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At least 19 recordsLinked to original sources
PubMed2026

Climate Gradients and Habitat Discontinuity Structure Genetic Variation in a Spring-Specialist Plant.

BACKGROUND AND AIMS: Groundwater-dependent ecosystems support disproportionate biodiversity in arid regions, yet the population genetics of spring-specialist plants remains poorly understood. Here, we present the first species-wide genetic dataset for crimson monkeyflower (Mimulus verbenaceus, Phrymaceae), a spring-specialist plant distributed in seeps, springs, and associated riparian areas across desert regions of North America. We aim to relate landscape features and climate gradients to the spatial genetic structuring within this system. METHODS: Using genome-wide reduced representation sequencing data consisting of 10,760 SNPs from 175 individuals across 17 populations, we characterized the patterns of genetic differentiation and diversity. Population structure was assessed using ADMIXTURE and Principal Component Analysis. We examined the contributions of climate to range-wide genetic variation in crimson monkeyflower using redundancy analysis. KEY RESULTS: Patterns of genetic differentiation were more consistent with those of spring-specialist animal taxa than those of upland plants or generalist riparian plants. We found strong population structure at both broad regional scales and at fine local scales. While geographic and spatial structuring was a primary driver of genetic structure across all scales, riparian connectivity influenced local patterns of diversity, and adaptation to local climatic variation was more influential at regional scales, with temperature, relative humidity, and a monsoon-driven climate gradient contributing to genetic differentiation. CONCLUSIONS: Our findings highlight the distinctive association with isolated perennial groundwater sources, as well as climate gradients, with genetic variation in this spring-specialist plant. These findings suggest that spring-specialist plants deserve special consideration in ecological theory, management, and conservation.

Mimulus↗
PubMed2026

Differences in structural color and population genetic structure of Western and Central Palearctic Polyommatus icarus populations.

The blue structural coloration of male Polyommatus icarus butterflies functions as a sexual signaling trait and exhibits remarkable spectral stability within populations despite being generated by highly complex photonic nanoarchitectures. The correlation of the blue sexual signaling color and population genetic variation of the butterflies was investigated across the Western and Central Palearctic regions. Dorsal wing reflectance spectra was measured for 95 male specimens and compared with the population genetic structure revealed in 99 specimens by 18 recently developed microsatellites. Reflectance measurements indicated a clear separation between the European and Central Asian populations, consistent with our previous findings, while the intermediate populations near the Ural Mountains exhibited distinct European spectral characteristics. In contrast, genetic variation showed limited structuring and correlated primarily with geographic distance, as indicated by a significant isolation-by-distance pattern. Thus, although both reflectance and genetic variations are geographically structured, spectral properties are only weakly correlated with genetic differentiation. Populations near the Ural Mountains exhibited genetic ancestry linked to Central Palearctic groups, while displaying distinct Western Palearctic coloration, suggesting that the focal species' sexual signaling is strongly influenced by local factors. These findings suggest that sexual signaling coloration may evolve at least partially independently of the neutral genetic background, offering additional insight into evolutionary divergence across broad geographic scales.

Animals↗
PubMed1978

Variation in the genetic structure of Peromyscus populations. I. Genetic heterozygosity--its relationship to adaptive divergence.

The genetic structure of nine Peromyscus maniculatus nebrascensis demes from southeastern Wyoming was determined by analyzing allozymes encoded by 23 genetic loci with polyacrylamide gel electrophoresis. Genetic variability is extremely high for two genetic parameters; the proportion of loci polymorphic per deme averaged 0.41. Previous estimates of genetic heterozygosity for species within the genus Peromyscus have a mean of 0.06. The results of the present study suggest that genetic heterozygosity is considerably higher within P. maniculatus demes than within demes of other species in the genus. Geographic range is correlated with heterozygosity among Peromyscus species, as is adaptive divergence into broad-niched species. These correlates suggest that high heterozygosity may reflect an adaptation to a variable environment.

Adaptation, Physiological↗
PubMed2026

Whole-Genome Sequencing Reveals Population Structure, Genetic Diversity, and Selection Signatures in Kazakh Dromedary and Bactrian Camels.

Understanding the genomic basis of environmental adaptation is essential for the conservation and genetic improvement of domestic camels. In this study, we investigated the population structure, genetic diversity, and genomic variation potentially associated with environmental adaptation of Kazakh dromedary and Bactrian camels using whole-genome sequencing. Whole-genome sequencing data were generated for Kazakh camels (15 dromedaries and 16 Bactrian camels) and integrated with 131 publicly available genomes representing camel populations from the Arabian Peninsula, Iran, Xinjiang, Inner Mongolia, and Mongolian wild camels. Population structure, genetic diversity, and genome-wide selection were evaluated using principal component analysis, ADMIXTURE, nucleotide diversity, linkage disequilibrium, runs of homozygosity, genomic inbreeding (FROH), and selection scans based on FST, θπ ratio, and XP-EHH. Population genomic analyses revealed clear differentiation between dromedary and Bactrian camels, whereas Kazakh camel populations exhibited higher nucleotide diversity (θπ = 1.307-1.551 × 10-3), and lower genomic inbreeding (median FROH: 0.037-0.056) than Arabian populations. Genome-wide selection analyses identified MC4R as the prominent candidate gene in Kazakh dromedaries and RYR1 as a prominent candidate gene in Kazakh Bactrian camels. Functional enrichment analyses highlighted pathways related to energy metabolism, thermogenesis, calcium signaling, skeletal muscle function, mitochondrial activity, and oxidative stress response. These findings provide new insights into genomic variation potentially associated with environmental adaptation in Kazakh camels and offer valuable genomic resources for future conservation, breeding, and evolutionary studies.

MC4R↗
PubMed2026

Inference of Genetic Structure and the Process of Population Formation in Nepalese Native Goats Using Uniparental and Genome-Wide Markers.

Nepal is a small, landlocked country with marked elevational variation from the Terai plains to the Himalayas. Here, four indigenous goat populations (Chyangra, Sinhal, Khari, and Terai) are raised at different elevations. This study aimed to clarify the genetic structure of these populations and how they are formed and propagated across the Himalayan region. We analyzed 136 Nepalese goats using mitochondrial (mt) DNA D-loop and sex-determining region Y (SRY) 3'-untranslated region (UTR) sequences, as well as 50 K SNP array data. The mtDNA haplogroups D (0.162) and G (0.03) were detected only in Chyangra, whereas haplogroup B was predominant in Sinhal (0.42), followed by Khari (0.260). Regarding SRY haplotypes, Y2B was detected in all populations, whereas Y1AB (0.42) was found only in Chyangra. Genome-wide SNP analysis showed that Chyangra was genetically related to Tibetan and Central Asian goats, while Terai resembled South Asian goats. Interestingly, Sinhal formed a distinct cluster, whereas Khari exhibited an admixed genetic structure. These findings suggest that Nepalese goats originate from at least three ancestral lineages and that an additional migration route may have existed through the southern Himalayas.

50K SNP↗
PubMed2026

Phylogenetic Constraints and Environmental Filtering Jointly Drive Adaptive Evolution in Phragmites australis: From Genetic Structure to Trait Decoupling on the Mongolian Plateau.

The Mongolian Plateau, a typical arid and semi-arid zone in Eurasia, is characterized by highly heterogeneous and fragmented wetland habitats. Phragmites australis, a common wetland species in this region, exhibits remarkable adaptability. Unraveling the coordination between phylogenetic history and local environmental filtering is crucial for elucidating its adaptive mechanisms. Integrating landscape genomics and trait-based phylogenetic analyses, we analyzed transcriptome-wide SNPs, multidimensional functional traits, and environmental variables across 90 individuals from 30 natural P. australis populations. This study aims to reveal the genetic and phenotypic variation patterns underlying population genetic structure and trait variation, specifically distinguishing the roles of geographic isolation, environmental filtering, and phylogenetic history. Results reveal a significant drainage-dependent pattern in genetic structure. Populations in hydrologically connected basins show extensive admixture, whereas those in isolated endorheic basins form distinct lineages. While geographic isolation underpins genetic differentiation, environmental filtering independently explains ~33.84% of the genetic variation, driven primarily by moisture heterogeneity (precipitation seasonality and soil moisture). Crucially, we observed differentiated evolutionary trajectories across functional traits. Structural traits (e.g., plant height, leaf thickness) are phylogenetically conserved; in contrast, physiological traits (e.g., water use efficiency) are decoupled from phylogeny, showing patterns consistent with high plasticity regulated by local environments. This evolutionary decoupling strategy enables P. australis to flexibly adapt to heterogeneous habitats while maintaining structural stability. This study uncovers the synergistic mechanisms by which geographic isolation and environmental filtering jointly shape the genetic patterns of this cosmopolitan species at a regional scale, clarifies that its evolutionary responses may depend heavily on the differentiated plasticity of trait types, and provides valuable regional insights into how widespread wetland species adapt to heterogeneous environments under global change.

Mongolia Plateau↗
PubMed2026

Genetic structure and selection signatures of Beijing-You chicken populations provide insight into breed conservation.

Preserving genetic diversity and maintaining population viability are critical yet challenging goals that demand rigorous evaluation of conservation strategies. Beijing-You chicken, as the sole indigenous chicken breed originating from Beijing, China, is currently maintained as four independent populations under distinct conservation programs. How different conservation regimes have shaped its genomic architecture remains largely unknown, limiting evidence-based evaluation. Here, we generated whole-genome resequencing data from 240 individuals representing four Beijing-You chicken populations to assess population structure, genetic diversity, and signatures of selection over decades of conservation. All four populations formed distinct clusters, reflecting measurable differentiation after decades of separate conservation. The differences in genetic diversity were broadly consistent with the variation in effective population size estimates. Runs of homozygosity and linkage disequilibrium decay patterns further characterized each population, with extended values indicating reduced effective population size and increased inbreeding under long-term conservation. We applied the fixation index (FST) and pairwise diversity ratio (θπ) methods to identify selection signatures. A total of 171 genes were identified as candidates. These genes were enriched in pathways related to reproduction, growth regulation, and environmental adaptation. These findings highlight patterns of reduced diversity and skewed relatedness, which could arise from management-related factors such as breeding preferences or mating strategies. Still, they are also compatible with neutral processes, including drift and founder effects. Regardless of the underlying cause, integrating scientifically informed conservation strategies with routine genomic monitoring across generations is essential for sustaining genetic diversity in Beijing-You chicken and other indigenous breeds.

Beijing-You chicken↗
PubMed1978

[Genetic structure of Staphylococcus epidermidis strain No. 17 possessing penicillinase and bacteriocinogenic activity].

The studies on the genetic structure of Staphylococcus epidermidis, strain 17 showed that this strain possessed a factor of bactericinogenicity of the one type, which was an extrachromosomal element not bound with penicillinase activity. The loss of the bacteriocinogenicity factor spontaneously or under the effect of acridine orange at a temperature of 37 degrees C was not observed. Passages of the strain at a temperature of 44 degrees C for 5 days and acridine orange proved to be the most effective eliminating factors. The loss of the bacteriocinogenicity plasmid did not result in changing any biochemical properties of the strain but was accompanied by a loss of the immunity to bacteriocin of the initial strain. The study of the growth regularities of the initial strain and its variant deprived of the bacteriocinogenicity plasmid showed that multiplication of the cells in the presence of the plasmid practically started without the latent period.

Acridine Orange↗
PubMed2026

Novel bacterial hosts and mobile genetic structure of tet(X) variants in tetracycline-contaminated aquatic environment uncovered by culture and long-read metagenomics.

Clinically important tigecycline (3rd-generation tetracycline) resistance tet(X) variants were inferred to have evolutionarily originated from environmental bacteria, and have been recognized among environment, human and animals. However, genetic basis for environmental proliferation and dissemination of tet(X) variants remains ambiguous. This study profiled tet(X) variants at gene, contig, isolate, and community levels in environmental community subjected to long-term stepwise increasing oxytetracycline (1st-generation tetracycline) or tigecycline pressure using long-term microcosm experiments, quantitative PCR, bacterial isolation, whole-genome sequencing, and Nanopore-based long-read metagenomics. We confirmed that both oxytetracycline and tigecycline enriched the abundance of tetracycline resistance genes especially oxytetracycline-enriched tet(X3). Unexpectedly diverse bacterial hosts and genetic structure of tet(X)-positive mobile elements in the environment microbiome were identified using bacterial isolation and long-read Nanopore metagenomics. Pseudomonas defluvii was first reported to carry tet(X3) in the chromosome, forming IS26-tet(X3)-res-ISCR2 circular intermediate to transfer between different DNA molecules. Database mining revealed similar mobile segments have prevailed among animal-derived Acinetobacter species. Unlike the widely reported ISCR2-mediated transfer of tet(X6), we identified a novel mobile multidrug transposon TnAs3 where tet(X6) and class 1 integron co-transferred as its passenger region. Mobile tet(X2)-ere(D)-aadS-erm(F)-blaOXA-347 segment was annotated in Runella, and co-occurrences of tet(X2) and ere(D), aadS, blaOXA-347 were also found in Flavobacterium, Arsenicibacter, Chryseobacterium and Pedobacter. Overall, tetracycline-contaminated aquatic microbiome harboured diverse mobile tet(X)-positive segments which have not yet been acquired by clinical pathogens, and thus served as the genetic pool of tet(X) variants together with indigenous bacterial hosts, especially the newly reported Pseudomonas defluvii. Reducing pollution of older-generation tetracyclines would be a proactive way to mitigate environmental evolution and possible clinical effects of tet(X) variants.

Metagenomics↗
PubMed2022

Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa.

African populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multi-generational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within Africa as well as how within-Africa variation can be informative for broader variant interpretation; many variants that are rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity across Africa.

Africa, Southern↗
PubMed2025

Genetic structuring and estimation of reproductive adults in Onchocerca volvulus: A genome-wide analysis across hosts and regions.

Genomic analysis of parasites can deepen our understanding of their transmission, population structure, and important biological characteristics. Onchocerciasis (river blindness), caused by the parasitic nematode Onchocerca volvulus, involves adult worms residing in subcutaneous nodules that produce larval-stage microfilariae (mf), which are routinely detected in the skin for diagnosis. Whole-genome studies of mf are limited; most analyses have focused on the mitochondrial genome. We conducted a genome-wide analysis with 94% median nuclear genome coverage, analyzing 171, 37, and 98 mf from 16, 3, and 5 individuals from Ghana, Liberia, and the Democratic Republic of Congo, respectively. These data were used to investigate population differentiation, estimate the number of reproductive adult worms, and analyze genetic variation across chromosomes. Population genetic analyses across hosts and countries showed that nuclear genome diversity can reveal fine-scale genetic structure, even between geographically close countries, providing more resolution than mitochondrial haplotype data. By reconstructing maternal and paternal sibships, we estimated the number of reproductively active adult filariae. Comparisons between adult worm estimates from genetic data and nodule observations showed that genetics-based estimates were higher or equal to observed worm counts in 8 out of 9 hosts for female worms and 7 out of 9 hosts for male worms. Our analysis also revealed lower-than-expected X chromosome diversity, consistent with neo-X chromosome fusions in filarial species. This study represents an important step in using nuclear genome data from mf to support onchocerciasis elimination efforts and in developing genetic tools that could inform mass drug administration programs.

Onchocerca volvulus↗
PubMed1978

[The smallpox vaccination strain MVA: marker, genetic structure, experience gained with the parenteral vaccination and behavior in organisms with a debilitated defence mechanism (author's transl)].

The MVA virus is a lab virus ideally suited for vaccination of both man and animal which can be differentiated from the known Vaccinia strains by the use of numerous biological markers. Its reduced virulence for the chick embryo, for experimental animals and for man is a particularly characteristic feature. With the exception of chick embryo fibroblasts, the MVA virus grows in cell cultures only abortively. This applies particularly to cells of human origin in which the cytopathic effect and plaque formation are completely missing. The restriction analysis of the DNS of the MVA virus demonstrates that its genetic structure differs from that of the CVA basic virus and other orthopox viruses. In contrast to the WHO reference strain Elstree, the MVA virus has a genome shortened by about 9 per cent. The use of the MVA virus for human vaccination is particularly indicated in persons to be vaccinated for the first time and likely to entail a risk (on account of allergies etc.) because it brings about a state of revaccination without complications. The MVA virus can be administered in intracutaneous, subcutaneous or intramuscular injections. Innocuoursness and successful vaccination have been demonstrated in more than 120000 persons. While other Vaccinia strains, such as the Elstree virus, experience a drastic increase of virulence in the immunosuppressed organism (subjected to whole-body irradiation), the MVA virus cannot be activated not even in this situation.

Animals↗
PubMedDate not supplied

[Phage T4 partial diploidy obtained with the method of DNA interrupted injection. I. Analysis of the genetic structure and phage progeny reproduction process].

Phage T4 chromosome fragmentation is shown to take place when DNA injection is interrupted, a fragment length being strictly controlled by the interval from the moment of adsorbtion till the moment of an interruption. Populations of the bacteria cells infected by the phage T4 partial diploids are produced with the method of DNA interrupted injection. In the population a merodiploid involves some phage T4 amber mutant and a phage "wild" type chromosome fragment of the size controlled. To construct merodiploids the amber mutant in gene 43 and the mutant in gene 32 with the higher and the lower recombination frequency, accordingly, are used. Every merodiploid which is the heterozygote by one of these genes or which is the heterozygote by the late genes is determined to reproduce mixed phage progeny. Both the mean of the burst and the parent genotypes ratio in progeny either in the E. coli CR-63 cells or in the E. coli B depend on neither the heterozygote genetic structure nor the diploid region size. The results obtained conclude that phage genes express their function in the small fragments and the fragment recombination with the mutant partner whole chromosome follows their autonomous replication.

Chromosomes↗
PubMed2026

High-Density SNP Genotyping Reveals High Population Connectivity and Limited Spatial Genetic Structure in Apodemus flavicollis and Apodemus sylvaticus.

High-density SNP arrays are increasingly used in ecological and evolutionary studies, yet their application in wild species remains challenging. In this study, we evaluated the performance of the Affymetrix Axiom Mouse HD array, originally developed for Mus musculus, in two wild small mammals, Apodemus flavicollis and Apodemus sylvaticus, with particular focus on genetic diversity and population connectivity across seven sampling sites within a fragmented landscape. A total of 96 individuals (43 A. flavicollis and 53 A. sylvaticus) were genotyped using a 616K SNP array. After quality control filtering for missingness and minor allele frequency, more than 160,000 high-quality autosomal SNPs were retained for each species. Despite being designed for a different species, the array effectively discriminated between A. flavicollis and A. sylvaticus, with principal component analysis clearly separating the two species. Levels of genetic diversity were comparable across sites, with mean observed heterozygosity around 0.33 and consistently negative F IS values, indicating a slight excess of heterozygotes. Population structure analyses revealed extremely weak spatial genetic differentiation. ADMIXTURE supported a single genetic cluster (K = 1) within each species, while analysis of molecular variance attributed more than 99% of genetic variation to within-individual components. Pairwise relationship analyses showed that related individuals were not confined to single sites but occurred across sampling locations, supporting ongoing gene flow even across the fragmented landscape. No significant isolation-by-distance pattern was detected. Overall, our results indicate high population connectivity and limited spatial genetic structuring in both species across the study area, consistent with the documented dispersal capacity of these species at the spatial scale investigated. Moreover, this study demonstrates that high-density SNP arrays can provide powerful genomic tools for investigating dispersal dynamics and population structure in closely related wildlife species under habitat fragmentation, where subtle genetic patterns may otherwise remain undetected.

Apodemus species↗
PubMed2025

Genomic-based revelation of genetic structure and adaptive characterization of Schizopygopsis malacanthus in the Jinsha River and Yalong River.

BACKGROUND: As a highly specialized class of schizothoracine fishes, Schizopygopsis malacanthus has attracted much attention due to its widespread distribution. To investigate the impact of the Qinghai‒Tibet movement on S. malacanthus, we analyzed the genetic evolutionary history of this species. RESULTS: These results showed that there was a high level of genetic differentiation between Jinsha River (JSR) populations and Yalong River (YLR) populations. The genetic diversity of intra-YLR populations was higher than that of the intra-JSR populations. There was gene exchange of the Suwalong population to the Huoqu and Ganzi populations. Furthermore, both of the JSR and YLR populations exhibited a gradual increase in the genetic differentiation index from low to high altitudes, and the effective population of high-elevation populations has gradually expanded. In high-altitude populations, the selected genes were enriched in DNA repair, light transduction, and energy metabolism, reflecting the genetic basis for their migration to higher altitudes. CONCLUSIONS: S. malacanthus populations had the higher genetic differentiation and genetic diversity in the JSR and its main tributary YLR. Therefore, we should preserve high-elevation natural river sections as much as possible and reserve habitats for their migration and diffusion.

Animals↗
PubMed1979

Genetic structure of the Greek gypsies.

Data are presented on several polymorphic genetic markers in 200 Greek gypsies. Polymorphic loci studied were: the ABO, MN, Rhesus, Kell and Duffy blood groups, hemoglobin, and ceruloplasmin. A survey for congenital malformations and hereditary diseases was also carried out on this group. The ABO, Rhesus, MN and Duffy system frequencies varied significantly from the figures obtained for the Greek population. However, there is a characteristic similarity between various gypsy groups studied in other nations and the distribution of polymorphic traits in the Punjab region of India. Cystic fibrosis, renal tubular acidosis, 21-hydroxylase deficiency, Hoty-Oram syndrome and homozygous beta-thalassemia were diagnosed within the gypsy group studied.

ABO Blood-Group System↗