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At least 19 recordsLinked to original sources
PubMed2025

Comparative Analysis of Mammalian Adaptive Immune Loci Revealed Spectacular Divergence and Common Genetic Patterns.

Adaptive immune responses are mediated by the production of adaptive immune receptors, antibodies, and T-cell receptors, which bind antigens, thus causing their neutralization. Unlike other proteins, adaptive immune receptors are not fully encoded in the germline genome and result from a complex of somatic processes collectively called V(D)J recombination affecting germline immunoglobulin (IG) and T-cell receptor (TR) loci consisting of template genes. While various existing studies report extreme diversity of antibodies and T-cell receptors, little is known about the diversity of germline IG and TR loci. To overcome this gap, the first comparative analysis of full-length sequences of IG/TR loci across 46 mammalian species from 13 taxonomic orders was performed. First, germline gene counts were shown to correlate in immunoglobulin heavy chain immunoglobulin heavy chain (IGH)/immunoglobulin lambda (IGL) loci and T-cell receptor alpha (TRA)/T-cell receptor beta (TRB) and anticorrelate in immunoglobulin kappa (IGK)/IGL, possibly indicating coevolution between corresponding chains. Second, structures of IG/TR loci were analyzed, and it was shown that IG/TR loci formed by long arrays of high multiplicity repeats are more common for species that have experienced population bottlenecks. Finally, haplotypes of IG/TR loci with little or no sequence similarity within a species were found, suggesting that they may have a limited potential for homologous recombination. These results demonstrate that IG/TR loci are rapidly evolving genomic regions whose structural variation is shaped by the population history of the species and open new perspectives for immunogenomics studies.

Animals↗
PubMed2025

Harnessing Landscape Genomics to Evaluate Genomic Vulnerability and Future Climate Resilience in an East Asia Perennial.

In this era of rapid climate change, understanding the adaptive potential of organisms is imperative for buffering biodiversity loss. Genomic forecasting provides invaluable insights into population vulnerability and adaptive potential under diverse climatic conditions, thereby facilitating management interventions and bolstering shaping species-specific germplasm conservation strategies. We primarily employed landscape genomics approaches, leveraging single-nucleotide polymorphisms obtained through whole-genome resequencing of 201 individuals across 43 Rheum palmatum complex populations, to pinpoint adaptive variation and its significance in the context of future climates, delineate seed zones, and establish guidelines for ex situ germplasm conservation. The species complex exhibited strong signatures of local adaptation and differential genomic vulnerabilities across its distribution range, with eastern lineage populations facing significant maladaptation risks under future climate scenarios. Using diverse datasets of putatively adaptive loci and climate change scenarios, we delineated three distinct seed zones within the species' range, estimated varying sample sizes per zone to capture most adaptive diversity, and predicted shifts in seed zone centroids ranging from 48.3 to 359.3 km from historical distributions to mitigate climate change impacts. Collectively, our findings underscore the importance of integrating genomic and environmental data to forecast the adaptive trajectory of an East Asian perennial under anticipated climate changes, guide seed zone delineation for germplasm conservation and enhance population resilience. These results provide a blueprint for designing targeted conservation strategies and restoration plans in other imperilled species.

Climate Change↗
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 = 0.18, p = 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↗
PubMed2026

Seasonal fluctuations in fitness result in severe reductions in effective population size.

Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection acting on standing genetic variation under a recently developed model and examine its effect on the variance effective population size (Ne) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to ∼50% genome-wide reductions in Ne. We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models.

Drosophila melanogaster↗
PubMed2026

Seasonal fluctuations in fitness result in severe reductions in effective population size.

Genetic evidence for fluctuating selection has begun to accumulate for different species over the past few decades, especially for the Drosophila genus where studies have reported hundreds of loci undergoing putatively adaptive oscillations across successive seasons. However, most theoretical and simulation studies of fluctuating selection have relied on abstract or weakly parameterized models, making it difficult to assess their relevance for natural populations. In this study, we simulate multilocus seasonally fluctuating selection under a recently developed model and examine its effect on the variance effective population size (Ne ) at a genome-wide scale. By recapitulating genomic, demographic, and evolutionary parameters from natural Drosophila populations in our simulations, we were able to reproduce allele frequency oscillations reported in recent studies and show that these lead to ~50% genome-wide reductions in Ne . We also demonstrate that Ne reductions are well predicted by the maximum frequency amplitude among all adaptively fluctuating loci, and that the frequency amplitudes are largely determined by the number of adaptively fluctuating loci and the strength of their epistatic interactions. Our results demonstrate that fluctuating selection can substantially reduce effective population size and underscore the importance of temporally variable selection in shaping genome-wide patterns of variation beyond classical models.

Drosophila melanogaster↗
PubMed2026

Landscape Genomics Reveals Divergent Adaptation Modes and Predicts Climate Vulnerability in Xinjiang Indigenous Sheep.

Climate change increasingly endangers precious indigenous sheep germplasm resources distributed across diverse Chinese landscapes, and systematically decoding their polygenic climate-adaptive genetic mechanisms is essential for targeted breed conservation and long-term sustainable pastoral production. Whole-genome resequencing data from 93 individuals covering six representative local sheep breeds were analyzed in this work. After filtering highly collinear climate variables, three mature landscape genomic approaches were jointly applied to identify environment-linked gene variants, while two predictive metrics across ten CMIP6 future climate scenarios quantified each breed's long-term adaptive risks. Six temperature- and water-related environmental factors jointly drove sheep population genetic differentiation, with temperature fluctuation indices showing markedly stronger explanatory power. Detected adaptive genes were significantly enriched in ion transport, energy metabolism and cellular stress response pathways. Future projections indicated western breeds (Bayinbuluke, Cele Black, Xiahe) face severe maladaptation risks under high-emission SSP370 scenarios by 2100, whereas central and eastern breeds possess much broader climate tolerance. This study systematically reveals the core genomic basis of ovine climate adaptation and quantifies distinct breed-specific climate vulnerability, providing solid reliable theoretical support for precision germplasm conservation and selective breeding of climate-resilient sheep varieties.

adaptive loci↗
PubMed2011

Adaptation to climate across the Arabidopsis thaliana genome.

Understanding the genetic bases and modes of adaptation to current climatic conditions is essential to accurately predict responses to future environmental change. We conducted a genome-wide scan to identify climate-adaptive genetic loci and pathways in the plant Arabidopsis thaliana. Amino acid-changing variants were significantly enriched among the loci strongly correlated with climate, suggesting that our scan effectively detects adaptive alleles. Moreover, from our results, we successfully predicted relative fitness among a set of geographically diverse A. thaliana accessions when grown together in a common environment. Our results provide a set of candidates for dissecting the molecular bases of climate adaptations, as well as insights about the prevalence of selective sweeps, which has implications for predicting the rate of adaptation.

Acclimatization↗
PubMed2026

From colonization to infection: Genomic evolution of Clostridioides difficile pathogenesis.

Clostridioides difficile is a spore-forming, toxin-producing anaerobe that is a leading cause of healthcare-associated infections. Its success as a pathogen reflects a complex interplay between bacterial evolution, virulence regulation, ecological adaptation, environmental selection, and host susceptibility. Comparative genomics has revealed deep C. difficile lineage diversification, driven by mobile genetic elements and selective pressures from antibiotics and host environments. These events affect strain-specific virulence by shaping the organization and regulation of the pathogenicity toxin loci, metabolic adaptations for nutrient utilization, and enhanced spore resilience. This review integrates evolutionary and genomic perspectives to illustrate how adaptive diversification has sculpted C. difficile pathogenesis and epidemic success.

CP: microbiology↗
PubMed2026

Genetically diverse populations hold the keys to climatic adaptation in the Western barn owl (Tyto alba).

Although local adaptation influences species distributions, its role in driving evolutionary resilience under climate change remains unclear. Current predictive models focus on genetic adaptation to present climates, providing limited insight into future adaptive capacity. We hypothesise that historical responses to climatic shifts can reveal candidate loci for local adaptation in the future. Combining ecological niche modelling and genomic analyses, we investigate spatiotemporal patterns and mechanisms of local adaptation of the Western Palearctic barn owl (Tyto alba). Ecological modelling reveals that barn owls now occupy a broader climatic niche than during the Last Glacial Maximum. Genomic analyses indicate ongoing adaptation, with regions under selection linked to environmental factors across all populations. We find that local adaptation drives evolutionary changes across populations, enabling colonisation of new habitats and shaping responses to climate change in resident populations. We show that standing genetic diversity plays a crucial role in adaptation to past, present, and future environmental shifts.

Animals↗
PubMed2025

Experimental Validation of Genome-Environment Associations in Arabidopsis.

Identifying the genetic basis of local adaptation is a key goal in evolutionary biology. Allele frequency clines along environmental gradients, known as genotype-environment associations (GEA), are often used to detect potential loci causing local adaptation but are rarely followed by experimental validation. Here, we tested loci identified in three moisture-related GEA studies on Arabidopsis. We studied 42 GEA-identified genes using t-DNA knockout lines under drought and tested effects on flowering time, an adaptive trait, and genotype-by-environment (GxE) interactions for performance and fitness. In total, 16/42 genes had significant effects on traits involved in local adaptation or performance responses to the environment. We found that wrky38 mutants had significant GxE effects for fitness; lsd1 plants had a significant GxE effect for flowering time, and 11 genes showed flowering time effects with no drought interaction. However, most GEA candidates did not exhibit GxE. In the follow-up experiments, wrky38 caused decreased stomatal conductance and specific leaf area under drought, indicating potentially adaptive drought avoidance. Additionally, GEA identified natural putative LoF variants of WRKY38 associated with dry environments, as well as alleles associated with variation in LSD1 expression. While only a few GEA-identified genes were validated for GxE interactions for fitness, we likely overlooked some genes because experiments might not well represent natural environments and t-DNA insertions might not well represent natural alleles. Nevertheless, GEAs apparently identified some genes contributing to local adaptation. GEA and follow-up experiments are straightforward to implement in model systems and demonstrate prospects for GEA discovery of new local adaptations.

Arabidopsis↗
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

Large Haplotypes Linked to Climate and Life History Variation in Divergent Lineages of Atlantic Salmon (Salmo salar).

Advances in sequencing are revealing that linked genomic architectures, enabling the evolution of co-adapted alleles at multiple loci, often shape complex phenotypes. Several recent studies have identified such architectures (e.g., chromosomal rearrangements and supergenes) contributing to adaptation or divergence across diverse species, from plants to mammals. Specifically, within Atlantic salmon (Salmo salar ), genomic studies are revealing large haplotypes and structural variants that may underpin local adaptation in the species. Using data from > 4000 individuals from 134 locations spanning the North Atlantic Ocean, we identify a large (~3 Mbp) genomic region on Ssa18 showing patterns of differentiation and linkage disequilibrium (LD) indicative of a large haplotype block containing three divergent haplotypes (herein A, B and C haplotypes). In Europe, haplotypes A and B were common, whereas A and C were more common within North America, suggesting a shared 'ancestral' A haplotype, with different continent-specific alternative haplotypes. Data support independent origins of divergent haplotypes in each continent, as well as signals of trans-oceanic introgression of haplotypes. Haplotype frequency is strongly associated with latitude, climate and life history (smolt age); however, the strength and direction of these relationships vary across continents. Overall, our analyses were consistent with other studies that identify chromosomal rearrangements; however, long-read sequence data did not find evidence of a structural variant, and instead an ancestral fusion may explain the formation and maintenance of the observed haplotypes. Our study contributes to ongoing efforts to understand the evolutionary role of linked genomic architecture in Atlantic salmon and its significance in salmonid diversification.

Climate Change↗
PubMed1977

Genic similarity of American and European species of the lobster Homarus.

European lobsters (Homarus gammarus) from the Norway coast and from the Irish Sea are examined for electrophoretically detectable genetic variation in seventeen functionally different proteins. Forty-one loci encoding these proteins are homologous with loci studied in a previous survey of eight populations of H. americanus. Progeny hatched from ovigerous Norway females show variation in three enzymes, but Mendelian inheritance is confirmed only for triosephosphate isomerase and for one of the phosphoglucose isomerases. Complex PGI phenotypes are described. The average amounts of genetic variability in European and American lobster populations appear to be equivalent. More than one allele is detected at 20% of the loci, the average number of alleles detected per locus is 1.2 and the average proportion of loci heterozygous per individual is 4.0%. While much less genically variable than other invertebrates, Homarus is not atypical when compared with eleven decapod species that average 5.8% heterozygosity. This is consistent with hypotheses relating genetic variability to adaptive strategy. At thirty loci H. gammarus is monomorphic for the common H. americanus allele. Two acid phosphatase systems are fixed or nearly fixed for alternative alleles in the two species while the remaining polymorphic loci show various degrees of interspecific divergence. Unique H. gammarus alleles are detected at five loci but only contribute significantly to species differences at the Acph-5, Me, and Pgi-4 loci. Acph-1, Est-2, Pgi-3, and Pgm-1 are polymorphic for the same alleles in both species, but again, with various differences in allelic frequencies. In sum, average genetic identity and average genetic distance are: I = 0.896 +/- 0.007 and D = 0.110 +/- 0.007, respectively. Compared to the values for conspecific population comparisons, I = 0.994 +/- 0.001 and D - 0.006 +/- 0.001, it is clear that a small but significant amount of genetic divergence separates the European and American lobster. Based on the premise that protein differences between existing species reflect the amount of time since they shared a common ancestor, it can be speculated that the European and American lobsters were isolated during the Pleistocene. The apparent weakness of reproductive isolating barriers suggests that these populations have evolved allopatrically. Finally, quantification of species' genetic differences, together with recent successes in interspecific laboratory matings, implicates species hybridization as a potentially important breeding practice in lobster aquaculture.

Animals↗
PubMed1976

Biochemical adaptations for flight in the insect.

1. Flight by insects is characterized by the most intense respiration known in biology and also the most controlled. Thus insect flight muscle may be the tissue of choice for the study of biochemical adaptation in the control of catabolism and biological oxidations, and many of the results obtained with insects have a significance and a relevance that transcend the boundaries between classes. In insects, such as the blowfly, flight is distinguished additionally by high wingbeat frequencies and an asynchronous type of excitation-contraction coupling. In spite of this intense muscular work, metabolic processes are not limited by the availability of oxygen. Also of importance is the morphological organization of the flight muscle and mitochondria, which have evolved ultrastructurally and biochemically into an effective catabolic machine. 2. In the fly, carbohydrate, principally glycogen, is the sole metabolic fuel; fats are not used in flight and enzymes concerned with fatty acid utilization are virtually lacking. Glycogenolysis does not lead to lactic acid; instead, the end products of glycolysis are pyruvate and alpha-glycerophosphate. The alpha-glycerophosphate cycle provides a mechanism not only for the reoxidation of glycolytically produced NADH but also for the stoicheiometric formation from each molecule of hexose equivalent of two molecules of pyruvate, which are then available for oxidation via the tricarboxylate cycle. The absence of dicarboxylate and tricarboxylate carriers from the mitochondria ensures that tricarboxylate-cycle intermediates do not exit from the mitochondrion but that pyruvate is oxidized to completion. On initiation of flight, mitochondrial oxidation of pyruvate is impeded by the lack of tricarboxylate-cycle intermediates for the generation of oxaloacetate. This is circumvented by the oxidation of proline. 3. The controls on metabolism in flight muscle, i.e. (1) glycogenolysis at phosphorylase and phosphorylase kinase, (2) glycolysis at phosphofructokinase, (3) alpha-glycerophosphate dehydrogenase, (4) proline dehydrogenase and (5) tricarboxylate cycle at isocitrate dehydrogenase, are effected by the phosphate potential and/or Ca2+. It is suggested that the metabolic changes, such as those seen in the rest-to-flight transition, are achieved by the concerted actions of these effectors at the different loci.

Adaptation, Physiological↗
PubMed2025

Genomic prediction of agronomic traits in perennial ryegrass (Lolium perenne L.) and genotype x environment interactions at the limit of the species distribution.

KEY MESSAGE: Perennial ryegrass shows extensive genotype x environment interactions at the limit of its ecological niche. Accounting for GxE may improve prediction even when environmental and genetic samples are highly diverse. BACKGROUND: In breeding the aim is to identify and accumulate beneficial variants. However, detection of these variants may be challenging in the presence of extensive genotype x environment interactions (GxE). METHODS: The study assesses the performance of 264 diploid perennial ryegrass accessions in a multi-environment field trial. We investigate the extent of GxE, for yield (total dry matter) and persistence traits under environmental conditions experienced in Nordic and Baltic regions at the limit of the species distribution. Two different approaches to modelling GxE were tested and validated under three different breeding scenarios. RESULTS: Our analysis documented the presence of significant GxE for all traits. Validation showed improvements in prediction accuracy when accounting for GxE: up to 4% for yield when predicting in unobserved environments, and up to 22% and 9% for spring cover and winter kill, respectively, when predicting unobserved germplasm. Genome-wide-association-studies (GWAS) were utilized to detect genetic variants with marginal effects (environment-independent effect) and conditional effects (environment-dependent effects). Results showed the presence of large-effect genetic variants with marginal effects, in addition to few Quantitative Trait Loci (QTL) whose effects were adaptive under specific environmental conditions while neutral or deleterious under different environmental conditions. CONCLUSION: This study demonstrates the usefulness and limitations of genomic prediction models for predicting GxE in highly diverse samples and describes the extent of GxE at the limit of species distribution for perennial ryegrass. Our study points towards adaptive variation which may enhance persistence of perennial ryegrass populations in Nordic and Baltic growing conditions.

Lolium↗
PubMed2026

VDJ-Insights: simplifying the annotation of genomic immunoglobulin and T cell receptor regions.

MOTIVATION: Accurate annotation of germline immunoglobulin (IG) and T cell receptor (TCR) loci is critical for understanding adaptive immunity. RESULTS: VDJ-Insights provides a user-friendly software package for characterizing these complex immune regions. In addition, it assesses gene segment functionality, identifies recombination signal sequences, and annotates complementarity-determining regions 1 and 2. VDJ-Insights achieved over 99% concordance with curated annotations from multiple species, outperforming existing annotation tools. When applied to 95 haplotypes from the Human Pangenome Reference Consortium, VDJ-Insights identified 652 and 275 novel IG and TCR alleles, respectively, highlighting its scalability for large immunogenetic studies. AVAILABILITY AND IMPLEMENTATION: Datasets and software package are available in the VDJ-insights repository, https://github.com/BPRC-Bioinfo and https://doi.org/10.5281/zenodo.17588835. Additional intermediate datasets used and analyzed during the current study are available from the corresponding authors upon reasonable request.

Software↗
PubMed2024

Genetic investigation of population structure in Atlantic chub mackerel, Scomber colias Gmelin, 1789 along the West African coast.

Sustainable management of transboundary fish stocks hinges on accurate delineation of population structure. Genetic analysis offers a powerful tool to identify potential subpopulations within a seemingly homogenous stock, facilitating the development of effective, coordinated management strategies across international borders. Along the West African coast, the Atlantic chub mackerel (Scomber colias) is a commercially important and ecologically significant species, yet little is known about its genetic population structure and connectivity. Currently, the stock is managed as a single unit in West African waters despite new research suggesting morphological and adaptive differences. Here, eight microsatellite loci were genotyped on 1,169 individuals distributed across 33 sampling sites from Morocco (27.39°N) to Namibia (22.21°S). Bayesian clustering analysis depicts one homogeneous population across the studied area with null overall differentiation (F ST = 0.0001ns), which suggests panmixia and aligns with the migratory potential of this species. This finding has significant implications for the effective conservation and management of S. colias within a wide scope of its distribution across West African waters from the South of Morocco to the North-Centre of Namibia and underscores the need for increased regional cooperation in fisheries management and conservation.

Animals↗
PubMed1979

[Brightness power function and equal brightness contour for dark- and light-adapted eye in the peripheral visual field (author's transl)].

To test whether the equal brightness contour at supra-threshold runs parallel with the contour at threshold, magnitude estimation and the staircase procedure were employed for estimating brightness power function under dark- and light-adaptation. The luminance was changed from 43 to 83 dB re 10(-6) cd/m2 with the light adapting luminance at 53 dB. The retinal loci tested were 0 degrees to 70 degrees periphery in steps of 10 degrees. The exponent of the power function gradually increased from .37 to .73 as eccentricity and adapting luminance increased. The equal brightness contour decreased for dark-adaptation and increased for light-adaptation as eccentricity increased at supra-threshold but at threshold did not follow the parallel hypothesis for both adapting conditions.

Adaptation, Ocular↗