Distribution Of Genetic Variation Research Articles

Phylogenetic Insights into H7Nx Influenza Viruses: Uncovering Reassortment Patterns and Geographic Variability

Influenza A viruses (IAVs), which belong to the Orthomyxoviridae family, are RNA viruses characterized by a segmented genome that allows them to evolve and adapt rapidly. These viruses are mainly transmitted by wild waterfowl. In this study, we investigated the evolutionary processes of H7Nx (H7N1, H7N2, H7N3, H7N4, H7N5, H7N6, H7N7, H7N8, H7N9) viruses, which pose a significant pandemic risk due to the known cases of human infection and their potential for rapid genetic evolution and reassortment. The complete genome sequences of H7Nx influenza viruses (n = 3239) were compared between each other to investigate their phylogenetic relationships and reassortment patterns. For the selected viruses, phylogenetic trees were constructed for eight genome segments (PB2, PB1, PA, HA, NP, NA, M, NS) to assess the genetic diversity and geographic distribution of these viruses. Distinct phylogenetic clades with remarkable geographic patterns were found for the different segments. While the viruses were consistently grouped by subtype based on the NA segment sequences, the phylogeny of the other segment sequences, with the exception of the NS segment, showed distinct grouping patterns based on geographic origin rather than formal subtype assignment. Reassortment events leading to complex phylogenetic relationships were frequently observed. In addition, multiple cases of previously undescribed reassortments between subtypes were detected, emphasizing the fluidity of H7Nx virus populations. These results indicate a high degree of genetic diversity and reassortment within H7Nx influenza viruses. In other words, H7Nx viruses exist as constantly changing combinations of gene pools rather than stable genetic lineages.

Comparative Efficacy of Current and Emerging Therapies for Cutaneous and Visceral Leishmaniasis: A Global Perspective

Leishmaniasis treatment has faced challenges with pentavalent antimonials, historically used but now showing resistance and high failure rates. The World Health Organization (WHO) recommended higher doses, but resistance in Nepal and misuse persist. Antimonials are no longer the preferred treatment for visceral leishmaniasis (VL) in the Indian subcontinent but are still used for cutaneous leishmaniasis (CL). Amphotericin B, especially liposomal amphotericin B (L-AmB), has become the preferred treatment for VL in the Indian subcontinent, with high efficacy and shorter treatment courses. Genetic insights into leishmaniasis reveal that parasite species and host immune responses are key factors in disease variation. Genetic analysis of atypical parasite isolates shows that genetic variations can lead to different disease patterns. Whole genome sequencing and proteomic analyses offer fresh insights into how parasite genes and proteins impact drug resistance, post-kala-azar dermal leishmaniasis (PKDL), and unusual disease presentations. Variations in hereditary unit copy numbers and single nucleotide polymorphisms contribute to genetic diversity and distinct tissue distribution, leading to distinct disease patterns. Genomic markers for drug resistance in Leishmania parasites include ATP-binding cassette (ABC) transporters, amino acid permease 3 (AAP3), and proteins like phosphoglycerate kinase (PGK) and mitogen-activated protein kinase (MAPK). These markers are associated with efflux of thiols and metals, antimony resistance, and protection against oxidative stress. Additionally, key proteins and enzymes in antioxidant defense mechanisms, such as iron superoxide dismutase-A (FeSOD-A), folate transporter 1 (FT1), and heat shock protein 83 (HSP83), play roles in drug resistance and parasite survival.

Spatio-temporal distribution and international context of bovine viral diarrhoea virus genetic diversity in France

Bovine viral diarrhoea (BVD) is one of the most economically damaging livestock enzootic diseases in the world. BVD aetiological agents are three pestiviruses (BVDV-1, -2 and HoBi-like pestivirus), which exhibit high genetic diversity and complex transmission cycles. This considerably hampers the management of the disease, which is why eradication plans have been implemented in several countries. In France, a national plan has been in place since 2019. Our understanding of its impact on the distribution of BVDV genotypes is limited by the availability of French genetic data. Here, we conducted a molecular epidemiology study to refine our knowledge of BVDV genetic diversity in France, characterise its international relationships, and analyse national spatio-temporal genotypic distribution. We collated 1037 BVDV-positive samples throughout France between 2011 and 2023, with a greater sampling effort in two major cattle production areas. We developed a high-throughput sequencing protocol which we used to complete the 5’UTR genotyping of this collection. We show that two main BVDV-1 genotypes, 1e and 1b, account for 88% of genotyped sequences. We also identified seven other BVDV-1 genotypes occurring at low frequencies and three BVDV-2 samples (genotype 2c). Phylogenetic analyses indicate different worldwide distribution patterns between the two main BVDV-1 genotypes. Their relative frequencies present no major changes in France since the 1990s and few variations at the national scale. We also found some degree of local spatial structuring in western France. Overall, our results demonstrate the potential of large-scale sequence-based surveillance to monitor changes in the epidemiological situation of enzootic diseases.

Fine-scale phylogeography of Tripneustes gratilla revealed a core-periphery pattern in the South China sea

The Core-Periphery Hypothesis (CPH) is a theoretical framework in phylogeography used to examine the spatial distribution of genetic diversity. The tropical Indian-Western Pacific (IWP), serving as a prominent marine biodiversity hotspot, constantly exports species and evolutionary novelties to peripheral habitats. Many species display genetic patterns consistent with CPH predictions from the IWP to periphery regions. However, the presence of CPH’s genetic signals in intermediate distribution zones remains underexplored. Here, we collected four sea urchin populations of Tripneustes gratilla in the South China Sea and analysed their population structure and evolutionary patterns using 13 morphological parameters, one mitochondrial 16S rRNA gene and nine polymorphic microsatellites. The results revealed substantial genetic homogeneity among the populations, implying a single origin from a glacial refugium. Nonetheless, morphological and microsatellite data distinctly differentiate the northernmost Fengjiawan population from the others, which could be attributed to increased environmental selection pressures such as temperature. Analysis of genetic diversity variation along latitudinal gradients and the relationship between geographic and genetic distances align with CPH expectations for both 16S and microsatellites, albeit to varying degrees of significance. This study enhances our understanding of tropical marine invertebrate evolution and supports the applicability of the CPH model at a fine-scale level.

Genome-Based Analysis of Genetic Diversity, Antimicrobial Susceptibility, and Virulence Gene Distribution in Salmonella Pullorum Isolates from Poultry in China.

Pullorum disease, caused by Salmonella enterica serovar Pullorum (S. Pullorum) infection, is a major pathogenic threat to the poultry industry. In this study, 40 S. Pullorum isolates from seven provinces of China were comprehensively analyzed in terms of antigenic type and antimicrobial susceptibility, and their drug-resistance genes and virulence genes were identified with whole-genome sequencing (WGS). We show that all these isolates were standard antigenic types, with ST92 the predominant genotype (92.5%). Disk diffusion assays revealed high resistance rates to streptomycin (92.5%), ciprofloxacin (82.5%), and ampicillin (80%), and the resistance rates to streptomycin, gentamicin, ampicillin, and cefotaxime were higher in isolates from sick chickens than in those from healthy chickens. In addition, gyrA mutations and eight acquired resistance genes were identified, with aac(6')-Iaa the most prevalent, followed by blaTEM1β, sul2, and the GyrA S83F mutation. The resistance phenotypes to streptomycin, ampicillin, and ciprofloxacin correlated strongly with the presence of the aac(6')-Iaa resistance gene, blaTEM1β resistance gene, and gyrA mutations, respectively. Analysis of the virulence genes showed that the isolates expressed numerous factors associated with secretion systems, including SPI-1 and SPI-2. Overall, this study extends our understanding of the epidemiology and antibiotic resistance of S. Pullorum in China.

The characterization, pathotype distribution and genetic diversity of Xanthomonas oryzae pv. oryzae in rice production centers of the Special Region of Yogyakarta, Indonesia

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogenic bacterium that induces bacterial leaf blight in rice. This disease is challenging to treat due to the presence of multiple pathotypes that can harm the plants. Characterizing and determining the distribution of pathotypes and genetic diversity of Xoo in the Special Region of Yogyakarta is essential for evaluating the appropriate approach to managing rice leaf blight in different districts of Yogyakarta. This study aimed to ascertain the characterization, distribution of pathotypes, and genetic diversity of Xoo in the Special Region of Yogyakarta. This study involved the isolation and characterization of Xoo from various rice production centers in Yogyakarta. The distribution of Xoo pathotypes was determined using five differential varieties (Tetep (4251), PB 5 (4827), Java 14 (11022), Kencana Bali (4477), and Kuntulan (1529)). Pathogenicity testing was conducted on six common varieties used by Yogyakarta farmers (IR64, Ciherang, C4, Mekongga, Menthik Wangi, and Inpari 42). Additionally, molecular characterization of Xoo was performed. The bacterial leaf blight that affects rice plants in the Yogyakarta region, caused by Xoo, is identified by yellow circular colonies. It exhibits a negative Gram staining response, positive catalase activity, negative oxidase activity, and does not hydrolyse starch. The Xoo pathotypes identified in Yogyakarta are IV, VIII, and XI. All six prevalent cultivars utilized by farmers in Yogyakarta are susceptible to Xoo. Out of each pathotype, four isolates were chosen, and they were divided into two distinct groups based on the DNA banding pattern they formed. Among these isolates, three had the lowest base sequence at 200 bp, while one isolate had a different DNA banding pattern with the lowest base sequence between 250–300 bp.

The characterization, pathotype distribution and genetic diversity of Xanthomonas oryzae pv. oryzae in rice production centers of the Special Region of Yogyakarta, Indonesia

Xanthomonas oryzae pv. oryzae (Xoo) is a pathogenic bacterium that induces bacterial leaf blight in rice. This disease is challenging to treat due to the presence of multiple pathotypes that can harm the plants. Characterizing and determining the distribution of pathotypes and genetic diversity of Xoo in the Special Region of Yogyakarta is essential for evaluating the appropriate approach to managing rice leaf blight in different districts of Yogyakarta. This study aimed to ascertain the characterization, distribution of pathotypes, and genetic diversity of Xoo in the Special Region of Yogyakarta. This study involved the isolation and characterization of Xoo from various rice production centers in Yogyakarta. The distribution of Xoo pathotypes was determined using five differential varieties (Tetep (4251), PB 5 (4827), Java 14 (11022), Kencana Bali (4477), and Kuntulan (1529)). Pathogenicity testing was conducted on six common varieties used by Yogyakarta farmers (IR64, Ciherang, C4, Mekongga, Menthik Wangi, and Inpari 42). Additionally, molecular characterization of Xoo was performed. The bacterial leaf blight that affects rice plants in the Yogyakarta region, caused by Xoo, is identified by yellow circular colonies. It exhibits a negative Gram staining response, positive catalase activity, negative oxidase activity, and does not hydrolyse starch. The Xoo pathotypes identified in Yogyakarta are IV, VIII, and XI. All six prevalent cultivars utilized by farmers in Yogyakarta are susceptible to Xoo. Out of each pathotype, four isolates were chosen, and they were divided into two distinct groups based on the DNA banding pattern they formed. Among these isolates, three had the lowest base sequence at 200 bp, while one isolate had a different DNA banding pattern with the lowest base sequence between 250–300 bp.

Molecular detection and genotyping of Toxoplasma gondii in stray cat feces from Khorramabad, West Iran

Cats, being the definitive host of Toxoplasma gondii, have a significant impact on the spread and outbreaks of the parasite. An essential factor in comprehending the transmission pattern of this parasite is an analysis of the genetic diversity distribution in cats infected with T. gondii. This study was aimed at determining the prevalence rate and genotyping of T. gondii in stray cat feces from Khorramabad, West Iran. In the years 2016–2017, 200 cats were sampled to get fresh feces specimens. Parasitological methods were utilized for the identification of oocysts. The DNA was isolated from the feces using a commercially available Genomic Mini Kit. In order to identify the genetic composition of T. gondii, we employed PCR-RFLP, sequencing, and phylogenetic analysis of the GRA6 target gene. No one of the samples tested positive for parasitology techniques. A total of 6.5 % (13/200) samples were positive when using the GRA6-PCR method. Based on PCR-RFLP results, all 13 samples were of T. gondii type III genotype. The nucleotide sequences of two samples from this study were found to be 5 % different from those of 12 references of T. gondii and one strain of Hammondia hamondi that was used as an external control. Based on the findings, molecular tests are more sensitive than parasitological methods. The RFLP approach revealed that type III of T. gondii is the prevailing and important genotype in Khorramabad, West Iran.

Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes.

Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.

Contrasting patterns of spatial genetic structure in endangered southern damselfly (Coenagrion mercuriale) populations facing habitat fragmentation and urbanisation

AbstractAimHuman‐induced environmental changes result in habitat loss and fragmentation, impacting wildlife population genetic structure and evolution. Urbanised and geographically peripheral areas often represent unfavourable environments, reducing connectivity among populations and causing higher population genetic differentiation and lower intra‐population genetic diversity. We examined how geographic peripherality and anthropogenic pressures affect genetic diversity and genetic differentiation in the protected southern damselfly (Coenagrion mercuriale, Odonata), which has low dispersal capabilities and specific habitat requirements and whose populations are declining.LocationWe studied two areas: one in semi‐natural habitats at the periphery of the species geographic range (northern France) and the other more central to the species' range, in an urbanised area surrounding the city of Strasbourg (Alsace, eastern France).MethodsWe genotyped 2743 individuals from 128 populations using 11 microsatellite loci. We analysed the spatial distribution of neutral genetic diversity (allelic richness, heterozygosity, levels of inbreeding and genetic relatedness), the extent of genetic differentiation and population affiliations (sPCAs) within the two areas. We also examined fine‐scale patterns of gene flow in the urbanised area of Alsace by investigating patterns of isolation by distance and estimating effective migration surfaces (EEMS) method.ResultsNorthern peripheral populations showed lower levels of genetic diversity and higher levels of genetic differentiation than central Alsacian populations. Although located in anthropised habitats, geographically central Alsacian populations showed high levels of gene flow, with dispersal events mainly occurring overland and not restricted to watercourses. However, the highly urbanised city of Strasbourg negatively impacted nearby populations by reducing levels of genetic diversity and increasing population genetic differentiation.Main ConclusionsThese results showed the need for management action by restoring breeding sites and creating migratory corridors for peripheral southern damselfly populations. However, our results also highlighted the resilience of southern damselfly in central range populations facing strong urbanisation pressures.

Genetic diversity and geographic distribution patterns of Malus landraces from 5 cultivated species under climate change in China

China is the largest center of genetic diversity of apple (Malus Mill.), with rich germplasm resources. In the process of evolution and domestication, a large number of apple landraces appeared, and they played a very important role before the introduction of modern cultivated apple varieties to China. However, the habitat of Malus landraces is under serious threat. In this study, 19 pairs of polymorphic simple sequence repeat primers were used to analyze the genetic structure and genetic relationships of Malus landraces and the potential distribution was predicted according to eight environmental variables using MaxEnt modeling. The results showed that the genetic variation of Malus landraces was high (Ho = 0.728 and He = 0.884), and the genetic differentiation was mainly distributed within respective populations and with almost no differentiation among populations. The five population groups were ranked, from highest genetic diversity level to lowest, as follows: Malus domestica subsp. chinensis > Malus prunifolia > Malus robusta > Malus asiatica > Malus micromalus. The 216 germplasms were divided into five groups based on Nei's genetic distance, whereas the Bayesian structure analysis categorized them into two groups. Population structure and principal coordinate analyses showed that Malus domestica subsp. chinensis, Malus asiatica and Malus prunifolia may be derived from similar genetic sources. In the modeling analysis, the cumulative contribution of temperature to the distribution of Malus landraces in suitable growth areas reached 66.1 %, and BIO4 (temperature seasonality) was identified as the major factor influencing the distribution of Malus landraces. Under four future emission scenarios, the potential distribution range of Malus landraces basically unchanged, but the total potential distribution area is projected to grow greatly over time and will tend to shift to higher latitudes.

A novel tomato interspecific (Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm.

We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

Pond area and availability safeguard amphibian genetic diversity across Iberia's largest protected wetland

Abstract Wetland ecosystems worldwide are threatened by habitat alteration, climate change and the introduction of invasive species, even within protected areas. Unravelling the reliance of sensitive wetland‐dwelling species, such as amphibians, on habitat characteristics is thus essential to identify conservation targets. Here we assess the distribution of genetic diversity of two strongly aquatic amphibians (Pelophylax perezi and Pleurodeles waltl) in association with habitat features across the most extensive, protected wetland of the Iberian Peninsula: Doñana National Park. Despite inhabiting a protected area free from anthropogenic barriers, the genetic diversity of P. perezi and P. waltl is not homogeneously distributed across the wetland, but instead concentrates in core areas, mainly in the northern zone. Both genetic diversity and connectivity (as opposed to genetic differentiation) showed significant positive associations with the area of the breeding sites and the flooded area surrounding the breeding sites within the dispersal potential of either species, that is nearby pond availability. Large water bodies connected to abundant temporary ponds are key for the maintenance of amphibian genetic diversity. Nevertheless, the core populations of our target species, which show markedly aquatic habits, are concentrated in areas colonised by invasive species, which could compromise their long‐term viability. Our results highlight that maintaining widely connected arrays of ponds of different hydroperiods, including large breeding sites free from invasive predators and competitors, is paramount for amphibian conservation in Mediterranean wetlands.

Riverscape features determining the genetic structure of the Yellow‐Spotted Amazon River Turtle (Podocnemis unifilis) in Brazilian Amazonia

AbstractLandscape characteristics can influence gene flow depending on the species ability to disperse. This imposes different levels of resistance to movement, determining the genetic structure and diversity of populations. Waterfalls and rapids in the Amazon basin have been suggested as contributing factors to the diversification and genetic structure of freshwater species, including turtles. Thus, along some main rivers of the Brazilian Amazon: Juruá, Madeira, Amazonas, Trombetas, Tapajós, Xingu, Tocantins, and Araguaia, we evaluated the spatial distribution of genetic diversity and characterized the population structure of Podocnemis unifilis, a widely distributed and endangered Amazonian turtle, using the mitochondrial DNA control region. We tested for isolation by geographic distance and by resistance models through an integrative approach using genetic, geographic, and ecological data, comparing these matrices with genetic distance. We found heterogeneous levels of genetic diversity and no spatial patterns. Results supported the isolation by resistance hypothesis, where the movement of individuals was influenced by freshwater, vegetational, climatological, and geomorphological variables, explaining the genetic distance of P. unifilis. Rapids and waterfalls impose greater resistance although they are barriers with different levels of permeability to the P. unifilis gene flow. Thus, the idiosyncrasies of each sub‐basin must be considered in the interpretation of the patterns found in assessing phylogeographic history.Abstract in Portuguese is available with online material.

Genetic diversity and haplotype distribution patterns analysis of cytb and RAG2 sequences in Rana hanluica from southern China.

Rana hanluica: an endemic amphibian of China, is found in the hills and mountains south of the Yangtze River. In this comprehensive study, we collected 162 samples from 14 different localities to delve into the genetic diversity of Rana hanluica using mitochondrial Cytb and nuclear RAG2 as genetic markers. Our findings reveal that the Nanling Mountains, specifically regions like Jiuyi Shan, Jinggang Shan, Mang Shan, and Qiyun Shan, are genetic hotspots harboring remarkable diversity. The research results also indicate that there is gene flow among the various populations of the species, and no distinct population structure has formed, which may be due to migration. Moreover, populations in some regions, as well as the overall population, show signs of a possible genetic bottleneck, which we speculate may have been caused by climate change. However, given the exploratory nature of our study, further investigations are warranted to confirm these observations. Through phylogenetic analyses, we uncovered indications that R. hanluica might have originated within the Nanling region, dispersing along the east-west mountain ranges, with a significant contribution originating from Jiuyi Shan. The genetic distributions uncovered through our research reflect historical migratory patterns, evident in the distinct haplotypes of the RAG2 gene between the western and eastern parts of the studied area. Moreover, Heng Shan and Yangming Shan exhibited unique genetic signatures, possibly influenced by geographic isolation, which has shaped their distinct genotypes. The insights gained from this study hold profound implications for conservation efforts. By identifying regions rich in genetic diversity and crucial gene flow corridors, we can develop more effective conservation strategies. Preserving these genetically diverse areas, especially within the Nanling Mountains, is vital for maintaining the evolutionary potential of R. hanluica. In conclusion, our research has laid a solid foundation for understanding the genetic landscape of R. hanluica, shedding light on its origins, population structures, and evolutionary trajectories. This knowledge will undoubtedly guide future research endeavors and inform conservation strategies for this endemic amphibian.

Unravelling the role of oceanographic connectivity in the distribution of genetic diversity of marine forests at the global scale

AbstractAimGenetic diversity of marine forests results from complex interactions of eco‐evolutionary processes. Among them, oceanographic connectivity driven by dispersal through water transport is hypothesized to play a pivotal role, yet its relative contribution has not been addressed at the global scale. Here, we test how present‐day oceanographic connectivity is correlated with the distribution of genetic diversity of marine forests across the ocean.LocationGlobal.Time periodContemporary.Major taxa studiedMarine forests of brown macroalgae (order: Fucales, Ishigeales, Laminariales and Tilopteridales).MethodsThrough literature review, we compiled a comprehensive dataset of genetic differentiation, encompassing 699 populations of 30 species. A biophysical model coupled with network analyses estimated multigenerational oceanographic connectivity and centrality across the marine forest global distribution. This approach integrated propagule dispersive capacity and long‐distance dispersal events. Linear mixed models tested the relative contribution of site‐specific processes, connectivity and centrality in explaining genetic differentiation.ResultsWe show that spatiality‐dependent eco‐evolutionary processes, as described by our models, are prominent drivers of genetic differentiation in marine forests (significant models in 91.43% of the cases with an average R2 of 0.50 ± 0.07). Specifically, we reveal that 18.7% of genetic differentiation variance is explicitly induced by predicted contemporary connectivity and centrality. Moreover, we demonstrate that long‐distance dispersal is key in connecting populations of species distributed across large water masses and continents.Main conclusionsOur findings highlight the role of present‐day oceanographic connectivity in shaping the extant distribution of genetic diversity of marine forests on a global scale, with significant implications for biogeography and evolution. This understanding can pave the way for future research aimed at guiding conservation efforts, including the designation of well‐connected marine protected areas, which is particularly relevant for sessile ecosystems structuring species such as brown macroalgae.

Genetic Diversity and Haplogroup Distribution of Three Ethnic Groups Tay, Thai, and Nung

The mitochondrial genome, with outstanding characteristics such as maternal inheritance, non-recombination and high mutation rate, is of great importance in population genetics and evolution research. To study the genetic diversity and the distribution of haplogroups of the Tai – Kadai language group, blood samples of 108 men from three ethnic groups Tay, Thai and Nung were collected. Total DNA extracted from blood samples was used for library preparation and whole mitochondrial genome sequencing using NGS. Comparing the obtained mitochondrial genome sequence with the RSRS (Reconstructed Sapiens Reference sequence) from Genbank (NC_012920) revealed 3929 distinct variants in 108 individuals with 1663 variants in the Tay ethnic group, 905 variants in the Thai ethnic group and 1361 variants in the Nung ethnic group. Nucleotide diversity (π) and haplotype were highest in the Thai ethnic group, being 0.0023 and 0.989, respectively. The genetic distances between each ethnic group pair (Tay-Nung, Tay-Thai and Thai-Nung), as shown by the FST values, were 0.03101; 0.00447 and 0.03282, respectively. Haplogroup analysis showed that 108 studied individuals belonged to 33 different haplogroups, belonging to 2 groups of haplogroups M and N. The most frequent haplogroups in Tay Thai and Nung were B4, F1 and M7, respectively. The results of this study show that although belonging to the same Tai - Kadai language family, the mitochondrial genomes among the three ethnic groups Tay, Thai, and Nung still have notable differences.

Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease.

Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.

Revisiting the genotypes of Theileria equi based on the V4 hypervariable region of the 18S rRNA gene.

Equine theileriosis, an economically important disease that affects horses and other equids worldwide, is caused by a tick-borne intracellular apicomplexan protozoa Theileria equi. Genotyping of T. equi based on the 18S rRNA gene revealed the presence of two, three, four or five genotypes. In previous published reports, these genotypes have been labelled either alphabetically or numerically, and there is no uniformity in naming of these genotypes. The present study was aimed to revisit the phylogeny, genetic diversity and geographical distribution of T. equi based on the nucleotide sequences of the V4 hypervariable region of the 18S rRNA gene available in the nucleotide databases. Out of 14792 nucleotide sequences of T. equi available in the GenBank™, only 736 sequences of T. equi containing the complete V4 hypervariable region of the 18S rRNA gene (>207 bp) were used in multiple sequence alignment. Subsequently, a maximum likelihood phylogenetic tree was constructed based on the Kimura 2-parameter model (K2+I). The phylogenetic tree placed all the sequences into four distinct clades with high bootstrap values which were designated as T. equi clades/ genotypes A, B, C and D. Our results indicated that the genotype B of Nagore et al. and genotype E of Qablan et al. together formed the clade B with a high bootstrap value (95%). Furthermore, all the genotypes probably originated from clade B, which was the most dominant genotype (52.85%) followed by clades A (27.58%), and C (9.78%) and D (9.78%). Genotype C manifested a comparatively higher genetic diversity (91.0-100% identity) followed by genotypes A (93.2-99.5%), and B and D (95.7-100%). The alignment report of the consensus nucleotide sequences of the V4 hypervariable region of the 18S rRNA gene of four T. equi genotypes (A-D) revealed significant variations in one region, between nucleotide positions 113-183, and 41 molecular signatures were recognized. As far as geographical distribution is concerned, genotypes A and C exhibited far-extending geographical distribution involving 31 and 13 countries of the Asian, African, European, North American and South American continents, respectively. On the contrary, the genotypes B and D exemplified limited distribution with confinement to 21 and 12 countries of Asian, African and European continents, respectively. Interestingly, genotypes A and C have been reported from only two continents, viz., North and South America. It was observed that genotypes A and C, and B and D exhibit similar geographical distribution. The present study indicated the presence of only four previously described T. equi genotypes (A, B, C and D) after performing the molecular analyses of all available sequences of the complete V4 hypervariable region of the 18S rRNA gene of T. equi isolates in the GenBank™.

Genotype identification and genetic diversity of the ompA gene among Chlamydia trachomatis

This study aimed to identify the distribution and analysis of genetic diversity of Chlamydia trachomatisgenotypes in infertile Vietnamese women. A total of 119 endocervical swabs were isolated from infertile women at the National Hospital of Obstetrics and Gynecology, Vietnam, during the period from January 2020 to December 2021, and was diagnosed with Chlamydiatrachomatis infection. 81 sequences of the ompA gene with a size of approximately 1,100 bp were used to determine the Chlamydia trachomatis genotypes by the currently reference sequences from GenBank. Sequence analysis of the ompA gene from the 81 positive patients showed nine genotypes, including E, D/Da, F, G/Ga, J, H, K, B/Ba, and I/Ia. In that, E, D/Da, and F were most prevalent (61.74%). Genotypes E, F, and G/Ga were highly conserved, showing 100% similarity to the alternative reference sequences, whereas ompA sequences of genotypes B/Ba, D/Da, H, I/Ia, J, and K displayed from one to ten nucleotide substitutions. In total, nineteen nucleotide changes were detected, seven of which led to amino-acid substitutions. The findings of the current study showed high prevalence of the genotypes E, D/Da, and F of C. trachomatis in infertile Vietnamese women.