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PubMed2026

Genomic-Environmental Integration Predicts Climate Vulnerability and Adaptive Potential of Tibetan Plateau Herpetofauna.

The herpetofauna of the Tibetan Plateau, home to Earth's highest-elevation ectothermic vertebrates, face escalating threats from rapid climate change. However, conventional conservation strategies often overlook intraspecific genetic variation and adaptive potential, limiting their predictive accuracy and effectiveness. Here, we integrate whole-genome resequencing data with environmental modeling to assess climate vulnerability in two endemic species: Nanorana parkeri (Tibetan frog) and Thermophis baileyi (hot-spring snake). Results suggest that the western populations of the two species exhibit higher genomic offsets under future climate, while some eastern populations of the Tibetan frog face a decrease in niche suitability, and the hot-spring snake will experience varying degrees of loss of suitable habitats. Furthermore, heterozygosity, genetic diversity, and genetic load demonstrate significant correlations with genomic offsets, suggesting that low genetic diversity and high genetic load may weaken the potential to adapt to environmental changes. Based on a genome-niche index that combines genomic offsets with niche suitability change, we identified evolutionary rescue populations that are potentially tolerant to climate change. Our findings underscore the importance of integrating genomic and environmental data to forecast the adaptive potential and enable effective conservation management of high-altitude herpetofauna under rapid climate change.

Animals↗

PubMed2025

Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations.

With the impact of climate change and anthropogenic activities, the underlying threats facing populations with different evolutionary histories and distributions, and the associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal populations and/or those showing admixture. Here, we re-sequence genomes of 102 individuals from 21 locations for Rhododendron vialii, a threatened species distributed in the subtropical forests of southwestern China that has suffered from habitat fragmentation due to deforestation. Population structure results revealed that R. vialii can be divided into five genetic lineages using neutral single-nucleotide polymorphisms (SNPs), whereas selected SNPs divide the species into six lineages. This is due to the Guigu (GG) population, which is identified as admixed using neutral SNPs, but is assigned to a distinct genetic cluster using non-neutral loci. R. vialii has experienced multiple genetic bottlenecks, and different demographic histories have been suggested among populations. Ecological niche modeling combined with genomic offset analysis suggests that the marginal population (Northeast, NE) harboring the highest genetic diversity is likely to have the highest risk of maladaptation in the future. The marginal population therefore needs urgent ex situ conservation in areas where the influence of future climate change is predicted to be well buffered. Alternatively, the GG population may have the potential for local adaptation, and will need in situ conservation. The Puer population, which carries the heaviest genetic load, needs genetic rescue. Our findings highlight how population genomics, genomic offset analysis, and ecological niche modeling can be integrated to inform targeted conservation.

Rhododendron↗

PubMed2026

Climate-Driven Niche Tracking and Genomic Resilience Shape Future Distribution of a Widespread Agricultural Weed.

Understanding how agriculturally important species respond to environmental change is critical for maintaining productivity, mitigating agroecosystem threats and sustaining resilience. While crops have traditionally been the focus in agroecosystems, agricultural weeds are integral components that often face even stronger selective pressures, making them powerful models for investigating ecological and evolutionary responses to climatic and human-mediated challenges. Insights from how weeds adapt rapidly under these pressures can inform strategies to improve agricultural outcomes, since both pests and crops evolve under the same multivariate selective pressures. Here, we integrate two centuries of distribution records with whole-genome sequencing from natural populations of the most damaging weed in Europe-Alopecurus myosuroides (blackgrass) - to examine its ecological and evolutionary responses in agroecosystems. Blackgrass largely maintained its historical climatic niche, expanding its range primarily by tracking environments analogous to those it historically occupied. Genome-wide analyses revealed a polygenic basis of environmental responses, with most loci linked to single environmental variables and a subset showing limited environmental pleiotropy, indicating modular adaptation to the complex selective pressures of managed agricultural landscapes. Coupling these genomic-environment relationships with projected climate change and genomic offset analyses indicated that most blackgrass populations will remain well aligned with future conditions. Our 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.

Plant Weeds↗

PubMed2025

Comparative genomic analysis of Acer tsinglingense and A. davidii provides insights into nervonic acid biosynthesis, population evolution and genome vulnerability of endangered A. tsinglingense.

Global biodiversity is facing threats from climate change, habitat fragmentation, and anthropogenic activities-pressures that particularly endanger endemic and narrowly distributed species. In this study, the high-quality chromosome-level genomes of two ecologically divergent maples were assembled: the endangered and range-restricted Acer tsinglingense (791.40 Mb) and its widespread congener Acer davidii (1291.99 Mb). Phylogenomic analysis indicates that the two species diverged ~16.3 million years ago, with A. tsinglingense showing notable gene family expansions in secondary metabolite pathways. Notably, the 3-ketoacyl-CoA synthase gene family, which is involved in nervonic acid biosynthesis, underwent significant expansion and tandem duplication in A. tsinglingense, exhibiting high expression in buds. Population genomic analysis revealed that, compared with the widely distributed A. davidii, A. tsinglingense possesses lower genetic diversity, higher harmful mutation load, and signatures of a severe population bottleneck during the Late Pleistocene. Genome-environment association analysis further identified climate-adaptive genomic variations linked to five key environmental factors and projected potential genomic offsets under future climate scenarios. The southern lineage of A. tsinglingense exhibited greater climate sensitivity and genomic vulnerability under strong selective pressures, underscoring its importance as a conservation priority. Our research reveals that metabolic specializations in A. tsinglingense (such as the synthesis of nervonic acid) may confer competitive advantages in specific habitats. However, factors including its restricted distribution, historical population bottlenecks, and accumulated genetic load severely constrain its evolutionary potential to cope with rapid climate change. These findings emphasize the importance of elucidating the genomic basis and mechanisms of endangerment in metabolically specialized and threatened plant species to inform effective conservation strategies.

Genome, Plant↗

PubMed2026

Population and landscape genomics provide insights into the adaptive genetic variation and future climate-induced vulnerability of the endangered tree species Phoebe bournei.

Elucidating the genomic underpinnings of adaptive variation is highly important for the conservation, landscape application, and management of ornamental trees against the backdrop of global climate change. However, research on the genetic mechanisms underlying climate adaptation in Phoebe bournei-a near-threatened subtropical tree species endemic to China, which is endowed with exceptionally high ornamental and ecological value-remains scarce. Whole-genome resequencing was conducted on 362 individuals from 27 natural populations across the geographical range of the species. Genome-environment association analyses were employed to identify 1556 climate-associated variants and 167 candidate genes associated with temperature and precipitation variables. Through functional annotation and expression profiling, pivotal genes, including TRX-M4 and FBD1, were identified as integral to drought and heat stress responses, with adaptive alleles displaying distinct geographic frequency distributions and significant phenotypic differentiation. Divergent evolutionary trajectories were deduced among populations, with southeastern populations distinguished by elevated genetic diversity and strong signatures of local adaptation. Nevertheless, projections derived from the Risk of Non-Adaptedness and gradient forest models suggest that these southeastern populations will face substantial genomic offset under future climate scenarios, signaling heightened vulnerability and the need for prioritized conservation and management. This study provides the first genome-wide perspective into the adaptive evolution of P. bournei and offers a robust foundation for its conservation and climate-resilient management.

Journal Article↗

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↗

PubMed2025

Eco-Evolutionary Genomics Reveal Mountain Range-Specific Adaptation and Intraspecific Variation in Vulnerability to Climate Change of Alpine Endemics.

Alpine plants restricted to rocky habitats exhibit intraspecific diversification due to range fragmentation during Holocene warming, complicating predictions of their climate vulnerability. A lack of understanding of eco-evolutionary mechanisms driving their response to climate change results in ineffective conservation efforts. To uncover the genomic basis of their diversification and explain spatial patterns of their vulnerability, we combine landscape genomics and species distribution modelling. Our model, the Campanula lehmanniana complex, occurs in three distinct central Asian mountain ranges, considered both a biodiversity hotspot and a vascular plant diversity darkspot. Genome-environment association confirmed the adaptive basis of intraspecific diversification, driven by numerous loci of small effect. Genomic and ecological data indicate mountain range-specific climate sensitivity driven by altitude, temperature and precipitation. The cold-dry adapted group from Zeravshan-Hissar Mts will face niche decline but show a higher degree of preadaptation to future climate, while the temperate-humid group from Tian Shan shows an opposite response, with a higher risk of maladaptation despite predicted niche expansion. Maladapted populations at northern margins may require an influx of adaptive variation to cope with predicted changes. However, limited landscape connectivity between island-like habitats, combined with long migration distances required to minimise genotype-environment disruption, highlights the role of human-assisted migration in enabling evolutionary rescue. These results underscore the need to facilitate gene flow from pre- to maladapted populations and the importance of population-specific approaches to inform effective conservation strategies in heterogeneous mountain ecosystems. The results may be relevant to numerous Central Asian mountain species that show similar phylogeographic patterns.

Climate Change↗

PubMed2023

Targeting Borrelia burgdorferi HtpG with a berserker molecule, a strategy for anti-microbial development.

Conventional antimicrobial discovery relies on targeting essential enzymes in pathogenic organisms, contributing to a paucity of new antibiotics to address resistant strains. Here, by targeting a non-essential enzyme, Borrelia burgdorferi HtpG, to deliver lethal payloads, we expand what can be considered druggable within any pathogen. We synthesized HS-291, an HtpG inhibitor tethered to the photoactive toxin verteporfin. Reactive oxygen species, generated by light, enables HS-291 to sterilize Borrelia cultures by causing oxidation of HtpG, and a discrete subset of proteins in proximity to the chaperone. This caused irreversible nucleoid collapse and membrane blebbing. Tethering verteporfin to the HtpG inhibitor was essential, since free verteporfin was not retained by Borrelia in contrast to HS-291. For this reason, we liken HS-291 to a berserker, wreaking havoc upon the pathogen's biology once selectively absorbed and activated. This strategy expands the druggable pathogenic genome and offsets antibiotic resistance by targeting non-essential proteins.

Borrelia burgdorferi↗

PubMed1992

Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus).

Southern blot analysis was used to quantify the extent of mtDNA D-loop length variation in two populations of white sturgeon, Acipenser transmontanus. Over 42% of individuals were heteroplasmic for up to six different mtDNA length variants attributable to varying copy numbers of an 82-bp repeat sequence. Chi-square analyses revealed that the frequencies of length genotypes and the incidence of heteroplasmy were significantly different between Fraser and Columbia River sturgeon populations but not between restriction site haplotypes. Heteroplasmic fish have, on average, higher copy number than homoplasmic fish. Forty-five of 101 homoplasmic individuals carry only a single copy of the repeat, while none of the 73 heteroplasmic fish has the single repeat as the predominant variant. On the basis of differences in frequency distributions of copy number within and between fish, we suggest that (1) heteroplasmy is maintained by high recurrent mutation of multiple copy genomes, favoring increased copy number and (2) the mutation pressure toward higher copy number heteroplasmy is partially offset by selection to reduced genome size and segregation to the homoplasmic condition.

Animals↗

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↗

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 10 000 years. Spearman correlation indicated a strong negative relationship between effective population size and human population density (rpopulation density = -0.90, P < 0.001) as well as cropland use (rcropland use = -0.89, P < 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↗

PubMed1989

Arterial pressure and aging.

Systolic arterial pressure increases with aging. This increase encompasses both the clinically normal and hypertensive ranges of pressure and is due in part to arterial stiffening. To what extent it may be modulated by life style changes that accompany aging is unknown. The stiffer arterial tree transmits the pulse wave with a higher velocity such that reflected waves return to the aortic root during the ejection period. This causes the aortic impedance to increase at this time, leading to a late peak in systolic pressure. Cardiac adaptation to these vascular changes include left ventricular hypertrophy and prolonged Ca2+ activation of contractile proteins leading to prolonged contraction. The resultant delayed contractile relaxation, in part, leads to a slower velocity of early left ventricular filling; however, this is offset by an enhanced atrial contribution to filling. These myocardial adaptations with aging, which in animal models appear, in part at least, to be controlled from within the genome permit a relatively normal heart volume and ejection fraction in the presence of chronically elevated afterload. These changes that occur with aging in otherwise healthy individuals can occur at a younger age in clinical hypertensives and can be produced in young experimental animals by hypertension. Thus, aging has sometimes been referred to as blunted hypertension, or hypertension as accelerated aging.

Aging↗

PubMed2025

Common gardens reveal genomic susceptibility and vulnerability to climate change in Eucalyptus.

Accelerated global climate change and increased species introduction across international scales have raised concerns about the potential for trees to experience maladaptation or lagging adaptation in response to these environmental shifts. However, our knowledge regarding the relationship between the genomic metrics used to predict maladaptation and actual fitness proxies in trees remains limited. Here, we present a population genomic analysis of 295 families from 28 provenances of Eucalyptus pellita, a widely cultivated fast-growing tree species, and conducted two common garden experiments. Genomic susceptibility encompassing individual heterozygosity (H), genomic inbreeding (FROH), and genomic load (inferred from deleterious mutations) exhibited distinct geographic patterns, shedding light on the origin and evolutionary history of E. pellita. The genetic basis of local adaptation was elucidated through genotype-environment associations and genome-wide association studies, including 198 loci associated with climate and 2388 loci regulating different traits. Furthermore, Australian provenances have higher genomic vulnerability under prospective climate alterations than Papua New Guinea and Indonesia provenances. By integrating phenotypic data across two common gardens, the relationship between leaf functional traits and predicted metrics of maladaptation was closer than growth attributes. Notably, pronounced natural selection signals linked to leaf morphogenesis have been identified by comparing two lineages spanning the oceans. This study underscores the immense potential of leveraging genomic susceptibility and genomic vulnerability to decipher the local (mal)adaptation of forest trees.

Eucalyptus↗

PubMed1990

Similar myocardial effects of aging and hypertension.

Aging has sometimes been referred to as 'blunted hypertension', and hypertension as 'accelerated aging'. Systolic arterial pressure increases with aging; the increase encompasses both the clinically normal and hypertensive ranges of pressure and is due in part to arterial stiffening. Cardiac changes that occur with aging in otherwise healthy individuals can occur at a younger age in clinically hypertensive individuals and can be produced in young animals by experimental hypertension. Such cardiac adaptations in hypertension and aging include left ventricular hypertrophy and prolonged Ca2+ activation of contractile proteins, leading to a prolonged force-bearing capacity. This is mediated by a prolongation of the cytosolic Ca2+ transient, due to a reduced rate of Ca2+ sequestration by the sarcoplasmic reticulum. The action potential is also prolonged. The resultant delayed contractile relaxation, in part, leads to a slower velocity of early diastolic left ventricular filling; however, this is offset by enhanced atrial filling. Cardiac muscle of the aging and hypertensive heart are also less sensitive to beta-adrenergic stimulation. These myocardial adaptations with aging and hypertension, in part, are controlled from within the genome and permit a relatively normal heart volume and ejection fraction in the presence of chronically elevated afterload.

Action Potentials↗

PubMed2026

Cohesin cofactor dosage sets the rate of loop extrusion, rendering genome folding tunable yet vulnerable to genetic disruption.

Genome folding is not static but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here, we show that extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and for the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

Cell Cycle Proteins↗

PubMed1992

Sequencing by hybridization: towards an automated sequencing of one million M13 clones arrayed on membranes.

An immediately applicable variant of the sequencing by hybridization (SBH) method is under development with the capacity to determine up to 100 million base pairs per year. The proposed method comprises six steps: (i) arraying genomic or cDNA M13 clones in 864-well plates (wells of 2 mm); (ii) preparation of DNA samples for spotting by growth of the M13 clones or by polymerase chain reaction (PCR) of the inserts using standard 96-well plates, or plates having as many as 864 correspondingly smaller wells; (iii) robotic spotting of 13,824 samples on an 8 x 12 cm nylon membrane, or correspondingly more, on up to 6 times larger filters, by offset printing with a 96 or 864 0.4 mm pin device; (iv) hybridization of dotted samples with 200-2000 32P-labeled probes comprising 16-256 10-mers having a common 8-mer, 7-mer, or 6-mer in the middle (20 probes per day, each hybridized with 250,000 dots); (v) scoring hybridization signals of 5 million sample-probe pairs per day using storage phosphor plates; and (vi) computing clone order and partial-to-complete DNA sequences using various heuristic algorithms. Genome sequencing based on a combination of this method and gel sequencing techniques may be significantly more economical than gel methods alone.

Bacteriophage M13↗

PubMed2025

Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption.

Genome folding is not static, but emerges from dynamic processes that control transcription, replication, recombination, and repair. DNA loop extrusion by cohesin is central to genome organization, yet it remains unclear how cells can tune extrusion kinetics to achieve precise and functional chromosome folding patterns. Here we discover extrusion rate acts as a tunable biophysical parameter in cells, quantitatively dialed by the respective dosage of the cohesin cofactors NIPBL and PDS5. Modulation of extrusion rate can offset changes in cohesin lifetime to buffer steady-state chromosome structure and transcriptional states, even in the face of abnormal extrusion dynamics. These findings provide a long-sought mechanistic basis for the genetic interactions between cohesin cofactors and the molecular origin of haploinsufficiency in cohesinopathies, such as Cornelia de Lange syndrome.

Journal Article↗

PubMed2024

Interspecific transfer of genetic information through polyploid bridges.

Hybridization blurs species boundaries and leads to intertwined lineages resulting in reticulate evolution. Polyploidy, the outcome of whole genome duplication (WGD), has more recently been implicated in promoting and facilitating hybridization between polyploid species, potentially leading to adaptive introgression. However, because polyploid lineages are usually ephemeral states in the evolutionary history of life it is unclear whether WGD-potentiated hybridization has any appreciable effect on their diploid counterparts. Here, we develop a model of cytotype dynamics within mixed-ploidy populations to demonstrate that polyploidy can in fact serve as a bridge for gene flow between diploid lineages, where introgression is fully or partially hampered by the species barrier. Polyploid bridges emerge in the presence of triploid organisms, which despite critically low levels of fitness, can still allow the transfer of alleles between diploid states of independently evolving mixed-ploidy species. Notably, while marked genetic divergence prevents polyploid-mediated interspecific gene flow, we show that increased recombination rates can offset these evolutionary constraints, allowing a more efficient sorting of alleles at higher-ploidy levels before introgression into diploid gene pools. Additionally, we derive an analytical approximation for the rate of gene flow at the tetraploid level necessary to supersede introgression between diploids with nonzero introgression rates, which is especially relevant for plant species complexes, where interspecific gene flow is ubiquitous. Altogether, our results illustrate the potential impact of polyploid bridges on the (re)distribution of genetic material across ecological communities during evolution, representing a potential force behind reticulation.

Polyploidy↗