The diamondback terrapin (Malaclemys terrapin) is a mid-sized turtle that serves as a keystone predator in salt marsh ecosystems of eastern North America. The terrapin has historically faced population declines due to habitat loss and overharvesting, which has resulted in its listing under multiple jurisdictions across the northern part of its range. To characterize levels and partitioning of terrapin genetic variation throughout the northeast region, we used restriction site-associated DNA sequencing (RADseq). We analyzed genetic variation among 116 individuals sampled across 18 sites. Within-population genetic diversity was relatively low (He = 0.080 to 0.122), and we observed a strong negative correlation between diversity and latitude. Furthermore, levels of genetic differentiation were moderate (pairwise FST = 0.00 to 0.19), with the mean pairwise FST of each population exhibiting a strong positive correlation with latitude. Together, these results are consistent with a model of serial colonization from a Pleistocene refugium in the mid-Atlantic. Spatial genetic variation was best explained by a landscape model that considered migration to be limited to coastal habitats, where northern range-edge populations maintained comparatively low genetic diversity and were more genetically distinct than populations to the south-consistent with their greater geographic isolation. Admixture analyses revealed weak genetic clustering, with the distribution of genetic clusters reflecting the combined historical effects of isolation-by-distance and human-mediated translocations. Regional efforts to restore terrapin habitat or reintroduce captive individuals should consider patterns of historic gene flow, cognizant of the relatively distinct and isolated populations at the northeastern range edge.

The unnatural selection: Plant evolution and adaptation in the Chernobyl and Fukushima Exclusion Zones.

Geographic origin and post-invasion genetic divergence of Mytilus galloprovincialis in China.

Genetic connectivity and regional differentiation of Calanus sinicus in Korean coastal wates with a focus on Yeosu Bay

Genetic differentiation of habitat-forming kelp Ecklonia radiata across an urban estuary.

Genome-based phylogenetics and species delimitation for the narrowly distributed Pachyhynobius salamander (Caudata: Hynobiidae) reveal cryptic biodiversity.

Differential copper stress responses in populations of the golden kelp Ecklonia radiata.

From the 1950s to the 1970s, approximately 80,000 kg of tea seeds were introduced from mainland China to the Xizang Autonomous Region for experimental cultivation. To assess the genetic diversity patterns of these tea accessions following more than half a century of acclimatization to plateau environments, we analyzed genetic variation, population structure, and genetic distinctiveness among fifty tea germplasm using nine phenotypic traits and 30 SSR markers. Phenotypic analysis revealed a moderately high level of genetic diversity, as indicated by the mean Shannon diversity index (H′ = 1.29). Principal component analysis (PCA) indicated that phenotypic variation was not geographically structured across the collection sites. The SSR markers exhibited a high degree of polymorphism, with an average polymorphic information content (PIC) of 0.610 and a genetic diversity index (I) of 1.437, indicating substantial genetic variation. Analysis of molecular variance (AMOVA) revealed that genetic differentiation occurred predominantly within populations, accounting for 91.49% of the total genetic variation. Similarly, 97.86% of the variation was attributed to differences within elevational gradients. Discriminant analysis of principal components (DAPC) and Bayesian population structure modeling (STRUCTURE) both identified two genetic clusters among the studied genotypes. Our results have practical implications for tea breeding programs by providing guidance for parental selection, informing germplasm collection management, and supporting the conservation of genetic resources.

The European Mudminnow ( Umbra krameri )—a species adapted to slow-flowing, oxygen-poor backwaters and marshes with dense vegetation—was declared extinct in Austria in 1975. However, it has since been rediscovered at two isolated sites: Fadenbach in the Nationalpark Donau-Auen and Jesuitenbach. Captive breeding programs have since been initiated to support reintroduction and safeguard remaining genetic diversity. To inform conservation strategies, we assessed genetic diversity, structure, and effective population sizes (Ne) using polymorphic microsatellite markers. Preliminary results reveal significant genetic differentiation between the two wild populations and between captive stocks and their presumed source in Fadenbach. Overall genetic diversity is low, and Ne estimates suggest a high risk of inbreeding, genetic drift, and further loss of adaptive potential. Although sample sizes are limited, these findings point to critical conservation concerns, especially for the Fadenbach population. Importantly, this study emphasizes the utility of genetic monitoring as a central tool for evidence-based conservation planning—supporting adaptive management, preventing further genetic erosion, and promoting the long-term survival of this critically endangered species in Austria and beyond.

Hop (Humulus lupulus) production in the eastern United States has increased in recent years, prompting the need to understand emerging fungal pathogens in this region. This study is the first population genetics analysis of Diaporthe humulicola, a recently described pathogen causing halo blight. A total of 71 D. humulicola isolates from Michigan, New York, Minnesota, and Canada were sequenced and analyzed using Illumina 150 x 150 bp reads with a 10x coverage. Single nucleotide polymorphisms were discovered and filtered using the Genome Analysis Toolkit. After filtering and clone correction, 63 isolates remained for downstream analysis. Population structure was determined to have three clusters and was supported using STRUCTURE, principal component analysis, and discriminant analysis of principal components. Analyses show that Michigan isolates are closely clustered with isolates from Canada and New York, and one isolate from Minnesota. The rest of the Minnesota isolates clustered in an independent cluster. Minnesota isolates appear to have high levels of population differentiation when compared to the different populations exhibiting a high fixation index, a measure of population differentiation and low nucleotide diversity. Mating type was determined for each isolate, with the Mat1-2-1 present in 61.9 percent of the whole population. We also detected signals of recombination in each of the fungal populations with higher levels in Michigan and Canada. These findings highlight the genetic complexity and regional differentiation of D. humulicola populations, with implications for disease management and hop breeding programs.

The Latvian Dark-head (Latvijas tumšgalve; LT) is the only sheep breed developed in Latvia. It is fully adapted to the country’s climatic conditions. As the sole national breed, it holds notable cultural importance by supporting traditional husbandry practices, landscape preservation, and regional identity. However, the dominance of commercial breeds threatens local genetic resources. Small-scale farms, where the LT population is concentrated, are especially vulnerable to population decline and possible extinction. This study assesses the genetic diversity within the LT breed and compares it with that of other major sheep breeds in Latvia. For the first time, lambs from sire rams of major breeds in Latvia underwent genotyping using the Illumina Ovine SNP50 BeadChip® (San Diego, CA, USA). Genetic diversity was assessed with minor allele frequency (MAF) analysis. Breed-specific markers were identified by detecting fixed SNPs (MAF = 0) unique to each breed. In total, 27,561 highly polymorphic SNPs (MAF 0.3–0.5) were identified in the LT breed. This indicates substantial genetic differentiation from other sheep breeds raised in Latvia. Among the analyzed SNPs, 2668 (5.45%) were fixed in the LT breed. Of these, 55–131 were unique compared with other breeds. The OvineSNP50 panel is an effective tool for characterizing the genetic structure of the LT breed. It enables the detection of distinct genetic traits and interbreed differences. These results establish a genomic basis for targeted conservation and selective breeding strategies. Such strategies maintain the genetic integrity and competitiveness of the Latvian Dark-head.

The genetic diversity and variation of two naturally distributed Camellia sinensis var. madoensis populations in Phu Yen, Vietnam, were analyzed using start codon targeted polymorphism (SCoT), inter simple sequence repeat (ISSR), and conserved DNA derived polymorphism (CDDP) techniques, and combined data. Based on the combined data, the entire variety possessed the following genetic diversity parameters: expected heterozygosity (He) = 0.2691, Shannon index (I) = 0.4085, and proportion of polymorphic bands (PPB) = 92.37%. The Cu Mong population demonstrated higher genetic diversity (He = 0.2223, I = 0.3387, PPB = 75.1%) than the Cao Phong population (He = 0.1531, I = 0.2358, PPB = 54.62%). Low gene flow (Nm = 1.2088) led to a significant genetic differentiation index (GST = 0.2926) and genetic distance (D = 0.2113) between the two survey populations. The distribution of genetic variation within the populations (WP = 54%) was slightly higher than that among populations (AP = 46%). Each DNA fingerprinting technique had distinct strengths and weaknesses in assessing genetic diversity and variation. However, the SCoT technique emerged as the most suitable for this study based on its overall utility.

BackgroundBasella alba L. a widely consumed green leafy vegetable, exhibits considerable nutritional and therapeutic potential attributed to its bioactive constituents. Prior investigations revealed significant variation in phytochemical and antioxidant activity across agro-climatic zones in Sri Lanka, suggesting potential genetic influence. This study is designed to explore underlying genetic variation using RAPD markers to investigate the correlations and contributions of genotype on previously reported bioactivity variation.ResultsFrom a screening of 15 RAPD primers, four primers (OPA 9, OPA 10, OPA 16, and OPB 10) produced, polymorphic, consistent and clearly scorable banding profiles (under optimized PCR conditions) in B. alba L. collected from 15 Sri Lankan locations. These primers collectively yielded 36 bands, 35 of which were polymorphic, resulting in a high polymorphism rate of 97.2%, confirming the informativeness of the selected primers for genetic diversity analysis. Genetic similarity was assessed using Jaccard’s coefficient in NTSYSpc.v2·10e, revealing values ranging from 0.44 to 0.97, with the highest similarity from the samples from Ratnapura and Kandy and the lowest similarity in Ratnapura and Kalutara. A dendrogram constructed via UPGMA grouped the samples into two major clusters and five sub-clusters, demonstrating substantial genetic differentiation influenced by geographic origin. Cluster I included Ratnapura and Kandy, while the remaining samples formed Cluster II and its subgroups, each representing different ecological zones. When compared to the phytochemical and antioxidant clustering data of the previous study, partial correspondence was observed. A Mantel test comparing genetic diversity and biochemical/antioxidant potential revealed a weak negative correlation which was not significantly different. Some of the locations within similar genetic cluster shared similar biochemical traits, while others diverged significantly, indicating that environmental conditions also influence bioactive compound synthesis. Notably, Cluster I (Ratnapura and Kandy) showed both genetic similarity and lower antioxidant traits. Samples from Ella and Polonnaruwa showed similar bioactive traits even though they were grouped into different genetic clusters.ConclusionThese findings suggest that both genetic makeup and environmental adaptation contribute to observed biochemical diversity in B. alba L. with a clear geographical correlation. This study highlights the value of integrating molecular and biochemical analyses to develop regionally adapted B. alba L. cultivars with enhanced nutritional traits, supporting sustainable agriculture in Sri Lanka and beyond.Supplementary informationThe online version contains supplementary material available at 10.1186/s12863-025-01385-4.

The genus Medicago, which includes the widely cultivated forage crop alfalfa, is of significant agricultural and ecological importance. Understanding genetic diversity in Medicago is essential for the conservation of its germplasm and its utilisation in plant breeding. This study aimed to assess the genetic diversity and population structure of the Medicago germplasm collection at the German Federal Ex situ Gene Bank. Genotyping-by-sequencing was used to analyse 1234 accessions of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), representing 40 Medicago species. After filtering, a high-quality dataset of 23,315 single nucleotide polymorphisms (SNPs) was generated. Our analyses revealed distinct genetic clusters corresponding to Medicago species and sections, with cultivated M. sativa L. and M. × varia Martyn clustering together with less genetic diversity compared to their wild counterparts. This reflects the shared genetic composition and extensive gene flow between M. sativa and M. × varia, commonly considered a hybrid between M. sativa and M. falcata L. Wild species displayed a more complex genetic structure, with polyphyletic patterns indicating higher genetic differentiation that reflects their diverse evolutionary histories and ecological adaptations. In conclusion, the comprehensive diversity analysis of the IPK Medicago collection provides valuable insights for gene bank management, targeted conservation efforts and strategic breeding initiatives.

ABSTRACTDefining appropriate conservation units is crucial to the protection and management of biodiversity. These delineations deliver further benefit when they include assessments of population vulnerability to extinction from pressures such as climate change. However, delineations and vulnerability assessments are particularly difficult within highly diverse species, such as the salmonid fish Arctic charr (Salvelinus alpinus), that show extensive phenotypic and genetic variation within and across locations, variable and complex life histories and broad geographic distributions. As yet, the nature and scope of Arctic charr diversity has not been characterised at the scale needed to delineate key conservation units in Scotland. To identify evolutionarily significant and vulnerable populations to prioritise for conservation, we conducted a genomic study of Arctic charr populations across Britain and Ireland with a focus on Scottish populations (N = 64 populations; 24,878 SNPs; 410 individuals). We found that most lake populations represented distinct genetic clusters, with limited gene flow between them and resulting in substantial genetic differentiation. Higher level groupings of genetic similarity across catchments likely reflect historic anadromy and migration, with populations primarily grouping east or west of the central watershed divide in Scotland. Analysing genetic offset, also known as genomic vulnerability, we identified strong inverse correlations between genetic vulnerability and latitude and distance to the sea, suggesting that more southern and more inland populations are more vulnerable to the effects of climate change. Additionally, patterns of vulnerability across several additional metrics identified other populations that may be at higher risk of loss. We further used our genetic data, along with phenotypic and geographic information, to identify populations of greatest evolutionary significance. This highlighted that the most important ones to protect are those in locations with multiple ecotypes, a key facet of functional Arctic charr biodiversity, and populations that are the only ones in their Hydrometric Area.

ABSTRACTApocynum venetum L., a saline‐alkali‐tolerant plant valued for its high‐quality bast fiber in textile manufacturing and medicinal compounds in traditional medicine, serves as a key economic species in saline‐alkali regions with additional phytoremediation applications. However, its natural populations are becoming increasingly threatened by rapid environmental change and anthropogenic activities. To inform conservation and sustainable utilization, we generated a chromosome‐level genome assembly of A. venetum (234.73 Mb; contig N50 = 19.11 Mb, scaffold N50 = 20.46 Mb) using PacBio HiFi, Illumina and Hi‐C technologies, and performed whole‐genome resequencing of 109 individuals spanning China's saline‐alkali regions. Population genetic analyses revealed that the Xinjiang population exhibited the highest level of genetic diversity and strong genetic differentiation from the other populations. Demographic analyses indicated that most populations underwent significant population declines during the late Last Glacial Maximum, followed by recovery in western and northern populations, whereas the eastern coastal populations maintained consistently low effective population sizes. Genome‐environment association analyses identified candidate adaptive loci, including a flavonol 4′‐sulfotransferase (4′‐ST) gene, potentially linked to saline‐alkali tolerance and flavonoid biosynthesis. Our findings provide critical insights into the evolutionary history and adaptive mechanisms of A. venetum, offering genomic tools for conservation prioritization and the development of stress‐resilient cultivars through marker‐assisted breeding.

Ternstroemia sylvatica inhabits several temperate and tropical montane forests in eastern Mexico. Its current discontinuous distribution results from both natural and anthropogenic fragmentation. We assessed the genetic diversity and population differentiation of T. sylvatica across its distribution range using 18 microsatellite markers. We sampled 366 individuals from 16 populations, analyzing genetic diversity (He) and population structure via STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Our results revealed high genetic differentiation (FST = 0.21), with most genetic variation occurring within populations (79.50%). STRUCTURE analysis identified two major genetic clusters: a northern group, comprising the populations with the lowest genetic diversity, and a southern group with higher genetic diversity (He = 0.59–0.73) geographically structured into ten subgroups. Additionally, the results suggest historical fragmentation, limited gene flow among populations and inbreeding, as a heterozygote deficit is prevalent across populations. The high genetic diversity in specific populations indicates potential hybridization with other sympatric Ternstroemia species.

To characterize molecular profiles of Salmonella isolates from the Meishan region (2014-2024) via whole-genome sequencing, focusing on serotype distribution, antimicrobial resistance genes (ARGs), virulence genes, and genetic differentiation based on coding-region single nucleotide polymorphisms (cgSNPs), and provide a molecular epidemiological basis for precise prevention, control, and source tracing of Salmonella infections. Sixty Salmonella strains from distinct sources (food surveillance = 2, food poisoning = 7, intestinal surveillance = 23, pathogen surveillance = 17, healthy population surveillance = 2, and other surveillance = 9) (2014-2024), Table 1, were sequenced on Illumina NextSeq 500. Serotypes (SISTR v1.1.0), multilocus sequence typing (MLST v2.0), ARGs/virulence genes (Abricate v1.2.0; CARD v3.2.7, VFDB v202310), and a cgSNP-based phylogenetic tree were constructed using Snippy v4.6.0 with the Salmonella Typhimurium reference genome (GCA_020714865.1). Twelve serotypes were identified; with Salmonella Typhimurium (65.0%, 39/60) as the dominant serotype, widely distributed across clinical, food, and outbreak sources, followed by Salmonella Enteritidis (13.3%, 8/60). Salmonella Typhimurium had prevalent ST34 (59.0%) and ST19 (38.5%); ST34 was confirmed as a locally dominant clone compared to the globally common ST19. All Salmonella Enteritidis were ST11. Five ARG categories (60 types) were detected: aminoglycoside resistance genes (96.7%) were most common, followed by β-lactam (65.0%) and sulfonamide (63.3%) resistance genes. Notably, Salmonella Typhimurium exhibited a high multidrug resistance (MDR) rate of 64.1%, which was significantly higher than that of Salmonella Enteritidis (12.5%). Core virulence genes (e.g., SPI-1, TTSS-1) were ≥95% conserved; serotype-specific genes (e.g., cdtB) were strain-specific. The 60 strains were divided into 14 clusters, with 76.7% (46 strains) assigned to 3 major clusters, confirming epidemiological links between outbreaks and sources. Salmonella Typhimurium ST34/ST19 with a high MDR rate is the dominant epidemic clone in the Meishan region, posing significant public health risks. cgSNPs are useful for source tracing. Targeted surveillance of dominant clones and stricter antibiotic regulation are imperative.

The diversity, genetic differentiation, and cophylogeny of avian protozoa of the genus Leucocytozoon and their black fly vectors (Diptera: Simuliidae) in Thailand were investigated. Leucocytozoon infections were detected in 46 (11.2%) of 410 black flies representing six species: Simulium asakoae, S. chumpornense, S. khelangense, S. siamense complex, S. yvonneae, and S. gombakense. The latter three species represent the first reports of having Leucocytozoon infections, suggesting their potential role in parasite transmission. A total of 12 Leucocytozoon lineages was identified, including novel lineages with low sequence similarity (92%) to previously known records in the S. siamense complex and S. yvonneae. These findings indicate uncharacterized parasite diversity in wild birds of Thailand. Genetic differentiation among Leucocytozoon populations was minimal across different geographic populations, but highly significant among parasites in different species of black flies, even when collected from the same location. Cophylogeny analyses revealed significant co-phylogenetic relationships between Leucocytozoon lineages and their potential black fly vectors, despite similarities in host-blood sources. These findings emphasize that parasite-vector specificity is shaped not only by host preference, but also by coadaptation mechanisms between black flies and Leucocytozoon species. Further studies on avian hosts, bloodmeal sources, and parasite-vector interactions are necessary for understanding Leucocytozoon transmission dynamics in Southeast Asia.

Abstract Phenotypic plasticity refers to the capacity of an organism’s phenotype to vary in response to changes in environmental conditions, without any change in the individual genotype. Sea urchins (Echinoidea) are well-known for their morphological and behavioural plasticity in response to changing habitats or trophic environments. Phenotypic plasticity has been little studied in directly developing species, in which low levels of phenotypic plasticity are usually expected as a consequence of high levels of genetic differentiation among populations and local genetic adaptation. In the present work, we report a significant plasticity in the direct-developing and brooding sub-Antarctic species Ctenocidaris ( Eurocidaris ) nutrix (Echinoidea, Cidaridae) through morphological and trophic analyses of gut contents and δ 13 C and δ 15 N isotopic compositions. Molecular data (COI mtDNA) confirm that the different phenotypes of C. nutrix , the short-spined C. nutrix nutrix and the long-spined C. nutrix longispina , are a single species restricted to sub-Antarctic waters. As formerly demonstrated in broadcasting echinoid species, morphological plasticity appears to be mainly linked to depth and swell exposure, specimens from exposed and shallow sites showing shorter spines and larger apical systems compared to specimens from sheltered or deep sites. Significant differences in the diet and trophic niche of the different phenotypes suggest that prey type and food diversity may also be a factor promoting distinct phenotypic responses, both in the feeding behaviour and morphology of echinoids.