Biology subjects

Kapheim, K. M.

Publications and source records attributed to Kapheim, K. M..

10 recordsLinked to original sources

bioRxiv2025

Reproductive and Seasonal Impacts on Rock Iguana Health: A Cross-sectional Study of Microbiome Changes

In this study, we examined how natural seasonal cycles and sex-based differences interact together using wild northern rock iguana as a study system. We collected samples during two seasons: reproductive (June) and post-reproductive (September) in 2016, this chapter demonstrates that sex and season both shaped microbiome composition. Reproductive females exhibited reduced microbial diversity during breeding compared to males and post-reproductive females, likely reflecting reproductive demands and dietary shifts. Physiological metrics including triglycerides, glucose, oxidative stress, and body mass index also influenced microbiome diversity, though the microbial community remained relatively stable across seasons.

microbiology↗

bioRxiv2024

Convergent evolution associated with the loss of developmental diapause may promote extended lifespan in bees

Diapause has long been proposed to play a significant role in the evolution of eusociality in Hymenoptera. Recent studies have shown that shifts in the diapause stage precede social evolution in wasps and bees, however, the genomic basis remains unknown. Given the overlap in molecular pathways that regulate diapause and lifespan, we hypothesized that the evolutionary loss of developmental diapause may lead to extended lifespan among adults, which is a prerequisite for the evolution of eusociality. To test this, we compared 27 bee genomes with or without prepupal diapause. Our results point to several potential mechanisms for lifespan extension in species lacking prepupal diapause, including the loss of the growth hormone PTTH and its receptor TORSO, along with convergent selection in genes known to regulates lifespan in animals. Specifically, we observed purifying selection of pro-longevity genes and relaxed selection of anti-longevity genes within the IIS/TOR pathway in species that have lost prepupal diapause. Changes in selection pressures on this pathway may lead to the evolution of new phenotypes, such as lifespan extension and altered responses to nutritional signals, that are crucial for social evolution. SignificanceDiapause has long been proposed to play a significant role in the evolution of eusociality in Hymenoptera. Recent studies have shown that the loss of diapause during the prepupal stage precedes social evolution in wasps and bees. However, the genomic mechanisms underlying this phenomenon remain unknown. Through comparative genomics, we showed that the convergent loss of prepupal diapause is associated with mechanisms that may promote lifespan extension, a prerequisite for social evolution. These mechanisms include genes losses and signals of selection on genes related to aging.

evolutionary biology↗

bioRxiv2022

Maternal body condition and season influence RNA deposition in the oocytes of alfalfa leafcutting bees (Megachile rotundata)

Maternal effects are an important source of phenotypic variance, whereby females influence offspring developmental trajectory beyond direct genetic contributions, often in response to changing environmental conditions. However, relatively little is known about the mechanisms by which maternal experience is translated into molecular signals that shape offspring development. One such signal may be maternal RNA transcripts (mRNAs and miRNAs) deposited into maturing oocytes. These regulate the earliest stages of development of all animals, but are understudied in most insects. Here we investigated the effects of female internal (body condition) and external (time of season) environmental conditions on maternal RNA in the maturing oocytes and 24 hr old eggs of alfalfa leafcutting bees. Using gene expression and WGCNA analysis, we found that females adjust the quantity of mRNAs related to protein phosphorylation, transcriptional regulation, and nuclease activity deposited into maturing oocytes in response to both poor body condition and shorter day lengths that accompany the late season. However, the magnitude of these changes was higher for time of season. Females also adjusted miRNA deposition in response to seasonal changes, but not body condition. We did not observe significant changes in maternal RNAs in response to either body condition or time of season in 24-hr-old eggs, which were past the maternal-to-zygotic transition. Our results suggest that females adjust the RNA transcripts they provide for offspring to regulate development in response to both internal and external environmental cues. Variation in maternal RNAs may, therefore, be important for regulating offspring phenotype in response to environmental change.

developmental biology↗

bioRxiv2021

Convergent selection on juvenile hormone signaling is associated with the evolution of eusociality in bees

Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here, we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two proteins that bind and transport juvenile hormone (JH) - a key regulator of insect development and reproduction. We find one of these JH binding proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behavior and suggest eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral, developmental hormone may have been co-opted during one of lifes major transitions. More broadly, our results highlight how trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.

evolutionary biology↗

bioRxiv2020

Composition and acquisition of the microbiome in solitary, ground-nesting alkali bees

Increasing evidence suggests the microbiome plays an important role in bee ecology and health. However, the relationship between bees and their bacterial symbionts has only been explored in a handful of species. We characterized the microbiome across the life cycle of solitary, ground-nesting alkali bees (Nomia melanderi). We find that feeding status is a major determinant of microbiome composition. The microbiome of feeding larvae was similar to that of pollen provisions, but the microbiome of post-feeding larvae (pre-pupae) was similar to that of the brood cell walls and newly-emerged females. Feeding larvae and pollen provisions had the lowest beta diversity, suggesting the composition of larval diet is highly uniform. Comparisons between lab-reared, newly-emerged, and nesting adult females suggest that the hindgut bacterial community is largely shaped by the external environment. However, we also identified taxa that are likely acquired in the nest or which increase or decrease in relative abundance with age. Although Lactobacillus micheneri was highly prevalent in pollen provisions, it was only detected in one lab-reared female, suggesting it is primarily acquired from environmental sources. These results provide the foundation for future research on metagenomic function and development of probiotics for these native pollinators.

ecology↗

bioRxiv2019

Brain microRNA expression associated with social evolution in bees

Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologs in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.

genomics↗

bioRxiv2019

Loss of developmental diapause as a prerequisite for social evolution in bees

Diapause is a physiological arrest of development ahead of adverse environmental conditions and is a critical phase of the life cycle of many insects. In bees, diapause has been reported in species from all seven taxonomic families. However, they exhibit a variety of diapause strategies. These different strategies are of particular interest since shifts in the phase of the insect life cycle in which diapause occurs has been hypothesized to promote the evolution of sociality. Here we provide a comprehensive evaluation of this hypothesis with phylogenetic analysis and ancestral state reconstruction of the ecological and evolutionary factors associated with diapause phase. We find that social lifestyle, latitude, and voltinism are significant predictors of the life stage in which diapause occurs. Ancestral state reconstruction revealed that the most recent common ancestor of all bees likely exhibited developmental diapause and shifts to adult or reproductive diapause have occurred in the ancestors of lineages in which social behavior has evolved. These results provide fresh insight regarding the role of diapause as a prerequisite for the evolution of sociality in bees.

evolutionary biology↗

bioRxiv2018

Draft genome assembly and population genetics of an agricultural pollinator, the solitary alkali bee (Halictidae: Nomia melanderi)

Alkali bees (Nomia melanderi) are solitary relatives of the halictine bees, which have become an important model for the evolution of social behavior, but for which few solitary comparisons exist. These ground-nesting bees defend their developing offspring against pathogens and predators, and thus exhibit some of the key traits that preceded insect sociality. Alkali bees are also efficient native pollinators of alfalfa seed, which is a crop of major economic value in the United States. We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. Repetitive content makes up more than one-third of this genome, and previously uncharacterized transposable elements are the most abundant type of repetitive DNA. We predicted 10,847 protein coding genes, and identify 479 of these undergoing positive directional selection with the use of population genetic analysis based on low-coverage whole genome sequencing of 19 individuals. We found evidence of recent population bottlenecks, but no significant evidence of population structure. We also identify 45 genes enriched for protein translation and folding, transcriptional regulation, and triglyceride metabolism evolving slower in alkali bees compared to other halictid bees. These resources will be useful for future studies of bee comparative genomics and pollinator health research.

genomics↗

bioRxiv2018

Investigating the viral ecology of global bee communities with high-throughput metagenomics

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate the impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 5 continents and Oceania. We developed a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences corresponding to (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 29 represented by >0.1 % of the reads in a given sample. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for metagenomics analysis of viruses, and greatly expands our understanding of the diversity of viruses found in bee communities.

genomics↗

bioRxiv2017

Juvenile Hormone, But Not Nutrition Or Social Cues, Affects Reproductive Maturation In Solitary Alkali Bees (Nomia melanderi)

Eusocial insect colonies are defined by extreme variation in reproductive activity among castes, but the ancestral conditions from which this variation arose are unknown. Investigating the factors that contribute to variation in reproductive physiology among solitary insects that are closely related to social species can help to fill this gap. We experimentally tested the role of nutrition, juvenile hormone, and social cues on reproductive maturation in solitary alkali bees (Halictidae: Nomia melanderi). We find that alkali bee females emerge from overwintering with small Dufour's glands and small ovaries, containing oocytes in the early stages of development. Oocyte maturation occurs rapidly, and is staggered between the two ovaries. Lab-reared females reached reproductive maturity without access to mates or nesting opportunities, and many had resorbed oocytes. Initial activation of these reproductive structures does not depend on pollen consumption, though dietary protein or lipids may be necessary for long-term reproductive activity. JH is likely to be a limiting factor in alkali bee reproductive activation, as females treated with JH were more likely to develop mature oocytes and Dufour's glands. Unlike for related social bees, the effects of JH were not suppressed by the presence of older, reproductive females. These results provide important insight into the factors that influence reproductive activity in an important native pollinator, and those that may have been particularly important in the evolution of reproductive castes.

physiology↗