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Application of laser ablation ICPMS to trace the environmental history of chum salmon Oncorhynchus keta.

Trace element levels in otoliths of chum salmon Oncorhynchus keta were examined by means of laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). A close linear relationship in the Sr:Ca ratios between EPMA (X-ray analysis with an electron microprobe) and LA-ICPMS analyses was found (p<0.0001), suggesting that the latter technique could be used to separate the marine and freshwater life phases. Mg:Ca, Cr:Ca, Zn:Ca and Ba:Ca ratios in either the core region or the oceanic growth zone of the otoliths varied among sites. These differences suggest that elemental compositions may reflect environmental variability among spawning (breeding) or habitat sites. Thus, those element ratios demonstrate the potential to be used to distinguish between fish spawning (breeding) sites and habitats for this species of salmon.

Animal Migration↗

Functional diversity of nematode communities in the southwestern North Sea.

A range of biological traits of nematode species were combined to identify patterns in the functional composition of their assemblages collected at 19 soft-bottom stations in the southwestern North Sea with the primary aim to determine which environmental variables control communities. We used 19 categories of five biological traits thought or known to represent an important ecological function. These were related to buccal morphology, tail shape, body size, body shape and life history strategy. Data on trait membership was provided by biological information on species and genera. A total of 79 different trait combinations were recorded. Results from correlation analyses revealed several significant relationships between traits. Some trait combinations were shared by different species and genera, and the ratio of realised versus total number of possible trait combinations of < 1 suggested that some trait combinations were not represented by the nematode fauna from this region. The functional composition of nematodes was strongly linked to median particle diameter and silt content of the sediment and water depth. The approach adopted and our attempts at defining and analysing functional attributes of nematode communities raised a number of conceptual and methodological issues which are discussed.

Animals↗

Functional convergence of rTCA-related carbon-fixation potential and biochemical residue accumulation in seagrass sediments.

Seagrass meadows are globally significant blue carbon ecosystems, yet the microbial and biochemical mechanisms driving sediment organic carbon (SOC) accumulation remain poorly understood. To address this, we employed an integrated approach combining metagenomic sequencing, biochemical assays, and structural equation modeling to investigate carbon cycling in the seagrass and adjacent unvegetated sediments of Swan Lake, China. A total of 115,179 carbon fixation genes and 119,615 decomposition genes were identified, revealing distinct microbial community structures among the habitats. Seagrass sediments harbored more diverse carbon-fixing (CFMs) and decomposing microorganisms (CDMs), with 83 medium-to high-quality metagenome-assembled genomes (MAGs) recovered. While neutral community model analysis indicated that stochastic processes predominantly governed community assembly, functional analyses highlighted specific drivers of sequestration. The reductive tricarboxylic acid (rTCA) cycle emerged as the dominant carbon fixation pathway, with key genes (e.g., aclA, korA) showing strong positive correlations with SOC. Conversely, decomposition pathways for starch and lignin were negatively associated with SOC. Furthermore, seagrass sediments exhibited elevated concentrations of total amino sugars (TAS) and lignin phenols (TLP), which linked significantly to carbon fixation rather than decomposition. PLS-SEM revealed statistically significant associations among seagrass traits, environmental variables, microbial carbon-fixation potential, biochemical residue pools, and SOC, supporting a mechanistic pathway in which enhanced microbial functional potential drives the accumulation of recalcitrant biochemical residues, thereby facilitating long-term carbon retention in sediments. These findings emphasize the pivotal role of microbial anabolism and the accumulation of biosynthetic residues in sediment carbon storage, suggesting a functional convergence in seagrass-driven carbon sinks.

Metagenomics↗

Impacts of dredged material disposal on a tropical soft-bottom benthic assemblage.

The soft-bottom benthic macrofauna in a spoil-ground of dredged material in Cleveland Bay, North Queensland, Australia, was studied to detect possible impacts of the disposal of sediments. The spatial distribution of the assemblage was studied in relation to the source of the impact at 28 stations on four occasions during 1998 and 1999. Additionally, environmental variables were measured on each occasion at each station. Macrobenthic assemblages inside the spoil-ground were different from assemblages outside the spoil ground only immediately after (15 days) the disposal of dredged material. Given the decrease in the abundance of organisms and number of species, it is suggested that this effect was due to direct burial of the macrobenthic assemblage inside the spoil-ground. Macrobenthic assemblages inside the spoil ground were not different from assemblages outside the spoil ground 3 months after dumping. These results suggest that the soft-bottom macrobenthic assemblages may respond quickly to the disturbance associated with the dumping of dredged material.

Animals↗

Gene therapy for the circumvention of inborn errors of metabolism (IEM) caused by single-nucleotide-polymorphisms (SNPs).

Single nucleotide polymorphisms (SNPs) are the result of point mutations in nuclear (and mitochondrial) DNA. Such localised damage to DNA (and its replicative mechanisms) may not be excised fully by the DNA repair mechanism in the genome: and therefore can become inheritable; subsequently to manifest later as an inborn error of metabolism (IEM). Causes of mutagenic damage to the DNA can include background radiation (such as emitted by radon gas), and by reactive oxygen species (ROS): and also by mutagenic chemicals that occur naturally (inter alia in the diet). Other causes of DNA damage are variable environmental hazards such as solar-derived short wave ultraviolet light A. Gene therapy involves the placement of missing genes into particular tissues by the harnessing of suitable vectors (originally these were animal viruses such as SV40). For example, gene therapy in the rat for diabetes has succeeded by liver-production of insulin (using genes obtained from pancreatic Islets of Langerhans cells). Many inborn errors of metabolism could be treated in this way: examples may include 100 haemoglobinopathies (such as sickle cell anaemia), phenylketonuria; and other diseases caused by lack of tissue-production of a particular enzyme (in its catalytically-active conformation).

Diabetes Mellitus↗

The possible role of female sex hormones in milk from pregnant cows in the development of breast, ovarian and corpus uteri cancers.

The continued increase in incidence of some hormone-related cancers worldwide is of great concern. Although estrogen-like substances in the environment were blamed for this increase, the possible role of endogenous estrogens from food has not been widely discussed. We are particularly concerned about cows' milk, which contains a considerable quantity of estrogens. When we name cows' milk as one of the important routes of human exposure to estrogens, the general response of Western people is that "man has been drinking cows' milk for around 2000 years without apparent harm." However, the milk that we are now consuming is quite different from that consumed 100 years ago. Unlike their pasture-fed counterparts of 100 years ago, modern dairy cows are usually pregnant and continue to lactate during the latter half of pregnancy, when the concentration of estrogens in blood, and hence in milk, increases. The correlation of incidence and mortality rates with environmental variables in worldwide countries provides useful clues to the etiology of cancer. In this study, we correlated incidence rates for breast, ovarian, and corpus uteri cancers (1993-97 from Cancer Incidence in Five Continents) with food intake (1961-97 from FAOSTAT) in 40 countries. Meat was most closely correlated with the breast cancer incidence (r=0.827), followed by milk (0.817) and cheese (0.751). Stepwise multiple-regression analysis (SMRA) identified meat as the factor contributing most greatly to the incidence of breast cancer ([R]=0.862). Milk was most closely correlated with the incidence of ovarian cancer (r=0.779), followed by animal fats (0.717) and cheese (0.697). SMRA revealed that milk plus cheese make the greatest contribution to the incidence of ovarian cancer ([R]=0.767). Milk was most closely correlated with corpus uteri cancer (r=0.814), followed by cheese (0.787). SMRA revealed that milk plus cheese make the most significant contribution to the incidence of corpus uteri cancer ([R]=0.861). In conclusion, increased consumption of animal-derived food may have adverse effects on the development of hormone-dependent cancers. Among dietary risk factors, we are most concerned with milk and dairy products, because the milk we drink today is produced from pregnant cows, in which estrogen and progesterone levels are markedly elevated.

Administration, Oral↗

Data-driven approaches in green microbiology: strategies for plant growth-promoting bacteria.

Plant growth-promoting bacteria (PGPB) are gaining attention as scalable biological solutions to enhance crop productivity and resilience. However, accurately identifying and characterizing PGPB remains challenging, particularly under variable environmental conditions where microbial functions are context-dependent and shaped by complex plant-microbe interactions. Advances in high-throughput sequencing have shifted the field from culture-dependent approaches to genome-informed strategies, enabling large-scale taxonomic and functional profiling. Although trait-based databases support the prediction of plant-beneficial genes, they capture only a fraction of the underlying biological complexity and often require labor-intensive analyses. Machine learning (ML) and deep learning (DL) have emerged as powerful tools to integrate genomic, physiological, and ecological data, enabling the prioritization of candidate strains with plant growth-promoting potential. To evaluate advances in the field, we conducted a systematic review of studies integrating ML and DL with PGPB characterization, assessing algorithm selection, performance, and target plant systems. Across 248 observations, only 6.0% of studies directly addressed PGPB screening, whereas the majority (77.4%) focused on plant disease detection, revealing a substantial gap in the application of AI to beneficial microorganisms for plant growth. Convolutional neural networks (CNNs) were the most frequently applied algorithms, largely driven by image-based phenotyping tasks. Overall, the field is constrained by limited datasets, high computational demands, and challenges in modeling multispecies and host-associated interactions. We highlight the need for integrative and interpretable ML and DL frameworks that bridge genomic data and functional validation. Such approaches represent a promising path toward scalable, data-driven discovery and deployment of bioinoculants in sustainable agriculture.

Agriculture↗

Steroid-dependent plasticity in the medial amygdala.

Behavioral sex differences have traditionally been thought to arise from gonadal steroids during a neonatal sensitive period. However, it is possible to sex-reverse certain behaviors by reversing the levels of circulating androgen in adult males and females. These results suggest that the sexually dimorphic substrates of sex behavior are subject to a high degree of plasticity, even in adulthood. I have found that circulating androgen exerts a trophic effect on the Nissl-stained morphology of an important nucleus in the control of sex behavior, namely, the posterodorsal subnucleus of the medial amygdala. First, sex-reversing the level of circulating androgen reversed the sex difference in soma size and regional volume of the posterodorsal subnucleus of the medial amygdala in adult rats. Interestingly, activation of both androgen and estrogen receptors was necessary for the post-castration maintenance of a masculine phenotype in terms of posterodorsal subnucleus of the medial amygdala cell size, whereas only estrogen receptor activity was necessary to maintain a masculine posterodorsal subnucleus of the medial amygdala volume. Then, we showed that seasonal variation in androgen was correlated with morphologic plasticity in the posterodorsal subnucleus of the medial amygdala of the Siberian hamster. However, if the experimental males were housed with females, their posterodorsal subnucleus of the medial amygdalas failed to regress in response to winter-like short daylengths. Furthermore, when male hamsters were castrated and treated with testosterone, the posterodorsal subnucleus of the medial amygdala responded to the hormone only if the animals were in summer-like photoperiods. Overall, these findings indicate that circulating androgens are critical for the maintenance of greater posterodorsal subnucleus of the medial amygdala regional volumes and soma sizes, and that environmental variables can regulate testosterone secretion and responsiveness.

Amygdala↗

Prenatal exposure to methylmercury and child development: influence of social factors.

BACKGROUND: In the Seychelles Child Development Main Study (SCDS), at 19 months of age, enhanced MDI scores were associated with increasing methylmercury (MeHg) exposure in higher caregiver IQ groups at several levels of family income. We performed a similar analysis of the 66-month evaluations to determine if the modifying influences of social and environmental factors were consistent with those previously observed. METHODS: Prenatal MeHg exposure was determined by analysis of maternal hair growing during pregnancy. Children in the cohort (N=711) were evaluated for cognitive ability (McCarthy Scales of Children's Abilities), language development (Preschool Language Scale), drawing and copying (Bender Gestalt Test), scholastic achievement (the Woodcock-Johnson Test of Achievement), and behavior (the Child Behavior Checklist). Interactions between prenatal MeHg exposure and caregiver intelligence, socioeconomic status (SES), home environment, and gender were examined by multiple regression analysis. RESULTS: The median prenatal MeHg exposure was 5.9 ppm (range=0.5-26.7 ppm). Gender significantly influenced the association between prenatal exposure and drawing and copying; however, the effects were not consistent. Prenatal exposure interacted with one or more social or environmental covariates for general cognitive ability, overall language ability, and prearithmetic achievement. Again, the effects were not consistent across either endpoints or covariate categories. CONCLUSIONS: Evidence of a small influence by social and environmental variables at 66 months is neither internally consistent nor consistent with earlier results. Overall, a consistent pattern of effect modification (EM) has not been observed, suggesting that the results may be due to chance.

Achievement↗

Adult cortisol response to immature offspring play in captive squirrel monkeys.

Variable environmental and social conditions influence hypothalamic-pituitary-adrenal activity in captive animals. Socially separated and individually housed animals generally experience increased cortisol secretion compared to animals housed with conspecifics, and social companionship can buffer the stress response when exposed to challenges such as introduction to novel environments. Nevertheless, the presence of conspecifics may also be the cause of stress because social dynamics impact individuals. Squirrel monkeys (Saimiri spp.) readily form same-sex affiliative social relationships, but in captivity, the presence of immature offspring severely disrupts affiliative associations among adults. We examined behavioral and physiological effects of the presence of immature offspring on adults by comparing two groups of adults with immature offspring to an all-adult group. We conducted behavioral observations and collected urine from adult members, and urine was assayed for cortisol at the Wisconsin National Primate Research Center. Adults in groups with immature offspring received an average of 18 play attempts per hour from the offspring, experienced a fivefold decrease in adult affiliation, and showed higher urinary cortisol levels compared to the all-adult group. A principal components analysis showed that adults characterized by receiving play attempts, rejecting play attempts, and lacking affiliative contact with other adults showed the highest mean urinary cortisol levels. Further analyses demonstrated that the persistent play attempts by immature offspring, not the resulting lack of adult huddling, were primarily responsible for the observed increase in urinary cortisol levels. Taken together, these data suggest that the disruptive effect of immature offspring produces a chronic cortisol increase in captive adult squirrel monkeys.

Animals↗

Astronomical and meteorological parameters and rest-activity rhythm in the spider monkey Ateles geoffroyi.

UNLABELLED: All animals including primates show regular variations in their behavioural activities and physiological functions. In numerous species diel, ultradian, infradian, annual and/or lunar rhythms have been established; however, the use of the focal sampling method does not provide information on hour-to-hour nor day-to-day variations. In behavioural field studies dealing with primate activity rhythms and their modulation by environmental variables the possible dual, synchronizing and/or masking effect of these variables is often ignored. In the present study, we analyze the relation between astronomical and meteorological parameters and various parameters of the rest-activity rhythm in Ateles geoffroyi, a species scarcely investigated with respect to biological rhythms. These Ateles were kept under semi-natural conditions, exposed to natural light, temperature and humidity cycles, and sky state. Motor activity was recorded with actiwatch accelerometers during 180 days (5-min intervals), starting from the autumn equinox. RESULTS: Ateles is active throughout the day, rests during the night and presents bimodal activity. Activity time, onset and end of activity as well as the times of their two activity peaks were significantly correlated with duration of the solar day and sunrise or sunset time. The behavioural parameters also correlated with ambient temperature. Climate factors and sky-state significantly influenced the duration and times of onset and end of activity. Our findings identified a clear modulation of the rest-activity pattern by astronomical variables serving as Zeitgebers, such as the natural light-dark cycle, and by masking effects of meteorological factors (temperature, weather and cloudiness), as well as of artificial variables introduced by the interaction with man.

Animals↗

Factors related to the attraction of flies at a biosolids composting facility (Bariloche, Argentina).

The composting process is used to treat biosolids from the Wastewater Treatment Plant of Bariloche (NW Patagonia, Argentina). Since 1998, an odourless, innocuous and stable organic amendment has been produced at the Biosolids Composting Plant of Bariloche. However, volatile compounds produced during this process, attract different vectors, mainly insects belonging to the Order Diptera, particularly in summer. To evaluate factors associated with the attraction of Diptera to composting windrows, volatile compounds, wind velocity, ambient and windrow temperatures were measured and their relationships with the taxa of flies found were determined. Sampling was conducted several months on newly formed windrows during 3 weeks of the thermophilic composting period. Composite samples from each windrow were taken on the first day of each sampling week, from November 1999 to March 2000 to analyze volatile compounds using an 'electronic nose'. Windrow and ambient temperatures and wind velocity were recorded on three consecutive days of each week, from January to March 2000; also the capture of flies was performed in this period. A weekly mean value was calculated for each environmental variable. Canonical Correspondence Analysis was employed to determine relationships between taxa of flies and the studied factors. The electronic nose discriminated among odours emitted, differentiating windrows by the bulking agent employed and by week of the thermophilic composting period. Ambient temperatures increased slightly during the sampling weeks; the highest values of wind velocity were registered during the second sampling week while windrow temperatures were sustained approximately 60 degrees C. Canonical Correspondence Analysis showed that attraction of flies to composting windrows was related to minimum and maximum ambient temperatures and volatile compounds for Muscina stabulans, Fannia sp. and Acaliptratae and to wind velocity for Ophyra sp., Sarcophaga sp., Cochliomyia macellaria and Phaenicia sericata.

Animals↗

How to analyze and understand the human immune system.

To enhance our understanding of the pathogenesis of diseases, including rheumatic diseases, and to improve disease control, it is essential to attain a thorough understanding of the human immune system, alongside mouse immunology. Historically, the investigation of the human immune system has posed significant challenges due to methodological limitations. Nonetheless, recent advancements in genomic studies of multifactorial diseases have elucidated that numerous risk-associated genetic variants affecting quantitative differences in cell-specific gene expression. In light of these findings, we are currently examining individual genetic variations in both healthy individuals and patients, as well as categorizing cells into distinct subsets in order to construct a comprehensive dataset concerning the human immune system. This is accomplished by combining data on gene expression, factors influencing the expression mechanisms, protein expression, metabolomics, and environmental variables pertinent to immune functionality-such as gut microbiota. These datasets will facilitate the comprehensive characterization of the human immune system. Using these datasets and through the integrative analyses of data related to risk genetic variations and gene expression profiles of each disease and individual, we anticipate uncovering novel insights into the human immune system, the heterogeneity of diseases, immune function mechanisms, and their regulatory strategies that may not be achievable through murine models.

Humans↗

Enzymatic variability of Candida krusei isolates in a course of fungal infection in a liver transplant recipient.

Transplant recipients are at high risk of fungal infections. The main site of fungal infections in patients undergoing liver transplantation is the abdominal cavity. One factor determining the pathogenicity of fungi is their ability to secrete hydrolytic enzymes. The aim of this study was to assess the enzymatic activity of Candida krusei, which caused an infection in a liver transplant recipient. The clinical specimens included swabs of throat, nose, and two drains, as well as bile, stool, and abdominal cavity aspirate. The yeast-like fungi isolated were identified by an ID 32 C test (bioMérieux) and their enzymatic activity assayed with the use of an API-ZYM test. Two biotypes of C. krusei were identified, depending on the source of the clinical specimen. The C. krusei isolates cultured from a throat swab, a nasal swab, and one of the drains secreted esterase lipase C8 (enzyme IV) and valine arylamidase (enzyme VII), in contrast to those isolated from the bile, abdominal cavity fluid, another drain, and stool. Characterization of two biotypes of C. krusei isolates cultured from different clinical samples from several infection sites indicated an ability of C. krusei to adapt to variable environmental conditions.

Candida↗

Ecology of the free-living stages of major trichostrongylid parasites of sheep.

Significant developments over recent decades make it timely to review the ecology of the major gastrointestinal nematode (GIN) species of sheep. These include the relentless development and spread of anthelmintic resistance in all of the major sheep production regions of the world, and the consequent drive towards integrated parasite management (IPM) systems incorporating non-chemotherapeutic strategies such as grazing management. The success of such programs is dependent on a detailed understanding of the environmental influences on the free-living stages of the nematode lifecycle. Major reviews of the subject were conducted prior to 1980, however considerable work has been completed since, including the development of mathematical models describing the epidemiology of GIN infection. Knowledge of the temperature thresholds for free-living development has also improved, while investigations of moisture influences and interactions with temperature have allowed more effective exploitation of environmental effects for IPM. This review re-evaluates our understanding of the factors that determine the success or failure of the free-living phases of the lifecycle in light of these developments. Temperature and moisture are the dominant influences on the free-living stages of Haemonchus contortus, Teladorsagia circumcincta and Trichostrongylus colubriformis, with the effects of pasture conditions playing a significant modulating role. Early in the free-living phase, the developmental success of the three GIN species is limited by susceptibility to cold temperatures. In general, H. contortus is most susceptible, followed by T. colubriformis and then T. circumcincta. The length of the development cycle is dependent largely on temperature, with development rate increasing at warmer temperatures. However, in order for development to proceed to the infective larval stage, addition of moisture is generally required. There has been considerably less work quantifying the effects of moisture on free-living development, although it is clear that H. contortus is most susceptible to desiccation during the pre-infective stages. Once the infective stage is reached, the influences of temperature and moisture on survival are less important, resulting in considerable survival times under conditions lethal to pre-infective stages. However, hot, dry conditions can be lethal for infective larvae of all three species, while extreme cold is also lethal with significant species variation. While the existing body of knowledge is substantial, the interpretation of many studies and comparison between them is complicated by inadequate description of, or variation in, the environmental measurements used. Confounding the effects of environmental variables on development to infective stage is the migration of larvae from the faeces and subsequent survival on pasture. There is a need to build on recent efforts to explore interaction between the effects of temperature and moisture, and also the trend to more closely simulate field conditions in laboratory studies. We propose a logical framework for future ecological investigations to overcome some of these problems, facilitate the development of a more integrated dataset on the subject and improve prediction of free-living development.

Animals↗

Modelling particle size distribution dynamics in marine waters.

Numerical simulations were carried out to determine the particle size distribution (PSD) in marine waters by accounting for particle influx, coagulation, sedimentation and breakage. Instead of the conventional rectilinear model and Euclidean geometry, a curvilinear collision model and fractal scaling mathematics were used in the models. A steady-state PSD can be achieved after a period of simulation regardless of the initial conditions. The cumulative PSD in the steady state follows a power-law function, which has three linear regions after log-log transformation, with different slopes corresponding to the three collision mechanisms, Brownian motion, fluid shear and differential sedimentation. The PSD slope varies from -3.5 to -1.2 as a function of the size range and the fractal dimension of the particles concerned. The environmental conditions do not significantly alter the PSD slope, although they may change the position of the PSD and related particle concentrations. The simulation demonstrates a generality in the shape of the steady-state PSD in the ocean, which is in agreement with many field observations. Breakage does not affect the size distribution of small particles, while a strong shear may cause a notable change in the PSD for larger and fractal particles only. The simplified approach of previous works using dimensional analysis still offers valuable approximations for the PSD slopes, although the previous solutions do not always agree with the simulation results. The variation in the PSD slope observed in field investigations can be reproduced numerically. It is argued that non-steady-state conditions in natural waters could be the main reason for the deviation of PSD slopes. A change in the nature of the particles, such as stickiness, and environmental variables, such as particle input and shear intensity, could force the PSD to shift from one steady state to another. During such a transition, the PSD slope may vary to some extent with the particle population dynamics.

Geologic Sediments↗

Modulation of prolactin but not corticosterone responses to stress in relation to parental effort in a long-lived bird.

We tested the hypothesis that parental effort modulates the magnitude of corticosterone and prolactin responses to stress in a long-lived bird, the Black-legged kittiwake (Rissa tridactyla). To do so, we compared corticosterone and prolactin responses to capture/restraint stress between chick-rearing birds and failed breeders (no parental effort). We predicted that (1) the increase in plasma corticosterone levels in response to stress should be lower in chick-rearing birds, (2) the decrease in plasma prolactin levels in response to stress should be lower in chick-rearing birds, and (3) as both sexes care for the chick, there should be no sex difference in the hormonal response to stress. Baseline plasma corticosterone and prolactin levels were higher in chick-rearing birds and were not influenced by body condition. Failed breeders were in better condition than chick-rearing individuals. Corticosterone response to stress was unaffected by parental effort as both chick-rearing and failed birds exhibited a robust corticosterone increase. Prolactin response to stress was however clearly influenced by parental effort: chick-rearing birds showed a modest 9% prolactin decrease whereas in failed birds prolactin concentrations fell by 41%. Body condition did not influence hormonal responses to stress. When facing stressful condition, breeding kittiwakes attenuate their prolactin response to stress while enhancing their secretion of corticosterone. Increasing corticosterone secretion triggers foraging efforts and diminishes nest attendance whereas an attenuation of prolactin response to stress maintains parental behavior. We suggest that this hormonal mechanism facilitates a flexible time-budget that has been interpreted as a buffer against environmental variability.

Adaptation, Physiological↗

Genome-wide SNP data reveal geographic structure and landscape-associated genomic differentiation in a widespread lizard in arid Eastern Central Asia.

Arid landscapes provide important systems for examining how geographic structure and environmental heterogeneity shape genomic differentiation. In topographically complex desert regions, however, it remains challenging to determine whether population structure primarily reflects landscape resistance, geographic distance, or contemporary environmental variation. Here, we use genome-wide SNP data to investigate population structure, phylogenetic relationships, historical gene flow, demographic history, and landscape correlates of genomic differentiation in the variegated racerunner (Eremias vermiculata), a widespread lacertid lizard across arid Eastern Central Asia. Analyses of 164 individuals recovered six geographically structured nuclear clusters associated with major desert basins and mountain-bounded regions. Nuclear phylogenies resolved two broad regional clades corresponding to northeastern and southwestern parts of the species' range, while PCA and ADMIXTURE analyses recovered six finer-scale genetic clusters. Mitochondrial phylogenies, based on combined NCBI-derived Cyt b and COI sequences from the same individuals, recovered four deeper maternal lineages. These patterns indicate overall phylogeographic agreement between nuclear and mitochondrial datasets, with genome-wide SNPs providing finer-scale resolution of population structure. Demographic reconstructions further uncovered regionally heterogeneous Late Pleistocene histories among clusters, including signals of expansion, stability, and decline. Landscape genomic analyses revealed that genomic differentiation is primarily associated with landscape resistance, particularly elevation and land cover, as well as geographic distance, whereas contemporary environmental variables explained comparatively little variation after controlling for spatial structure. Together, our results suggest that genomic differentiation in E. vermiculata reflects the interplay of persistent landscape configuration, historical connectivity, and region-specific demographic histories across arid Eastern Central Asia. More broadly, this study highlights the value of integrating phylogeographic and landscape genomic approaches for understanding population differentiation and evolutionary history in topographically heterogeneous desert ecosystems.

Arid Eastern Central Asia↗