How biotic and abiotic selective pressures shape adaptive genomic variation is revealed and a framework for forecasting evolutionary responses to future global change is provided.
Abstract
Predicting whether populations can persist under rapid environmental change requires identifying the ecological drivers of local adaptation, uncovering their genetic bases, and understanding how adaptive variation will respond to future selection. Here, we combine landscape genomics, environmental data, and evolutionary simulations to identify the selective forces shaping adaptation across 1,500 km of the west coast of North America in the low-dispersing coastal dogwhelk Nucella canaliculata, determine their genomic bases, and forecast future evolutionary responses. We found strong associations of genome-wide variation with both abiotic (i.e., mean pH) and biotic variation (i.e., cross-sectional shell thickness of the mussel prey species, Mytilus californianus). These patterns are underlain by two large-effect loci, including a biomineralization gene associated with pH tolerance and a locus near a thiamine transporter associated with prey shell thickness. Genomic offset analyses and population genetic simulations further predict that ongoing ocean acidification will disrupt existing adaptive patterns and generate maladaptation in high latitude populations, with evolutionary outcomes strongly influenced by gene flow, which determines the rate at which adaptive alleles spread across the species range. Together, these findings reveal how biotic and abiotic selective pressures shape adaptive genomic variation and provide a framework for forecasting evolutionary responses to future global change.
Understanding how plants adapt to elevational niches is essential for uncovering mechanisms of natural selection and diversity patterns in mountain systems. Integrating genomic and ecological approaches is therefore important for advancing our knowledge of plant adaptation and informing conservation under climate change. In this study, we investigate 15 populations of an alpine shrub Rhododendron intricatum in the Mt. Gongga region of the eastern Hengduan Mountains, focusing on genomic and phenotypic responses across elevations. Genotype-environment association analyses identified multiple outlier genomic regions associated with elevation, consistent with polygenic responses to environmental gradients, and candidate genes were broadly linked to functions such as signalling, stress responses, metabolism and reproductive regulation. Distinct allele turnover patterns along precipitation seasonality and mean annual temperature further indicate the combined effects of climatic heterogeneity in shaping genomic responses. Concurrently, systematic trends were detected in phenotypic traits along elevation, including increased leaf spectral reflectance, shifts in vegetative dimensions and changes in floral morphology. Predictive models under future climate scenarios reveal increasing genetic offset through time, and projected mismatch becomes uniformly severe across the entire elevational gradient by the end of the century. Together, multiple lines of evidence reveal coordinated genomic and phenotypic responses to shared environmental gradients. Our findings demonstrate generalized ecological strategies in mountain systems and highlight the extreme vulnerability of alpine endemics to ongoing climate change.
Qin Li, Kai-Ning Hu, Ji Wang et al.· Molecular Ecology· 0 citations
Saline habitats, which include both coastal and inland, host specialised halophytic communities that can withstand high salinity. Coastal communities are shaped by tidal inundation and marine connectivity, whereas inland saline habitats are driven by evaporation, groundwater salinisation, and greater landscape isolation. These contrasting hydrological and environmental variables likely drive divergent patterns of genetic diversity, influencing local adaptation, connectivity, and evolutionary divergence, which is important for understanding species persistence and guiding conservation of saline ecosystems under environmental change. This systematic review brings together phylogeographic studies on halophytic species from both environments to uncover global drivers of genetic difference. A systematic search of Web of Science, Scopus, and PubMed was done, and 20 studies were identified focusing on key genera including Salicornia, Sarcocornia, Suaeda, and Triglochin. Distinct genetic clades were often associated with habitat type or geographic region, indicating repeated divergence linked to coastal–inland environmental gradients. Genetic differentiation between coastal and inland halophyte populations is primarily driven by habitat fragmentation, restricted gene flow, historical refugia and recolonisation, salinity-mediated adaptation, and differences in dispersal capacity. As a result, coastal populations are generally more genetically connected, whereas inland populations tend to be more isolated, structured, and evolutionarily divergent. The data also showed a strong regional bias; while research is well established in Europe, Asia, and North America, African inland saline ecosystems are critically understudied. We conclude that habitat connectivity and dispersal pathways are the primary determinants of halophyte genetic structure. Future research must integrate ecological niche modelling and landscape genetics to resolve the evolutionary dynamics of these taxa, particularly in under-sampled regions such as southern Africa, to support effective conservation of saline biodiversity. However, the synthesis is constrained by the small number of eligible studies (n = 23) and their uneven geographic distribution, with limited representation from Africa, South America, and Australia, which restricts the ability to draw fully global conclusions. Recognising and protecting these systems is essential for safeguarding global saline biodiversity.
Nomcebo T. Mngomezulu, D. Veldkornet· Coasts· 0 citations
Climate change is increasing drought and heat stress in European forests, raising concerns about the capacity of long-lived tree species to respond to rapidly changing environmental conditions. While local adaptation has been documented in many forest trees, it remains unclear whether newly established seedlings, which form the forests of the future, are able to persist and adapt to these new climatic conditions. Here, we investigated genomic differences between naturally regenerated seedlings and trees of European beech (Fagus sylvatica) across the three regions of the German Biodiversity Exploratories using low-coverage whole-genome sequencing (∼5x) of 1,032 individuals. Population structure was primarily driven by geographic region, whereas genetic diversity was similar across life stages. Despite this genome-wide similarity, we detected allele frequency shifts between trees and seedlings, concentrated in narrow genomic windows. These shifts were strongest in surviving seedlings, suggesting that environmental filtering during early establishment may contribute to shaping the genetic composition of regenerating populations. The strongest signals were observed within the Swabian Alb, where sampled seedlings were 2-years old and had experienced a longer period of potential filtering prior to sampling. Genotype–environment association analyses identified loci associated with climatic variables, and subsequent GO enrichment analyses of genes linked to these loci revealed significantly more enriched GO terms in seedlings than in trees, suggesting stronger environmental filtering by the current climate in seedlings. In particular, we found associations with maximum air temperature, relative humidity, soil moisture, and precipitation, affecting genes involved in stress responses, growth, metabolism, and developmental processes. Together, our results demonstrate that young cohorts of European beech differ genetically from trees and reveal genomic patterns consistent with life-stage-dependent environmental filtering. These findings suggest that the genetic composition of early life-stages is already altered by current environmental conditions, possibly contributing to adaptation to new climatic conditions.
Marieke Lenga, L. Opgenoorth, K. Heer et al.· bioRxiv· 0 citations
Findings show that ecological niche tracking and polygenic adaptation allow agricultural weeds like blackgrass to persist under rapid environmental change, offering insights relevant not only for weed management but also for designing resilient cropping systems under future climates.
Célia Neto, Quan-Jing Zheng, Paul Neve· bioRxiv· 0 citations
Clear genomic differentiation among regions and populations is suggested, as well as an uneven spatial distribution of adaptive alleles associated with drought and heat stress, together suggesting different degrees of local adaptation to climate across the landscape.
Francisco J. Velásquez-Puentes, W. Durka, Colin E. Hughes et al.· Evolutionary Applications· 1 citation
Understanding adaptation to environmental variation is fundamental to climate-resilient agriculture. Here, we analyzed a georeferenced collection of 167 Dioscorea accessions spanning a wide range of bioclimatic and biophysical variation, from dry sahelian environment to rainforest environment. Genome-wide association analyses revealed that the genetic architecture of environmental adaptation is largely driven by large-effect loci, although precipitation-related traits were associated with many small-effect loci. This mixed architecture could lead to multiple breeding strategies, including marker-assisted backcrossing and the targeted use of wild and semi-wild relatives. We identified a core collection of accessions that captures much of the genetic and environmental diversity, and highlighted accessions as potential parents for abiotic stress tolerance. Projections under future climate scenarios using genomic offset identified regions and accessions at elevated risk of maladaptation, as well as others with broad adaptive potentiality. Maximizing the use of available material may facilitate the development of climate-resilient cultivars. Plain Language Summary Yam is an ancient staple crop grown across the tropics, but there is still much room for plant breeders to understand how yam species adapt to their environments. We studied 167 wild and cultivated yam samples from West Africa, spanning dry Sahelian conditions to rainforest, exploring the relationship of these samples’ local climate and soil data. Adaptation appears shaped mainly by a handful of strong-effect genes, plus many small-effect genes tied to rainfall. We identified a smaller “core” set of samples capturing most of the genetic and environmental diversity, and flagged accessions especially promising as parents for breeding stress-tolerant yam. We also predicted which populations face the greatest risk under future climate change. Together, these findings give breeders practical tools for developing climate-resilient yam varieties from existing genebank collections.
B. Adhikari, R. Akakpo, Anna Halpin-McCormick et al.· bioRxiv· 0 citations
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