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At least 19 recordsLinked to original sources
PubMed2025

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

Quercus↗
PubMed2025

Genome sequencing and population genetics provide insights into local adaptation of Opisthopappus species on cliff environments of Taihang Mountains.

Local adaptation represents a pivotal theme in evolutionary biology. The Opisthopappus genus, comprising Opisthopappus longilobus and O. taihangensis, thrives on the cliffs of the Taihang Mountains. During their evolutionary history, two species are hypothesized to have locally adapted to their cliff habitats. In the present study, we employed a combined approach of whole-genome sequencing of O. taihangensis and population genomic analysis from both species to gain deeper insights into their patterns of local adaptation. Our results revealed that the expansive genome of O. taihangensis (3010.18 Mb), a consequence of a whole-genome duplication (WGD) event, coupled with a high proportion of repetitive sequences (82.70%), was postulated as one of its adaptive strategies. A clear differentiation between O. taihangensis and O. longilobus was observed, with the two species diverging approximately 17.57 million years ago (Mya), with O. longilobus serving as the ancestor. Since their divergence, limited gene flow was observed between the two species. Post-divergence, the effective population sizes of both species expanded, yet underwent a dramatic reduction at approximately 0.07 Mya. Furthermore, a total of 798 adaptive genes were identified, of which 207 overlapped with expanded genes, and eight genes were found to be under positive selection. These genes primarily regulated the growth and development of both species via pathways such as oxidation-reduction and ubiquitin-proteasome, enabling them to withstand climate changes. These findings provide profound insights into the local adaptation of Opisthopappus species to the cliff environments and offer valuable clues for further exploring the local adaptation among various cliff-dwelling organisms.

Adaptation, Physiological↗
PubMed2026

Haplotype Blocks Are Associated With Rapid Local Adaptation to Environmental Shifts in Wild Barley.

Genomic mechanisms of local adaptation must be highly responsive in geographic regions where climate is changing rapidly. The Levant region is a critical biodiversity hotspot and the distribution edge for many species, including the wild ancestor of domesticated barley. This region is under an accelerated desertification process, thus enforcing a rapid genomic response to the projected environmental changes. To elucidate the genomic basis of rapid local adaptation, we studied wild barley populations using an ecological-genetic sampling design that decouples environmental variation from demographic background. We collected and sequenced 300 wild barley individuals and evaluated the phenotypes of 3600 progeny plants over 3 years. Our genomic analyses revealed that local adaptation is associated with clusters of candidate genes forming haplotype blocks. These clusters are enriched with environment and stress responsive genes, including flowering time regulators, drought and heat responsive genes. We identified six candidate adaptive haplotype blocks which span 1-8 Mbp and are distributed across chromosomes 1H, 2H, 4H and 5H, each segregating as two major haplotypes. Additionally, we integrated over 2600 occurrence records into ecological and evolutionary modelling to assess the genomic vulnerability of populations to projected future climates. Our study identifies candidate genomic regions and environmental drivers of local adaptation in wild barley and highlights the advantage of haplotype blocks architecture in orchestrating an efficient response to rapid environmental change. We highlight the ecological factors most strongly associated with the observed evolutionary responses and provide insights and guidelines for biodiversity conservation and implementation of crop wild relatives in breeding.

Hordeum↗
PubMed1975

Local adaptation in the ventral photoreceptors of Limulus.

Local adaptation was demonstrated in the ventral photoreceptors of Lumulus using either flashes or continuous illumination. Spots of light locally desensitized the region of the photoreceptor on which they were focused. In dark-adapted photoreceptors where "quantum bumps" were clearly discernible, local adaptation of the quantum bumps was observed. Local adaptation could induce differences of threshold of 1 decade over distances of 50-80 mum. With continuous local illumination these gradients could be maintained from 2 s to 30 min. In addition, the decrease in time scale associated with light adaptation was also found to be localized to the region of illumination.

Adaptation, Ocular↗
PubMed2026

No evidence of fine-scale local adaptation of winter moths to variable tree phenology.

Spatial variation in plant phenology can impose strong selective pressures on herbivorous insects whose fitness relies on synchrony with host plants, promoting local adaptation to host timing. Winter moths (Operophtera brumata) have been shown to synchronize egg hatching with host budburst, but whether this reflects local adaptation remains unclear. We used three complementary approaches to assess small-scale local adaptation of winter moths to oak phenology in Wytham Woods, UK, a 385-hectare woodland with repeatable variation in individual oak budburst phenology. We experimentally investigated whether host tree phenology predicts hatch timing using common gardens across multiple temperatures, evaluated fitness benefits of synchrony using translocations, and assessed population structure and gene-environment associations using whole-genome sequencing. We found no support for local adaptation to individual trees. Common garden experiments revealed systematic differences in hatch timing which were unrelated to host budburst, while translocations indicated no fitness consequences of asynchrony. Genetic analyses showed no detectable population structure or association with budburst timing. Local adaptation to host phenology therefore appears not to arise on individual trees but may instead occur at broader spatial scales. Understanding the scale of local adaptation is essential for predicting how insect-plant synchrony will respond to environmental change across heterogeneous landscapes.

Animals↗
PubMed2025

Genetic Differentiation is Constrained to Chromosomal Inversions and Putative Centromeres in Locally Adapted Populations With Higher Gene Flow.

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside-a nonmodel fish with extensive local adaptation across a steep latitudinal gradient-as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.

Gene Flow↗
PubMed2025

Genomic insights into the demographic history and local adaptation of wild boars across Eurasia.

Wild boars exhibit genetic and phenotypic diversity shaped by migrations and local adaptations. Their expansion across Eurasia, especially in Central Asia, remains underexplored. Here, we present newly sequenced whole-genome data of 47 wild boars from Eastern Asia, Central Asia, and Europe, combined with 49 existing genomes, creating a comprehensive dataset of 96 individuals. Our analyses show that Asian wild boars and Southeast Asian Suids split ∼3.6 million years ago (mya), with Central Asian and Southern Chinese ancestors diverging ∼1.8 mya. The split between Central Asian and European-Near East ancestors occurred ∼0.9 mya, followed by a European-Near East divergence ∼0.6 mya. We identify signatures of local adaptation in Central Asian populations, including two positively selected variants in LPIN1, associated with lipid metabolism, and a missense mutation in ALPK2, linked to meat traits. These findings provide insights into wild boar dispersal and adaptation and shed light on domestic pig breeding.

Animals↗
PubMed2026

Pathogen local adaptation shapes Pierce's disease of grapevines outcomes under field conditions.

Climate change is broadly expected to increase the range of many plant diseases, yet the current status of local thermal adaptation in many pathogens is poorly understood. Xylella fastidiosa (Xf) is a global bacterial plant pathogen that causes Pierce's disease (PD) of grapevines and infects over 700 other host plant species, impacting both agricultural and natural ecosystems. In a common garden experiment with 477 vines in the field, we compared PD outcomes from a local (colder climate in CA) vs non-local (warmer climate in CA) bacterial strain in 13 Mediterranean grapevine varieties over 3 years. Relative to the local strain, there was 77% lower overwinter survival in the non-local strain from a warmer climate, strongly indicating local adaptation in these CA Xf populations. Host genotype also had a significant effect on pathogen winter survival, and grapevine varieties differed in PD susceptibility. Additionally, we assessed in planta evolution of the two pathogen strains over 3 years by whole-genome sequencing 58 field-derived isolates. There were convergent loss-of-function mutations in genes encoding minor Type IV pilin (T4P) proteins, which control twitching motility and other virulence phenotypes, suggesting rapid adaptive evolution. Our results suggest local adaptation to cold temperatures in a bacterial plant pathogen and a possible role for minor Type IV pilins in thermal adaptation. These findings demonstrate the urgent need to incorporate X. fastidiosa evolution and local thermal adaptation into global models of PD spread. Differentiating pathotypes with distinct thermal adaptations will improve disease forecasting and inform quarantine decisions.IMPORTANCEForecasting the movement of plant pathogens is a critical issue under global warming to effectively manage future plant disease outbreaks. Yet, current plant pathogen local thermal adaptation is often unaccounted for, especially in bacterial pathogens. Our study examines local adaptation to temperature in a bacterial plant pathogen, Xylella fastidiosa, that causes disease in grapevines in addition to infecting 700 other plant species. In a large-scale field experiment across 13 grapevine varieties, we demonstrate local adaptation in pathogen winter survival in distinct Xylella fastidiosa strains. Additionally, we found evidence of adaptive evolution in just 3 years, as we observed convergent mutations after resequencing strains that evolved in the field. Our results suggest that X. fastidiosa populations-even within a small geographic area-have distinct adaptations to winter temperatures and may exhibit differential responses to warming winters.

Type IV pili↗
PubMed2026

Genomic insights into local adaptation of indigenous chickens.

Indigenous chickens are an essential part of biodiversity and a vital protein resource to humans, yet global warming and environmental changes pose serious threats to their survival and productivity. Therefore, assessing population adaptive capacity under shifting environments is crucial for breeding resilient animals, and guiding conservation strategies. Here, we integrated ecological and whole-genome resequencing data from 1 022 chickens from 44 Chinese indigenous populations to reveal genomic signatures of local adaptation. From 87 agroclimatic variables, we identified eight dominant environmental factors including solar radiation, precipitation, diurnal temperature range, and five landcover variables (cropland areas, water areas, trees coverage, bare ground and shrubs coverage) that shape ecological niches of indigenous chickens. Landscape and comparative genomics analyses revealed both known and novel candidate genes, such as UNC80, PTPRO, NCOR2, CSF2RB, NXT2 and PALLD for the solar radiation, precipitation, diurnal temperature range, cropland areas, trees coverage and bare ground, respectively. Particularly, adaptive non-coding variants harbored in these genes exhibited spatial allelic changes across populations and acted as regulatory elements via chromatin accessibility and DNA methylation, influencing adaptation in a tissue-specific manner. Our findings underscore the rich genetic diversity of Chinese indigenous chickens and provide new insights into genomic mechanisms of local adaptation, offering valuable references for domestic animal breeding, conservation, and climate resilience.

Animals↗
PubMed2026

Comparisons Between Large-Scale Genomic Variants and SNPs in Driving Population Divergence and Local Adaptation.

Genomic variations, such as indels (2-49 bp) and structural variants (SVs, ≥50 bp), are larger-scale mutations than single nucleotide polymorphisms (SNPs) and can substantially impact evolutionary processes, including speciation, adaptation, and phenotypes. Despite their functional importance, integrative population genetic analyses that jointly consider genome-wide SNPs, indels, and SVs remain under-explored. The ground tit (Pseudopodoces humilis), an endemic species to the Qinghai-Tibet Plateau (QTP), exhibits divergence across distinct glacial refugia, accompanied by habitat and morphological divergence, making it an excellent example for investigating how different types of genomic variants contribute to population divergence and local adaptation. Here, by retrieving 81 whole-genome sequence data, over 13 million SNPs, 2 million indels, and 22,101 SVs were identified. Variants were unevenly distributed across the genome, characterized by distinct hotspot regions. Indels and SVs revealed four genetic clusters consistent with previous SNP-based results, thereby validating the reliability of our variant datasets. FST and genotype-environment association (GEA) analyses independently revealed numerous candidate indels and SVs; each showed minimal overlap with previously identified SNPs, and were enriched in similar functional pathways such as signal transduction, skeletal muscle development, water transport, DNA repair, reproduction, nervous system development, and immunity. Collectively, our results demonstrated that indels and SVs could capture additional signatures besides SNPs. Furthermore, similar but distinct gene functions among different types of genomic variants collectively and complementarily drive genomic divergence across environmental gradients in such a high-elevation endemic species, underscoring its evolutionary relevance in local adaptation.

indels↗
PubMed2025

Heat-Induced Secondary Dormancy Contributes to Local Adaptation in Arabidopsis thaliana.

Seeds should not germinate in conditions unsuitable for seedling growth. Dormancy, which allows seeds to remain inactive in an environment that would otherwise enable germination, helps optimise the timing of germination. Primary dormancy, developed during seed maturation on the parent plant, prevents immediate germination post-dispersal, regardless of external conditions. Secondary dormancy, however, is triggered post-dispersal when seeds face unfavourable conditions, enabling them to re-enter dormancy even if initially non-dormant. This mechanism allows seeds to fine-tune germination according to environmental conditions. In this study, we examined the role of heat-induced secondary dormancy in local adaptation by analysing natural variations within 361 Arabidopsis thaliana accessions from across Europe. We discovered that secondary dormancy acquisition varies with primary dormancy levels and after-ripening. Both primary and heat-induced secondary dormancy exhibited adaptive clines along temperature and precipitation gradients, with secondary dormancy showing a steeper cline, indicating its significant role in local adaptation. Using species distribution models, we predicted that genotypes with high secondary dormancy would show greater resilience to future climate changes. Additionally, we identified specific genomic regions controlling secondary dormancy levels including a novel candidate gene for secondary dormancy variation. Our findings show that secondary dormancy is a complex adaptive mechanism and a predominant contributor to the dormancy trait syndrome that favours plant survival in habitats exposed to harsh summers.

Arabidopsis↗
PubMed2015

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

We present the first genome-wide study of recent evolution in Culex pipiens species complex focusing on the genomic extent, functional targets and likely causes of global and local adaptations. We resequenced pooled samples of six populations of C. pipiens and two populations of the outgroup Culex torrentium. We used principal component analysis to systematically study differential natural selection across populations and developed a phylogenetic scanning method to analyse admixture without haplotype data. We found evidence for the prominent role of geographical distribution in shaping population structure and specifying patterns of genomic selection. Multiple adaptive events, involving genes implicated with autogeny, diapause and insecticide resistance were limited to specific populations. We estimate that about 5-20% of the genes (including several histone genes) and almost half of the annotated pathways were undergoing selective sweeps in each population. The high occurrence of sweeps in non-genic regions and in chromatin remodelling genes indicated the adaptive importance of gene expression changes. We hypothesize that global adaptive processes in the C. pipiens complex are potentially associated with South to North range expansion, requiring adjustments in chromatin conformation. Strong local signature of adaptation and emergence of hybrid bridge vectors necessitate genomic assessment of populations before specifying control agents.

Adaptation, Biological↗
PubMed2025

Genome sequencing and population genomics provide insights into the demographic history, genetic load, and local adaptation of an endangered Tertiary relict.

Endangered Tertiary relict trees represent an exceptional evolutionary heritage with small and isolated populations, yet little is known about how demographic history, local adaptation, and genetic load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Ulmus elongata L. K. Fu & C. S. Ding, an endangered Tertiary relict tree endemic to East Asia. By integrating genomes from U. elongata and seven other endangered trees from public databases, we identified rate-decelerated genes across endangered trees and genes under positive selection of U. elongata associated with tissue development, detoxification, and immune response, and signal transduction and regulation mechanisms potentially leading to endangered status. Demographic analyses revealed continuous population decline from the late Miocene to present, especially during the last glacial maximum (LGM) and last 10&#x2009;000&#x2009;years. Spearman correlation indicated a strong negative relationship between effective population size and human population density (rpopulation density&#x2009;=&#x2009;-0.90, P&#x2009;<&#x2009;0.001) as well as cropland use (rcropland use&#x2009;=&#x2009;-0.89, P&#x2009;<&#x2009;0.001). Genotype-environment association (GEA) analyses identified a set of candidate genes associated with temperature and precipitation, supporting a polygenic adaptation model in U. elongata. Overall, our findings underscore the severe population bottlenecks that have led to the fixation of strongly deleterious mutations and inbreeding, further compromising the adaptive potential and long-term viability of U. elongata. Furthermore, assessments of genomic vulnerability under future climate scenarios revealed higher genetic offsets in northern region of Fujian and Jiangxi populations, suggesting these regions require prioritized conservation efforts due to reduced adaptive capacity.

Endangered Species↗
PubMed2025

Genomic Insights Into Local Adaptation Across Heterogeneous Understory Habitats and Climate Change Vulnerability.

Understanding adaptive evolution and survival risks in understory herbs is crucial for the effective conservation of biodiversity. How environmental gradients shape species local adaptation patterns is not well understood, nor is how populations of understory herbs respond to a changing climate. In this study, we conducted population genomic analyses of Adenocaulon himalaicum (Asteraceae) with a pan-East Asian distribution, representing a good model for dominant understory herbs to elucidate adaptation mechanisms in heterogeneous forest ecosystems. Based on 34,398 putatively neutral single nucleotide polymorphisms (SNPs) across 27 populations, we identified three genetic lineages accompanied by high levels of genetic differentiation between populations. Our isolation by environment results (IBE) indicated a significant effect of environmental gradients on genomic variation of A. himalaicum (r&#x2009;=&#x2009;0.18, p&#x2009;=&#x2009;0.03). To decompose the relative contributions of climate, geography and population structure in explaining genetic variance, our partial RDA found that the prominent contribution of environmental effects (climatic and soil variables) explained 29% and 36% of the neutral and adaptive genetic variation, respectively. Using two genotype-environment association (GEA) methods, we identified 13 SNPs as candidates for core climate-related adaptation loci, with two of these loci further validated by qRT-PCR experiments. Projections of spatiotemporal genomic vulnerability under different future climate scenarios revealed that populations in the southeastern edge of the Himalayas, near the Sichuan Basin, the southernmost region of Northeast China and the northern Korean Peninsula, as well as northern Japan, were identified as the most vulnerable and should be prioritised for conservation. Therefore, our current study provides the genomic foundations for conservation and management strategies to elucidate how these understory herbs cope with future climate changes.

Climate Change↗
PubMed1973

Phototropism and local adaptation in Phycomyces sporangiophores.

Phototropic responses to unilateral ultraviolet stimuli were studied to determine whether the response of one side of the cell is affected by the previous exposure of the opposite side to ultraviolet. It has been found that the direction of bending is not parallel to the stimulus direction, but is along a straight line rotated 17 degrees clockwise from the stimulus direction. This deviation indicates that the photoreceptors may be in a state of continual clockwise rotation. If before the stimulus the cell is exposed briefly to ultraviolet and rotated through 90 degrees , the response is not along the 17 degrees line, but is deviated a greater or lesser amount, depending on whether the 90 degrees rotation is clockwise or counterclockwise. This difference is evidence that the first ultraviolet exposure leaves a persistent patch of light-adapted receptors and the shaded part of the cell remains dark adapted. The phototropic stimulus straddles the edge between light- and dark-adapted regions, and the differing responses of the two regions affects the direction of phototropic bending. A phototropic mechanism is proposed which combines the features of local adaptation and photoreceptor rotation.

Dark Adaptation↗
PubMed1976

[Local adaptation curves evoked by the pupillo-motor reflex].

We have studied local dark-adaptation curves using the pupillary reflex. The results obtained indicate that the dark-adaptation curves produced by central and peripheral stimulation are variable and are in principle similar to the psychophysical curves obtained in matching conditions. This result demonstrates that the pupillary reflex is triggered by two different types of receptors which have the same characteristics as the cones and the rods, and that the system of the pupillary receptors and the optical pathways is identical.

Adult↗
PubMed1991

Local adaptations of two naturally occurring neuronal conductances, gK + (A) and gK + (Ca), allow for associative conditioning and contiguity judgements in artificial neural networks.

Features of two potassium conductances implicated in the acquisition of conditioned reflexes, the slow calcium dependent conductance (gK + (Ca] and the fast transient conductance (gK + (A], were incorporated into a 6 x 6 element artificial neural network. Adaptive algorithms derived from observations of cortical neurons during associative learning changed gK + (A) in proportion to the product of this current and an EPSP-induced second messenger concentration, and changed gK + (Ca) as a function of a spike-induced second messenger concentration. This network concurrently acquired two distinct representations in response to presentation of stimuli: one resembled associative conditioning (defined in terms of its sensitivity to forward pairing vs. simultaneous or backward pairing); the other reflected contiguous pairings of stimuli. The acquisition of one representation did not markedly interfere with acquisition of the other. This network may accordingly serve as an example of a self-organizing system which minimizes the postulated inherent cross talk between functionally dissiminar representations (Minsky and Papert 1988).

Acclimatization↗