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1. Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

   https://doi.org/10.1038/s41598-023-41896-7  

   Rahman, Sarthok Rasique; Lozier, Jeffrey D. (September 2023, Scientific Reports)

   Abstract Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble beeBombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wildBombussuggests that the function of methylation in niche adaptation would be worth further investigation. 

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2. Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

   https://doi.org/10.1111/mec.17125  

   Heraghty, Sam D.; Jackson, Jason M.; Lozier, Jeffrey D. (September 2023, Molecular Ecology)

   Abstract Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation inBombus vosnesenskii, a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find thatB. vosnesenskiiexhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicateB. vosnesenskiiis an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change. 

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3. Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis

   https://doi.org/10.1093/hr/uhab059  

   Hu, Yuxi; Feng, Chao; Yang, Lihua; Edger, Patrick P; Kang, Ming (January 2022, Horticulture Research)

   Abstract The crop wild relative Fragaria nilgerrensis is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve as a useful guide in the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibiting the highest genetic diversity. Redundancy analysis suggested that both environment and geographic variables shaped a significant proportion of the genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, which present a unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweep scans and genome–environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis. 

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4. Local adaptation across a complex bioclimatic landscape in two montane bumble bee species

   https://doi.org/10.1111/mec.15376  

   Jackson, Jason M.; Pimsler, Meaghan L.; Oyen, Kennan J.; Strange, James P.; Dillon, Michael E.; Lozier, Jeffrey D. (February 2020, Molecular Ecology)

   Abstract Understanding evolutionary responses to variation in temperature and precipitation across species ranges is of fundamental interest given ongoing climate change. The importance of temperature and precipitation for multiple aspects of bumble bee (Bombus) biology, combined with large geographic ranges that expose populations to diverse environmental pressures, make these insects well‐suited for studying local adaptation. Here, we analyzed genome‐wide sequence data from two widespread bumble bees,Bombus vosnesenskiiandBombus vancouverensis, using multiple environmental association analysis methods to investigate climate adaptation across latitude and altitude. The strongest signatures of selection were observed inB. vancouverensis, but despite unique responses between species for most loci, we detected several shared responses. Genes relating to neural and neuromuscular function and ion transport were especially evident with respect to temperature variables, while genes relating to cuticle formation, tracheal and respiratory system development, and homeostasis were associated with precipitation variables. Our data thus suggest that adaptive responses for tolerating abiotic variation are likely to be complex, but that several parallels among species can emerge even for these complex traits and landscapes. Results provide the framework for future work into mechanisms of thermal and desiccation tolerance in bumble bees and a set of genomic targets that might be monitored for future conservation efforts. 

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5. Pervasive Genomic Signatures of Local Adaptation to Altitude Across Highland Specialist Andean Hummingbird Populations

   https://doi.org/10.1093/jhered/esab008  

   Lim, Marisa C; Bi, Ke; Witt, Christopher C; Graham, Catherine H; Dávalos, Liliana M (February 2021, Journal of Heredity)

   Chapman, Mark (Ed.)

   Abstract Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow, and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether the selection is strong enough to influence functional differentiation of subpopulations differing by a few hundred meters in elevation. We used targeted capture of 12 501 exons from across the genome, including 271 genes previously implicated in altitude adaptation, to test for adaptation to local elevations for 2 highland hummingbird species, Coeligena violifer (n = 62) and Colibri coruscans (n = 101). For each species, we described population genetic structure across the complex geography of the Peruvian Andes and, while accounting for this structure, we tested whether elevational allele frequency clines in single nucleotide polymorphisms (SNPs) showed evidence for local adaptation to elevation. Although the 2 species exhibited contrasting population genetic structures, we found signatures of clinal genetic variation with shifts in elevation in both. The genes with SNP-elevation associations included candidate genes previously discovered for high-elevation adaptation as well as others not previously identified, with cellular functions related to hypoxia response, energy metabolism, and immune function, among others. Despite the homogenizing effects of gene flow and genetic drift, natural selection on parts of the genome evidently optimizes elevation-specific cellular function even within elevation range-restricted montane populations. Consequently, our results suggest local adaptation occurring in narrow elevation bands in tropical mountains, such as the Andes, may effectively make them “taller” biogeographic barriers. 

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