The sky island mountain ranges of the southwestern United States offer a natural setting for examining how climate and geography impact population structure and gene flow. The jewel scarab, Chrysina gloriosa, is a charismatic beetle restricted to high-elevation habitats in these mountains, where isolation and environmental change may be driving population divergence. We used low-coverage whole-genome resequencing and species distribution modelling to study population structure, gene flow, and demographic history across five mountain ranges in Arizona and West Texas. Our results indicate strong genetic differentiation among most populations, with recent gene flow detected only between two neighbouring ranges, possibly through male-mediated dispersal. Demographic analyses reveal a decline in effective population size following late Pleistocene climate shifts, consistent with habitat contraction inferred from paleo-vegetation records. Future climate projections suggest further habitat loss and increasing isolation. Together, these results show how past and ongoing climatic changes have and continue to shape population structure in C. gloriosa, with important implications for its long-term evolutionary potential. These findings mirror patterns documented across sky-island taxa globally, supporting a general model in which climate-driven habitat dynamics and dispersal limitation interact to generate recurrent cycles of population fragmentation, genetic erosion, and demographic instability in montane systems.

ABSTRACTMountain systems are natural laboratories for evolution, where rugged topography and ecological heterogeneity restrict gene flow. In the Hengduan Mountains, Neotetracus sinensis (N. sinensis), the sole species of its genus, occupies cool montane forests and has limited dispersal. Here we assemble a high‐quality reference genome and resequenced individuals from two isolated ranges in Yunnan, specifically Gaoligong Mountains (GLG) and Wuliang Mountains (WL), to test how geographic isolation shapes genomic variation. Genome‐wide SNPs reveal clear population structure, with PCA and phylogeny concordantly resolving two distinct clades. Relatedness analysis shows no close‐kin duplicates, and ROH are uniformly short, indicating outbred genomes. Demographic reconstructions show a shared trajectory marked by expansion ~1.0 Mya and a prolonged decline through the Middle‐Late Pleistocene. Despite a lower long‐term Nₑ, WL population displays contemporary nucleotide diversity (π), consistent with very recent gene flow or rapid post‐bottleneck recovery. To robustly assess genomic differentiation and mitigate biases from the small WL sample size, we employed a strict two‐tiered filtering approach. The intersection of the top 1% relative (Fst) and absolute (Dxy) divergence windows identified 5 core genomic islands, notably highlighting the DNA repair gene MGMT as a key candidate for environmental adaptation. Concurrently, functional enrichment of the broader top 1% Fst regions indicated an overrepresentation of pathways associated with synaptic and neuromodulatory signaling, cytoskeleton‐linked intracellular transport, and circadian regulation. These results provide a genomic framework for understanding how geographic isolation and montane environments shape divergence in N. sinensis.

Reconstruction of the genetic history of the Austro-Asiatic- and Dravidian-speaking tribal populations of South Asia.

The reintroduction of a species into its historical range can present challenges for wildlife managers, particularly when it occurs near the edge of that species’ range and the population is isolated from others. One important aspect of reintroductions is the selection of source populations that best suit local conditions. Additionally, movement and gene flow between reintroduced and extant populations is important for maintaining genetic diversity and evolutionary processes but can be highly influenced by habitat quality, quantity, intactness, and landscape permeability. The reintroduction of pronghorn (Antilocapra americana) into the Flint Hills region of east-central Kansas from the late 1970s through the early 1990s resulted in the establishment of a small population (~ 30 individuals) originating from southwest Wyoming and southeast Colorado. We collected pronghorn fecal samples from the Flint Hills region and from a historical population in western Kansas for DNA analysis to compare, predict, and model genetic diversity, gene flow, isolation, and genetic drift within the Flint Hills population since reintroduction. Our results indicated the average observed heterozygosity from the Flint Hills (0.68) was slightly higher than in western Kansas (0.61), and the average number of alleles per locus were similar (6.1 and 6.2 respectively). Pairwise FST (0.09, p = 0.00001) and G”ST (0.15) indicated slight restriction of gene flow, but not complete isolation between the two groups. Shared ancestry was detected between both groups which may be either through recent gene flow, historical gene flow or similar source populations. The higher genetic diversity found in the Flint Hills population may be attributed to behavioral isolation between the two source populations, the underestimation of their population size, or long-distance immigration from other populations. Additionally, changes in agricultural practices and higher habitat fragmentation in western Kansas may be limiting local and regional pronghorn movement and gene flow. Our results provide additional insight into potential factors influencing the diversity and structure within small, isolated populations when considering future reintroductions of pronghorn and other wildlife species.

The Turkestan ground-jay (Podoces panderi), a corvid endemic to Central Asia's deserts and steppes, exemplifies how extreme environments drive speciation. Our study provides the first comprehensive high-resolution genomic analysis of this species, using complete mitochondrial genomes (49 individuals) to decode its population structure and demographic past. Our analyses revealed three highly divergent genetic clusters with strong geographic structure. The P. p. iliensis population (Cluster_3) showed particularly pronounced genetic distinctiveness, with significant differentiation from P. p. panderi (Cluster_2 and Cluster_1) populations. This clear genetic separation supports the taxonomic validity of P. p. iliensis as a distinct evolutionary lineage. Demographic reconstruction indicated that Cluster_2 likely represents the ancestral group, with subsequent southward expansion into the Karakum region. The isolated P. p. iliensis population exhibited signatures of long-term isolation, including reduced genetic diversity and absence of recent gene flow with other clusters. These results provide strong evidence that P. p. iliensis represents a distinct evolutionary unit. The genetic structuring into three clusters reflects historical isolation in desert refugia during Pleistocene climatic fluctuations. Notably, we detected asymmetric gene flow among three clusters. These findings redefine P. panderi as a model for desert adaptation, where climatic extremes forged genetic fragmentation amid limited dispersal. Beyond taxonomy, our work highlights how aridification sculpted biodiversity in Asia's interior, urging conservation attention for these evolutionarily distinct lineages.

ABSTRACT Aim To reconstruct the colonisation dynamics of silver fir in the Pyrenees during the Holocene using genetic and paleoecological data. Location Abies alba forests in the Pyrenees and Northeastern Iberia. Taxon Silver fir ( Abies alba Mill.). Methods Palaeoecological data from 43 pollen diagrams were used to elucidate the appearance and persistence of silver fir during the Holocene. Additionally, 43 forests were sampled in the southern Pyrenees to perform genetic analyses using 65 SNPs derived from a total of 273 SNPs sourced from a transcriptome assembly. Linear regressions of pairwise population statistics ( F ST ) against geographical distances were performed to examine the presence of isolation by distance. An assumption‐free approach was also employed to explore the genetic structure of the populations and coalescence analyses were carried out to infer past demography history. Results We identified Pyrenean eastern and western genetic groups, which originated from an ancestral population located in the eastern Pyrenees. From this population, a westward colonisation took place, during which isolation by distance led to genetic divergence among populations. The eastern group diverged from a common ancestor shared with Alpine populations approximately 110,250 years (3150 generations) ago. The divergence between the eastern and western groups began around 40,250 years ago, coinciding with a reduction in effective population size to 1/2 of its ancestral value. Subsequently, a secondary contact occurred approximately 8575 years ago, resulting in admixed populations in the central Pyrenees. Main Conclusions We identified a single eastern origin for Pyrenean silver fir populations, followed by westward expansion and spatial differentiation, with recent gene flow between previously isolated genetic groups. This scenario aligns with palaeoecological evidence and shows how the Pyrenees acted as a longitudinal corridor for postglacial colonisation. The resilience and genetic diversity of Pyrenean silver fir populations underscore their importance for the conservation of the species in Europe.

The Pacific nudibranch Hermissenda crassicornis (sensu lato) is a well-known model organism in neuroscience. This species was recently split into three pseudocryptic species based on differences in genetics, morphology, and behavior. We used ddRADSeq data from 33 individuals (2354 loci) and coalescent isolation-with-migration models alongside forward simulations to estimate and evaluate the demographic history of the clade. We inferred (1) a novel phylogenetic tree topology with the North American species as sisters, (2) relatively old divergence times (0.55 and 1.29 mya), (3) a much larger population size in the southern species H. opalescens, and (4) no recent or current gene flow between the sympatric species H. crassicornis and H. opalescens. Then we examined behavioral differences between sympatric H. crassicornis and H. opalescens to characterize possible mechanisms promoting their reproductive isolation. Mating experiments showed that both H. crassicornis and H. opalescens display assortative mating, consistent with the existence of a prezygotic reproductive barrier. Our results support the splitting of H. crassicornis (sensu lato) and reinforce the need to reassess previous studies that used the species complex as a model organism.

India-specific cardiogenetic aspects: Focus on cardiomyopathies and inherited arrhythmia syndromes.

Glaciers have been proposed as evolutionary hotspots for microbial evolution; however, direct evidence for glacial microbial population formation and genomic loci undergoing selective sweeps remains limited. To address this knowledge gap, we investigated the genomic diversity, evolutionary pressures, and adaptive strategies of Cryobacterium, a representative genus of glacier environments. Based on recent gene flow analysis, 18 distinct populations of Cryobacterium were identified, each exhibiting clear discontinuities in gene flow and genetic boundaries. Selective pressure analyses revealed purifying selection within populations, maintaining genetic stability, and positive selection between populations, suggesting adaptive divergence from environmental differences. Notably, half of the populations spanned geographically distant glaciers, suggesting widespread dispersal mechanisms such as atmospheric circulation or glacial fauna migrations. We identified 17 genes under strong selective sweeps, involved in metabolic enzymes, transporters, and gene regulation. Based on the reverse ecology principles, these genes (e.g., glucose-6-phosphate dehydrogenase assembly and RNA polymerase-binding gene), are likely to be critical for cold adaptation. This study provided clear genomic evidence of glacial microbial population formation driven by recent gene flow, significantly enhanced our understanding of microbial adaptation in extreme cold ecosystems, and emphasized the importance of deep genomic sequencing in ecological and evolutionary research.

BackgroundDespite Anopheles funestus s.s. being a highly competent and widespread malaria vector in Africa, its population structure remains largely understudied in many countries, including Tanzania. Herein, we examine the genetic diversity, geographic isolation, and gene flow of An. funestus populations across ten administrative regions in mainland Tanzania.MethodsWe employed 12 previously used microsatellite DNA markers to describe genetic diversity, isolation by distance, and gene flow patterns among ten An. funestus s.s. populations (n = 654) and one An. parensis population (n = 28), used as an outgroup, sampled across ten regions in mainland Tanzania.ResultsOverall, allelic richness (Na) and genetic diversity (HS) did not differ significantly among populations. Although some loci and populations showed significant departures from Hardy–Weinberg equilibrium, the patterns were not indicative of substructuring within locations. Pairwise genetic divergence (FST) values indicated clear separation between An. parensis and An. funestus s.s., with values exceeding 0.2, consistent with species-level differentiation. Among An. funestus s.s. populations, the highest divergence was observed between southeastern coastal populations (Mtwara, Ruvuma, Lindi) and inland populations, with FST values up to 0.288. There was no evidence of isolation by distance. Instead, patterns of genetic divergence suggested connectivity across the Rift Valley and heterogeneity among southeastern populations. Neighbor-joining analysis and Bayesian genotype clustering identified three distinct population groups: (i) An. parensis (Dodoma), (ii) a genetically distinct An. funestus s.s. population from Mtwara, and (iii) a more homogeneous cluster comprising the remaining An. funestus s.s. populations. Notably, the Mtwara population appeared highly differentiated, with divergence approaching that between An. funestus s.s. and An. parensis, supporting its distinctiveness but not undermining the role of An. parensis as an outgroup.ConclusionsExcept for the Mtwara population, whose status will need to be clarified through whole-genome sequencing, moderate genetic divergence was found among An. funestus s.s. populations across Tanzania, despite geographical separation and the Rift Valley. The observed genetic structure suggests that anthropogenic gene flow may play a key role in shaping population divergence. Future studies should aim to delineate the effects of local adaptation from recent gene flow to further explore these dynamicsGraphical Supplementary InformationThe online version contains supplementary material available at 10.1186/s13071-025-07080-8.

Plio–Pleistocene range dynamics of the spotted sand lizard ( <i>Pedioplanis lineoocellata</i> ) sheds light on taxonomic uncertainty

The taxonomy of Chilean Myotis has long been contentious, particularly regarding the status of M. arescens relative to M. atacamensis and M. chiloensis . Here, we use an integrative framework combining genome‐wide single nucleotide polymorphisms (SNPs), morphometrics, and bioacoustics to reassess lineage boundaries and evolutionary relationships in Chilean Myotis . We analyzed 19,707 high‐quality SNPs from 80 specimens spanning the full latitudinal distribution of the group, 10 external and craniodental measurements from 123 specimens, and 825 echolocation pulses from free‐flying bats. Population genomic analyses revealed three genetic clusters, but only M. atacamensis formed a deeply divergent and well‐supported lineage, with no detectable recent gene flow to southern taxa. In contrast, M. arescens and M. chiloensis showed shallow genetic differentiation, strong asymmetric gene flow, and a latitudinal gradient of shared ancestry. Phylogenetic reconstruction based on SNPs failed to recover reciprocal monophyly between M. arescens and M. chiloensis , and process‐based species delimitation strongly supported a two‐lineage model comprising M. atacamensis and a single southern lineage ( M. chiloensis + M. arescens ). Morphometric and bioacoustics analyses mirrored these patterns: M. atacamensis was clearly differentiated in skull size and echolocation calls, whereas M. arescens and M. chiloensis formed overlapping morpho‐acoustic continua. Together, our results indicate that M. atacamensis is an independently evolving desert‐adapted lineage, while M. arescens represents a northern population within a geographically structured M. chiloensis . We therefore recommend recognizing only two Myotis species in Chile and interpreting M. arescens as a population‐level unit within M. chiloensis , with important implications for taxonomy, biogeography, and conservation assessments.

ABSTRACT Objective The Common Snook Centropomus undecimalis is a species widely distributed throughout the western Atlantic, playing a key ecological role in coastal and estuarine ecosystems. Despite its broad distribution from Florida to southeastern Brazil, little is known about the genetic patterns underlying its population connectivity. This study aimed to characterize the genetic structure of this species and to infer patterns of genetic diversity and connectivity across its range. Methods A total of 100 individuals collected from Florida to southeastern Brazil were genotyped at 11 microsatellite loci. Genetic structure was assessed using Bayesian clustering analysis, discriminant analysis of principal components, and analysis of molecular variance. Genetic differentiation among populations was estimated by pairwise FST, and recent gene flow was inferred from migration proportions among the identified genetic profiles. Results Three distinct genetic profiles were identified: one exclusive to the southern Gulf of Mexico (Gulf Profile) and two along the Atlantic coast (Northern and Southern profiles), both contributing to a central mixed zone in northern South America. Analysis of molecular variance revealed greater variation within populations (68.8%). When admixed individuals (&amp;lt;80% assignment) were excluded, the variation among groups increased to 27.2%, while within-group variation remained high (68.4%). The Gulf Profile showed strong differentiation from the others (FST = 0.33–0.39), whereas differentiation between the Northern and Southern profiles was lower but significant (FST = 0.038). Recent migration analysis indicated high genetic self-recruitment within each profile (68–99%) and limited gene flow among them, except for significant migration from the Southern Profile to the Northern Profile (migration rate = 0.301). Genetic diversity was high across all profiles, with greater allelic richness and heterozygosity in the Gulf Profile and lower values in the Southern Profile; 90 private alleles were identified, most of them in the Gulf Profile. Conclusions The Common Snook exhibits an isolated stock in the southern Gulf of Mexico, likely maintained by historical processes and local oceanographic dynamics, such as the Loop Current and cyclonic vortices. Along the Atlantic coast, two distinct genetic profiles (Northern and Southern) are connected by a transitional zone in northern South America characterized by extensive genetic admixture. Atlantic connectivity appears to be facilitated by ocean currents and the species’ broad ecological plasticity, including tolerance to salinity variation and diadromous migrations. These findings provide valuable insights for conservation and fisheries management strategies throughout the distributional range of this species.

Contrasting whole-genome diversity patterns and adaptation in honeybees from two southern European glacial refugia

Avian Influenza (AI) remains a critical threat to livestock production in Oceania, with recent outbreaks of Highly Pathogenic Avian Influenza (HPAI) H7 subtypes in Australia and New Zealand. Historically, AI detections in these countries were largely confined to wild birds. However, since 2024, multiple outbreaks in commercial poultry populations have been reported, with the emergence of HPAI H7N3, H7N8, and H7N9 in Australia and H7N6 in New Zealand. To investigate the epidemiological links of these outbreaks, we retrieved all publicly available H7 hemagglutinin (HA) gene sequences from animals in Oceania between 2014 and 2025 that were deposited in GISAID and NCBI databases. Phylogenetic reconstruction using maximum likelihood methods revealed distinct Australian and New Zealand clades, suggesting local viral evolution rather than recent transboundary introductions. The absence of phylogenetic clustering between Oceanian and Asian H7 sequences suggests limited recent gene flow between regions, particularly in the HA gene segment. These local viral mutations can pose a threat to the poultry industry; therefore, continuous genomic surveillance in commercial farms and wild bird reservoirs is crucial. Such efforts support the One Health framework by enabling early detection of pathogenic variants and reducing zoonotic spillover risks for animal and public health.

Alpaca (Vicugna pacos) is a large camelid that originated in South America. However, its evolutionary origin is debated, with hypotheses suggesting domestication from vicuña (V. vicugna) or guanaco (Lama guanicoe) or descent from extinct wild species with introgression from these two camelids. We show by means of phylogenetic, population and demographic genomic analyses, that the alpaca is a homoploid hybrid species that originated following hybridization between vicuña and the ancestor of wild guanaco and domesticated llama (L. glama). This event occurred during the mid-Holocene (~6.3 thousand years ago [Ka]) and shortly before the two Lama species diverged from each other (~5.9 Ka). Following its origin, the alpaca occasionally interbred with both llama and vicuña with recent gene flow and introgression. In addition, we identify alleles of many genes in alpaca that are derived alternately from its two parents. In combination, these alleles may have contributed to the reproductive isolation of the alpaca from its parents due to their effects on body size and sperm development, respectively. While attempting to domesticate camelids in South America, it is likely that humans may have retained hybrid offspring that exhibited preferred traits from both parents. This selective retention, along with the alternately inheriting highly diverged genes, may have led to the establishment of a new homoploid hybrid species in the case of alpaca, as sexual reproduction was restored through iterative evolution.

The impact of strongly differentiated populations on species delimitation due to limited or sex-biased dispersal remains challenging and under-explored in the framework of integrative taxonomy. The Mediterranean chafer beetle genus Pachypus is remarkable for its extreme female philopatry, with entirely wingless and subterranean females. This makes Pachypus an interesting case study. Based on a dataset of over 900 protein-coding genes (metazoan universal single-copy orthologs; mzl-USCOs), we investigated phylogeny, species delimitation, gene flow, and population differentiation to provide an integrative assessment of species boundaries. Integrative consideration of all results led to the recognition of 14 mostly morphologically cryptic species, including several new taxa. Most inferred speciation events occurred in the time between the end of the Messinian salinity crisis (about 5.3 million years ago) and the early Pleistocene. Phylogenetically old species and lack of recent speciation was unexpected because of the extreme philopatry, the morphological similarity of the species, and the high degree of differentiation observed among populations of the same species. Speciation was partly associated with the disruption of previously more connected ranges after the Messinian salinity crisis (MSC). This also helps clarify the extent to which the Mediterranean dried out during the MSC, since land connections in the circum-Tyrrhenian region must have persisted long enough for flightless Pachypus females to disperse across drifting land areas connecting the Apennine Peninsula and Africa. We found evidence for historical gene flow between species, while more recent gene flow between populations is low, which is potentially the cause of considerable over-splitting found in the Bayesian Phylogenetics & Phylogeography (BPP) species delimitation analysis. We showed that integrating the outcome of the BPP species delimitation with genealogical divergence index (gdi) values proved to be helpful in some cases but was inconclusive in many others. Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) analyses were less prone to over-splitting. This illustrates how species delimitation analyses of cases with restricted or sex-biased dispersal and highly differentiated populations can serve as empirical tests of the utility and robustness of delimitation approaches.

Abstract For about the past 120 years, Apiomorpha crispa (Fuller, 1896) has been considered to be a junior synonym of A. strombylosa (Tepper, 1893). Although some morphological variation among specimens of A. strombylosa has been recognised across its range, geographic separation and different host associations led to coccidologists treating the variation as belonging to two forms rather than there being distinct species. Here, we use allozyme electrophoresis and DNA sequencing of mitochondrial and nuclear genes to test the hypothesis that A. strombylosa, as currently treated, is a single biological species. We find that the ‘eastern’ and ‘western’ forms of A. strombylosa sens. lat. are distinct species with no evidence of recent gene flow despite both forms sometimes being in close geographic proximity. The two species are morphologically distinct and induce galls on different Sections of Eucalyptus L'Herit. We hereby resurrect Brachyscelis (=Apiomorpha) crispa (Fuller, 1896) reinst. stat. from synonymy with Brachyscelis (=Apiomorpha) strombylosa (Tepper, 1893) and provide a revised description of the species.

South Asian populations are genetically well stratified due to multiple waves of migration, admixture events, and endogamy. India remains a rich resource for population genomics studies with many small and socio-culturally homogeneous communities whose origins and demographic histories are largely unknown. In this study, we analysed such a small Sindhi settlement in the Thane district in Maharashtra of West coast India using genome-wide autosomal SNP data from 13 healthy Sindhi individuals using both frequency- and haplotype-based approaches. Our analyses suggest that the West coast Indian Sindhi community is very unique and has significant population affinity with a group more closely related to the Pakistani Burusho than to the Pakistani Sindhi, as it has an additional East/Southeast Asian component. Furthermore, the sharing of haplotypes and Identity by Descent (IBD) suggests recent gene flow from the local Konkani population on the west coast of India into Indian Sindhi. Admixture modelling suggested that Indian Sindhi admixture with the East/Southeast Asian source group could be 40-50 generations before present (GBP), explaining their current unique demographics. However, apart from this additional admixture, they share the basic genetic composition of the Pakistan/Northwest Indian groups, as reflected in Principal Component Analysis (PCA), outgroup F3 and IBD sharing. Our new findings suggest that Indian Sindhi settlement from the Thane in Maharashtra in West coast of India derive their genetic ancestry not directly from Pakistani Sindhis but from other groups related to Burusho in Pakistan. The study therefore encourages further research to identify the heterogeneous nature of migrations to the Indian subcontinent and thus further decipher its unique demographics.

Climatic fluctuations during glacial periods have profoundly shaped the demographic history and gene flow dynamics of many taxa. This study integrated high-throughput sequencing of 67 individuals with comprehensive genomic analyses to investigate biogeographic patterns, genetic divergence and demographic trajectories in the Opisthotropis latouchii species complex, a group of mountain stream snakes distributed across Central China. Our analyses revealed substantial genetic divergence, identifying four distinct lineages, each confined to one of the four major mountain ranges in Central China, including one previously unrecognised species. These lineages exhibited distinct demographic signatures, with population bottlenecks occurring during Quaternary glaciations. Initial isolation in the glacial refugia of the southern regions of these mountains during the Late Pliocene was followed by postglacial expansions along a northward trajectory, with further divergence along a latitudinal gradient associated with mountain distribution. Notably, the mountain ranges of Central China acted as critical refugia during glacial periods, promoting rapid speciation, and as dispersal corridors during interglacial periods, facilitating range expansion and enabling recent gene flow. These findings highlight the profound impact of Quaternary climatic oscillations on genetic structure, demographic history and gene flow patterns of these endemic taxa.