core microbiome consisting of Actinobacterial genera (Streptomyces, Nocardiodes) and the fungus Moniliella spathulata. Dormant (diapausing) larval bees hosted the most abundant and distinctive bacteria and fungi, attaining 33 and 52 times their initial copy number, respectively. We tested two adaptive hypotheses regarding microbial functions for diapausing bees. First, using isolated bacteria and fungi, we found that Streptomyces from brood cells inhibited the growth of multiple pathogenic filamentous fungi, suggesting a role in pathogen protection during overwintering, when bees face high pathogen pressure. Second, sugar alcohol composition changed in tandem with major changes in fungal abundance, suggesting links with bee cold tolerance or overwintering biology. We find that A. bomboides hosts a conserved core microbiome that may provide key fitness advantages through larval development and diapause, which raises the question of how this microbiome is maintained and faithfully transmitted between generations. Our results suggest that focus on microbiomes of mature or active insect developmental stages may overlook stage-specific symbionts and microbial fitness contributions during host dormancy. 

Abstract Most pesticide research has focussed on risk to managed honeybees, but other managed and wild bees are also exposed to pesticides. Critically, we know little about the magnitude and sources of risk to honeybees compared with other bees during crop pollination.To compare pesticide exposure and risk across wild and managed bees, we sampled the main bee groups present during bloom in 20 apple orchards, including managed honeybees (Apis mellifera), managed bumblebee workers (Bombus impatiens), wild mining bees (Andrenaspp. andAndrena [Melandrena]spp.), bumblebee foundress queens (Bombus impatiens) and eastern carpenter bees (Xylocopa virginica). We screened all bees for 92 pesticides and computed a Risk Quotient using available toxicity data (honeybee LD₅₀s), adjusting for differences in toxicity known to scale with body mass. To gain insight into exposure origin, we compared residues in bees to those in focal orchard apple and dandelion flowers.Nearly all bee samples contained pesticides (95%), with the average contamination level ranging from 7.1 ± 2.8 parts per billion (ppb) inB. impatiensworkers to 388.4 ± 146.2 ppb inAndrena. Exposure profiles were similar for all bees exceptA. mellifera, whose unique exposure profile included high levels of the neonicotinoid insecticide thiamethoxam.All bee groups except wildB. impatiensqueens had at least one sample exceeding a US Environmental Protection Agency or European Food Safety Authority exposure level of concern.Apis melliferaexperienced significantly greater risk than other bee groups, with 63% and 81% of samples exceeding an acute or chronic exposure level of concern, respectively. Risk to honeybees was driven primarily by high thiamethoxam levels not found in focal orchard flowers and likely originating outside the orchard.Synthesis and applications: We find that pesticide exposure and risk differ between honeybees and other managed and wild bees during apple pollination. Furthermore, pesticide exposure is a landscape‐scale phenomenon and therefore measures to reduce exposure must consider the surroundings beyond focal farms. Limiting orchard sprays, while reducing on‐farm exposures, will not protect far‐foraging bees from off‐farm exposures such as thiamethoxam, which we hypothesize is coming from nearby seed‐treated corn fields planted during apple bloom. 

Abstract Sequence data assembly is a foundational step in high‐throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under‐studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE‐only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided‐assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally moveClavinomiato Dieunomiini and renderEpinomiaonce more a subgenus ofDieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better‐performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.