Phylogeography and genetic structure of avian isospora based on mitochondrial COI gene sequences from 17 countries.

Genetic diversity of the Australian paralysis tick (Ixodes holocyclus) causing paralysis in the endangered spectacled flying fox (Pteropus conspicillatus).

Genetic diversity of Culex pipiens complex populations from different geographic regions of China based on mtDNA-COI.

Enterobius vermicularis (pinworm) is a globally distributed intestinal nematode that primarily infects children. Despite its high prevalence, information on the molecular diversity of human-derived E. vermicularis populations remains limited, particularly in geographically diverse regions such as Türkiye. This study aimed to characterize genotype and haplotype diversity based on the mitochondrial cytochrome c oxidase subunit 1 (COI) gene in E. vermicularis egg isolates collected from humans in different regions of Türkiye. A total of 71 microscopy-positive samples were analyzed by nested PCR, and 40 COI amplicons (397 bp) yielded high-quality sequences for further evaluation. Sequence analysis revealed 16 distinct haplotypes defined by 20 polymorphic sites. Overall haplotype diversity was high (Hd = 0.871), whereas nucleotide diversity was low (π = 0.00714). Among the regional populations, the highest haplotype diversity was observed in Kars (Hd = 0.895), while the highest nucleotide diversity was detected in Balıkesir/Edremit (π = 0.00927). Maximum-likelihood phylogenetic analysis demonstrated that all Türkiye haplotypes belonged to Genotype B and formed three subclusters together with previously reported human-derived reference sequences from Europe and the Middle East. Seven haplotypes showed no 100% match in GenBank and were therefore considered novel, whereas the remaining haplotypes were identical to genotype B sequences previously reported from Greece, Bulgaria, Iran, Iraq, and Türkiye. To our knowledge, this study presents the first COI-based haplotype dataset of E. vermicularis egg isolates from multiple regions of Türkiye and demonstrates substantial intraspecific genetic diversity despite the predominance of a single mitochondrial genotype. These findings expand current knowledge of the genetic structure of human-derived E. vermicularis in Türkiye and provide a basis for future large-scale molecular epidemiological studies. Further studies including larger sample sizes and additional genetic markers are needed.

X-chromosome Short Tandem Repeats (X-STR) have been utilized in forensics and population genetics studies for more than two decades, particularly in cases involving complex kinship analysis, disaster victim identification, sexual assault, and incest. Nevertheless, the genetic landscape of India remains underexplored using X-STR markers. In the present study, blood samples of 420 unrelated participants (133 females and 287 males) were analyzed from the Brahmin community of Gujarat, India. For the amplification of X-STR loci, the Investigator® Argus X-12 QS Kit was utilized. 186 unique alleles were identified, suggesting high genetic diversity of the Brahmin population. Locus DXS10135 (PIC = 0.930) was the most polymorphic, and locus DXS7423 was the least polymorphic (PIC = 0.553). On analyzing the haplotype diversity, Linkage Group-1 (LG1) was found to have the highest haplotype diversity (0.997). Notably, LG1 was also the most informative and polymorphic linkage group (PIC = 0.994), preceded by LG4 (PIC = 0.989), LG2 (PIC = 0.988), and LG3 (PIC = 0.983). Based on the allelic and haplotype frequencies, the combined estimates for PDF, PDM, MECDesmarais, MECKishida, MECKruger, and MECDesmarais duo were ≥ 0.999, demonstrating high discriminatory power of all the loci. Furthermore, inter-population phylogenetic analysis revealed high genetic affinity of Gujarat's Brahmins with other populations of the Indian subcontinent, encompassing Madhya Pradesh's Bhil tribe and Punjab's Jat Sikh. The Gujarat Brahmins also have a shorter genetic distance with other South Asian populations, including the Bangladeshi population. This research indicates that the studied X-STR markers are highly polymorphic, offering significant insights for individual identification in forensics.

Preimplantation genetic testing for monogenic disorders (PGT-M) can prevent transmission of severe α-thalassaemia, but conventional workflows remain limited by family-specific assay design for direct variant detection, dependence on additional family samples for haplotype construction, and labour-intensive multi-step procedures across several platforms. Targeted long-read sequencing-based PGT-M for α-thalassaemia (tlrPGT-α-thal) integrates direct variant detection and haplotype linkage analysis within a single assay, but prospective clinical validation is lacking. This prospective clinical study enrolled 103 families at high risk of transmitting α-thalassaemia at a reproductive medicine centre between August 2024 and March 2025. All families underwent blinded parallel analysis using both conventional NGS-based PGT-M (comparator) and tlrPGT-α-thal. In the primary concordance analysis, tlrPGT-α-thal was fully concordant with conventional NGS-based PGT-M (507/507, 100.0%; exact 95% CI, 99.3-100.0). Direct variant detection was successful in 501/507 embryos (98.82%; 95% CI, 97.4-99.6), haplotype linkage was established in 505/507 embryos (99.61%; 95% CI, 98.6-100.0), and one meiotic recombination event was identified. Among 93 families proceeding to embryo transfer, 57 pregnancies underwent invasive prenatal diagnosis, and all were concordant with the corresponding tlrPGT-α-thal results. Of the 26 comparator-inconclusive embryos, tlrPGT-α-thal resolved 6 complex cases, including cases with incomplete pedigrees or insufficient informative SNPs. Among the remaining 20 embryos with HBA-region aneuploidies, genotype and parental origin could be determined in 12. The findings show that tlrPGT-α-thal enables direct detection of diverse α-thalassaemia-causing variants together with efficient haplotype linkage analysis within a single workflow, without requiring family-specific assay design or additional family samples. The method demonstrated high diagnostic accuracy while providing added value in complex scenarios. Taken together, tlrPGT-α-thal represents a simplified and broadly applicable strategy for α-thalassaemia PGT-M.

Classical HLA allele and haplotype frequency estimates in US populations.

Host-pathogen interplay of Orientia tsutsugamushi: pathomolecular epidemiology and phylo-immuno profiling in naturally infected rodents and shrews.

Lysine-rich membrane associated Plasmodium helical interspersed subtelomeric gene (phistb) is a member of the phist family of genes which encodes exported proteins essential for the parasite's survival within infected red blood cells. Recent studies suggest the phistb gene as a promising malaria vaccine candidate, however, its genetic diversity remains understudied. This study assessed the genetic diversity of the phistb gene in regions of varying malaria transmission aiming to generate data and improve our understanding of this promising malaria vaccine candidate gene. Genomic data from 1472 Plasmodium falciparum samples from Tanzania, Kenya, Uganda, and Ethiopia were retrieved in variant Calling file format (VCF) format from the MalariaGEN Pf7 database. Variants were filtered to include only biallelic Single Nucleotide Polymorphism (SNPs) with Variant Quality Score Log- Odds (VQSLOD) > 1 and "PASS" status. Genetic diversity, differentiation, and selection signatures were analyzed using population genetics metrics. After filtering, 1312 samples were retained. Wright's inbreeding coefficient (Fws) showed that 875 (66.7%) samples had monoclonal infections, with the highest proportion of monoclonal infections in Ethiopia (95.3%), followed by Tanzania (67.2%), Kenya (65.7%), and Uganda (50%). Among the 875 monoclonal samples, 88 haplotypes were identified, with Hap_1 (renamed PF3D7)and Hap_13 comprising 37.9 and 21.5 of the samples, respectively. Nucleotide and haplotype diversity were relatively higher in Kenya with 0.097, and 0.88 respectively, compared to the other study populations. The overall fixation index (Fst) was < 0.05, and Principal Component Analysis revealed no clear population sub-structure among countries. Negative Tajima's D values in Tanzania, Kenya, and Ethiopia indicated an excess of low-frequency alleles. This study reports low genetic diversity of the phistb gene in the four countries despite varying malaria transmission intensities among them, thus making it a suitable candidate gene for malaria vaccine. Further studies should be conducted to assess individual antibodies recognition of the phistb variants and the ability to elicit cross reactivity to further support its potential as a vaccine candidate.

Aedes aegypti is the principal vector of several medically important arboviruses, including dengue virus (DENV) and chikungunya virus (CHIKV), both of which remain endemic in Thailand. However, studies on arbovirus surveillance and mitochondrial genetic diversity of Ae. aegypti populations across broad geographic scales remain limited. This study aimed to assess the detection ofDENV and CHIKV andcharacterize the mitochondrial genetic diversity of Ae. aegypti across multiple regions of Thailand. A total of 303 adult Ae. aegypti mosquitoes collected from eight provinces across five geographic regions of Thailand were screened for DENV and CHIKV RNA. Mitochondrial cytochrome c oxidase subunit I (COI) genetic diversity was assessed using haplotype network analysis and analysis of molecular variance (AMOVA). CHIKV RNA was detected in 51 mosquitoes (16.8%) from four provinces, with the highest detection rates observed in Prachuap Khiri Khan and Bangkok. DENV RNA was not detected in any sample. COI analysis revealed moderate to high mitochondrial haplotype diversity and geographic variation in haplotype distribution among populations. Both widely shared and province-specific haplotypes were identified. AMOVA indicated that most genetic variation occurred within populations (93.19%), with significantgenetic differentiation among populations (ΦST = 0.068, P < 0.001). CHIKV RNA was detected in Ae. aegypti populations from multiple regions of Thailand, whereas DENV RNA was not detected. Mitochondrial COI analysis revealed substantial haplotype diversity and geographic variation among populations. These findings contribute to current knowledge of arbovirus occurrence and mosquito genetic diversity in Thailand and provide a foundation for future vector surveillance studies.

The GmCYCLOPS paralogs regulate soybean nodulation and exhibit signatures during domestication.

ObjectivesCystic echinococcosis (CE), caused by the Echinococcus granulosus larval stage, poses health problems in the world, including Iran. This study is aimed at investigating the epidemiological and molecular characterization of E. granulosus collected from CE samples in Urmia, the northwest of Iran.MethodsIn this cross‐sectional study, the demographic information of 295 hydatid cyst patients who underwent surgery between 2010 and 2021 was recorded and analyzed statistically. Due to time and financial constraints, a total of 74 samples were evaluated. DNA of FFPE (formalin‐fixed paraffin‐embedded) hydatid cyst samples was extracted, and PCR was performed using mitochondrial genes cox1 and nad1. PCR products were electrophoresed and sequenced, and sequence analysis was performed using BioEdit and BLAST software.ResultsAmong 295 cases studied, 173 (58.64%) were female and 122 (41.36%) male, respectively, and the CE frequency was significantly higher in patients aged 20–30 (n = 24/295; 8.1%), villagers (n = 70/295; 23.7%), and low educated cases (n = 82/295; 27.8%). The most group affected by CE was the housewives (n = 33/295; 11.2%), followed by the illiterate people (n = 82/295; 27.8%) and the farmers (n = 17/295; 5.8%). The liver (n = 52/295; 17.6%) and the lung (n = 40/295; 13.6%) were the most common sites for cyst formation, followed by the abdomen (n = 9/295; 3.1%), kidney (n = 4/295; 1.4%), thorax (n = 2/295; 0.7%), spleen (n = 2/295; 0.7%), and the pancreas (n = 3/295; 1.0%). DNAs from all 74 paraffinized hydatid cyst samples were extracted successfully. Of the whole FFPE samples amplified by PCR assay using nad1 and cox1 genes, only 27 and 25 FFPE samples were sequenced, respectively. The 9.1% (n = 27) for cox1 and the 8.4% (n = 25) for nad1 were sequenced. All samples′ analyses resulted G1. In addition, analysis of cox1 and nad1 genes did not identify any haplotypic variation. DNAs from all 74 paraffinized hydatid cyst samples were extracted successfully. Of the whole FFPE samples amplified by PCR assay using nad1 and cox1 genes, only 27 and 25 FFPE samples were sequenced, respectively. The 9.1% (n = 27) for cox1 and the 8.4% (n = 25) for nad1 were sequenced. All samples analyzed resulted G1. In addition, analysis of cox1 and nad1 genes did not identify any haplotypic variation.ConclusionsMolecular findings identified the G1 genotype as the predominant genotype involved in E. granulosus transmission in the northwest region of Iran.

Rhesus macaques play a valuable role in biomedical research, and their genetic characterization is critical for effective colony management. Levels of genetic diversity, genomic admixture, and genetic substructure can all impact the suitability of macaques for biomedical research. The Southwest National Primate Research Center (SNPRC) houses one of the largest rhesus macaque colonies in the United States. Their genetic management includes the ongoing assessment of genetic diversity, ancestral origin (India or China), and deep sequencing of the major histocompatibility complex (MHC). A goal of the SNPRC has been the reduction of levels of admixture between Indian- and Chinese-origin macaques and the prevalence of simian immunodeficiency virus (SIV) refractory MHC haplotypes while maintaining overall genetic and MHC haplotype diversity. This has been achieved by targeted sequencing of the MHC and removing animals with haplotypes more prevalent in Chinese-origin macaques from breeding. We investigated the impact of management strategies on admixture, population genetic structure, genetic diversity, and inbreeding using whole exome sequencing of founding and colony-born animals (n = 488). Admixture analysis of founders showed one animal to be of Chinese origin and an additional 37 considered admixed (> 15% Chinese ancestry; range 16.3-84.5%) with population substructure closely reflecting primate research center source. The levels of Chinese ancestry in the colony declined over time, though genetic diversity remains high (heterozygosity = 0.320). We characterized the MHC through targeted sequencing of 1,069 SNPRC macaques born over a twelve-year period. MHC management strategies reduced the prevalence of SIV-refractory MHC haplotypes, with Mamu-B*008 reaching significance (p = 0.027), while overall haplotype diversity was maintained (Mamu-A, h = 0.907; Mamu-B, h = 0.952). Finally, we performed genome-wide scans for genetic selection over time. We identify numerous genomic regions where allele frequencies have shifted significantly, supporting the presence of short-term adaptation under colony management. We show that colony management strategies have been successful without reducing genetic diversity of the MHC or exonic regions. We also show that colony genetic substructure is related to animal colony source and that mergers and migrations have reduced inbreeding and increased overall genetic diversity.

Genetic divergence along elevational gradients between mainland and island populations provides an opportunity to test the island genetic erosion model, which predicts reduced genetic diversity and increased differentiation in island populations. We examined two moth species, a geometrid moth (Alcis angulifera) and an erebid moth (Hydrillodes morosa), sampled along elevational gradients on Mt. Jirisan (mainland) and Mt. Hallasan (island) in southern South Korea. A total of 155 individuals were analyzed using mitochondrial cytochrome oxidase subunit I (mt COI) sequences. We identified 61 haplotypes across both species. A. angulifera exhibited similarly high genetic diversity on the mainland and island, whereas H. morosa showed overall lower diversity relative to A. angulifera but pronounced regional differences, with significantly higher haplotype and nucleotide diversity on the island. Mantel tests revealed significant genetic divergence between mainland and island populations but not within individual mountains, suggesting ongoing gene flow within elevational gradients. AMOVA indicated moderate differentiation in A. angulifera (FCT = 0.08) and stronger differentiation in H. morosa (FCT = 0.14), with most genetic variation occurring within populations. Gene flow estimates further highlighted contrasting patterns, with high connectivity in A. angulifera (Nm = 5.49) and restricted migration in H. morosa (Nm = 0.08). Together, these results indicate that while A. angulifera maintains genetic cohesion across regions, H. morosa exhibits stronger geographic and elevational structuring due to limited gene flow. Our findings do not support a universal reduction in genetic diversity in island populations; instead, they highlight the importance of species-specific ecological traits and geographic context in shaping genetic diversity patterns, suggesting that the island genetic-erosion pattern is more context-dependent than previously appreciated.

The current study is the first of its sort to evaluate the mitochondrial DNA (mtDNA) control region i.e. Displacement Loop (D-loop) in Damani sheep breed of Khyber Pakhtunkhwa Province, Pakistan. Limited work had been done on Damani sheep being recognized based on morphology and SSRs (Same Sequence Repeats) markers, which have not provided information about its origin. Thus, the current study was designed to investigate genetic diversity, relationship and matrilineal lineage of Damani sheep. Thirty (30) pure breed Damani sheep male and female were selected for blood sampling. The DNA was extracted from blood samples using Non-enzymatic salting out method and then (PCR) Polymerase Chain Reaction was performed for amplification of D-loop 910bp region. The amplicons were purified and then sequenced using Sanger sequencing technique. The sequences of D-loop revealed sixty-seven (67) polymorphic positions which were further subdivided into six haplotypes. The mean composition of D-loop nucleotides sequences were A/T and G/C contents (62.08 and 38.56%, respectively). Mean haplotype (HD) and nucleotides diversity (π) of D-loop was 0.853, and 0.02867, respectively. Two main clades were detected in Phylogenetic tree of D-loop sequences including the wild sheep (Ovis ammon) and domestic sheep (Ovis aries). The clustering pattern of Damani sheep D-loop haplotypes showed common matrilineal lineage with Chinese and Russian native sheep further it was concluded that population of this breed harbors considerable genetic diversity. The findings of this study will be a baseline for effective breeding strategies and conservation management of this breed in future.

Chloroquine resistance in Plasmodium falciparum (Pf) driven by mutations in the Pf chloroquine resistance transporter (Pfcrt) gene continues to pose a challenge to malaria control in endemic regions like India. Understanding the genetic diversity and evolutionary patterns of Pfcrt is important for guiding malaria surveillance and future national drug policy. This study analysed 979 Indian (exon 2) and 719 global full-length Pfcrt sequences using molecular tools to assess genetic diversity, selection pressure and population structure. Comparative and temporal analyses were conducted across Indian states and global regions to explore evolutionary trends. Indian sequence analysis revealed regional and temporal variations in haplotype diversity with both widespread and region-specific variants. Haplotype networks identified three major haplotypes namely CVIET, SVMNT and CVMNK, with CVIET predominating, particularly in the North-East, while SVMNT and CVMNK showed variable prevalence across regions and time periods. The greatest diversity was recorded between 2010-2019 despite reduced malaria incidence, suggesting ongoing selection pressure. Mizoram exhibited the highest Tajima's D value (D = 3.310, p < 0.01) and Pfcrt sequences from North-East region showed a unique genetic structure reflecting a likely role of selection pressures from the Greater Mekong Subregion. Globally, 65 haplotypes were detected with highest diversity in Cambodia with strong genetic differentiation observed across countries. Distinct genetic clusters and limited haplotype sharing across countries suggest that region-specific evolutionary pressures have shaped Pfcrt diversity. Positive selection at 6 codons and linkage disequilibrium between key SNPs indicate functional adaptation under drug pressure. This study highlights the variation in Pfcrt shaped by national drug policies and regional malaria transmission patterns. Continued molecular surveillance is essential to monitor emerging resistant lineages and guide effective malaria treatment strategies. This study highlights the variation in Pfcrt shaped by national drug policies and regional malaria transmission patterns.

ABSTRACTIn honey bees (Apis mellifera), the ancient and multifunctional protein Vitellogenin (Vg) is tightly linked to colony health. Vg contributes to several key traits, including nutrient transport, immunity support, and regulation of social behavior. However, the role of selective forces in shaping natural variation in this gene is poorly understood. To address this, we use a population genetic approach based on long‐read sequences to characterize full‐length vg haplotype variation. Using sequences from 543 honey bees sampled in Europe and the USA, including different subspecies and multiple geographical locations and we test whether patterns of variation and divergence are compatible with selection. Our findings show that vg segregates into two main haplotype versions (haplogroups), defined by 65 common polymorphisms, which together account for 69% of the sampled haplotypes. One haplogroup is abundant in A. m. mellifera conservatory samples. At the protein level, the haplogroups differ at only seven positions, all of which are in the protein's lipid‐binding cavity. This concentration at a single functional region motivates the hypothesis that haplogroup differences may affect lipid binding or transport. The remaining 58 polymorphisms are synonymous or in noncoding regions, which could influence gene expression and splicing. We further find that comparisons of variation across our samples are compatible with a history of positive selection at vg, in line with prior work. Taken together, our results document substantial vg haplotype structure across sampled honey bees and identify protein‐coding differences concentrated in the lipid‐binding cavity. This provides a foundation for future work linking vg genetic variation to Vg function and colony‐related phenotypes.

As with other locally adapted species, Philippine mallard ducks risk populationfragmentation and indiscriminate hybridization. To allow for targeted breed improvement,this study aimed to unravel the maternal genetic relationships, phylogeny, and levels ofgenetic diversity in Philippine mallard ducks. We sequenced the mitochondrial DNA D-loopregion of 118 ducks sampled from the Southern Leyte, Samar, and Cebu Provinces. Sequencedata analysis revealed nine transition base substitutions and eight distinct haplotypes.Overall haplotypic diversity (Hd = 0.666 ± 0.038) exceeded that reportedfor Javanese ducks, but was comparable to that of Thai, Chinese, and Indian domestic duckpopulations. The matrilineal phylogenetic tree positioned all Philippine mallard duckswithin the Old-World Haplogroup A. Specifically, they clustered into subhaplogroup A3(75/118), together with domestic ducks from China and Southeast Asia; putative ancestralsubhaplogroups A0 (6/118) and A1a (5/118) in a basal position, showing close geneticaffinities with Eurasian wild mallards and Eastern spot-billed ducks; and subhaplogroupA1b (6/118), showing genetic relatedness to the Indian Runner duck. Notably, 26individuals formed a distinct cluster corresponding to subhaplogroup A2, which appeared tobe unique to this population. This study provides the first mitochondrial DNA D-loop-basedgenetic characterization of Philippine mallard ducks, placing this population within thebroader Haplogroup A lineage and highlighting how its genetics was shaped by islandbiogeography. Collectively, these results establish the basis for future research onanimal genetic resources and phenomics, supporting the sustainable management of mallardduck populations in the Philippines.

PremiseAdvances in long‐read sequencing offer new possibilities to investigate haplotype diversity across multiple genes in plants and other taxa through multi‐locus, long‐read amplicon sequencing (multi‐locus LRAS). Despite this progress, there is a notable absence of dedicated bioinformatics pipelines for assembling diploid haplotypes of heterozygous individuals from such multi‐locus LRAS datasets, which is required for highly polymorphic populations.MethodsWe first evaluated various de novo and reference‐based assembly methods, culminating in a custom pipeline (HapAsmbl) to assemble haplotypes from Oxford Nanopore Technologies (ONT) LRAS data of five flowering genes (FT3, FTL9, VRN1, VRN2A, and VRN2B) generated from perennial ryegrass, a highly heterozygous species. After verifying the efficacy using a simulated heterozygous dataset, the HapAsmbl pipeline was used to explore haplotype diversity of CO, FT3, and VRN1 across multiple ryegrass populations.ResultsHapAsmbl outperformed existing tools by reliably reconstructing diploid haplotypes across multiple loci, enabling efficient haplotype characterization and novel allele discovery in genetically diverse populations.DiscussionHapAsmbl simplifies haplotype resolution from complex LRAS datasets from heterozygous individuals, allowing routine use of ONT long‐read sequencing for scalable haplotype analysis. HapAsmbl will enable researchers to uncover novel alleles and relate these to phenotype, supporting plant‐breeding efforts in non‐model crops.

While the biogeographic patterns of animals and plants are well defined, the distribution of the microbial eukaryotic world remains contentious. Classically, protists were assumed to be cosmopolitan, dispersing everywhere with little geographic constraint. We tested this hypothesis by compiling 88 marine cytochrome oxidase subunit I metabarcoding studies to perform a global population-genetic analysis. We uncovered a fundamental biogeographic divide: most animal (Metazoa) and plant (Archaeplastida) phyla have haplotype diversity that is strictly concentrated within specific ocean basins, while most protist phyla share identical haplotypes across multiple, distant oceans. The combination of large geographic ranges with moderate among-ocean genetic differentiation in protists is inconsistent with strict historical cosmopolitanism and is compatible with high connectivity and range expansion dynamics, including, but not limited to, recent colonization events. Our findings provide a unified population-genetic perspective on marine eukaryotic biogeography and refine current views of microbial dispersal at ocean-basin scales.