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1. Gene flow in the anemone Anthopleura elegantissima limits signatures of local adaptation across an extensive geographic range

   https://doi.org/10.1111/mec.15506  

   Cornwell, Brendan H. ( July 2020 , Molecular Ecology)

   Species inhabiting marine environments face a wide range of environmental conditions that vary spatially across several orders of magnitude. The selective pressures that these conditions impose on marine organisms, in combination with potentially high rates of gene flow between distant populations, make it difficult to predict the extent to which these populations can locally adapt. Here, I identify how selection and gene flow influence the population genetic structure of the anemoneAnthopleura elegantissimaalong the Pacific coast of North America. Isolation by distance is the dominant pattern across the range of this species, with a genetic break near Pt. Conception, CA. Furthermore, demographic modelling suggests that this species was historically confined to southerly latitudes before expanding northward. Outlier analyses identify 24 loci under selection (out of ~1,100), but the same analysis on simulated genetic data generated using the most likely demographic model erroneously identified the same number of loci under selection, if not more. Taken together, these results suggest that demographic processes are the dominant force shaping population genetic patterns inA. elegantissimaalong the Pacific coast of North America. I discuss these patterns in terms of the evolutionary history ofA. elegantissima, the potential for local adaptation, and their consequences with respect to interactions with the endosymbiontBreviolum muscatineiacross their geographic range.

    

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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)

   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. The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard ( Phrynosoma platyrhinos )

   https://doi.org/10.1111/mec.16070  

   Farleigh, Keaka ; Vladimirova, Sarah A. ; Blair, Christopher ; Bracken, Jason T. ; Koochekian, Nazila ; Schield, Drew R. ; Card, Daren C. ; Finger, Nicholas ; Henault, Jonathan ; Leaché, Adam D. ; et al ( July 2021 , Molecular Ecology)

   Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large‐scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post‐glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.

    

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4. Landscape genomics of Quercus lobata reveals genes involved in local climate adaptation at multiple spatial scales

   https://doi.org/10.1111/mec.15731  

   Gugger, Paul F. ; Fitz‐Gibbon, Sorel T. ; Albarrán‐Lara, Ana ; Wright, Jessica W. ; Sork, Victoria L. ( December 2020 , Molecular Ecology)

   Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and rangewide sampling to (a) identify genetic variation underlying local adaptation to environmental gradients in the California endemic oak,Quercus lobata; (b) examine whether putatively adaptive SNPs show signatures of selection at multiple spatial scales; and (c) map putatively adaptive variation to assess the scale and pattern of local adaptation. Of over 10 k single‐nucleotide polymorphisms (SNPs) generated with genotyping‐by‐sequencing, we found signatures of natural selection by climate or local environment at over 600 SNPs (536 loci), some at multiple spatial scales across multiple analyses. Candidate SNPs identified with gene–environment tests (LFMM) at the rangewide scale also showed elevated associations with climate variables compared to the background at both rangewide and elevational transect scales with gradient forest analysis. Some loci overlap with those detected in other oak species, raising the question of whether the same loci might be involved in local climate adaptation in different congeneric species that inhabit different geographic contexts. Mapping landscape patterns of adaptive versus background genetic variation identified regions of marked local adaptation and suggests nonlinear association of candidate SNPs and environmental variables. Taken together, our results offer robust evidence for novel candidate genes for local climate adaptation at multiple spatial scales.

    

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5. Genetic trade‐offs underlie divergent life history strategies for local adaptation in white clover

   https://doi.org/10.1111/mec.16180  

   Wright, Sara J. ; Goad, David M. ; Gross, Briana L. ; Muñoz, Patricio R. ; Olsen, Kenneth M. ( October 2021 , Molecular Ecology)

   Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defence polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately‐outcrossing herbaceous legume, white clover (Trifolium repens). This widespread species displays a well‐studied chemical defence polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate‐associated cyanogenesis clines throughout its range. Two biparental F₂ mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade‐offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade‐offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL×E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL colocalization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favoured early investment in flowering at the cost of multiyear survival in the southernmost site versus delayed flowering and multiyear persistence in the northern environments. Our findings demonstrate that multilocus genetic trade‐offs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.

    

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