Microsatellite-based assessment of genetic variation, bottleneck signatures and population structure in Omani and exotic goats

Native bacterial endosymbionts in aphids have been studied for many years but it is only recently that transinfections across species are being investigated from an applied perspective. Here we consider the impact of a Rickettsiella viridis transinfection originally from the pea aphid Acyrthosiphon pisum, in an important pest of cereals, Rhopalosiphum padi, that causes feeding damage and transmits barley yellow dwarf virus (BYDV). Our main aims were to quantify the fitness and dispersal consequences of the transinfection, assess its transmission dynamics, and determine whether Rickettsiella influences BYDV acquisition or transmission. The transinfected strain had fitness costs in its new aphid host, with an intrinsic rate of increase (rm) value around 20% lower, and showed horizontal transmission. Rickettsiella did not transmit vertically with complete fidelity, although it persisted in population cages for at least 11 weeks. Although Rickettsiella did not affect transmission of BYDV, it reduced the production of alates by 10% or more depending on aphid density. Aphids carrying Rickettsiella showed a slower rate of movement to adjacent plants compared with those without Rickettsiella. The body colour of aphids with Rickettsiella was also darker. This Rickettsiella transinfection imposes deleterious host effects, while retaining the capacity to persist in populations through horizontal transmission. Although it does not influence BYDV transmission, the reduced alate formation and slower movement suggest potential impacts on pest spread and population structure. These findings advance our understanding of symbiont-host interactions and highlight the potential for endosymbiont manipulations to influence aphid ecology and management. © 2026 Society of Chemical Industry.

Extended-spectrum β-lactamase-producing Escherichia coli are globally disseminated pathogens whose success is driven by clonal expansion and horizontal gene transfer. However, the population structure and evolutionary relationships of these organisms in the United Arab Emirates remain insufficiently characterized. In this study, we applied a population genomic and phylogenomic approach to investigate ESBL-producing E. coli causing bloodstream infections and their genetic relatedness to strains from non-human reservoirs within a One Health framework. Forty-five ESBL-producing E. coli isolates recovered from bloodstream infections between 2021 and 2024 were analyzed, with whole-genome sequencing performed on 29 representative isolates. Genomic analyses revealed the predominance of internationally disseminated high-risk lineages, particularly sequence types ST131 and ST1193, largely associated with the ESBL gene blaCTX-M-15. Conserved genetic contexts of blaCTX-M-15 in these lineages suggested stable vertical inheritance, whereas greater diversity of mobile genetic elements was observed among non-ST131 isolates, indicating ongoing horizontal gene transfer. Additional resistance determinants, including blaDHA-1, blaSHV-12, and notably the carbapenemase gene blaNDM-5, contributed to multidrug-resistant genotypes, indicating the coexistence of ESBL and carbapenemase activity in a subset of isolates. Phylogenomic comparisons based on core genome variation demonstrated close genetic relatedness between clinical isolates and E. coli from food, poultry, and environmental sources in the United Arab Emirates. These findings indicate that bloodstream infections are associated with shared circulating ESBL-producing E. coli lineages exhibiting genetic relatedness across human and non-human reservoirs. The results highlight the evolutionary connectivity of E. coli populations and emphasize the importance of integrated genomic surveillance to track and limit the spread of multidrug-resistant pathogens.

Ancient mitochondrial genomes from Coastal Patagonia: Population structure and human dispersal in the Southern Cone

Tuberculosis (TB) remains a major global public health burden, exacerbated by the continued emergence and spread of drug-resistant Mycobacterium tuberculosis. Despite the rapid expansion of publicly available whole-genome sequencing data, gaps remain in the consistent characterization of global population structure, dominant sequence-type (ST) distributions, accessory genome variability, and antimicrobial resistance (AMR) gene profiles, largely due to fragmented and uneven sampling across regions and time periods. This study aimed to conduct a large-scale in silico analysis of publicly available M. tuberculosis whole-genome sequences to descriptively characterize global ST structure, accessory genome diversity, AMR gene landscapes, and their geographic and temporal distributions, while integrating available phenotypic susceptibility data. We conducted the largest genomic analysis of M. tuberculosis to date, examining 7890 high-quality genomes from 82 countries (1900-2024) retrieved from NCBI GenBank. Rigorous quality filtering using CheckM ensured retention of genomes with >90% completeness and <5% contamination. Comprehensive genomic characterization included assembly metrics, annotated gene features, multi-locus sequence typing, AMR profiling using AMRFinderPlus (v4.0.23; database 2025-07-16.1), temporal trend analysis, geographic distribution mapping, and gene presence pattern (GPP) clustering to assess accessory genome diversity. Analysis of 7890 high-quality M. tuberculosis genomes from 77 countries (1900-2024) revealed a highly conserved global population dominated by a few epidemic clones. Although 158 ST were identified, three ST (ST 215, ST 279, ST 276) accounted for 84.9% of all isolates, with ST 215 alone representing 58.0%, indicating a strong global clonal bottleneck, while 90.5% of ST were rare (≤10 isolates each). Most isolates were human-derived (93.7%), and genome size (∼4.38Mb) and gene content (∼4149 genes) showed minimal variation worldwide. AMR analysis identified 27 AMR genes, but >99.6% of isolates carried only three core genes (erm(37), blaC, and aac(2')-Ic), whereas all other resistance genes occurred in <0.25% of genomes, including a single vancomycin-resistant isolate (0.01%). Phenotypic data showed high susceptibility to first-line drugs (97-98%), but substantial non-susceptibility to several second-line agents, particularly fluoroquinolones (ciprofloxacin and ofloxacin) and the second-line drugs capreomycin and ethionamide. Overall, while global M. tuberculosis is driven by a few dominant clones with a conserved core genome, rare lineages and resistance profiles highlight important hidden genomic diversity. GPP analysis identified 146 recurrent patterns, with GPP1 dominating ST 215, ST279, and ST276, suggesting limited accessory genome diversification. This large-scale in silico analysis reveals a highly skewed global sequence-type distribution of M. tuberculosis, with pronounced geographic structuring and widespread presence of conserved, intrinsic chromosomal resistance-associated genes. The findings emphasize the importance of cautious interpretation of resistance gene prevalence and phenotypic non-susceptibility patterns derived from heterogeneous public datasets, and highlight key methodological considerations for global genomic analyses of M. tuberculosis.

UCE phylogenomics reveals orogenic vicariance and introgression shaping diversification in the montane Mexican lizard genus Barisia (Squamata: Anguidae).

Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.

Continental diversification and insular speciation in a widespread passerine (Troglodytes musculus) in southern South America.

To characterize the genetic diversity and evolutionary patterns of four Weining chicken strains from Guizhou Province, China, we generated genome-wide single nucleotide polymorphisms (SNPs) using dd-RAD sequencing. We found that Weining chicken exhibited moderate genetic diversity, with observed heterozygosity (Ho = 0.267) lower than expected heterozygosity (He = 0.312) and a positive inbreeding coefficient (FIS ≈ 0.14), indicating some degree of inbreeding across the population. Among strains, HM showed the highest diversity while HT had the lowest. Analyses of population structure, phylogeny, principal component analysis, and admixture consistently revealed weak genetic differentiation (FST < 0.06) and frequent gene flow among strains. Kinship analysis demonstrated mostly low pairwise relatedness, with a minority of individuals exhibiting closer kinship. Selection signature scans identified multiple candidate regions; genes within these regions were significantly enriched for biological processes and pathways related to immune response (e.g., IL-17 signaling) and metabolic regulation (e.g., MAPK signaling), which were consistently highlighted in both GO and KEGG enrichment analyses. These results demonstrate that Weining chicken has moderate genetic diversity, low population differentiation, and evidence of inbreeding and gene flow, with candidate selection signals in immune and metabolic pathways (e.g., IL-17 and MAPK signaling), providing a quantitative basis for conservation and breeding programs.

This article presents the results of a study of the materials recovered from the Medieval cemetery in Vologda, dating to the 15th–16th centuries. In contrast to previously examined collections, the sample derived from the Ilyinsky Monastery cemetery is confined to a relatively narrow chronological range. This feature enhances the potential for a more precise assessment of how local historical circumstances influenced the demographic structure of the urban population. The sample comprises the remains of 121 individuals. The study was conducted in accordance with standard anthropological methods. The mortality distribution of the individuals within the sample reveals some deviations from a typical pattern. In particular, the group features a high proportion of children (63 %), with infants under one year of age accounting for 52 % of all children. Among adults, a predominance of males has been identified (70 % vs 30 %). The mortality distribution within the male subgroup exhibits two peaks: the first in early adulthood (25–29 years) and the second in the older age category (50+ years). Furthermore, a considerably lower average age at death among females has been revealed compared to other contemporaneous population groups in Vologda.

The genus Linum comprises over 230 species, with L. usitatissimum valued for linen and oil, yet crop wild relatives (CWRs) remain underutilized due to limited availability and poor molecular characterization. In this study, 96 accessions representing 16 wild and one cultivated species were evaluated using 49 SSR markers to assess genetic diversity and cross-species transferability (CST). A total of 473 alleles were detected, with allelic richness ranging from 1 to 22 alleles per locus and polymorphic information content (PIC) values reaching up to 0.91, underscoring the discriminatory power of the markers. High genetic diversity parameters, including Shannon's index (up to 1.296), revealed substantial allelic variation in species such as L. bienne and L. lewisii. Population structure analysis indicated moderate differentiation (global Fst = 0.186) and the presence of admixed individuals, reflecting complex evolutionary histories shaped by multiple gene flow events and introgression. Cluster analysis proved effective for uncovering pedigree relationships among genotypes and offered advantages over PCoA, while CST rates ranged from 45.45 to 100% across species. The high CST observed within sections (Linum, Dasylinum) highlights conserved genomic regions, whereas variable amplification in Linastrum points to divergent evolutionary trajectories. Together, these findings demonstrate that SSR markers not only capture allelic richness and population structure but also illuminate evolutionary processes such as speciation, introgression, and lineage divergence. The study establishes a valuable foundation for integrating Linum CWRs into breeding programs, thereby broadening the genetic base in cultivated linseed. These findings can enhance the scope and effectiveness of future breeding initiatives, particularly where such markers are lacking.

This study investigate the molecular epidemiology and population characteristics of 184 Acinetobacter baumannii clinical isolates collected in Zhejiang (2015-2020), shedding light on the persistence and success of ST208-KL2 lineage. Whole-genome sequencing and bioinformatic analysis characterized the population structure and transmission dynamics of 184 A. baumannii. Plasmid analysis identified the surrounding structures of blaOXA-58 and blaNDM-1 genes. Serum inhibition assays and Galleria mellonella virulence experiments, combined with global epidemiological analysis, explored the persistence and dominance of ST208-KL2. Of the isolates, approximately 78.8% (145/184) exhibited carbapenem resistance, primarily driven by blaOXA-23, blaOXA-72, blaOXA-58, and blaNDM-1. The A. baumannii population was divided into 2 clusters, distinguished by differences in ST types and resistance islands profiles. Cluster2 accounted for 71 department-time transmission events, mainly involving long-term interdepartmental spread, particularly in the rehabilitation medicine department and intensive care unit. Recombination analysis revealed that recombination occurred mainly in capsular locus (KL) regions, prophage regions, and predicted protein regions. Phenotypic experiments found that ST208-KL2 isolates displayed increased virulence and greater resistance to serum inhibition compared to ST208-KL7 isolates. This finding likely explains its persistently higher prevalence throughout the study period, except in 2019. Cluster2 isolates demonstrated significant advantages in ARG prevalence, resistance rates, and transmission capacity. ST208-KL2, with its superior serum resistance and virulence compared to ST208-KL7, has emerged as a dominant lineage with global implications for infection control and public health.

Pathogenic Escherichia coli and Salmonella threaten poultry production and human health through zoonotic transmission. Whole-genome sequencing of multidrug-resistant isolates from Bangladeshi poultry provides critical insights into antimicrobial resistance and population structure, supporting integrated One Health approaches to combat antimicrobial resistance.

Abstract Lebanon cedar ( Cedrus libani ) is a keystone conifer of eastern Mediterranean mountains, and an important species for forest conservation and restoration. However, range-wide patterns of population structure in C. libani remain poorly resolved, limiting evidence-based management and conservation efforts. In this study, we investigate the genetic structure and diversity of C. libani across its main distribution range of Anatolia and its closely related taxon, C. brevifolia (Cyprus cedar). Using 15 nuclear microsatellite markers (nSSRs), we analyzed seed lots from 14 stands across Türkiye and trees from one natural population of C. brevifolia in Cyprus. Our results reveal a significant genetic differentiation between C. brevifolia and C. libani (pairwise FST 0.063 to 0.114), as well as high genetic diversity within both taxa (mean expected heterozygosity H E ≈ 0.507; mean allelic richness Ar = 6.97). STRUCTURE analyses identified K = 3 as the primary level of population subdivision, separating C. brevifolia from C. libani and revealing a clear east–west separation within Anatolian C. libani . Subsequent hierarchical analyses resolved five genetically distinct clusters of C. libani , corresponding to major geographic regions of the Taurus Mountains (Antalya, Isparta, Konya, Mersin, and Kahramanmaraş). These clusters reflect pronounced spatial structuring and region-specific genetic diversity potentially influenced by macro-scale tectonic and climatic barriers. This study provides a comprehensive assessment of the spatial genetic structure of C. libani in Anatolia offering valuable insights for sustainable forest management and gene conservation.

Hybridization and introgression play crucial roles in evolution and adaptation. Although the influence of ploidy differences on interspecific hybridization has been documented, most studies have focused on single pairs of hybridizing species, thereby limiting our understanding of broader patterns of interspecific gene flow. Here, we investigate hybridization among six partially sympatric Betula species to examine patterns of genetic admixture involving diploid, tetraploid and octoploid species occupying diverse microhabitats. We sampled 148 populations across China, representing three diploid species (B. ashburneri and B. costata from section Costatae, and B. platyphylla from section Betula), two tetraploid species (B. ermanii and B. utilis from section Costatae), and one octoploid species (B. dahurica from section Dahuricae), and genotyped 2,610 individuals at 15 microsatellite loci. We assessed population structure and compared levels of genetic admixture among the six Betula species using pairwise analyses. Genetic diversity increased with ploidy level and was positively correlated with latitude. Analyses of population genetic structure revealed genetic admixture among Betula species with different ploidy levels. The proportion of hybrids among species within section Costatae was significantly higher than that among sections, although it was not significantly associated with phylogenetic distances between species. Higher genetic diversity in northern populations of the six Betula species suggests the existence of glacial refugia at higher latitude. The comprehensive dataset for six Betula species not only enables investigation of patterns of genetic admixture across ploidy levels but also fosters novel hypotheses regarding the origins of polyploid lineages and the factors influencing the dynamics of interspecific hybridization.

ABSTRACT Though information on the population dynamics and reproduction of the endemic delectable soft-furred mouse, Praomys delectorum, abound, the impact of anthropogenic disturbances on these parameters is still not known. This study investigated the impact of anthropogenic disturbances on the breeding pattern, population structure, and sex ratios of P. delectorum. The capture-mark-recapture technique was used to trap rodents from June 2018 to February 2020 in the Ukaguru Mountains within the Eastern Arc Mountains, Tanzania, where four 60 m × 60 m grids were set, two in intact sites and two in disturbed sites. More significant males were trapped in intact forests (χ2 = 10.71, df = 1, p = 0.001) compared to disturbed forests. The population density of P. delectorum varied temporally with peaks attained in the wet season in both habitats. Population structure showed few juveniles in most months and sub-adults accounted for the population increases in the wet seasons in all habitats. The proportion of reproductively active individuals varied temporally in both disturbed and intact forests while habitat disturbance showed no effect on the breeding activity of this species. Overall, these results suggest season as a factor responsible for the varying reproductive activity and population structure of P. delectorum in the landscape.

ABSTRACTGene flow affects the distribution of genetic variation of a species over time and thus can be crucial for a population's persistence and adaptive capacity. Given the importance of gene flow, it is key to understand the connectivity and genetic differentiation between populations of species with small and segregated breeding populations that are facing population declines, such as many long‐distance migratory birds. In this study, we explored population structure in Hudsonian Godwits (Limosa haemastica) from two geographically distinct breeding areas in the North American sub‐Arctic and two nonbreeding areas in South America using nuclear microsatellites. Despite being spatially and temporally segregated during most of the annual cycle, our results indicate no evidence of population differentiation between breeding populations, nor clustering between individuals from breeding and nonbreeding populations connected by migration. Considering the phenology of the species, godwits from both breeding populations could co‐occur during southward migration and/or throughout the oversummering period, likely in the Las Pampas ecoregion of Argentina. As with many other long‐distance migratory shorebirds, immature godwits stay in their nonbreeding areas until sexual maturity is reached, during which time they can explore, interact, and follow flocks of adults to different nonbreeding areas, thus increasing the chances of mixing between populations. This highlights the importance of recognizing the key role of early life period within the full life cycle of migratory birds for understanding their demography and evolutionary potential.

Pool-seq (pooled sequencing) combines DNA from multiple individuals prior to sequencing, enabling population-level allele frequency estimation without individual genotyping. When employed in a case-control Genome Wide Association Study (GWAS) framework, pool-seq faces a fundamental power limitation: Errors on allele frequency estimates are inversely proportional to sequence coverage and are large at modest coverage levels. Although this power limitation is appreciated, modestly sized pool-seq GWAS lacking unambiguous hits are often interpreted as showing a polygenic genetic architecture. We illustrate that this inference is unwarranted using empirical data from a Drosophila zinc resistance mapping study. Despite achieving >700× sequencing coverage in case and control pools, a directly ascertained SNP-based GWAS failed to reveal clear evidence for major-effect loci. A unique feature of the dataset is that an advanced intercross multiparent population, with known founders, was employed as the GWAS population. We leverage this unique population structure, in a manner that would not be possible in an outbred panel, to carry out two additional GWASs using imputed haplotype- or SNP-frequency estimates, which in contrast uncover localized regions of major effect. The key difference between approaches lies in statistical power: directly ascertained SNP counts have errors inversely proportional to sequencing coverage, whereas known founder imputation-based approaches can be considerably more accurate. In outbred populations where imputation cannot be used to obtain more accurate allele frequency estimates, substantially higher coverage than currently envisioned may be required to reliably detect modest allele frequency shifts. This work highlights that insufficiently powered GWAS studies can mask simple genetic architectures and create the illusion of polygenicity through statistical noise alone.

Wheat blast is a major threat to wheat production in tropical and subtropical regions of Brazil, yet the influence of epidemiological processes and population genetic structure on epidemic development remains unclear. Therefore, this study aimed to investigate, across different temporal and spatial scales, the genetic dynamics of Pyricularia oryzae Triticum lineage populations and their potential role in shaping wheat head blast epidemics. To investigate temporal genetic dynamics, we analyzed 270 isolates collected from wheat and co-occurring grasses at different crop growth stages within a single field. To evaluate potential tissue specialization and regional genetic structuring, an additional 97 isolates from leaves and spikes were sampled in two distinct regions of Minas Gerais. The analyses revealed a predominantly clonal population structure, with identical multilocus genotypes occurring within the same field, across geographic regions, and between plant tissues. The absence of genetic differentiation between leaf- and spike-derived isolates indicates a lack of tissue specialization, suggesting that the same genotypes can infect multiple organs throughout the crop cycle. Moreover, the detection of PoT-positive grasses both before and during wheat development highlights the potential contribution of grass-associated inoculum early in the epidemic. These findings support a scenario of low recombination, strong clonal expansion, and widespread dissemination of a few adapted genotypes, suggesting that early foliar infections and grass-associated inoculum may play a key role in initiating and sustaining wheat blast epidemics.

The role of isolation by distance in shaping population structure across space is well understood, and the same principles should operate over time. Allochrony, the isolation of populations due to separation in time, can be a source of genetic differentiation, but remains infrequently documented between yearly asynchronous populations. In this study, we investigate divergence between two putative sympatric populations of the alpine butterfly Oeneis chryxus ivallda at Castle Peak, CA, USA. We find clear genetic differentiation between butterflies collected in odd and even years, with limited instances of admixture. The observed GST of 0.05 between the two populations is approximately equivalent to 26 km based on pairwise GST values observed between O. chryxus populations across space. These results demonstrate a potential source of population differentiation in systems that promote multiple-year development in insects, often found in high-elevation and high-latitude environments.