Convergent genomic signatures of local adaptation across a continental-scale environmental gradient

Moreira, Lucas R.; Smith, Brian Tilston

doi:10.1126/sciadv.add0560

Cited by 6 publications

References 92 publications

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Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Sjodin,

Schmidt,

Galbreath

et al. 2024

Sci Rep

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Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37–193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.

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Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Sjodin,

Schmidt,

Galbreath

et al. 2024

Sci Rep

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Repeated global adaptation across plant species

Nocchi,

Whiting,

Yeaman

2024

Proc. Natl. Acad. Sci. U.S.A.

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Global adaptation occurs when all populations of a species undergo selection toward a common optimum. This can occur by a hard selective sweep with the emergence of a new globally advantageous allele that spreads throughout a species’ natural range until reaching fixation. This evolutionary process leaves a temporary trace in the region affected, which is detectable using population genomic methods. While selective sweeps have been identified in many species, there have been few comparative and systematic studies of the genes involved in global adaptation. Building upon recent findings showing repeated genetic basis of local adaptation across independent populations and species, we asked whether certain genes play a more significant role in driving global adaptation across plant species. To address this question, we scanned the genomes of 17 plant species to identify signals of repeated global selective sweeps. Despite the substantial evolutionary distance between the species analyzed, we identified several gene families with strong evidence of repeated positive selection. These gene families tend to be enriched for reduced pleiotropy, consistent with predictions from Fisher’s evolutionary model and the cost of complexity hypothesis. We also found that genes with repeated sweeps exhibit elevated levels of gene duplication. Our findings contrast with recent observations of increased pleiotropy in genes driving local adaptation, consistent with predictions based on the theory of migration-selection balance.

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Integrating Spatial Analyses of Genomic and Physiological Data to Understand Avian Responses to Environmental Change

Benham,

Beckman

2024

Integrative and Comparative Biology

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Projected rates of climate change over the next century are expected to force species to shift ranges, adapt or acclimate to evade extinction. Predicting which of these scenarios may be most likely is a central challenge for conserving biodiversity in the immediate future. Modeling frameworks that take advantage of intraspecific variation across environmental gradients can be particularly important for meeting this challenge. While these space-for-time approaches are essential for climatic and genomic modeling approaches, mechanistic models that incorporate ecological physiology data into assessing species vulnerabilities rarely include intraspecific variation. A major reason for this gap is the general lack of empirical data on intraspecific geographic variation in avian physiological traits. In this review, we outline the evidence for and processes shaping geographic variation in avian traits. We use the example of evaporative water loss to underscore the lack of research on geographic variation even in traits central to cooling costs in birds. We next demonstrate how shifting the focus of avian physiological research to intraspecific variation can facilitate greater integration with emerging genomics approaches. Finally, we outline important next steps for an integrative approach to advance understanding of avian physiological adaptation within species. Addressing the knowledge gaps outlined in this review will contribute to an improved predictive framework that synthesizes environmental, morphological, physiological, and genomic data to assess species specific vulnerabilities to a warming planet.

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Convergent genomic signatures of local adaptation across a continental-scale environmental gradient

Cited by 6 publications

References 92 publications

Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Repeated global adaptation across plant species

Integrating Spatial Analyses of Genomic and Physiological Data to Understand Avian Responses to Environmental Change

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