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.

The Greenland shark (Somniosus microcephalus) is known for its slow metabolism and deep-sea habitat. It is thought to be the longest-lived vertebrate on Earth, with an estimated lifespan of 392 ± 120 y. Despite its remarkable longevity and unusual lifestyle, no genomic studies are yet available for this species. Here, we report a chromosome-level assembly of the Greenland shark genome, which is 5.9 Gb in size with an N50 length of 233 Mb and a completeness score of 96.7%. Our analyses of gene family expansion and positive selection revealed classical longevity-related mechanisms, including immune enhancement, cancer resistance, and DNA repair, as well as additional features potentially associated with extended lifespan limits. Unique amino acid substitutions in the globular domain of linker histone H1.0 are predicted to enhance chromatin stability, and the species' distinctive gene repertoire provides a framework for generating hypotheses potentially linking ferroptosis to exceptional longevity. We also elucidate the dynamics of the effective population size (Ne) of the Greenland shark and its close relative, the Pacific sleeper shark (Somniosus pacificus). These genomic analyses offer insights into the molecular basis of the exceptional longevity of the Greenland shark and highlight potential genetic mechanisms that could inform future research into longevity.

Clonality, management, and geography shape genetic structure in a perennial species with restricted distribution.

Streptococcus pneumoniae serotype 24F has emerged as a major cause of invasive pneumococcal disease in Europe following the introduction of PCV13 yet remains absent from current paediatric vaccine formulations. We investigated the genomic epidemiology and phylodynamics of serotype 24F within Norway by focusing on the dominant strain Global Pneumococcal Sequence Cluster 6 (GPSC6) and placed these isolates in a global context using 972 genomes from 29 countries. GPSC6 is composed of distinct lineages, which we estimate to have diverged around the mid-twentieth century. Before the pneumococcal conjugate vaccine (PCV) era, Lineage 1 was composed predominantly of vaccine serotypes. The past success of Lineage 1 likely came from its antimicrobial resistance (AMR) gained in the 1980s. Since the introduction of PCVs in childhood immunization programmes, Lineage 2 has expanded rapidly, driven by clades with serotypes not covered by the PCVs. A time-calibrated phylogeny indicates that GPSC6-24F originated in the 1980s and expanded rapidly after the introduction of PCV7 in 2006. In Norway, two importations in the period 2007–2009 seeded most local transmissions. The effective population size of GPSC6 declined after PCV7 introduction, followed by expansion of non-vaccine serotypes, notably 24F and 11A. In silico AMR profiling revealed that GPSC6-24F isolates likely remain susceptible to β-lactams and other antimicrobial classes but are resistant to co-trimoxazole, contrasting the expansion of multidrug-resistant GPSC10-24F reported from high-antibiotic-use settings. Vaccine-driven selection rather than AMR seems to be shaping the GPSC6-24F dynamics in Europe and highlights the need for continued genomic surveillance, as 24F is not covered by paediatric PCV formulations.

Worldwide, the pig industry suffers financial losses due to the extremely contagious disease caused by the classical swine fever virus (CSFV). However, comprehensive and global genotyping information for CSFV remains scarce. A total of 1,053 full length E2 sequences of CSFV from the NCBI database were used in this study. According to phylogenetic analysis, the strains were grouped into dominant genetic subgroups. The positive selection pressures on the CSFV E2 envelope protein genes were also evaluated and a site-by-site examination of the dN/dS ratio was conducted to pinpoint certain codons that diversify under positive selection. Phylogenomic analyses using maximum likelihood (ML) and Bayesian inference (BI) confirmed that the 1,053 strains clustered within the previously defined five subgenotypes (1.1, 1.2, 2.1, 2.3 and 3.4). One positively selected site was identified at amino acid residue position 71. Bayesian coalescent analysis estimated an evolutionary rate of 1.364 × 10⁻³ substitutions per site per year (95% HPD: 1.1808 × 10⁻³-1.5602 × 10⁻³) and a tMRCA of approximately 1816 (95% HPD: 1796-1837). The effective population size of CSFV began increasing in the 1920s, continued to rise until the 1950s, and then remained stable thereafter. Sequence-based antigenic mapping was used to evaluate antigenic relationships among CSFV strains, revealing that most strains clustered closely together. Understanding the molecular epidemiology and functional significance of positively selected amino acid sites may aid in predicting changes in virulence and inform vaccine development and disease control strategies.

Genomic approaches can provide critical insights into the genetic health of endangered species and the impacts of long-term management on semi-captive populations. Asian elephants (Elephas maximus), listed as Endangered, include a large semi-captive population in Myanmar that may represent an important reservoir of genetic diversity. However, their genetic structure, levels of inbreeding, and relatedness remain poorly characterized. We assembled the largest genomic dataset to date for semi-captive Asian elephants, comprising reduced representation data (RADseq, N = 261) and whole-genome data (WGS, N = 64). Heterozygosity values showed no significant differences between wild-born and captive-born individuals. Both RADseq and WGS data revealed low to medium levels of inbreeding and no evidence of an increase among younger generations. Population structure analyses confirmed a homogeneous population with no geographic-based genetic structure, likely reflecting management practices and natural mating with wild bulls. Demographic inference indicated a sharp decline in effective population size (Ne) between 60 and 30 generations ago, consistent with a long-term population contraction, and current Ne was estimated as being very low. Relatedness analyses identified 657 first-cousin or closer relationships, including 124 first-degree pairs. We also uncovered 35 previously undocumented father-offspring pairs with some males having disproportionately high reproductive success. To facilitate future monitoring, we developed three reduced relatedness-informative marker (RIM) panels. The smallest panel (274 SNPs) provided sufficient resolution for reliable parentage assignment at reduced cost. Our findings demonstrate how genomic tools uncovered the genetic consequences of management of the largest semi-captive elephant population of Myanmar, highlighting the need for continuous monitoring to safeguard its genetic diversity. More broadly, this study illustrates how integrating WGS and RADseq can inform conservation planning for semi-managed populations and offers transferable approaches applicable to other endangered species.

Genetic drift and gene flow can give rise to a complex population genetic structure. The inverse problem of estimating the genetic drift and gene flow in the past, based on the present-day genomic population structure, can be solved using an admixture graph. This describes differentiated local populations in terms of population splits and migrations between populations. The history and associated levels of genetic drift and admixture can be estimated based on the genome-wide SNP allele frequency data. Here, we present a set of statistical methods based on the admixture graph. Applying a prior on the stochastic variation of the effective population size decomposes the genetic drift values that are associated with the non-migration edges into the timings of the population splits and the effective population sizes at those times. This decomposition facilitates downstream analyses such as reconstruction of ancestral allele frequencies via a Brownian motion model with admixture. To trace changes in allele frequencies on a world map, we estimated the geographic locations of the ancestral populations using Brownian motion, the rate of which depends on the genetic drift values. Mapping the history of putative adaptations onto a world map can illuminate factors responsible for regional population heterogeneity. We investigated the effectiveness of detecting adaptations with a numerical simulation that mimics human population history, and by analyzing the eQTLs of the MC1R gene, which is involved in regulation of skin and hair pigmentation.

The Pecos pupfish, Cyprinodon pecosensis, is an imperilled freshwater fish found in arid regions of Texas and New Mexico (USA). The species faces multiple challenges to persistence including reductions in suitable habitat, water shortages, as well as hybridization and competition with an introduced congener (sheepshead minnow, C. variegatus). As part of the current management strategy, refuge populations, seeded with non-introgressed individuals collected from Texas, are maintained at the Fort Worth Zoo and on private property in West Texas. Therefore, assessments of standing genetic variation within and among wild and refuge populations and levels of admixture in the wild are critical for future conservation and management planning. Fin clips were acquired in 10 locations in the wild, five in Texas, five in New Mexico and from two refuge populations in Texas (one maintained by Fort Worth Zoo and another on a private property in West Texas). In Texas, non-introgressed C. pecosensis were found in the wild at only one location Upper Salt Creek (USC); all other locations were composed of admixed individuals or non-introgressed C. variegatus. No admixed individuals were found in New Mexico. Significant genetic heterogeneity was detected between all locations of non-introgressed C. pecosensis, including the refuge populations, and estimates of divergence between Texas locations (USC and refuge populations) and New Mexico locations were relatively large (FST: 0.23-0.32). Estimates of contemporary effective population size for USC and the two refuge populations were less than 50, but greater than 500 for all New Mexico populations. In summation, while New Mexico populations look secure, the data suggest that C. pecosensis in Texas is currently imperilled by the threat of hybridization, as well as potential loss of genetic diversity on contemporary time scales. Deep divergence between Texas (including refuge populations) and New Mexico suggests that further study would be needed prior to any management plans that would involve assisted gene flow between the regions.

Although mass-spawning pooling systems are widely used for small yellow croaker (Larimichthys polyactis) aquaculture, they often induce severe genetic bottlenecks driven by reproductive skew. This study evaluated cross-generational genetic diversity and spawning patterns to propose an optimal genetic management strategy. We analyzed 1049 adult broodstock and 950 juvenile offspring using nine microsatellite markers. To mitigate reproductive skew, fertilized eggs were collected via multi-time sampling (19 times) over a two-month spawning season and reared to the juvenile stage. Genetic diversity was highly conserved across generations, with expected heterozygosity maintained at 0.860 in the offspring. Parentage assignment succeeded for 96.2% of the offspring (914 individuals), revealing 802 unique families, of which 89.9% (721 families) were singletons. Also, 60.9% of the broodstock contributed to reproduction, exhibiting a right-skewed participation distribution. Importantly, comparisons with a short-term single-event collection control group demonstrated that our multi-time strategy effectively prevented drastic reductions in effective population size (Ne). These patterns highlight the species asynchronous spawning physiology and confirm that the strategy approximates random mating with minimal genetic drift. We suggest this long-term, multi-time egg collection method as an effective protocol for the sustainable genetic management of multiple-spawning marine fish.

Insular (island-limited) populations typically show signatures of weak purifying selection, indicating high genetic load and reduced fitness compared with mainland populations. However, the source of this pattern is often unclear-it may reflect residual signatures from a temporary period of small effective population size (Ne) associated with island colonisation (founder effects), persistently small Ne due to the lower carrying capacity of islands (range limitations), or relaxed selective constraints unrelated to Ne. Here we disentangle these hypotheses by analysing the drivers of variation in evolutionary rates of nonsynonymous (dN) and synonymous (dS) sites in nine mitochondrial genes (8001bp) from 40 rail species (Aves: Rallidae). We find that insular species with short terminal branches (indicating recent island colonisation) have highly elevated mitochondrial dN/dS across multiple mitochondrial genes. In contrast, rails representing more ancient island colonisations have dN/dS ratios that are indistinguishable from mainland/widespread species. Furthermore, we find that island size is unrelated to dN/dS among island species. These results indicate that insular rails suffer a high initial cost of island colonisation and undergo a period of inefficient selection due to founder effects, but that there is little impact from longer-term range limitations or relaxed selection.

Sexual selection on males is expected to reduce genetic diversity via paternal inheritance because increased variance in male reproductive success lowers the male effective population size. It is plausible that sexual selection on males also affects genetic diversity via maternal inheritance, e.g., due to demographic processes. However, associations between sexual selection and maternally inherited genetic diversity were never tested for. Here, taking advantage of the fact that mitochondria are maternally inherited, we compare the diversity of two widely studied mitochondrial genes across 262 species of non-flying terrestrial mammals, for which male-biased sexual dimorphism is a good indicator of the intensity of sexual selection on males. We found that species with stronger male-biased dimorphism have lower mitochondrial diversity, after controlling for confounding effects. A plausible explanation for this result is that sexual selection on males can reduce female effective population size, giving rise to the change of allelic diversity in these mitochondrial genes. Our result thus suggests broader associations of sexual selection with demography and population genetic structure than previously recognized.

Coleoid cephalopods have convergently evolved many traits shared with vertebrates, including camera-type eyes, large brain-to-body size ratios, and complex behaviors. Most evolutionary studies of cephalopods have compared individual genomes of taxa that diverged tens to hundreds of millions of years ago, yet very few have examined more recent evolution from a population genetics perspective. Here we present a comparative population genomic analysis of the sympatric sister species Octopus bimaculatus and Octopus bimaculoides using whole-genome resequencing. Despite similar morphologies, these species differ substantially in their life histories, ecologies, and geographic distributions. Using demographic inference, we estimated that the two species diverged approximately one million years ago and that O. bimaculatus has maintained a consistently larger effective population size since divergence. Consistent with these demographic histories, we found stronger signatures of positive selection in O. bimaculatus , including a positive correlation between recombination rate and nucleotide diversity, more selective sweeps, and a higher proportion of mutations fixed by adaptation-all consistent with more efficient natural selection in larger populations. Protein-coding genes overlapping with selective sweeps were enriched for various functions that included many related to brain and eye development, suggesting that traits characteristic of coleoid cephalopods continue to be shaped by positive selection on recent timescales in these species. Comparing coding-sequence divergence on the Z chromosome to the autosomes, we also find evidence for a female-biased mutation rate, consistent with an independent estimate from a deeper-timescale cephalopod comparison.

The eastern chipmunk (Tamias striatus) is an abundant North American sciurid rodent and the only extant member of the subgenus Tamias. Despite its abundance, a reference genome has not been produced for this species. Here we present an assembled and annotated reference genome for the eastern chipmunk using PacBio HiFi long read sequencing data. We sequenced the genome of a vouchered male eastern chipmunk collected in Maine and stored at the National Museum. We compared the eastern chipmunk's genome with the genome of the Siberian chipmunk (Tamias sibiricus; subgenus Eutamias), the only other species in the Tamias genus with an annotated reference genome. The genomes were similar with 55.45% of genes showing collinearity and chromosomal rearrangements only occurring between chromosomes 4 and 8. We identified 219 genes under positive selection in the eastern chipmunk relative to the Siberian chipmunk. A coalescent analysis inferred the effective population size of the Maine eastern chipmunk may have steadily decreased through the Pleistocene epoch, consistent with a reduction in available habitat. We also generated short-read Illumina sequencing data from two additional eastern chipmunks collected in New Castle County, Delaware and Carbon County, Pennsylvania. We calculated nucleotide diversity over 10kb windows across the genome (mean = 0.0014 ± 0.0012s.d.) and identified genes with high nucleotide diversity. The eastern chipmunk reference genome will facilitate future population genetic and evolutionary studies including those investigating its role as a reservoir host for the bacterium that causes Lyme disease.

Assessing genetic diversity is essential for the characterization and conservation of livestock. This study investigates the genetic diversity of the three indigenous goat breeds from northern Belgium (Flanders), Kempische Geit, Vlaamse Geit, and Belgische Hertegeit, using pedigree and genomic data. Pedigree analyses estimated inbreeding and effective population size, while genomic data were assessed using runs of homozygosity (ROH) and population structure analyses (F st , principal component analysis (PCA) and ADMIXTURE). Pedigree-based results revealed moderate inbreeding (F ped = 10.3%, 7.4%, and 9.0%) and critically low effective population sizes (N e = 17, 28, and 43, respectively). Despite these constraints, population trends since 2017 show encouraging growth, with active breeding females increasing 153% (Kempische Geit) and active breeders rising 90% (Vlaamse Geit). Genomic data from 280 individuals (88–97 per breed), genotyped using the GGP Goat SNP array, revealed inbreeding coefficients based on ROH from 8% to 15%, with individual values reaching up to 39%. Several ROH islands were detected, including two in Vlaamse Geit on chromosomes 10 and 13, which overlap with regions reported in other international breeds. Linkage disequilibrium-based estimates of effective population sizes (N e = 21–22) further highlight the endangered status of these breeds. Genetic differentiation was substantial (F st from 0.10 to 0.14) which was supported by PCA and ADMIXTURE. This study provides the first integrated pedigree and genomic assessment of goat diversity in Flanders, offering critical insights for the conservation and sustainable management of these local breeds. These data support comparisons with international populations and inform future breeding strategies. • Flanders (Northern Belgium) has three local goat breeds • All three goat breeds were analyzed based on pedigree and genotype data • Inbreeding coefficients based on runs of homozygosity were between 8% and 15% • Effective population sizes remain below critical thresholds for viability • The three goat breeds are considered endangered

Man-made barriers impede fish movement up and downstream, between the channel and floodplain, and from marginal habitats to those that promote survival and reproductive output. Barriers also increase genetic isolation resulting in loss of genetic variation. Species with drifting eggs and larvae, like the endangered Rio Grande silvery minnow (Hybognathus amarus), are especially susceptible to disruptions to demographic and genetic connectivity. Using archived Rio Grande silvery minnow DNA from 25 temporal collections spanning 38 years, and targeted amplicon sequencing, we show that unidirectional stream flow and longitudinal position of populations affect patterns of Ne and genetic diversity. Ne is reduced in the upstream-most reach (Angostura) and there is a strong correlation between upstream and range-wide Ne suggesting impacts to the entire population. In the absence of population augmentation, allelic diversity was reduced upstream but stocking with captive-reared fish restored diversity. Long-term genetic analysis indicates: (1) that there is no longer sufficient spawning and rearing to maintain natural diversity in the Angostura reach; (2) upstream movement of adults is insufficient to recover diversity; and/or (3) there is higher variance in reproductive success in resident fish resulting in small values of Ne; all consequences of a highly engineered and disconnected river corridor. Similar impacts are predicted for species with pelagic life histories in altered rivers, underscoring the need for fish passage structures that facilitate connectivity and habitat restoration aimed toward propagule retention in upstream reaches. Long-term genetic data also show periodic recruitment bottlenecks compound losses to genetic diversity imposed by river regulation that cannot be restored by hatchery stocking alone.

Understanding the genomic architecture of species of conservation concern is essential for fostering effective conservation initiatives. Current biodiversity assessment approaches increasingly incorporate genetic metrics to evaluate the status of species and populations of conservation interest. However, due to the limited availability of conspecific genomes for most non-model species, previous studies have often depended on heterospecific genomes. This approach has been shown to significantly impact the precision of genetic metrics, resulting in inaccurate measurements and insights. However, it is currently unknown what the impact of using non-species-specific genomes is for the determination of genetic indicators in vulnerable marine fishes, such as red roman (Chrysoblephus laticeps). Red roman is a southern African endemic species, which, due to overexploitation, is currently considered Near Threatened on the International Union for Conservation of Nature (IUCN) Red List. Recent studies have shown significant life history and physiological differences between exploited and protected populations. Here, we present the first high-quality scaffold-level genome assembly and annotations for the red roman, using a combination of Oxford Nanopore and Illumina sequencing, and compared key genetic indicators (diversity, population structure and effective population size) obtained from reads mapped to the genomes of other Sparidae species, with well-established genomic resources. The final assembly had 1263 scaffolds, a total length of 758 Mb, with a scaffold N50 of 5.89 Mb and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 99.30%. As expected, comparative analyses with genomes of different sparid species revealed enhanced read alignment, genotyping accuracy and single nucleotide polymorphism (SNP) retention after filtering. Furthermore, there were significant overall differences across the genomes for the measures of observed heterozygosity (H O), nucleotide diversity (π), Tajima's D, F ST and estimates of effective population size (N e), with different genomes presenting different (and sometimes contrasting) genetic indicators metrics and, consequently, demographic histories for red roman. Our study not only significantly improved genomic resources for genomic conservation analyses in C. laticeps, but most importantly highlighted the importance of species-specific reference genomes for accurate evolutionary and conservation inference in highly variable marine fishes.

Genomic insights into the evolution and adaptation of Listeria monocytogenes in poultry production systems.

Adaptive VP1 sites 93 and 97 modulate antigenic evolution and receptor binding of Senecavirus A: Phylogenetic analysis and validation with recombinant viruses.

The endangered black-and-white snub-nosed monkey (Rhinopithecus bieti), endemic to high-altitude forests in southwest China, has increased from fewer than 1,500 individuals pre-1990 to over 3,500 post-2010. However, it faces severe habitat fragmentation, with at least 20 isolated groups. A comprehensive investigation of large-scale population genomic analysis is lacking. We present the first comprehensive genomic reassessment of this species using fecal-DNA and targeted capture sequencing to generate genome-wide single-nucleotide polymorphism data for 309 individuals. We identified five distinct genetic populations (Southwest, Southeast, Central, North-Central, and North) with strong geographic associations. Furthermore, we found previously unrecognized subpopulations, primarily associated with isolation within human-altered landscapes. Roads and human settlements were the primary barriers to contemporary genetic connectivity. Genetic diversity is highest centrally and declines peripherally, reflecting historical/recent barriers. Demographic inference suggests: (i) a possible southwestern origin and northward dispersal at ∼128.5 to 8.2 ka, probably driven by late Pleistocene climatic oscillations and local refugia; (ii) major subpopulation divergences within the last ∼610 to 120 years ago, likely due to human exploitation; and (iii) a sharp decline ∼300 years ago, leaving extremely low effective population size (40 to 314). Admixture origins of both Southeast and North-Central populations highlight their role in facilitating gene flow. Historically, habitats with high connectivity contrast with current severe fragmentation, particularly in the southern regions; this persistent suitability disparity suggests limited historical connectivity promoting genetic divergence between southern and central/northern populations. Our results provide critical insights into the population structure and evolutionary history of R. bieti, offering critical insights for conservation and demonstrating the power of fecal genomics in endangered species.

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.