Pairwise Distances Research Articles

Building shape-focused pharmacophore models for effective docking screening

The performance of molecular docking can be improved by comparing the shape similarity of the flexibly sampled poses against the target proteins’ inverted binding cavities. The effectiveness of these pseudo-ligands or negative image-based models in docking rescoring is boosted further by performing enrichment-driven optimization. Here, we introduce a novel shape-focused pharmacophore modeling algorithm O-LAP that generates a new class of cavity-filling models by clumping together overlapping atomic content via pairwise distance graph clustering. Top-ranked poses of flexibly docked active ligands were used as the modeling input and multiple alternative clustering settings were benchmark-tested thoroughly with five demanding drug targets using random training/test divisions. In docking rescoring, the O-LAP modeling typically improved massively on the default docking enrichment; furthermore, the results indicate that the clustered models work well in rigid docking. The C+ +/Qt5-based algorithm O-LAP is released under the GNU General Public License v3.0 via GitHub (https://github.com/jvlehtonen/overlap-toolkit).Scientific contributionThis study introduces O-LAP, a C++/Qt5-based graph clustering software for generating new type of shape-focused pharmacophore models. In the O-LAP modeling, the target protein cavity is filled with flexibly docked active ligands, the overlapping ligand atoms are clustered, and the shape/electrostatic potential of the resulting model is compared against the flexibly sampled molecular docking poses. The O-LAP modeling is shown to ensure high enrichment in both docking rescoring and rigid docking based on comprehensive benchmark-testing.Graphical

Gradual change of cortical representations with growing visual expertise for synthetic shapes

Abstract Objective: Visual expertise for particular categories of objects (e.g., mushrooms, birds, flowers, minerals, and so on) is known to enhance cortical responses in parts of the ventral occipitotemporal cortex. How is such additional expertise integrated into the prior cortical representation of life-long visual experience? To address this question, we presented synthetic visual objects rotating in three dimensions and recorded multivariate BOLD responses as initially unfamiliar objects gradually became familiar. Main results: An analysis of pairwise distances between multivariate BOLD responses (“representational similarity analysis,” RSA) revealed that visual objects were linearly discriminable in large parts of the ventral occipital cortex, including the primary visual cortex, as well as in certain parts of the parietal and frontal cortex. These cortical representations were present from the start, when objects were still unfamiliar, and even though objects were shown from different sides. As shapes became familiar with repeated viewing, the distribution of responses expanded to fill more of the available space. In contrast, the distribution of responses to novel shapes (which appeared only once) contracted and shifted to the margins of the available space. Conclusion: Our results revealed cortical representations of object shape and gradual changes in these representations with learning and consolidation. The cortical representations of once-viewed shapes that remained novel diverged dramatically from repeatedly viewed shapes that became familiar. This disparity was evident in both the similarity and the diversity of multivariate BOLD responses.

Genetic Diversity and Population Structure of Dülmen Wild, Liebenthal and Polish Konik Horses in Comparison with Przewalski, Sorraia, German Draught and Riding Horses.

The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the present study, genetic diversity was estimated for 101 Dülmen wild horses using multilocus genotypic information from a set of 29 autosomal microsatellites and compared with 587 horses from 17 different horse populations. Dülmen wild horses maintained a high degree of genetic diversity, with an average observed heterozygosity of 0.68, a mean number of 6.17 alleles, and heterozygote deficit of -0.035. Pairwise genetic distances (FST, Nei's standard, and Cavalli-Sforza distances) were closest to German coldblood breeds, Polish Konik, and Icelandic horses and most divergent from Sorraia and Przewalski's horses. Neighbor joining dendrogram and PCA plots showed a clear distinction of Dülmen wild horses from other populations, particularly from Przewalski horses. Posterior Bayesian analysis confirmed clear differentiation from other horse populations without an admixture pattern and a high membership index (0.92). It was possible to distinguish Dülmen wild horses from Dülmen and Polish Konik horses. In conclusion, Dülmen wild horses show a notable separation from other German horse breeds and primitive horse populations and may serve as a resource to study evolution of equine domestication.

Molecular identification and phylogenetic relationship of fishes belonging to the Family Danionidae from Brahmaputra Basin, Assam, Northeast India.

The Northeast India, being part of two global biodiversity hotspot namely the Indo-Burma and Eastern Himalayan Hotspots supports a wide variety of rich aquatic biodiversity including fishes. The family Danionidae is a widely diverse group inhabiting the upper colder stretches of river although few are abundant in the lower stretches. The persisting similarity in the morphological appearance and body colouration within the members of this family seeks an integrated method to identify the species correctly. In the present study, the mt-DNA barcode was generated for correct identification and confirmation of the species. A total of nine mitochondrial cytochrome c oxidase subunit I gene sequences were generated for each species under the study. The pairwise distance values ranged from 0.09 to 9.11% within species and 9.06-32.71% between species. A neighbour-joining tree was constructed based on the Kimura 2 parameter model. Two major groups were observed where Danioninae formed a sister group to the Chedrinae and Rasborinae. The present study is a preliminary work to document and identify the species under the family Danionidae from Brahmaputra basin, Assam, using molecular tools and establish the phylogenetic relationship.

Asian Mus musculus: subspecies divergence, genetic diversity, and historical biogeography

Abstract The House Mouse, Mus musculus, is a model organism that has greatly contributed to evolutionary research. Despite its significance, there remain gaps in our understanding of its phylogeography and population genetic structure in Asian regions. This comprehensive study aims to elucidate the evolutionary history, genetic diversity, and distribution patterns of M. musculus. A diverse data set of 281 M. musculus samples was collected from across Asia, covering 101 localities in 19 countries. Phylogenetic analysis using Cytochrome b and D-Loop region unveiled well-supported lineages. These lineages correspond to: M. m. musculus, M. m. domesticus, M. m. castaneus, and M. m. bactrianus. Also, validity of M. m. bactrianus was questioned. The analysis suggests a monophyletic origin of these subspecies approximately 0.59 million years ago (Mya), followed by 2 main lineages—one consisting of M. m. domesticus (~0.59 Mya) and the other comprising M. m. castaneus, M. m. bactrianus, and M. m. musculus (~0.56 Mya). Genetic diversity varied among subspecies, with M. m. domesticus exhibiting the highest diversity due to its extensive global distribution and M. m. bactrianus exhibiting the lowest diversity due to restriction in southwest Asia. Pairwise genetic distances and Fst values confirmed significant genetic differentiation among the subspecies, underlining their historical isolation. Additionally, a Mantel test indicated that geographical distance played a pivotal role in shaping genetic differentiation. Demographic analysis revealed evidence of population expansions in M. m. domesticus, M. m. musculus, and M. m. castaneus, while M. m. bactrianus showed characteristics of neutral selection and genetic drift. Species distribution modeling, assessing both Current Conditions and the Last Glacial Maximum, indicated habitat shifts and losses during glacial periods, particularly in the eastern and northern regions of Asia. However, each subspecies displayed unique responses to climatic changes, reflecting their distinct ecological adaptations. Historical biogeography analysis pointed to complex origins and a network of dispersal and vicariance events that led to the contemporary distribution of subspecies. Deserts and xeric shrublands emerged as critical areas for diversification and speciation. This study contributes to our understanding of the phylogeography and population genetics of M. musculus in Asia, highlighting the significance of geographical factors and climatic fluctuations in shaping its evolutionary history and genetic diversity.

Y-chromosome analysis recapitulates key events of Mediterranean populations

The remarkable geographical situation of the Mediterranean region, located between Europe, Africa, and Asia, with numerous migratory routes, has made this area a crucible of cultures. Studying the Y-chromosome variability is a very performant tool to explore the genetic ancestry and evaluate scenarios that may explain the current Mediterranean gene pool. Here, six Mediterranean populations, including three Balearic Islands (Ibiza, Majorca, and Minorca) and three Southern Italian regions (Catanzaro, Cosenza, and Reggio di Calabria) were typed using 23 Y-STR loci and up to 39 Y-SNPs and compared to geographically targeted key reference populations to explore their genetic relationship and provide an overview of Y-chromosome variation across the Mediterranean basin. Pairwise RST genetic distances calculated with STRs markers and Y-haplogroups mirror the West to East geographic distribution of European and Asian Mediterranean populations, highlighting the North-South division of Italy, with a higher Eastern Mediterranean component in Southern Italian populations. In contrast, the African populations from the Southern coast of the Mediterranean clustered separately. Overall, these results support the notion that migrations from Magna Graecia or the Byzantine Empire, which followed similar Neolithic and post-Neolithic routes into Southern Italy, may have contributed to maintaining and/or reinforcing the Eastern Mediterranean genetic component in Southern Italian populations.

Exploring genetic variation in saffron (Crocus sativus L.) accessions through two-locus DNA barcoding

Saffron (Crocus sativus L.) remains among the most costly spices worldwide due to its invaluable properties. Traditional breeding methods are restricted by saffron's male sterility and clonal multiplication, which may result in genetic deterioration and make genetic diversity within saffron populations cryptic. To overcome this cryptic diversity, we conducted a comprehensive genetic analysis of sixteen saffron accessions from Morocco, France, Greece, and Italy using two universal DNA barcodes: ITS2 and trnH-psbA. Our findings unveiled significant genetic diversity among examined accessions, characterized by considerable sequence variation. This led to the identification of a notable number of haplotypes (14 and 15) with a high haplotype diversity (HD) = 0.9, signifying extensive genetic variability. Moreover, Phylogenetic and network analyses illustrated distinct genetic clusters and evolutionary relationships among saffron populations, separating our accessions from Iranian saffron. Besides, Pairwise distance and principal component analyses confirmed the unique genetic profiles of the Assif Zimer population from Morocco. Notably, the study explores environmental factors as potential contributors to genetic differences across different regions. Finally, the assessment of ITS2 secondary structures and the generation of Two-Dimensional DNA Barcodes provided unique identities to accessions and gave valuable insights into sequence variability and molecular identification. Our study contributes to a deeper understanding of saffron genetics and provides essential information for conservation projects.

Two-sample testing with local community depth

AbstractIn this paper, we investigate nonparametric two-sample hypothesis testing with local community depth, a measure of data depth calculated from pairwise distances between observations. Unlike many common “center-outwards” measures of data depth, local community depth captures local features of a distribution such as multimodality and can adapt to modes with different scales. This gives local community depth greater power to detect scale changes in multimodal distributions, and importantly the method is parameter-free. The local depth employed supplements existing adaptations of depth to local regions and is computationally cheaper in high dimensions than many classic depths such as halfspace depth, regression depth, simplicial depth, and Mahalanobis depth. We test hypotheses by using local community depth in the Liu–Singh test and give conditions under which our method is consistent against fixed alternatives (and has a limiting null distribution). In simulations and an application to diagnosing dengue fever, we show that local community depth outperforms other depths when the underlying distribution is multimodal or asymmetric, and is comparable to other methods when the data is unimodal and symmetric.

INCEPT: A Framework for Duplicate Posts Classification with Combined Text Representations

Dealing with many of the problems related to the quality of textual content online involves identifying similar content. Algorithmic solutions for duplicate content classification typically rely on text vector representation, which maps textual information into a set of features. Ideally, this representation would capture all aspects of the underlying text, including length, word frequencies, syntax, and semantics. While recent advancements in text representation have led to improved performance, a comprehensive approach that explicitly incorporates all text features has not yet been proposed. In this study, we present the INCEPT framework that utilizes multiple representation methods to detect duplicate text pairs, taking advantage of their individual strengths. The core of our approach involves using a stacking ensemble of pairwise vector distance measurements that are computed from multiple text representation methods. A stacking classifier then utilizes these distance scores as input and learns to identify duplicate posts. We assess the proposed framework’s effectiveness in identifying duplicate posts in an online Question and Answer platform. By combining several text representation methods, INCEPT performs well in the duplicate posts classification task. Our experiments demonstrate that specific framework configurations outperform the accuracy scores obtained from individual text representation methods. Therefore, we also infer that no single text representation method can independently capture a text’s features.

First Insight into the Phylogenetic Diversity of Bovicola caprae Infesting Goats of Different Agro-climatic Locations in India.

Bovicola caprae is an important obligate ectoparasite of goats worldwide including India. The present study aimed at the molecular confirmation, phylogenetics and population structure analyses of B. caprae infesting goats of three different agro-climatic locations in India, by targeting the mitochondrial cytochrome C oxidase subunit 1 (cox1) genetic marker. The phylogenetic tree exhibited the presence of two different lineages of B. caprae. The sequences generated herein clustered in lineage 2 along with theGenBank™ archived sequences from China and Iran. The sequences generated herein also showed the circulation of sub-lineages of B. caprae in India based on the analysis of pairwise genetic distances between sequences and median-joining haplotype network. The population structure analyses revealed low nucleotide (0.00353 ± 0.00291 and 0.02694 ± 0.00363) and high haplotype (0.667 ± 0.314 and 0.618 ± 0.104) diversities for the present study isolates as well as for the complete dataset, respectively, which evinced a recent demographic expansion. High genetic differentiation (FST value = 0.97826) and low gene flow (Nm = 0.00556) were also recorded in the different lineages/populations. In conclusion, the present study addressed the research gap and provided the first insight into the phylogenetics of the goat louse B. caprae and highlighted the circulation of sub-lineages of the ectoparasite in India.

SnapFISH-IMPUTE: an imputation method for multiplexed DNA FISH data

Chromatin spatial organization plays a crucial role in gene regulation. Recently developed and prospering multiplexed DNA FISH technologies enable direct visualization of chromatin conformation in the nucleus. However, incomplete data caused by limited detection efficiency can substantially complicate and impair downstream analysis. Here, we present SnapFISH-IMPUTE that imputes missing values in multiplexed DNA FISH data. Analysis on multiple published datasets shows that the proposed method preserves the distribution of pairwise distances between imaging loci, and the imputed chromatin conformations are indistinguishable from the observed conformations. Additionally, imputation greatly improves downstream analyses such as identifying enhancer-promoter loops and clustering cells into distinct cell types. SnapFISH-IMPUTE is freely available at https://github.com/hyuyu104/SnapFISH-IMPUTE.

Genetic Links between Reproductive Traits and Amino Acid Pairwise Distances of Swine Leukocyte Antigen Alleles among Mating Partners in Microminipigs.

Previously, we found that a greater dissimilarity in swine leukocyte antigen (SLA) class I and class II alleles between mating partners resulted in increased farrowing rates in a highly inbred population of Microminipigs (MMPs). In this follow-up study, we have analyzed the effects of dissimilarity in SLA alleles between mating partners for seven different reproductive traits, including litter size and the number of stillborn and live or dead weaned piglets. We determined the relationships among reproductive traits within each mating event and the amino acid distances of SLA alleles as markers of diversity between mating partners. Our results indicate that mating partners with greater amino acid pairwise genetic distances in the SLA-1 class I gene or DQB1 class II gene alleles were associated with significantly larger litter sizes and higher numbers of live piglets at birth and weaning. Also, partners with greater pairwise distances in the SLA-2 class I gene alleles exhibited fewer pre-weaning deaths. These findings suggest that the dissimilarity in SLA class I and class II alleles between mating partners may affect not only farrowing rates but also other key reproductive traits such as litter size and improved piglet survival rates. Consequently, SLA alleles could serve as valuable genetic markers for selecting mating partners in breeding programs and for conducting epistatic studies on various reproductive traits in MMPs.

Tiwaripotamon keeae sp. nov. (Crustacea: Decapoda: Potamidae), a new miniature species of freshwater crab from the China-Vietnam border in Napo, Guangxi

A new miniature species of freshwater crab from the genus Tiwaripotamon Bott, 1970 (Potamidae), is described from a montane karst area in southern Napo, at the China-Vietnam border. It is the twelfth known species of the genus, and is also the smallest known, with the largest adult specimen observed barely exceeding 20 mm in carapace width. Apart from the small size, features of the eyes, carapace and ambulatory legs further set Tiwaripotamon keeae sp. nov. apart from its congeners. Pairwise genetic distances of the mitochondrial cytochrome oxidase subunit I (COI) gene also support it as a distinct species.

Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies.

The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang etal. 1993.

Pairwise Distances and the Problem of Multiple Optima.

Discrete optimization problems arise in many biological contexts and, in many cases, we seek to make inferences from the optimal solutions. However, the number of optimal solutions is frequently very large and making inferences from any single solution may result in conclusions that are not supported by other optimal solutions. We describe a general approach for efficiently (polynomial time) and exactly (without sampling) computing statistics on the space of optimal solutions. These statistics provide insights into the space of optimal solutions that can be used to support the use of a single optimum (e.g., when the optimal solutions are similar) or justify the need for selecting multiple optima (e.g., when the solution space is large and diverse) from which to make inferences. We demonstrate this approach on two well-known problems and identify the properties of these problems that make them amenable to this method.

Capturing MRSA Diversity by Integrating Genomic and Epidemiological Data of Patients and their Spaces

Background: Methicillin-resistant S. aureus (MRSA) is known to cause frequent and severe infections in community living centers, potentially resulting in significant mortality for elderly patients. More research is needed to understand how to utilize genomic and epidemiological data to understand characteristics that may lead to increased transmission. We hypothesized that combining genomic and epidemiological information to sample patients and their environments during long-term stays, we will be able to capture a diverse set of MRSA strains. Method: This work included genome sequencing of patient and environmental samples from 11 patients within the VA Ann Arbor Healthcare System from May 4, 2021- November 16, 2022. All 11 patients tested positive for MRSA during their stay (mean days = 31). Patient and environmental samples were taken throughout their stays, screened for MRSA, and whole-genome sequenced. Single nucleotide variants (SNVs) were identified by mapping reads and calling variants against strain-specific reference genomes. We used ape v5.6-2 in R v4.2.2 to analyze and infer evolution, acquisition, and transmission events based on pairwise SNV distances. Genomic clusters were determined using stats v3.6.2, with a SNV distance threshold of 20. Result: Samples that were collected from patient bodily sites were able to reveal 20 distinct genomic clusters of MRSA (patient hands: n = 10, nares: n = 7, groin: n = 3). Environmental samples from patient environments also revealed distinct genomic MRSA clusters (tv remote: n = 9, toilet seat and bed rail: n = 6, table top, bed control, and call button: n = 5, bed curtain: n = 4, pulse ox = 2, cell phone, tray, pulse ox, mat, body hoist wrap, and bed: n = 1). Conclusion: The identification of various genomic clusters from patients and their environmental reservoirs suggests intrahost variation that can only be captured by using a more holistic approach of integrating epidemiology and genomic sequencing. Developing studies that incorporate genomic data, various environmental sources, and multiple isolates over time within community living centers can increase our understanding of strains that are more likely to transmit, survive on living and non-living surfaces and therefore lead to improved recommendation for infection prevention interventions and drivers of endemicity.Disclosure: Lona Mody: NIH, VA, CDC, Kahn Foundation; Honoraria: UpToDate; Contracted Research: Nano-Vibronix

GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.

Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges. To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families. GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.

Ancient Grasshoppers: A revision of the genus Bullacris (Orthoptera: Pneumoridae)

The genus Bullacris in the family Pneumoridae was most recently revised by Dirsh in 1965 based on morphological comparisons between species. However, since that time, new information about the genus and the family has come to light, necessitating a revision of the genus. In addition, the species B. boschimana was originally described based on a single female specimen. Here we present and describe the male of the species for the first time. The aim of this study was to update the current species descriptions by including additional specimens and incorporating additional methods for a more comprehensive comparison. Analyses consisted of morphometric measurements from high-quality images of type specimens, existing South African museum specimens, as well as personally collected specimens. Acoustic signals are also presented and compared between species. In addition, phylogenetic analyses were conducted on the barcoding mitochondrial gene COI and two nuclear genes, namely ITS and 18S. Results show that according to morphological, acoustic and genetic data, B. discolor and B. serrata as well as B. intermedia and B. membracioides share notable similarities. Bullacris discolor and B. serrata share similar phenotypic traits, in which B. discolor can either appear uniform in colour or have a speckled variation that is very similar in appearance to B. serrata. Bullacris intermedia and B. membracioides have a 5% mitochondrial DNA pairwise distance, suggesting that they may have not be fully diverged; however, morphological analysis shows that these species are morphologically distinguishable. It is suggested that these species may have undergone spatial separation at one point; however, further investigation is required. Additional sampling across a wider geographic range is essential to clarify the relationships between B. discolor and B. serrata, as well as between B. intermedia and B. membracioides.

Identification and molecular characterization of Wanghe virus: A novel member of the Solinviviridae family from mosquitoes, China

Arboviruses have always been a significant public health concern. Metagenomic surveillance has expanded the number of novel, often unclassified arboviruses, especially mosquito-borne and mosquito-specific viruses. This report presents the first description of a novel single-stranded RNA virus, Wanghe virus, identified from mosquitoes that were collected in Shandong Province in 2022. In this study, a total of 4,795 mosquitoes were collected and then divided into 105 pools according to location and species. QRT-PCR and nested PCR were performed to confirm the presence of Wanghe virus, and its genomic features and phylogenetic relationships were further analyzed. Our results revealed that Wanghe virus was detected in 9 out of the 105 mosquito pools, resulting in a minimum infection rate (MIR) of 0.19 % (9/4,795). One complete genome sequence and three viral partial sequences were obtained from the Wanghe virus-positive pools. Pairwise distance analysis indicated that these amplified sequences shared high nucleotide identity. Phylogenetic analysis demonstrated that Wanghe virus is most closely related to Guiyang Solinvi-like virus 3, which belongs to Solinviviridae. Further analyses indicated that Wanghe virus is a new, unclassified member of Solinviviridae.

Genetic landscape of the people of Bangladesh depicted with 17 Y-Chromosome-Specific microsatellites

Seventeen microsatellite loci from the non-recombining region of the human Y chromosome were typed using AmpFlSTR® Yfiler® PCR amplification systems in 404 male subjects belonging to the three largest ethnic groups in Bangladesh. A total of 150 haplotypes from the Chakma, 144 from the Tripura, and 110 from the Khasia were detected with a corresponding discrimination capacity of 73.885%, 65.563%, and 81.250%, respectively. The highest allele frequency of 0.828 was detected in DYS391 locus in the Tripuras, while the lowest allele frequency of 0.009 was detected at the same locus for the Chakma population. The highest gene diversity (0.964) was observed at DYS385a/b locus in the Khasias, while the lowest gene diversity (0.301) was detected at DYS391 locus in Tripuras population. The overall haplotype diversity for the studied populations was 0.986141. Both the Neighbour-Joining tree and pairwise genetic distances showed that Chakma lies closer to a clade consisting of Tripuras (Khagrachari, Bangladesh) and Tripuri (Tripura, India). In contrast, the Khasias demonstrated a close affinity with the Oraon (Chhattisgarh, India), followed by the Santals. The Y-STR haplotype matching probabilities within and between populations demonstrated that the Chakma, Tripura, and Khasia were 100% genetically distinct. The studied ethnic populations exhibited higher frequency for haplogroups L and Q as opposed to haplogroups R1a, H, and L found in the mainstream Bengali population. The Median-joining networking showed haplogroups L and R1a have the most compact clustering within populations, followed by haplogroups Q and H. The presence of haplogroup R1a suggests that Bengali may have originated through west-to-east migration, whereas haplogroups L and Q distribution in the studied tribes reveal a very significant affinity with the South-East Asian populations and may have shared a common ancestral origin with the Mongoloid stock populations. Bioresearch Commu. 10(2): 1482-1488, 2024 (July)