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Abstract Bumble bees (Bombus) exhibit exceptional diversity in setal body color patterns, largely as a result of convergence onto multiple Mullerian mimicry patterns globally. When multiple species cross the same sets of mimicry complexes, they can acquire the same color polymorphisms, providing replicates of phenotypic evolution. This study examines the genetic basis of parallel color pattern acquisition in three bumble bee taxon pairs in western North America that shift between orange-red and black mid-abdominal segmental coloration in Rocky Mountain and Pacific Coastal mimicry regions: polymorphic Bombus vancouverensis and B. melanopygus, and sister species B. huntii and B. vosnesenskii. Initial gene targets are identified using a genome-wide association study, while cross-developmental transcriptomics reveals genetic pathways leading to final pigmentation genes. The data show all three lineages independently target the regulatory region of a segmental-fate determining Hox gene, Abdominal B (Abd-B), for this color transition. For B. vancouverensis and B. melanopygus, this involves different deletions in the same location, and all mimicry pairs differentially express Abd-B and ncRNAs in this locus. Transcriptomics reveals a shared core gene network across species, where Abd-B interacts with nubbin and pigment enzyme ebony to decrease black melanin production in favor of paler, redder morphs. Expression of multiple genes in the melanin biosynthesis pathway is modified to promote this phenotype, with differing roles by taxon. Replicated morphologies unveil key genes and a Hox gene hotspot, while enabling evolutionary tracking of genetic changes to phenotypic changes and informing how gene regulatory networks evolve. 

Abstract The gut microbiome is influenced by host species and the environment, but how the environment influences the microbiome of animals introduced into a new ecosystem has rarely been investigated. Freshwater mussels are aquatic fauna, with some threatened or endangered species propagated in hatcheries and introduced into natural systems as part of conservation efforts. The effects of the environment on the freshwater mussel gut microbiome were assessed for two hatchery-propagated species (Lampsilis ovata, Lampsilis ornata) introduced into rivers within their natural range. Mussels were placed in rivers for 8 weeks, after which one subset was collected, another subset remained in that river, and a third subset was reciprocally transplanted to another river in the same river basin for a further 8 weeks. Gut microbiome composition and diversity were characterized for all mussels. After the initial 8 weeks, mussels showed increased gut bacterial species richness and distinct community composition compared to hatchery mussels, but gut microbiome diversity then decreased for mussels that remained in the same river for all 16 weeks. The gut bacterial community of mussels transplanted between rivers shifted to resemble that of mussels placed initially into the recipient river and that remained there for the whole study. All mussels showed high proportions of Firmicutes in their gut microbiome after 8 weeks, suggesting an essential role of this phylum in the gut of Lampsilis species. These findings show that the mussel gut microbiome shifts in response to new environments and provide insights into conservation strategies that involve species reintroductions. 

Abstract Understanding the myriad avenues through which spatial and environmental factors shape evolution is a major focus in biological research. From a molecular perspective, much work has been focused on genomic sequence variation; however, recently there has been increased interest in how epigenetic variation may be shaped by different variables across the landscape. DNA methylation has been of particular interest given that it is dynamic and can alter gene expression, potentially offering a path for a rapid response to environmental change. We utilized whole genome enzymatic methyl sequencing to evaluate the distribution of CpG methylation across the genome and to analyze patterns of spatial and environmental association in the methylomes of two broadly distributed montane bumble bees (Bombus vancouverensis Cresson and Bombus vosnesenskii Radoszkowski) across elevational gradients in the western US. Methylation patterns in both species are similar at the genomic scale with ∼1% of CpGs being methylated and most methylation being found in exons. At the landscape scale, neither species exhibited strong spatial or population structuring in patterns of methylation, although some weak relationships between methylation and distance or environmental variables were detected. Differential methylation analysis suggests a stronger environment association in B. vancouverensis given the larger number of differentially methylated CpG's compared to B. vosnesenskii. We also observed only a handful of genes with both differentially methylated CpGs and previously detected environmentally associated outlier SNPs. Overall results reveal a weak but present pattern in variation in methylation over the landscape in both species. 

Abstract Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-rearedBombus vosnesenskiiworkers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species’ range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CT_MIN) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CT_MAX) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees.