The garden dormouse (Eliomys quercinus) is one of the fastest-declining mammals in Europe, and action is needed to prevent further population losses. The primary causes of declines are not well-understood, as the species experiences variable conditions and threats across its range, but likely include habitat fragmentation and loss. Previous genetic studies have provided evidence of highly structured garden dormouse populations in Western Europe, despite this region having been defined as a single clade with mitochondrial DNA analysis. Within Western Europe, the magnitude of declines has been recognized to be greater on the eastern edge of the species' range, which could explain differentiation within the clade as resulting from diversity loss and genetic drift for regions under greater risk of extirpation. Here, we focus on fine-scale genomic differentiation across the Western European clade to explore the consequences of genomic erosion on the eastern region and to help identify mechanisms driving genetic differentiation within this species. We found genetic differentiation both between and within major geographic regions. Populations located in the eastern edge of the species' range showed stronger signs of population isolation, including structure between spatially distant populations, lower genetic diversity, and greater rates of inbreeding. However, all populations exhibited signals of recent rapid population decline. Outlier analyses indicated that differentiation between regions was primarily due to genetic drift resulting from isolation-by-distance rather than adaptive differentiation. We also found genetic structuring between populations within the Rhine Valley, despite apparent lack of physical barriers preventing dispersal among groups within this region. Our findings indicate that population isolation following habitat loss and fragmentation has likely been a major contributor to garden dormouse declines. Dispersal among disparate garden dormouse sampling regions is restricted-even across local spatial scales-leading to loss of genetic diversity and potential erosion of evolutionary potential. With 21st century declines expected to continue across the species' range, even relatively common and well-connected populations are likely to follow the trajectory of the eastern populations, with increasing loss of diversity as populations contract and become more isolated.

The increasing frequency of castor bean or ricin-induced intoxication or terror events threatens public safety and national security, making the tracing of castor bean origins critical for law enforcement and counterterrorism efforts. Chemical attribution signatures (CAS) could address this issue by providing inherent and forensic links between ricin-containing samples and their geographical origins; however, practical implementations of this approach remain scarce. Omics data sets offer substantial potential to generate comprehensive biological insights and high-dimensional data for provenance attribution, where transcriptomics and proteomics profiling are better suited to castor beans than traditional genomics and metabolomics, regarding that castor beans exhibit low genetic diversity but high phenotypic polymorphism. In this work, toward castor bean samples from 14 provinces or autonomous regions in China and three international locations, including Ethiopia, Pakistan, and South Sudan, we proposed an integrated local-global data-mining strategy by systematically integrating RNA-seq transcriptomics and data-independent acquisition quantitative proteomics, and developed a straightforward feature-screening pipeline to prioritize 59 signature peptides as provenance-related CAS with distinct interregional and international expression patterns. A subsequent machine learning model trained on these CAS achieved 93.7% classification accuracy, identifying robust discriminative patterns among samples from different global regions, as well as fine-scale differences across altitude gradients and north-south divisions in China, in which the attribution index of altitude and latitude is reported for the first time. Finally, after validation by parallel reaction monitoring in nanoLC-HRMS/MS, we confirmed a minimum signature panel of 24 peptides as molecular CAS markers for the origin attribution of castor beans.

A novel core genome clustering method proposed for population structure analysis and genotyping of bacterial genomes.

ABSTRACTNon‐native species can be introduced to novel environments such as cities via wildlife trade. These populations may have conservation value—particularly if they are of a species threatened in its native range. Genetic tools can help assess the fitness of introduced populations by indicating if they are (1) suffering the consequences typically associated with small, isolated populations derived from few founders (e.g., inbreeding, low genetic diversity) or (2) they demonstrate gene flow indicative of mixed‐origin founders, successful breeding, and/or continual introductions of conspecifics. Such data can inform management interventions in the ex‐situ environment and highlight potential contributions of introduced populations to native‐range conservation. We examined multiple metrics of genetic health of a non‐native population of ca. 200 critically endangered Yellow‐crested Cockatoos (Cacatua sulphurea)—native to the eastern Indonesian archipelago—introduced to Hong Kong (HK) from the 1960s. We sequenced whole genomes and mitochondrial DNA of HK cockatoos and compared them to native‐range C. sulphurea, Sulphur‐crested Cockatoos (C. galerita) from Australia, and representatives from five additional wild parrot populations. Results indicate HK's cockatoos may have as yet evaded the severe negative genetic consequences of small, isolated populations, and currently have Ne and nucleotide diversity comparable to other wild parrot populations. Their genetic characteristics conform to those of young, mixed‐origin, non‐native populations: high individual‐level variance in relatedness and inbreeding/outbreeding, and influences of admixture. Given that C. sulphurea subspecies exhibit very low genetic distances, HK's city cockatoos are worthy of further examination as a potential genetic reservoir and rescue source for C. sulphurea.

Translocations and reintroductions aim to improve the viability of isolated populations and promote connectivity for large carnivores. However, there is no established framework for assessing their success. We used the Eurasian lynx (Lynx lynx) in western and central Europe to assess the impact of translocations on the viability of six populations and their interconnectivity. Lynx populations are small and isolated and have low genetic diversity. Population reinforcements have been carried out, but their impact has not been determined. We devised a workflow to evaluate how releasing new individuals affects population extinction probability and connectivity and patch colonization, and to estimate the minimum release population to create a stepping-stone network. To this end, we calibrated a spatially explicit, individual-based model with space use, survival, and reproductive rates observed in the populations and validated it with field data on population growth and expansion from the 1970s to 2020. We ran the model with the observed population structure in 1995-1996 to 2040 in two scenarios, with and without translocations. In both scenarios, most existing populations remained stable in our model for the next 20 years, but had low connectivity. Lynx translocations positively affected viability and connectivity on a population scale but did not increase connectivity between the eastern and western Alps. To create a stepping-stone population that would significantly improve connectivity across the Alps, we conservatively estimated that at least 13 males and 37 females should be released in the Italian southeastern Alps based on the assumption of negligible immigration rates between patches. Concerted transboundary management to improve the future survival of lynx populations in western and central Europe is still needed.

Type 1 diabetes (T1D) is a chronic autoimmune disease with variable incidence worldwide,. with a higher incidence in countries of European ancestry. The present study aimed primarily to evaluate differencesin genomic ancestry (GA) and genetic diversity (GD) betweenindividuals with T1D in Brazil and Portugal compared with healthy control. Secondarily, we aimed to compare theGA and to compare the GA of individuals with T1D from different regions of Brazil with those from Portugal. The sample included 1,698 Brazilians and 107 Portugueseindividuals with T1D, whose data were analyzed using Ancestry Informative Markers (46-AIMs-Indels) to estimate the proportion ofEuropean, African, and Native American (NAM) ancestry.Allele frequencies for short (1) and long (2) alleles were estimated for all individuals. Fragment genotyping was performed by capillary electrophoresis using the ABI 3500 sequencer (Applied Biosystems). The data were analyzed using GeneMapper V.4.1 (Life Technologies, USA). STRUCTURE v2.3.3 software was used to estimate individual ancestry, with K values ranging from 2 to 5 to assess the robustness of the inferred ancestry proportions based on the HGDP-CEPH diversity panel (H952 subset) as a reference for ancestral populations. Genetic parameters were estimated using the software Arlequin v3.5.2.2 RESULTS: The results revealed a predominance of European GA in both populations, with higher European GA in Portugal and higher African and NAM GA in Brazil. A higher GD was observed in individuals with T1D from Brazil compared with those from Portugal. Non-admixed individuals with T1D from Portugal exhibited high genetic homogeneity and low genetic diversity. Individuals with T1D from the Northern Region of Brazil presented the greatest genetic differentiation compared to regional control groups.. This study identifies differences in GA and GD among individuals with T1D from Brazil and Portugal. Considering the dynamics of migrations and admixture in both countries, our datashoulddrive future research areas related to identifying other genetic variants, such as the HLA system alleles (risk or protection) in Brazil and Portugal, which may contribute to a better understanding of the pathogenesis of the disease in both countries.

Porcine circovirus 3 (PCV3) has been detected worldwide in both healthy and diseased pigs, raising questions about its molecular diversity and potential genotype structure. Since its discovery, several genotyping schemes have been proposed; however, most of them rely on arbitrary criteria and often produce inconsistent or conflicting classifications. In this study, all high-quality PCV3 ORF2 sequences available at the GenBank to date were analyzed to evaluate whether consistent and reproducible genotyping criteria can be defined. Phylogenetic trees reconstructed using multiple algorithms and statistical comparisons of topological similarity revealed moderate-to-high incongruence among methods, limited phylogenetic signal, and a general decline in bootstrap support toward deeper nodes. Genetic distance distributions showed complete overlap between and within proposed genotypes, further questioning the biological meaning of such partitions. Overall, these findings indicate that the current genetic landscape of PCV3 does not support a robust or standardized genotyping framework. Given the low genetic variability of PCV3 and the absence of experimental evidence for genotype-specific differences in antigenicity, epidemiology, or virulence, the definition of formal genotypes appears challenging and premature, and likely unnecessary at this stage.

Studying how genetic variation is structured across space, and how it relates to divergence in phenotypic traits relevant to reproductive isolation, is important for our understanding of the speciation process. We used ddRAD-seq data to examine genetic variation across the distribution of an Andean warbler species complex (Myioborus ornatus-melanocephalus), which includes a known hybrid zone between two taxa with striking plumage differences. Genetic structure reflects geographic variation in head plumage, with some breaks coinciding with major topographic barriers in the Andes. We found that M. o. chrysops and M. m. bairdi, the two hybridizing taxa, were characterized by low overall genetic divergence. Based on our cline analyses of plumage and genomic hybrid indices, this hybrid zone extends for approximately 250 km, where advanced generation hybrids are likely most common. We also identified a slight difference in the geographic centers of the plumage and genetic ancestry clines, potentially suggesting asymmetric introgression of chrysops-like plumage traits. By studying genetic variation in a phenotypically diverse group distributed across a topographically complex area that includes a hybrid zone, we show how both geographic features and plumage traits potentially relevant to mate choice may contribute to species formation and maintenance in tropical mountains.

The critically endangered white-thighed colobus, Colobus vellerosus, is on the brink of extinction, necessitating the implementation of effective conservation management strategies. The population in Kikélé village serves as the primary remaining stronghold for this species in Benin, comprising around twenty-nine individuals in the small Kikélé Sacred Forest (KSF) and an additional eight individuals in the community-managed Okuta Kobunan Forest (OKF). The KSF is a well-established sacred forest managed by the Kikélé community and is situated an average of 7.5km from the OKF, which is currently being developed as a community-managed forest. These two populations are believed to have descended from a single founding pair introduced to the Kikélé region circa 1800. Given the small population size and the possible severe genetic bottleneck at its foundation, the genetic diversity might be extremely low. In our study, we conducted a first analysis of the genetic diversity of the two populations using mitochondrial markers, the complete cytochrome b (cytb) and a segment of the hypervariable control region (D-loop, 750bp). Our findings revealed only one cytb haplotype, along with two haplotypes that differ by just one site in the D-loop. We recommend a range-wide population genetic assessment of the species to explore the possibility of translocations as a potential genetic rescue strategy.

Ecoepidemiology of Angiostrongylus cantonensis in Mediterranean rats: spatial heterogeneity, low genetic diversity and precipitation-driven transmission.

ABSTRACTIn a rapidly warming Arctic, genetic variation might serve to buffer organisms against the effects of environmental change, such as sea ice loss and ocean warming. Yet, this concept remains largely unexplored because comprehensive genome‐wide studies across the full ranges of Arctic marine taxa are rare. Bowhead whales (Balaena mysticetus) have a strong association with sea ice and polar water masses, a long history of human exploitation, and a circumpolar distribution, making them a valuable model for evaluating how past environmental and anthropogenic factors have shaped contemporary population variation. We analysed both nuclear and mitochondrial genomes from bowhead whales sampled across the species' range, encompassing all four recognised stocks. Firstly, our results indicate the existence of three genetic groupings instead of four: (1) Okhotsk Sea; (2) East Greenland‐Svalbard‐Barents Sea; and (3) a population containing two recognised stocks—the Bering‐Chukchi‐Beaufort and East Canada‐West Greenland. We utilised high‐resolution ecological niche modelling and bowhead whale movement data to reconstruct inter‐stock habitat connectivity over the last 11,700 years, finding that this explains our identified genetic groupings. Bowhead whale populations exhibit little‐to‐no evidence of recent inbreeding and retain high genetic diversity relative to other mammalian species despite centuries of intensive commercial whaling. The most vulnerable population is that in the Okhotsk Sea, which has the lowest genetic diversity, most inbreeding, and the highest realised genetic load. Collectively, our findings elucidate the recent history and dynamics of bowhead whales, offering valuable baseline data and context on present‐day genetic structure and diversity to support effective conservation and management strategies.

Linguistic structures show uneven global distributions, but it remains unknown to what extent such distributions are driven by human population history at a global scale. Here, we track population history through population genetics and show that, adjusting for geography, phylogeny, and environment, genetic diversity (in terms of local homozygosity modeled across individuals) is inversely correlated with linguistic diversity (in terms of local entropy of structural features modeled across languages). This inverse correlation arises from the parallel impact of isolation vs. contact on both genomic and structural linguistic diversity: Isolation leads to low genetic diversity and promotes structural linguistic diversification, while contact and migration yield higher genetic diversity and promote linguistic homogenization. The extent of the correlation varies across world regions and aspects of language, but its overall global robustness highlights how hotspots of linguistic diversity can serve as a compelling example of the flexibility of human language, since they have been less affected by the increase of contact and migration that occurred over recent millennia and homogenized linguistic structures.

Understanding evolutionary relationships in domesticated crops and their wild relatives is often challenging because of their recent divergence, and still ongoing interspecific gene flow. These processes blur species boundaries and complicate phylogenetic reconstruction. The genus Sechium (Cucurbitaceae), which includes the cultivated chayote (S. edule ssp. edule), a Neglected and Underutilized Species (NUS), and its related wild taxa, represents one of such cases. Using genome-wide Single Nucleotide Polymorphisms (SNPs) analyzed under a population genomics framework, we explored the species barriers of Sechium and reconstructed its phylogeny using multispecies coalescent models. Our results clarify taxonomic boundaries within the genus, confirming S. edule ssp. sylvestre as the closest wild relative of the cultivated chayote, and supporting species-level distinction among wild taxa. Divergence within Sechium mostly occurred during the Pleistocene, and our data point to the "Oaxaca" biogeographic province, in southern Mexico, including parts of the states of Oaxaca, Puebla and Veracruz, as the most likely center of chayote domestication. Several metrics revealed low genetic diversity and small contemporary effective population sizes (Ne) in wild taxa, highlighting their vulnerability under ongoing tropical cloud forest loss. These findings emphasize the urgent need to integrate wild Sechium species into national and international conservation frameworks. More broadly, this study demonstrates how combining phylogenomics and conservation genomics can help resolve taxonomic uncertainty, trace domestication processes, and guide the preservation of Crop Wild Relatives (CWR); particularly those associated with NUS that remain vital for future food security and agroecosystem resilience.

Urbanisation is a pervasive form of anthropogenic environmental change and a driver of contemporary evolution. Yet, it remains unclear how demographic processes and environmentally associated genomic variation shape genomic patterns in cities and whether these responses depend on species-specific ecological traits. Here, we addressed this gap using whole-genome sequencing of two related, diet-specialised solitary bees (Andrena florea and Andrena vaga) that differ in dispersal-related traits, rarity and host-plant distribution, sampled along an urban intensity gradient. By integrating population and landscape genomic analyses, we quantified genetic diversity, demographic history, population structure and genotype-environment associations. Neutral genomic patterns differed strongly between species: A. florea showed lower genetic diversity, higher differentiation and a recent population decline, whereas A. vaga maintained higher diversity, connectivity and demographic stability. Genetic diversity was associated with species-specific landscape features (edge density in A. florea and semi-natural habitat in A. vaga), rather than with urban intensity per se. Despite weak population structure, genotype-environment association analyses identified loci associated with urban intensity, and haplotype-based scans detected genomic regions showing patterns consistent with positive selection. Functional annotation and cross-species comparisons revealed partial convergence in candidate genes and functional pathways. Together, these results show that genomic responses to urbanisation cannot be explained by urban intensity alone, but instead emerge from the interaction between gene flow, genetic drift and selection, mediated by species-specific ecological traits. This leads to divergent demographic trajectories but partly convergent genomic responses across species.

Human-driven biodiversity loss, intensified by illegal hunting and trafficking, has caused severe wildlife population declines and extinctions, necessitating studies on long-term genomic erosion to inform conservation strategies. While temporal genomic analyses using ancient and historical/museum DNA reveal generational impacts, sparse sampling often limits insights into prolonged declines, highlighting the need for time-resolved studies to understand sequential population decline and species persistence under sustained pressures. The Chinese pangolin (Manis pentadactyla), critically endangered as a result of historical overexploitation, has experienced severe continuous population decline pre-1979, 1980-1999, and post-2000. However, the temporal genetic consequences and associated extinction risks remain poorly understood. We analyzed 228 pangolin genomes (133 newly sequenced), spanning continuous population decline, to assess the dynamics of genomic erosion. Our results demonstrate that persistent population decline drives long-term genetic decline within populations, with the severity of population decline correlating directly with the degree of negative genetic impact (e.g. reduced diversity, increased inbreeding and genetic load) and extinction risk. Counterintuitively, however, between populations, those experiencing the most severe population decline (e.g. southwest China) exhibited less extreme relative genetic consequences compared to less severe population decline (e.g. south China), suggesting a stronger dependence on the history of effective population size before population decline. Critically, the contemporary South China population shows significantly lower genetic diversity, higher inbreeding, elevated genetic load, and consequently higher extinction risk, demanding urgent prioritization for conservation. This study provides novel insights into the complex genomic legacy of continuous population decline, elucidating anthropogenic impacts on genetic erosion and offering a scientific framework for targeted conservation strategies.

Choerospondias axillaris is an ecologically and economically important tree species, yet its phylogeographic pattern remains insufficiently understood. We analysed 29 natural populations of C. axillaris in China based on three chloroplast DNA (cpDNA) and internal transcribed spacer (ITS) sequences. The MaxEnt model was then employed to forecast changes in suitable habitats under four climate scenarios. The results show that C. axillaris exhibits moderate genetic diversity (cpDNA: H t = 0.585; ITS: H t = 0.301). CpDNA genetic variation mainly exists among populations (61.51%), whereas ITS genetic variation is primarily concentrated within populations (90.17%). This pattern indicates that seed dispersal is limited, but pollen-mediated gene flow is extensive. Neutrality tests and mismatch distribution analyses suggest that C. axillaris has undergone significant and recent population expansion in its history. We infer that the Xuefeng Mountains-Wushan region in central China may have served as a significant glacial refuge. After the Last Glacial Maximum, C. axillaris expanded southwards (such as Guangdong) from this region to establish the current distribution patterns. Future climate warming may drive its suitable habitats northwards to areas south of the Qinling Mountains. Therefore, priority should be given to protecting identified genetic diversity hotspots and potential refuge populations while implementing targeted management for populations with low genetic variation to ensure the species' evolutionary potential.

Climate change is driving major shifts in global snake biodiversity, yet large-scale assessments across taxonomic, phylogenetic, and genetic dimensions remain limited, hindering effective conservation. We compiled 3,486,894 records of 3044 species across seven biogeographic realms to evaluate current spatial patterns of diversity and to project future range dynamics and conservation priorities under different climate change scenarios. We constructed species distribution models for 1201 species to project range dynamics under four shared socioeconomic pathways across 10 global climate models and then applied generalized linear mixed models that integrated genetic and phylogenetic diversity to assess conservation priorities. Of 1201 species, 542 (45.1%) were projected to experience significant range contractions (a mean range loss of 11.62%). Of these, 175 species (14.6%) were projected to undergo both range loss and shifts of more than 400km, and 103 of 775 species (13.3%) were projected to exhibit range contraction and low genetic diversity. Range shifts were widespread, especially in the Palearctic, with >60% of genera expected to move >100km. Species in tropical forests and montane habitats were disproportionately at risk of range contraction and range shifts. Current protected areas (PAs) covered only 20-40% of the ranges of threatened snakes, and 81 of 341 genera (23.7%), such as Boa and Lachesis, were projected to lose habitat more rapidly inside PAs than outside. We identified four groups of conservation priority based on range vulnerability, genetic risk, and conservation gaps: taxa facing both range contraction and long-distance shifts; genetically vulnerable taxa with shrinking ranges; taxa inadequately covered by PAs; and taxa projected to lose habitat faster inside PAs than outside. These findings underscore the urgent need for spatially adaptive, genetically informed, and climate-resilient conservation strategies to protect the evolutionary potential of global snake diversity.

Abstract Snow scorpionflies ( Boreus ; Mecoptera: Boreidae) are cold‐adapted insects that are active on snow, yet basic ecological and phylogenetic information remains scarce for species from East Asia and the Russian Far East. In the Japanese archipelago, Boreus jezoensis Hori and Morimoto (1996) is the only recorded species of the genus and has been known solely from its type locality, Mt. Hirayama (Hokkaido), with no subsequent confirmed records. We conducted field surveys in montane areas of Hokkaido, including the type locality; 26 adult Boreus individuals were identified from exposed moss patches adjacent to snow. Morphological examinations confirmed that specimens from both mountains are B. jezoensis , representing the second record of the species and providing a new locality record approximately 170 km from the type locality. We also generated the first mitochondrial cytochrome c oxidase subunit I ( COI ) sequences for B. jezoensis and reconstructed a preliminary COI phylogeny of Boreus . The B. jezoensis samples formed a strongly supported clade with low genetic divergence between the two populations. Together, these findings extend the known distribution of B. jezoensis , provide foundational DNA barcode resources for East Asian Boreus , and offer basic ecological information for this poorly known species.

Introduction: The genus Pocillopora comprises coral species distributed throughout tropical and subtropical regions. In the Central Mexican Pacific region, Pocillopora verrucosa is the main reef-building species. In response to the recent decline in coral coverage, restoration protocols have been implemented over the past decade. However, to date, no genetic diversity records are available as potential markers to evaluate the effect of assisted recruitment on site dynamics in the area. Objective: Determine the genetic diversity of P. verrucosa in an insular (Islas Marietas National Park) and a coastal (Punta de Mita) restoration site within the Central Mexican Pacific. Methods: A 2 cm2 fragment from 15 colonies per site was collected. Mitochondrial markers for the COI and ATP6 genes were amplified. A total of 40 sequences of the COI (n = 19) and ATP6 (n = 21) genes were obtained, and the haplotype and nucleotide diversity were determined. Results: For the COI gene, two haplotypes shared between the sites were identified, with H1 being the most abundant. For the ATP6 gene, one exclusive haplotype was detected in Islas Marietas National Park, and one more abundant haplotype was shared between the two sites. The AMOVA results revealed a homogeneous pattern with Fst values of 0.21603 (p < 0.10655) for COI and Fst = 0.04174 (p < 0.3753) for ATP6. Conclusions: The low genetic diversity suggests that, as previously reported, asexual reproduction has been the predominant mode throughout the site’s history, and that the assisted propagation implemented may promote the maintenance of the individuals that have historically shown resistance to thermal stressors. However, it is essential to explore alternative propagation techniques in future restoration initiatives, as the long-term success of restoration also relies on reducing the vulnerability of these ecosystems to future environmental stressors.

Background/Objectives: The widespread adoption of short tandem repeat (STR) marker technology in genetic analysis has led to the collection of substantial STR data from diverse populations. Allele-frequency data provide robust forensic utility and support accurate likelihood ratio calculations, highlighting the importance of regional databases. Methods: The presented study aimed to determine the allelic frequencies and statistical parameters for 16 autosomal genetic STR markers included in the NGM DetectTM PCR Amplification Kit in a population sample of 220 unrelated individuals from the South-West region of the Republic of Bulgaria. Results: We found that the most polymorphic and informative marker for the Bulgarian population in the southwestern region is SE33, with the next most informative markers being D1S1656, D12S391, D18S51, and FGA. In contrast, D22S1045, D16S539, and D2S441 showed comparatively lower genetic variability and informativeness. At the same time, no deviations from the Hardy-Weinberg equilibrium were observed for the 16 loci studied. Conclusions: This work not only enriches knowledge of the genetic diversity of the Bulgarian population but also provides the Bulgarian and international justice systems with an objective, scientifically sound basis for expert decision-making.