Search Results (267)

The COVID-19 disease outbreak is the deadliest viral pandemic our generation has experienced, and much uncertainty remains over the varying vulnerability of different populations to the virus. This study investigates whether long-term evolutionary processes, such as genetic diversity and culturally embedded behavioural norms, can help explain why countries experienced different levels of COVID-19 infections and mortalities. Using a sample of 133 countries, we find that populations with higher expected genetic heterozygosity and greater historical exposure to infectious diseases are associated with lower COVID-19 case and death rates. We reveal two distinct pathways through which these effects manifest. Firstly, populations that migrated further from the evolutionary origins of Homo sapiens in East Africa exhibit lower genetic heterozygosity, which, in turn, is linked to greater susceptibility to COVID-19. Secondly, regions with higher historical disease prevalence tend to develop collectivist cultural norms and behaviours that are shaped to reduce disease transmission, which appear to mitigate the spread of COVID-19. These findings suggest that differences in vulnerability are not random but rather deeply rooted in genetic and cultural evolution. The analysis remains robust after accounting for socioeconomic, geographical, and institutional controls. Our findings offer policymakers fresh perspectives by integrating genetic theory and sociocultural dynamics into contemporary public health strategies. Full article

Background: Longfin batfish (Platax teira) is an important economic species in southern China. In recent years, its wild population has significantly declined due to overfishing. Around 2015, breakthroughs in the artificial large-scale seedling technology for P. teira have promoted the growth of its aquaculture scale in regions such as Hainan and Guangdong. Methods: To study the genetic diversity, inbreeding status, and population structure of the current P. teira farming populations in China, we performed whole-genome resequencing technology and high-density SNP markers to analyze the genetics of four main farming populations. A total of 109 individuals from four populations (NA, ZP, XL, and XC) were sequenced, identifying 5,384,029 high-quality SNPs. Results: The results showed that the nucleotide diversity (π) of each population ranged from 0.00155 to 0.00165 and observed heterozygosity (Ho) ranged from 0.253 to 0.282, which indicated low levels of genetic diversity. The results of the ROH analysis show significant inbreeding in the NA population. Genetic differentiation analysis revealed that the genetic differentiation among NA, XC, and ZP populations was relatively low (F_ST = 0.021–0.029). Conclusions: NA, XC, and ZP populations likely share a common origin of their fry stocks. Based on a phylogenetic tree, principal component analysis (PCA), and population structure analysis, the four populations were divided into four genetic groups. This study is the first analysis of the genetic diversity and population structure of P. teira farming populations in China, laying the foundation for the establishment of a base breeding population and the implementation of genetic improvement programs. Full article

Shanlan upland rice is a unique rice resource of the Li and Miao ethnic group in China and serves as a valuable gene pool adapted to tropical mountainous environments. To explore the genetic relationships of Shanlan upland rice from different geographical origins, 21 SSR markers were used to conduct genetic diversity and population structure analyses on 288 Shanlan upland rice accessions from 10 provinces (regions) in southern China. Results: The study revealed that the mean values of effective allele number (Ne), Shannon’s information index (I), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) for Shanlan upland rice were 1.616, 0.491, 0.74, 0.129, and 0.306, respectively. Genetic diversity analysis and molecular variance analysis (AMOVA) showed that the main source of variation between materials was the individual Shanlan upland rice plants. Genetic distance and differentiation results revealed the phylogenetic relationships among Shanlan upland rice populations. Both clustering and population structure analyses divided the materials into five subgroups, suggesting that the Shanlan upland rice from Qiongzhong, Hainan, might be the center of genetic diversity for the Hainan Shanlan upland rice, while rice from Dongfang, Hainan, and the inland populations exhibit genetic isolation. This study provides foundational data for the prioritized conservation and innovative utilization of Shanlan upland rice germplasm resources. Full article

Background: Inbreeding is a major genetic problem that reduces fertility and causes genetic disorders. Some breeders of dromedary camels use the same bull for many years due to its excellent characteristics, leading to mating with offspring and subsequent generations, resulting in increased homozygosity and genetic disorders. We hypothesize that inbreeding is associated with infertility in dromedary camels with normal and uninfected reproductive tracts. Methods: We genotyped 96 samples from seven camel breeds using the Illumina 55K SNP BeadChip, including five confirmed infertile individuals. Inbreeding coefficients (F) were calculated using PLINK based on heterozygosity and runs of homozygosity. Genome-wide association analysis using logistic regression was performed to identify potential genomic regions associated with infertility. Results: All five infertile camels showed significantly higher F values (>0.15) compared to 91 fertile individuals (<0.10, p < 0.001). The genome-wide association analysis failed to identify specific genomic regions linked to infertility, likely due to limited statistical power (n = 5 cases) and the polygenic nature of fertility traits. Population structure analysis revealed genetic differentiation related to coat color, with two significant SNPs on chromosome 3 near SLC30A5 (p < ${10}^{-7}$). Conclusions: Our results demonstrate that elevated inbreeding is strongly associated with infertility in dromedary camels. Future studies should employ larger sample sizes (≥50 infertile individuals) or whole-genome sequencing (35× coverage) to identify specific genomic regions. Implementation of breeding strategies avoiding related matings (F < 0.10) is recommended to maintain reproductive performance in camel herds. Full article

Acipenser dabryanus, once abundant in China’s freshwater ecosystems, is now extinct in the wild. Effective genetic tools are urgently needed to support conservation efforts under the Yangtze River Protection Law and the 10-year fishing ban. Traditional molecular markers (e.g., COI, SSR, SNP) often lack sufficient resolution for fine-scale population assessment. Here, we developed a high-resolution Multiple-Nucleotide Polymorphism (MNP) system for A. dabryanus, comprising 424 newly developed, highly polymorphic markers optimized for multiplex PCR and high-throughput sequencing. The MNP system demonstrated excellent performance in individual fin tissue samples, successfully distinguishing Acipenser sinensis and Acipenser ruthenus individuals from the A. dabryanus population. In addition, 41 characteristic alleles specific to A. dabryanus were further identified. Across samples, it achieved >90% MNP locus detection rate, with an average of 7.48 alleles per locus, 66.5% heterozygosity, >98% reproducibility, and 99% accuracy. A strong correlation was observed between DNA concentration and spike-in-based copy numbers (R² > 0.99), and sensitivity analysis confirmed reliable detection at ~1 copy/reaction. Application of the system across 97 samples, including 51 A. dabryanus tissue samples and 46 water environmental samples, revealed clear population structure with an average genetic differentiation of 70.45%, highlighting substantial genetic diversity within the sampled populations. Based on the above experimental results, the high-resolution MNP system has the potential to enable construction of population-specific allelic genotypes to distinguish wild individuals from released ones and, when applied to tissue and eDNA samples, to facilitate monitoring of migration pathways and habitat connectivity. Such applications could provide essential genetic information to evaluate release programs, guide conservation strategies, and inform habitat restoration for the recovery of A. dabryanus. Full article

Local livestock genetic resources are crucial for sustainable agriculture and biodiversity conservation. Dengchuan cattle, a nationally protected dairy breed in China, are esteemed for their high milk fat content and cultural significance. However, they have been threatened by crossbreeding with exotic high-yielding breeds, resulting in a decline in purebred resources. In this study, we evaluated the genetic diversity and structure of a conserved population using 100K SNP microarray data from 74 individuals. After implementing strict quality control measures, 78,460 loci were retained for principal component analysis (PCA), which identified 100 SNPs most associated with PC1. After calculating high-consistency loci using PLINK, based on allelic consistency, we selected 61 high-stability markers to represent 60 individuals for further analysis. Genetic diversity parameters indicated moderate polymorphism, with an effective population size (Ne) of 2.293, observed heterozygosity (Ho) of 0.300, expected heterozygosity (He) of 0.326, and an average polymorphic information content (PIC) of 0.261. A paired t-test confirmed a highly significant difference between Ho and He (p < 0.001). Runs of homozygosity (ROH) revealed a moderate level of inbreeding (F_ROH = 0.0928), with bulls exhibiting slightly higher values than females. Neighbor-joining (NJ) clustering further indicated clear lineage distinctions among bulls, but lower kinship among females. Overall, Dengchuan cattle exhibit moderate genetic diversity but face risks due to a small Ne and an unbalanced family structure. Targeted breeding strategies and genetic monitoring are recommended to ensure sustainable conservation and utilization. Full article

Background/Objectives: Mahachai Betta (Betta mahachaiensis) is a bubble-nesting fighting fish endemic to brackish habitats in Bangkok, Samut Sakhon, and Samut Prakan, where rapid urbanization and industrial growth threaten persistence. We evaluated genetic structure and diversity across 10 populations (81 individuals) to inform conservation planning. Methods: This study combined microsatellite genotyping (13 loci) with ecological niche modeling to assess genetic variability, population connectivity, and landscape–environmental drivers of differentiation. Results: Habitat loss and fragmentation were associated with reduced gene flow and decreased genetic diversity. Mean allelic richness was 2.65 and expected heterozygosity ranged from 0.20 to 0.46, with F_ST values up to 0.400. Forward simulations predicted severe erosion of diversity within the next 12.5–37.5 years. Populations showed clear genetic subdivision, most pronounced in Samut Prakan and Samut Sakhon, with two Samut Sakhon populations (SKN3 and SKN7) reflecting strong environmental heterogeneity. Conclusions: Improving habitat connectivity and intensifying local community engagement are priority actions to enhance the resilience and long-term persistence of Mahachai Betta. This study provides the first integrated genetic and landscape-based assessment of the species, highlighting its rapid genetic erosion under urbanization and offering a foundation for targeted, evidence-based conservation strategies. Full article

Prosopis cineraria (L.) Druce is a keystone tree species in the arid and semi-arid regions of West and South Asia, with critical ecological, cultural, and conservation significance. In the United Arab Emirates (UAE) and other regions of the Arabian Peninsula, this beneficial tree is called Ghaf. Despite its importance, genomic resources and population-level diversity data for the tree remain limited. Here, we present the first comprehensive population genomics study of Ghaf based on whole-genome resequencing of 204 individual trees collected across the UAE. Following Single-Nucleotide Polymorphism (SNP) discovery and stringent filtering, we analyzed 57,183 high-quality LD-pruned SNPs to assess population structure, diversity, and gene flow. Principal component analysis (PCA), sparse non-negative matrix factorization (sNMF), and discriminant analysis of principal components (DAPC) revealed four well-defined genetic clusters, broadly corresponding to geographic origins. The genetic diversity varied significantly among the groups, with observed heterozygosity (Ho), inbreeding coefficients (F), and nucleotide diversity ($\pi$) showing strong population-specific trends. Genome-wide fixation index F_ST scans identified multiple highly differentiated genomic regions, enriched for genes involved in stress response, transport, and signaling. Functional enrichment using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam annotations indicated overrepresentation of protein kinase activity, ATP binding, and hormone signaling pathways. TreeMix analysis revealed gene flow into one of the genetic clusters from both others, suggesting historical admixture and geographic connectivity. This work provides foundational insights into the population genomic profile of P. cineraria, supporting conservation planning, restoration strategies, and long-term genetic monitoring in arid ecosystems. Full article

The aim of this study was to assess the presence of heterogeneity of variance in milk yield in the first lactation of buffaloes and its subsequent influence on the genetic evaluation of Murrah breed sires. The analysis utilized a dataset comprising 2392 milk yield records of buffaloes involved in the Programa de Melhoramento de Búfalos do Brasil. The standard deviation classes were established by standardizing the averages of contemporary group levels, with positive values constituting the high standard deviation class and values equaling or less than zero comprising the low standard deviation class. The linear mixed model incorporated fixed effects of sire group, buffalo age at calving, and heterozygosity as covariates, along with additive genetic random effects. Variance components were estimated via Bayesian inference employing the Gibbs sampler to derive posterior means. The average posterior heritability obtained in analyses without considering heterogeneity of variances (i.e., the “general analysis”) was 0.21, while the averages 0.19 and 0.34 were obtained for the low and high standard deviation classes, respectively. The genetic correlation between standard deviation classes was 0.61. The genetic correlation estimates between the predictions of breeding values for milk yield were more closely aligned between the predictions obtained in the general analysis with the low standard deviation class, and more discrepant between the two standard deviation classes. In the animal genetic evaluation model, when heterogeneity of variance is disregarded, the variance components are substantially weighted towards the performance of individuals in the low phenotypic variability class. By disregarding the presence and heterogeneity of variance, the breeding values of the best sires were underestimated. Full article

Copaifera langsdorffii is a neotropical tree widely distributed in the Brazilian Atlantic Forest and Brazilian Savanna. Population genetic analyses can identify the scale at which tree species are impacted by human activities and provide useful demographic information for management and conservation. Using a Restriction site Associated DNA Sequencing approach, we assessed the genomic variability of six C. langsdorffii population relicts in a transition zone between the Seasonal Atlantic Forest and Savanna biomes in Southeastern Brazil. We identified 2797 high-confidence SNP markers from six remnant populations, with 10 to 29 individuals perpopulation, in a transition zone between the Seasonal Atlantic Forest and Savanna biomes in Southeastern Brazil. Observed heterozygosity values (0.197) were lower than expected heterozygosity (0.264) in all populations, indicating an excess of homozygotes. Differentiation among populations (F_ST) was low (0.023), but significant (0.007–0.044, c.i. 95%). A clear correlation was observed between geographic versus genetic distances, suggesting a pattern of isolation by distance. Bayesian inferences of population structure detected partial structuring due to the transition between the Atlantic Forest and the Brazilian Savanna, also suggested by spatial interpolation of ancestry coefficients. Through the analysis of F_ST outliers, 28 candidates for selection have been identified and may be associated with adaptation to these different phytophysiognomies. We conclude that the genetic variation found in these populations can be exploited in programs for the genetic conservation of the species. Full article

Factor XI (FXI) deficiency, or hemophilia C, is a rare bleeding disorder resulting from reduced levels or dysfunctional FXI protein due to mutations in the F11 gene. This study investigated the correlation between FXI activity levels, F11 genotype, and bleeding phenotypes. Clinical and genetic characteristics of 93 individuals from southern Italy diagnosed with congenital FXI deficiency, including 39 index cases and their relatives, were evaluated. FXI:C plasma levels were measured. Sanger sequencing of F11 was performed, and the pathogenicity of variants identified was assessed using in silico tools. FXI activity levels ranged widely (1–69%), with most cases being heterozygous and showing moderate deficiency. Only 12 individuals had severe FXI deficiency, typically associated with homozygosity or compound heterozygosity. Bleeding symptoms varied from mild to severe and occurred in 31% of subjects, though only a minority of those with severe deficiency experienced spontaneous or surgery-related bleeding. Sanger sequencing revealed 24 distinct F11 gene variants, predominantly missense mutations, with three novel variants (p.Val89*, p.Leu306Pro, and p.Trp515Gly). Common mutations included p.Glu135* and p.Glu315Lys. Variants were distributed across the gene, with no domain-specific clustering. No clear genotype–phenotype correlation was observed. FXI levels alone did not reliably predict bleeding risk, highlighting the influence of additional factors such as age, gender, and clinical history. This study reinforces the allelic and clinical heterogeneity of FXI deficiency and the limited utility of FXI:C levels alone for predicting bleeding severity. Further research is needed to clarify the complex genotype–phenotype relationships in FXI deficiency. Full article

The present research investigates the fine-scale spatial genetic structure (SGS) and gene flow dynamics in the endangered relict tree Tetracentron sinense, a keystone species in China’s montane ecosystems facing severe habitat fragmentation and genetic erosion. Utilizing genome-wide SNPs from 378 individuals across four natural populations (BMXS, MGFD, GLGS, SXFP), derived from ddRAD-seq, we quantified genetic diversity, SGS (Sp statistic), and dispersal patterns through spatial autocorrelation, parentage analysis, and age-class stratification. Results indicated critically low heterozygosity (observed heterozygosity, H_O = 0.019–0.022) and high inbreeding coefficient (Fis = 0.147–0.304), with moderate SGS (Sp = 0.0076–0.021) suggesting restricted gene flow (effective dispersal radius: 11–32 m). Seed-mediated dispersal was predominant, but topography and rainfall constrained dispersal (<5% beyond 50 m). Saplings exhibited stronger SGS, and the SXFP population experienced 100% sapling mortality due to inbreeding depression. Conservation efforts should prioritize assisted gene flow, habitat restoration, and ex situ sampling at distances greater than 115 m to preserve genetic diversity and adaptive potential. This study highlights the urgent need for genomics-informed conservation strategies in fragmented montane ecosystems. Full article

The genus Paphiopedilum (Orchidaceae) has high ornamental value due to its long flowering period, brilliant flower color, and peculiar floral morphology. Guangxi is the center of ecological diversity of Paphiopedilum, and therefore it is urgent to conduct rescue studies on the genetic resources and genetic structure of this genus in Guangxi. In this study, the genetic diversity of 39 populations from eight Paphiopedilum species in Guangxi was analyzed using ten selected EST-SSR primer pairs and fluorescent PCR amplification. The results show that genetic diversity varied among species, with large differences in expected heterozygosity (He). The highest genetic diversity was observed in P. barbigerum (I = 0.923; He = 0.480), while P. dianthum (I = 0.179; He = 0.098) showed the lowest diversity. From the genus perspective, molecular variance analysis (AMOVA) revealed that 57% of the genetic variation occurred among populations and 43% within populations, with inter-population variation being the main source of genetic variation. From a species perspective, genetic differentiation varied, with inter-individual differentiation ranging from 79% to 95%. The percentage of molecular variance indicated that genetic variation mainly occurred among individuals, which was the main source of total variation. According to the principle of maximum likelihood, the optimal K value was determined to be 6, and 760 Paphiopedilum samples were divided into six subgroups. The results of this study not only identify priority populations for conservation and establish a germplasm repository to preserve existing resources, but also provide references for research on asexual reproduction, seed propagation, and hybrid breeding of Paphiopedilum, thereby promoting the conservation and sustainable utilization of Paphiopedilum germplasm resources. Full article

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition often associated with genetic syndromes. Structural variants on the long arm of chromosome 15 (15q) are recurrently implicated in syndromic ASD, yet their phenotypic spectrum remains insufficiently characterized in diverse populations. We retrospectively analyzed clinical and molecular data from three patients with ASD treated at a Brazilian public reference center who also presented neurological and systemic comorbidities. Genetic investigations included G-banded karyotyping, chromosomal microarray analysis (CMA), methylation assays, and multiplex ligation-dependent probe amplification (MLPA) when indicated. Variants were classified according to ACMG guidelines and correlated with individual phenotypes. Case 1 showed an 8.4 Mb triplication at 15q11.2–q13.1 encompassing SNRPN, UBE3A, and GABRB3, which are associated with epilepsy, delayed neuropsychomotor development, and dysmorphic traits. Case 2 presented a 418 kb duplication at 15q13.3 involving CHRNA7 and OTUD7A, a variant of uncertain significance correlated with intellectual disability, speech apraxia, and self-injurious behavior. Case 3 demonstrated extensive loss of heterozygosity at 15q11.2–q13.1 and 15q21.3–q26.2, which is compatible with maternal uniparental disomy and Prader–Willi syndrome, manifesting hypotonia, seizures, and global delay. These findings underscore the potential involvement of the 15q region in syndromic ASD and related neurological comorbidities, highlighting the diverse pathogenic mechanisms and the importance of comprehensive genomic profiling for diagnosis, counseling, and individualized care. Full article

European black pine (Pinus nigra Arn. subsp. nigra) persists in scattered montane stands across Greece, where isolated populations harbour genetic variation shaped by local environments and demographic history. In this study, we assessed the genetic diversity and population structure of P. nigra using nuclear microsatellite markers (nSSRs) across four populations: Mt. Athos, Sithonia, Thassos, and Perama. A total of 67 individuals were genotyped, and seven high-quality polymorphic loci were retained after rigorous filtering. The Mt. Athos population exhibited the highest allelic richness and heterozygosity, with all loci being polymorphic and a low inbreeding coefficient after null allele correction. In contrast, the Perama population displayed reduced diversity, fewer polymorphic loci, and persistent heterozygote deficits. Principal Component Analysis (PCA) and Discriminant Analysis of Principal Components (DAPC) revealed weak overall population structure, with Perama genetically distinct from the other sites. Spatial Principal Component Analysis (sPCA) further uncovered an east–west cline within Athos and localized structure potentially shaped by both natural isolation and human influence. These findings highlight regional variation in genetic diversity within P. nigra and identify Athos as a genetically rich population of particular interest. The results provide a foundation for long-term monitoring and support informed strategies for the management and conservation of P. nigra in Greece. Full article