Gene Flow Research Articles

Cladistics of Rhipicephalus microplus and laboratory assessment of acaricidal efficacy of different Cassia fistula extracts against R. microplus larvae.

The present study aimed to analyze the cladistics and population structure analysis of Rhipicephalus microplus ticks infesting buffaloes in Haryana, India, as well as the assessment of the anti-tick efficacy of the ethanolic extracts of Cassia fistula (bark, pod pulp, and flowers) against R. microplus larvae. The molecular characterization and population structure analysis were performed by targeting the amplification of the partial mitochondrial cytochrome C oxidase subunit 1 (cox1) gene, whereas anti-tick efficacy was evaluated using a larval packet test. The sequences generated herein revealed a homology of 98.26-100% to the GenBank-archived R. microplus sequences. In population structure analysis, high haplotype (0.500 ± 0.265) and low nucleotide (0.002 ± 0.001) diversities were recorded for the sequences generated in this study. Significantly negative neutrality indices were recorded for the overall dataset. The extracts were found to significantly affect mortality rates in a dose-dependent manner, and the ethanolic extracts of the bark, pod pulp, and flowers of C. fistula exhibited median lethal concentration (LC50) values of 27.989, 40.457, and 49.43mg/mL, respectively. The LC50 value recorded for the combination of the ethanolic extracts of the bark, flower, and pod pulp of C. fistula was 19.724mg/mL, whereas the synthetic acaricide ivermectin had an LC50 value of 351.56mg/mL. In conclusion, R. microplus populations infesting cattle and buffalo hosts in India exhibited negligible genetic differentiation and high gene flow between them. Additionally, the combination of all C. fistula extracts could serve as a potential substitute for the synthetic acaricide.

Phylogeny and genetic diversity of Echinometra sea urchin in Taiwan

ABSTRACT Four closely related Echinometra species exist in the Indo-Pacific region, but little is known about their population genetics in Taiwan, an area rich in marine biodiversity. Echinometra dominates the Douziping coral reef off Liuqiu Island, where urchin barrens are also present. To understand the relationship between Echinometra species and urchin barrens, we investigated the genetic diversity of Echinometra species in Taiwan by using a nondestructive DNA extraction method on the spines of sea urchins. Mitochondrial DNA results showed that E. sp. C is the dominant species in Taiwan, with relatively high interspecific genetic distance. The E. sp. C is the only species in Douziping, and its population is expanding in accordance with the significantly low R2 value, the significantly negative Fu’s Fs values, and mismatch distribution analysis results. Gene flow estimates between the urchin populations in Taiwan and those in the neighbouring waters of Okinawa suggested that the Kuroshio Current could play an important role in Echinometra dispersal. This implies strongly connectivity between these populations. This study reports the first case of E. sp. C-associated urchin barrens in the tropics.

Genome-wide data reveal bi-direction and asymmetrical hybridization origin of a fern species Microlepia matthewii.

Natural hybridization is common and plays a crucial role in driving biodiversity in nature. Despite its significance, the understanding of hybridization in ferns remains inadequate. Therefore, it is imperative to study fern hybridization to gain a more comprehensive understanding of fern biodiversity. Our study delves into the role of hybridization in shaping fern species, employing Microlepia matthewii as a case study to investigate its origins of hybridization. We performed double digest Genotyping-by-sequencing (dd-GBS) on M. matthewii and its potential parent species, identifying nuclear and chloroplast SNPs. Initially, nuclear SNPs were employed to construct the three cluster analysis: phylogenetic tree, principal component analysis, and population structure analysis. Subsequently, to confirm whether the observed genetic mixture pattern resulted from hybridization, we utilized two methods: ABBA-BABA statistical values in the D-suite program and gene frequency covariance in the Treemix software to detect gene flow. Finally, we employed chloroplast SNPs to construct a phylogenetic tree, tracing the maternal origin. The analysis of the nuclear SNP cluster revealed that M. matthewii possesses a genetic composition that is a combination of M. hancei and M. calvescens. Furthermore, the analysis provided strong evidence of significant gene flow signatures from the parental species to the hybrid, as indicated by the two gene flow analyses. The samples of M. matthewii cluster separately with M. hancei or M. calvescens on the chloroplast systematic tree. However, the parentage ratio significantly differs from 1:1, suggesting that M. matthewii is a bidirectional and asymmetrical hybrid offspring of M. hancei and M. calvescens.

Phylogeography and paleoclimatic range dynamics explain variable outcomes to contact across a species' range.

Replicability of divergence after contact is a poorly characterized process, particularly in the contexts of phylogeography and postglacial range dynamics within species. Using contact zones located at the leading-, mid- and rear-edges of a species' range, we examined variation in outcomes to contact between divergent lineages of Campanula americana. We investigated whether contact zones vary in quantity and directionality of gene flow, how phylogeographic structure differs between contact zones, and how historic range dynamics may affect outcomes to contact. We found that all contact zones formed at similar times via primary contact yet detected significant admixture in only the rear-edge (RE) contact zone. In the northern leading-edge contact zone and the mid-range Virginia contact zone, gene flow was minimal and asymmetric. In the southern RE contact zone, gene flow was strong and symmetric. Asymmetric admixture in the leading-edge and Virginia contact zones matches the directionality of a known cosmopolitan cytonuclear incompatibility between lineages of C. americana. Our results emphasize the dependence of speciation processes on phylogeographic structure, evolutionary history and range dynamics.

Impact of patrilocality on contrasting patterns of paternal and maternal heritage in Central-West Africa

Despite their ancient past and high diversity, African populations are the least represented in human population genetic studies. In this study, uniparental markers (mtDNA and Y chromosome) were used to investigate the impact of sociocultural factors on the genetic diversity and inter-ethnolinguistic gene flow in the three major Nigerian groups: Hausa (n = 89), Yoruba (n = 135) and Igbo (n = 134). The results show a distinct history from the maternal and paternal perspectives. The three Nigerian groups present a similar substrate for mtDNA, but not for the Y chromosome. The two Niger–Congo groups, Yoruba and Igbo, are paternally genetically correlated with populations from the same ethnolinguistic affiliation. Meanwhile, the Hausa is paternally closer to other Afro-Asiatic populations and presented a high diversity of lineages from across Africa. When expanding the analyses to other African populations, it is observed that language did not act as a major barrier to female-mediated gene flow and that the differentiation of paternal lineages is better correlated with linguistic than geographic distances. The results obtained demonstrate the impact of patrilocality, a common and well-established practice in populations from Central-West Africa, in the preservation of the patrilineage gene pool and in the affirmation of identity between groups.

Genetic analyses and dispersal patterns unveil the Amazonian origin of guava domestication

Guava (Psidium guajava L.) is a semi-domesticated fruit tree of moderate importance in the Neotropics, utilized for millennia due to its nutritional and medicinal benefits, but its origin of domestication remains unknown. In this study, we examine genetic diversity and population structure in 215 plants from 11 countries in Mesoamerica, the Andes, and Amazonia using 25 nuclear microsatellite loci to propose an origin of domestication. Genetic analyses reveal one gene pool in Mesoamerica (Mexico) and four in South America (Brazilian Amazonia, Peruvian Amazonia and Andes, and Colombia), indicating greater differentiation among localities, possibly due to isolation between guava populations, particularly in the Amazonian and Andean regions. Moreover, Mesoamerican populations show high genetic diversity, with moderate genetic structure due to gene flow from northern South American populations. Dispersal scenarios suggest that Brazilian Amazonia is the probable origin of guava domestication, spreading from there to the Peruvian Andes, northern South America, Central America, and Mexico. These findings present the first evidence of guava domestication in the Americas, contributing to a deeper understanding of its evolutionary history.

Genetic diversity and connectivity of the invasive gastropod, Callinina georgiana (Caenogastropoda: Viviparidae) across a fragmented riverscape: A mitonuclear perspective

Abstract Aquatic invasive species are a significant threat to global freshwater biodiversity. This study focuses on the banded mystery snail, Callinina georgiana, an invasive species in the Adirondack region of northern New York—an important section of the New York Great Lakes Basin. This project aims to explore the genetic connectivity of C. georgiana within its invasive range using a combination of mitochondrial and nuclear markers. Sampling was conducted in the Raquette River and adjacent waterways, with a total of 229 snails collected from 16 distinct populations distributed across eight different waterbodies. Also included were two populations from the species' native range in the southern U.S.A. DNA was extracted, and a 710‐bp fragment of the mitochondrial DNA marker cytochrome c oxidase 1 and a 351‐bp fragment of nuclear marker histone‐3 were amplified. Population genetic analyses including haplotype patterning, AMOVA and genetic diversity estimates, neutrality tests and tests for isolation by distance were performed to assess connectivity patterns. Results showed moderate to high levels of genetic admixture within the snail's invasive range as indicated by the lack of geographic patterning of haplotypes and low to moderate levels of genetic differentiation across multiple sites. Demographic analyses combined with high numbers of private haplotypes indicate historic population expansion. Interestingly, a case of mitonuclear discordance was detected for native and invasive populations as evident by incongruent haplotype patterns for the cytochrome c oxidase 1 and histone‐3 markers. Callinina georgiana exhibits a high level of genetic connectivity in its invasive range. The presence of dams does not significantly affect apparent gene flow, indicating that anthropogenic activities, such as boat traffic might be key in dispersing the snails across this fragmented freshwater system. This study offers new insights into the dispersal and genetic structure of an invasive freshwater snail. It highlights the importance of considering anthropogenic factors when confronting complex patterns of genetic diversity. The findings are significant for biodiversity conservation and provide a basis for developing strategies to manage and contain the spread of aquatic invasive species such as C. georgiana, especially in regions with high human activity.

<i>FADS</i> gene polymorphism and the history of the formation of the indigenous populations of Siberia

The polymorphism of the rs174570, rs74771917, and rs7115739 FADS-gene loci in Siberian populations was studied. It was shown that the frequency of the rs174570-T variant marking haplotype A with a reduced level of fatty acid desaturase expression in the modern indigenous populations increases in the direction from the south to the north of Siberia. Similarly, an increase in the frequency of the TTT haplotype at the rs174570, rs74771917, and rs7115739 loci was observed in the northern direction. However, in ancient times, the populations of Eastern Siberia (its northeastern part, Baikal region, and Primorye) were characterized by an equally high frequency of the rs174570-T variant (over 80%). It was shown that the main influx of the rs174570-C allele (and the CCG haplotype) to northeast Siberia occurred relatively recently, over the past 300 years, as a result of mating contacts between indigenous populations and immigrant groups of predominantly eastern European origin. The gene flow intensity (for the rs174570-C allele) is estimated to be 1.5-4.4% per generation. The appearance of the rs174570-C variant in the population of the Baikal region has been registered since the Eneolithic epoch, which is apparently associated mainly with the advance of the Afanasievo culture tribes to the east of Siberia. Meanwhile, analysis of paleogenomic data showed that the TTT haplotype, with high frequency distributed in modern Eskimos and Amerindians, was present in the upper Paleolithic population of the Amur region, and therefore its carriers apparently took part in the formation of the ancient Beringian population.

Evaluating Two Sampling Methods for Mycoplasma Bovis Diagnosis in American Bison (Bison bison).

Mycoplasma bovis is a bacterial pathogen endemic to cattle. In the early 2000s, M. bovis emerged as a cause of respiratory disease in American bison (Bison bison), causing significant morbidity and mortality. Bison herds that experience an outbreak of M. bovis are at higher risk for subsequent outbreaks, suggesting that chronic, subclinical infections can be established. Antemortem testing is therefore crucial to disease management; however, the precise sampling method to maximize detection of M. bovis in bison is unknown. We evaluated two sample types-superficial nasal swabs and deep nasopharyngeal swabs-collected from apparently healthy or symptomatic bison from January 2021 through December 2022. We used real-time PCR to detect M. bovis in 76/938 bison (8.1%) from 11 herds. For bison testing positive on at least one swab type, M. bovis was detected in 63/76 (82.8%) deep nasopharyngeal swabs and 29/73 (38.1%) superficial nasal swabs. Agreement between swabs for positive bison was 21% (n=16, kappa coefficient 0.319). We conclude that deep nasopharyngeal swabbing is more sensitive than superficial nasal swabbing for detection of M. bovis in bison and that low agreement between methods may be related to stage of infection. We further tested pooled samples by PCR and found that pooling of up to five samples can be effective to increase throughput and minimize costs. Management of wild bison relies on the ability to relocate animals to maintain gene flow and healthy populations. Sensitive and specific diagnostic tests are needed to inform decisions and minimize risk of transmission, especially from subclinical carriers. This study provides valuable insight that will inform best practices for M. bovis testing, thereby supporting the conservation of bison as healthy wildlife, which in turn promotes ecological restoration, safeguards cultural practices of Tribal Nations, and upholds the bison as a unique American icon.

Molecular identification and genetic diversity of biting midges (Diptera: Ceratopogonidae) in the tropical environment on Hainan Island, China.

Biting midges are hematophagous arthropods responsible for zoonotic infectious diseases and have a wide distribution in temperate and tropical latitudes of the world. The genomic DNA of midge samples was extracted using the Chelex method and the ITS1gene was amplified by PCR to identify the midge species via BLAST. The sequence characteristics and the genetic diversity were analyzed using ClustalOmega, DnaSP, Arlequin, PopART, and TCS software tool. The validity of the ITS1 gene as a DNA barcode marker was evaluated using DAMBE. The phylogenetic relationship was established in the MEGA software. The ABGD web determined the species boundary and the SDT software visualized the pairwise sequence comparisons. A total of 39 midge samples possessed the range from 364 to 429 bp of the ITS1 sequences. The midge samples were identified as Culicoides imicola, Culicoides oxystoma, Culicoides peregrinus, Culicoides jacobsoni, Forcipomyia peregrinator, and Culicoides fulvus, respectively. The ITS1 sequences had 288 conserved sites (60.25%), 167 variable sites (34.94%), 141 parsimony-informative sites (29.50%), and 26 singleton sites (5.44%), with a considerable sequence variation with a high haplotype diversity. Populations in Lingao, Haikou, Tunchang were relatively independent, with a low level of gene flow. A separate population of Forcipomyia genus in Danzhou was observed. The biting midges in Hainan, a tropical island, had abundant genetic diversity. Timely surveillance is a crucial control measure for the spread of midge-borne diseases.

Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand

Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conduct a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identifies three dominant lineages, each with unique gene sets potentially enhancing bacterial fitness in the environment. We find that recombination drives lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage reveal increased expression of lineage-specific genes under environmental conditions in two out of three lineages. This underscores the potential importance of environmental persistence for these dominant lineages. The study also highlights the influence of environmental factors such as terrain slope, altitude, and river direction on the geographical dispersal of B. pseudomallei. Collectively, our findings suggest that environmental persistence may play a role in facilitating the spread of B. pseudomallei, and as a prerequisite for exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.

Population genetic structure of Culex tritaeniorhynchus in different types of climatic zones in China

BackgroundCulex tritaeniorhynchus is widely distributed in China, from Hainan Island in the south to Heilongjiang in the north, covering tropical, subtropical, and temperate climate zones. Culex tritaeniorhynchus carries 19 types of arboviruses. It is the main vector of the Japanese encephalitis virus (JEV), posing a serious threat to human health. Understanding the effects of environmental factors on Culex tritaeniorhynchus can provide important insights into its population structure or isolation patterns, which is currently unclear.ResultsIn total, 138 COI haplotypes were detected in the 552 amplified sequences, and the haplotype diversity (Hd) value increased from temperate (0.534) to tropical (0.979) regions. The haplotype phylogeny analysis revealed that the haplotypes were divided into two high-support evolutionary branches. Temperate populations were predominantly distributed in evolutionary branch II, showing some genetic isolation from tropical/subtropical populations and less gene flow between groups. The neutral test results of HNQH (Qionghai) and HNHK(Haikou) populations were negative (P < 0.05), indicating many low-frequency mutations in the populations and that the populations might be in the process of expansion. Moreover, Wolbachia infection was detected only in SDJN (Jining) (2.24%), and all Wolbachia genotypes belonged to supergroup B. To understand the influence of environmental factors on mosquito-borne viruses, we examined the prevalence of Culex tritaeniorhynchus infection in three ecological environments in Shandong Province. We discovered that the incidence of JEV infection was notably greater in Culex tritaeniorhynchus from lotus ponds compared to those from irrigation canal regions. In this study, the overall JEV infection rate was 15.27 per 1000, suggesting the current risk of Japanese encephalitis outbreaks in Shandong Province.ConclusionsTropical and subtropical populations of Culex tritaeniorhynchus showed higher genetic diversity and those climatic conditions provide great advantages for the establishment and expansion of Culex tritaeniorhynchus. There are differences in JEV infection rates in wild populations of Culex tritaeniorhynchus under different ecological conditions. Our results suggest a complex interplay of genetic differentiation, population structure, and environmental factors in shaping the dynamics of Culex tritaeniorhynchus. The low prevalence of Wolbachia in wild populations may reflect the recent presence of Wolbachia invasion in Culex tritaeniorhynchus.

Assessment of the genetic diversity and population structure in Moringa oleifera accessions using DNA markers and phenotypic descriptors

Moringa (Moringa oleifera Lam.) is one of the multipurpose trees with significant promise as a high-value crop of industrial importance, having nutritional, therapeutic, and prophylactic properties. Genetic diversity is a cornerstone of any crop improvement program and plays a key role in the selection of promising parental lines for hybrid breeding. Morphological and molecular markers have been proven to be potential tools for the evaluation of genetic diversity, crop genetic improvement, and conservation of plant genetic resources. In the current study, morphological descriptors, RAPD, and SCoT markers were used to determine genetic diversity among 28 M. oleifera accessions. Significant morphological variations were noted for several economic traits across the accessions studied. Four primary clusters were visible on the dendrogram based on phenotypic markers, indicating clustering of accession from a shared geographical habitat. No correlation was estimated between morphological traits, indicating an environmental influence. Three RAPD and seven SCoT primer sets produced 37 and 46 markers, with 53.2 and 71.3% polymorphisms, respectively. Based on genotypic data and the UPGMA approach, all 28 accessions were separated into two major clusters in the phylogenetic tree, irrespective of any geographical areas. The clustering pattern indicates widespread plant species and rapid gene flow through cross-pollination in Moringa populations. Three subpopulations of the involved accessions were identified by population structure analysis; however, there was only a weak link with the location of plant cultivation. The expected heterozygosity for the three subpopulations varied from 0.23 to 0.32, as per R-based structural analysis. AMOVA's attribution of 86% and 19% of all variations to within- and between-populations, respectively, indicates that there has been gene flow across geographic regions. The PCA showed a wide distribution of genotypes in the scatterplot, also suggesting huge genetic variation among the M. oleifera population. The study revealed a significant level of genetic diversity among M. oleifera accessions, which can be harnessed to conserve plant genetic resources and develop high-yielding, nutrient-dense Moringa cultivars.

Genetic and morphological evidence support the specific status of the endemic Ericaandevalensis (Ericales, Ericaceae).

Assessing the taxonomic status of closely related taxa is crucial in plant systematics and can have important implications for conservation and human plant use. Ericaandevalensis Cabezudo & Rivera is a metallophyte endemic species from highly metal-polluted soils of SW Iberian Peninsula, an area with a mining history going back more than 5,000 years. Ericaandevalensis is closely related to Ericamackayana Bab., a northern Iberian species also present in western Ireland. The status of E.andevalensis as a species or subspecies subordinated to E.mackayana is subject to debate. Here, we assessed the genetic and phenotypic relationship between both species, including the population structure of E.andevalensis. We used high throughput sequencing to determine genome-wide Single Nucleotide Polymorphisms (SNPs), and morphometric analyses from 35 reproductive and vegetative traits. The morphological analysis showed at least eight characters that can discriminate the two species, from which ovary hairiness and the size of leaf glandular hairs were the most informative. Genetic analyses showed that each species formed a monophyletic cluster with full support, separated by an interspecific genetic distance >4-fold higher than intra-specific distance. Population genetic analyses of E.andevalensis shows that populations are highly structured, with the Portuguese one as the most isolated and less variable. These results support the recognition of E.andevalensis as a distinct species with a highly constrained ecological requirements and a narrow geographic distribution, but with a limited gene flow between populations. We discuss the implications of these outcomes in conservation policies and potential uses of E.andevalensis such as decontamination of polluted soils.

Genome resequencing reveals population divergence and local adaptation of blacklegged ticks in the United States.

Tick vectors and tick-borne disease are increasingly impacting human populations globally. An important challenge is to understand tick movement patterns, as this information can be used to improve management and predictive modelling of tick population dynamics. Evolutionary analysis of genetic divergence, gene flow and local adaptation provides insight on movement patterns at large spatiotemporal scales. We develop low coverage, whole genome resequencing data for 92 blacklegged ticks, Ixodes scapularis, representing range-wide variation across the United States. Through analysis of population genomic data, we find that tick populations are structured geographically, with gradual isolation by distance separating three population clusters in the northern United States, southeastern United States and a unique cluster represented by a sample from Tennessee. Populations in the northern United States underwent population contractions during the last glacial period and diverged from southern populations at least 50 thousand years ago. Genome scans of selection provide strong evidence of local adaptation at genes responding to host defences, blood-feeding and environmental variation. In addition, we explore the potential of low coverage genome sequencing of whole-tick samples for documenting the diversity of microbial pathogens and recover important tick-borne pathogens such as Borrelia burgdorferi. The combination of isolation by distance and local adaptation in blacklegged ticks demonstrates that gene flow, including recent expansion, is limited to geographical scales of a few hundred kilometres.

Conservation genomics of the critically endangered Chinese pangolin.

The Chinese pangolin (Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters (MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.

Genetic diversity of North African populations in the 17q21 genomic region.

The demographic history of human populations in North Africa has been characterized by complex migration processes that have determined the current genetic structure of these populations. We examined the autosomal markers of eight sampled populations in northern Africa (Tunisia and Libya) to explore their genetic structure and to place them in a global context. We genotyped a set of 30 autosomal single-nucleotide polymorphisms (SNPs) extending 9.5Mb and encompassing the 17q21 inversion region. Our data include 403 individuals from Tunisia and Libya. To put our populations in the global context, we analyzed our data in comparison with other populations, including those of the 1000 Genomes Project. To evaluate the data, we conducted genetic diversity, principal component, STRUCTURE, and haplotype analyses. The analysis of genetic composition revealed the genetic heterogeneity of North African populations. The principal component and STRUCTURE analyses converged and revealed the intermediate position of North Africans between Europeans and Asians. Haplotypic analysis demonstrated that the normal (H1) and inverted (H2) polymorphisms in the chromosome 17q21 region occur in North Africa at frequencies similar to those found in European and Southwest Asian populations. The results highlight the complex demographic history of North Africa, reflecting the influence of genetic flow from Europe and the Near East that dates to the prehistoric period. These gene flows added to demographic factors (inbreeding, endogamy), natural factors (topography, Sahara), and cultural factors that play a role in the emergence of the diverse and heterogeneous genetic structures of North African populations. This study contributes to a better understanding of the complex structure of North African populations.

On the road to losing connectivity: Faecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India.

Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding, and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data are required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used faecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single-nucleotide polymorphism (SNP) data for 124 gaur and 99 sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred Karhandla Wildlife Sanctuary. Although sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although land cover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.

Plasmodium vivax populations in the western Greater Mekong Subregion evaluated using a genetic barcode.

An improved understanding of the Plasmodium vivax populations in the Great Mekong Subregion (GMS) is needed to monitor the progress of malaria elimination. This study aimed to use a P. vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics and explore the gene flow among P. vivax parasite populations in the western GMS (China, Myanmar and Thailand). A total of 315 P. vivax patient samples collected in 2011 and 2018 from four regions of the western GMS were genotyped for 42 SNPs using the high-throughput MassARRAY SNP genotyping technology. Population genetic analysis was conducted to estimate the genetic diversity, effective population size, and population structure among the P. vivax populations. Overall, 291 samples were successfully genotyped at 39 SNPs. A significant difference was observed in the proportion of polyclonal infections among the five P. vivax populations (P = 0.0012, Pearson Chi-square test, χ2 = 18.1), with western Myanmar having the highest proportion (96.2%, 50/52) in 2018. Likewise, the average complexity of infection was also highest in western Myanmar (1.31) and lowest in northeast Myanmar (1.01) in 2018. The older samples from western China in 2011 had the highest pairwise nucleotide diversity (π, 0.388 ± 0.046), expected heterozygosity (He, 0.363 ± 0.02), and the largest effective population size. In comparison, in the neighboring northeast Myanmar, the more recent samples in 2018 showed the lowest values (π, 0.224 ± 0.036; He, 0.220 ± 0.026). Furthermore, the 2018 northeast Myanmar parasites showed high and moderate genetic differentiation from other populations with FST values of 0.162-0.252, whereas genetic differentiation among other populations was relatively low (FST ≤ 0.059). Principal component analysis, phylogeny, and STRUCTURE analysis showed that the P. vivax population in northeast Myanmar in 2018 substantially diverged from other populations. Although the 42 SNP barcode is a valuable tool for tracking parasite origins of worldwide parasite populations, a more extended barcode with additional SNPs is needed to distinguish the more related parasite populations in the western GMS.

Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies.

Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.