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The illegal poaching of lions for their body parts poses a severe threat to lion populations across Africa. Poaching accounts for 35% of all human-caused lion deaths, with 51% attributed to retaliatory killings following livestock predation. In nearly half of the retaliatory killings, lion body parts are removed, suggesting that high demand for lion body parts may fuel killings attributed to human-lion conflict. Trafficked items are often confiscated in transit or destination countries far from their country of origin. DNA from lion parts may in some cases be the only available means for examining their geographic origins. In this paper, we present the Lion Localizer, a full-stack software tool that houses a comprehensive database of lion mitochondrial DNA (mtDNA) sequences sourced from previously published studies. The database covers 146 localities from across the African continent and India, providing information on the potential provenance of seized lion body parts. Lion mtDNA sequences of 350 or 1,140 bp corresponding to the cytochrome b region can be generated from lion products and queried against the Lion Localizer database. Using the query sequence, the Lion Localizer generates a listing of exact or partial matches, which are displayed on an interactive map of Africa. This allows for the rapid identification of potential regions and localities where lions have been or are presently being targeted by poachers. By examining the potential provenance of lion samples, the Lion Localizer serves as a valuable resource in the fight against lion poaching. The software is available at https://lionlocalizer.org. [ABSTRACT FROM AUTHOR]

Assessing genetic diversity, population connectivity, demographic patterns, and phylogeographic relationships is vital for understanding the evolutionary history of species and thus aid in conservation management decisions. Indian wolves (currently, Canis lupus pallipes and Canis lupus chanco) are considered ancient, unique and divergent lineages among grey wolves, yet their population genetics are poorly understood. To void this knowledge gap, we collected samples from Indian peninsular (n = 77) and Himalayan wolves (n = 24) and used a combination of maternal (mtDNA CR and Cyt b) and bi-parental (nuclear microsatellites) markers to estimate levels of genetic diversity, examine the patterns of genetic structuring between them and within their distribution range, and assess their demographic histories. Both the wolf populations showed moderate levels of genetic variability, comparable to other grey wolves. Low levels of genetic differentiation were observed within both the Indian peninsular and Himalayan wolves indicating high levels of gene flow within their populations. On the other hand, high levels of genetic differentiation were observed between the two wolves indicating absence of gene flow. Molecular analysis highlighted the uniqueness of both the Indian wolves which was further supported by the presence of unique haplotypes indicating no admixture between them. Demographic analysis using both mtDNA and microsatellites revealed decline in population sizes of both the wolf lineages and both have undergone bottlenecks. Estimates of past effective population size revealed recent population declines of both lineages of Indian wolves at around 25–50 generations corresponding to about 100–200 years ago. Our results further support the designation of both lineages of Indian wolves as two distinct species Canis pallipes and Canis himalayensis and suggest increasing conservation efforts to save the unique and ancient wolf species from extinction. [ABSTRACT FROM AUTHOR]

India has a centuries-old tradition of sheep production and breeding that accomplish economic, agricultural, and religious roles. In addition to the 44 registered sheep breeds, there is a fat-tailed sheep population referred to as Dumba. This study evaluated genetic variation in Dumba sheep and its differentiation from other Indian sheep breeds using mitochondrial DNA and genomic microsatellite loci. Haplotype and nucleotide diversity based on mitochondrial DNA analysis revealed substantially high maternal genetic diversity in Dumba sheep. Major ovine haplogroups A and B observed in sheep populations across the globe registered their presence in the Dumba sheep. The molecular genetic analysis using microsatellite markers also showed high measures of allele (10.125 ± 0.762) and gene diversity (0.749 ± 0.029). Results correspond to the non-bottleneck population that is near mutation-drift equilibrium despite some deficiency in the number of heterozygotes (FIS = 0.043 ± 0.059). Phylogenetic clustering confirmed Dumba to be a distinct population. Results of this study endow authorities with critical information imperative for sustainable utilization and conservation of Indian fat-tailed sheep, which is considered to be an untapped genetic resource contributing to the food security, livelihood, and economic sustainability of rural households in marginal areas of the country. [ABSTRACT FROM AUTHOR]

Background: Mitochondrial DNA (mtDNA) depletion syndromes (MDDS) are genetically and clinically variable disorders resulting from a reduction in mtDNA content in the cells, tissues, and organ systems, leading to symptoms related to energy deficits. Deficiency of the mitochondrial succinyl-CoA ligase/synthetase enzyme secondary to pathogenic variations in the SUCLG1 and SUCLA2 genes is a subtype of MDDS that presents with neurological manifestations and a specific biochemical profile. Methods: This cross-sectional series describes five patients with MDDS secondary to pathogenic variations in the SUCLG1 and SUCLA2 genes from two tertiary care centers in Canada and India. Clinical data concerning the course, investigations, and outcome were gathered through chart reviews. Results: All subjects presented in early infancy with neurological manifestations, including movement disorder, psychomotor regression, developmental delay, hearing loss, behavioral issues, or a combination thereof. Elevated methylmalonic acid metabolites, an abnormal acylcarnitine profile, and lactic acidemia were noted in the biochemical profile of each patient (n = 5/5, 100%). Molecular genetic testing disclosed the presence of pathogenic homozygous mutations in four subjects and compound heterozygosity in one subject. Conclusion: MDDS associated with SUCLG1 and SUCLA2 genes can be detected biochemically by the presence of methylmalonic aciduria besides the elevation of lactate, C3, C4DC, and C5-OH acylcarnitine. Conducting metabolic workups including MMA and acylcarnitine profiles in patients with heterogeneity of clinical symptoms associated with the presence of this biochemical marker may potentially reduce the time to diagnosis and management. [ABSTRACT FROM AUTHOR]

This study is the first time to perform molecular characterization in indigenous chickens, Sakini, of Nepal for studying genetic diversity and its relationship with its assumed progenitors. The first 522 nucleotides of hypervariable I (HVI) segment of the D-loop from 33 individuals were PCR amplified and subsequently sequenced. Fourteen haplotypes out of 33 sequences were identified from 20 polymorphic sites. Haplotype (gene) diversity (Hd) is 0.813 with SD 0.065 and nucleotide diversity (Pi) is 0.00525 with SD 0.00091. The neighbour joining tree indicated that Red Jungle Fowl from India is the progenitor of the Nepalese Sakini chicken. NETWORK analysis revealed that it can be grouped into four distinct Haplogroups (A1, E1, E2, and E3) respectively. Seventeen individuals belonged to E1, eight to E3, seven to E2, and one to A1. The high mitochondrial Dloop diversity in Nepalese Sakini chicken with multiple maternal origins serves the scientific basis for the development of rational policies supporting conservation efforts and provides directions for future research for developing sustainable genetic improvement approaches. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome of the freshwater fish species Labeo rajasthanicus was obtained, using Illumina NovaSeq 6000 with 2 × 150 bp paired-end sequencing. The mitogenome of L. rajasthanicus is 16,738 bp in length (GenBank accession no.: OQ834146), comprised of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region, i.e. D-loop. The arrangement of genes was found to be identical to other Cypriniformes fish mitogenome, available in the NCBI database. The taxonomic status of L. rajasthanicus as a valid species was debated by some researchers and it was considered a synonym of L. boggut. However, phylogenetic analysis in the present study supports the species validity of L. rajasthanicus, as it showed a distinct node well separated from L. boggut and supported by a high bootstrap value. Furtherly, the pairwise genetic divergence among studied species showed the divergence between L. rajasthanicus and L. boggut as 1.6% whereas the minimum divergence was found to be 0.13% with L. dussumieri followed by L. fimbriatus (0.58%) and L. gonius (0.63%). The complete mitogenome of L. rajasthanicus will also be useful as a baseline reference genome for the reconstruction and annotation of the mitogenome of other Labeo species. [ABSTRACT FROM AUTHOR]

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a unique autosomal recessive disorder characterized by mitochondrial changes resulting from mutations in the TYMP gene, responsible for encoding thymidine phosphorylase. Despite its genetic origin, the study indicates that the manifestation of MNGIE does not strictly adhere to a hereditary pattern. The investigation focused on a family from the Ernakulam district of Kerala, India, involving three members. The proband began experiencing gait difficulties at the age of 4, leading to a confirmed diagnosis of MNGIE at 17. Subsequent clinical assessments confirmed MNGIE in the two younger siblings, while the youngest remained unaffected. Common symptoms across all three included ptosis, limited eye movements, generalized muscle atrophy, and the absence of tendon reflexes. Elevated lactate levels were observed in both venous blood and cerebrospinal fluid, and magnetic resonance imaging scans revealed diffuse leukoencephalopathy. Emphasizing the importance of early identification of MNGIE patients, the study underscores the emerging therapeutic options that can positively impact survival and overall health outcomes. The findings highlight that prompt diagnosis and intervention contribute to improved prognosis and well-being in affected individuals. [ABSTRACT FROM AUTHOR]

The South American leafminer, Tuta absoluta is an exotic devastative pest on solanaceous vegetables, including tomatoes, which leads to a cent per cent economic loss in India. The molecular markers assist in assessing gene flow, migratory frequencies, and genetic variety, as well as helping to evaluate the genetic makeup and diversification of an exotic species population to indigenous ones. With this, the present study aimed to investigate the genetic divergence of T. absoluta in different districts of Tamil Nadu, India. The study depicted the examination of genetic divergence of T. absoluta by aiding amplified region of mitochondrial DNA encoding cytochrome oxidase I (COI) from the T. absoluta samples gathered from Coimbatore, Dharmapuri and Dindigul districts of Tamil Nadu. The findings showed that the phylogenetic tree constructed from all sequences of T. absoluta acquired from the NCBI (National Center for Biotechnology Information) and BOLD (The Barcode of Life Data System) databases exhibited 99 percent identity and aggregated together into a single clade. Hence, the present study revealed the great genetic uniformity in T. absoluta populations in India and corroborates that most of the globe rely on the partial COI gene, evidenced by minimal nucleotide diversity. [ABSTRACT FROM AUTHOR]

Mitochondrial dysfunction has long been associated with the pathogenesis of lung cancer (LC). Mitochondrial DNA (mtDNA) haplogroups have been reported to modify the risk of LC in a few different populations; however, no study has been done among the Indians. Here, we explore the relationship between mtDNA haplogroups and LC in a representative eastern Indian sample set. Different combinations of six mtDNA SNPs, which define the major Asian mtDNA haplogroups M and N, and their sub-haplogroups D, G, M7, R, and F were genotyped via polymerase chain reaction (PCR) – restriction fragment length polymorphism (RFLP) – sequencing approach in 94 smoker LC patients and 100 healthy smoker controls from an eastern Indian cohort. The distribution of 7 mtDNA haplogroups did not show any significant differences between patients and controls (p<0.05). We did not find sub-haplogroup M7 in our study population. Our study is the first to indicate that the major Asian mtDNA haplogroups have no significant (p<0.05) association with LC in East Indian population. [ABSTRACT FROM AUTHOR]

Background: Native chickens are dispersed in a wide geographical range and have hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular studies because of its quick advancement, matrilineal legacy, and simple molecular structure. Method and Results: We performed NGS sequencing to investigate mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in Indian native chicken breeds and Red Jungle fowl. The chicken breeds were genotyped using the D-loop region and 23 haplotypes were identified. When compared to Indian native breeds, more haplotypes were identified in the NADH dehydrogenase subunits, Cytochrome c oxidase, Cytochrome b, ATP synthase subunit 6, and Ribosomal RNA genes. The phylogenetic examination indicated that the analyzed chicken breedswere divided into six significant clades, namelyA, B,C, D, E, and F, of which the F clade indicated the domestication of chicken breeds in India. Additionally, our work affirmed that the Indian Red Jungle Fowl is the origin for both reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on the whole mtDNA and D-loop region. Indian Red Jungle Fowl is distributed as an outgroup, suggesting that this ancestry was reciprocally monophyletic. Conclusion: The mtDNA sequences of Indian native chickens provided novel insights into adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native birds. [ABSTRACT FROM AUTHOR]

• We have first time generated complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan. • One of the promising samples belonged to haplogroup M3a1 + 204, which is prevalent among medieval swat valley population and also in two Roopkund individuals. • In phylognalysis and haplotype network Parsi sample with M3a1 + 204 share clade with both Middle Eastern and South Asian samples. The rich cultural and genetic diversity of South Asia emerged from multiple migrations and cultural assimilation of multiple waves of migrants. The Parsi community of North-western India were one of those who migrated from West Eurasia in the aftermath of 7th century CE and assimilated into the local cultural framework. Earlier genetic studies further strengthened this notion with the finding that they harbour both Middle Eastern and South Asian genetic components. Although these studies covered both autosomal and uniparental markers, still maternal ancestry was not covered in depth and with good resolution of mitochondrial markers. Hence in our current study, we have first time generated a complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan and performed detailed phylogenetic analysis to infer their maternal genetic affinity. In our analysis, we found that the Parsi mitogenome with mtDNA haplogroup M3a1 + 204 shares clade with both Middle Eastern and South Asian modern individuals in both the Maximum Likelihood tree and Bayesian phylogenetic tree. This haplogroup was also prevalent among the medieval Swat valley population of present-day Northern Pakistan and was also observed in two Roopkund A individuals. In the phylogenetic network this sample share haplotype with both South Asian and Middle Eastern samples. So conclusively, the first Parsi settlers' maternal ancestry encompasses both South Asian and Middle Eastern genetic composition. [ABSTRACT FROM AUTHOR]

Trade and collection of edible frogs are banned in India. We used mitochondrial (16 and 12S DNA) and nuclear gene (Rag-1 and Rhodopsin) sequences to examine the population genetic and demographic structure of an edible frog species, Phrynoderma karaavali (Karaavali Skittering frog) from Kerala as it exist after the ban. Frogs from 11 sites show high mtDNA haplotype and nDNA diversity which indicates a stable or expanding population. The evolutionary demographic pattern suggests population expansion across its geographical range, even though the species is still subject to poaching. Two major population clusters were observed at the northern and southern end of the species range. Gene flow occurs despite of geographic barriers. Genetic distance increases with geographical distance. P. karaavali diverged from its sister species in Phrynoderma around 11 mya in the late Miocene. [ABSTRACT FROM AUTHOR]

Objectives: Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records. Methods: To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North‐western India have been sequenced. Results: Interestingly, three novel sub‐clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs. Conclusion: The haplotype‐based analysis suggests that the Kayastha population shares genetic affinities with the Indo‐European and Sino‐Tibetan populations found in the trans‐Himalayan region. The FST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub‐continent. Both mtDNA and Y‐chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations. [ABSTRACT FROM AUTHOR]

Geographic and anthropogenic barriers can result in creating population structure in primates. We hypothesized that such features in the Northeast India could have given rise to subpopulations with variable genetic structure and diversity in Western Hoolock gibbons, Hoolock hoolock. For testing this, we collected faecal and blood samples from 37 individuals from H. hoolock spreading their whole distribution, isolated DNA, amplified mitochondrial markers and constructed a median joining network and measured gene flow between subpopulations from the data. We found high haplotype diversity in mitochondrial markers as well as presence of three sub-populations. Due to high diversity parameters, the population of Western hoolock gibbons in India seems healthy and resilient to changes. We expect that the results will assist in in-situ conservation of the species and in captive breeding programs in various zoos of the region. [ABSTRACT FROM AUTHOR]

Leber's hereditary optic neuropathy (LHON) is a mitochondrial complex I disorder and causes inexorable painless vision loss. Recent studies from India reported that a significant proportion of LHON patients lack primary mitochondrial DNA mutations, suggesting that alternative genetic factors contribute to disease development. Therefore, this study investigated the genetic profile of LHON-affected individuals in order to understand the role of mito-nuclear genetic factors in LHON. A total of thirty probands displaying symptoms consistent with LHON have undergone whole mitochondrial and whole exome sequencing. Interestingly, whole mtDNA sequencing revealed primary mtDNA mutations in 30 % of the probands (n=9), secondary mtDNA mutations in 40 % of the probands (n=12) and no mitochondrial changes in 30 % of individuals (n=9). Further, WES analysis determined pathogenic mutations in 11 different nuclear genes, especially in cases with secondary mtDNA mutations (n=6) or no mtDNA mutations (n=6). These findings provide valuable insight into LHON genetic predisposition, particularly in cases lacking primary mtDNA mutations. [ABSTRACT FROM AUTHOR]

The Muscid flies belonging to the order Diptera, Family Muscidae, are notoriously famous for their ability to transmit disease-causing organisms to humans, livestock, and even plants. The huge species count of this group not only makes the classical method of identification laborious but also error-prone. Therefore, in this study, we analysed cytochrome oxidase 1 (cox1) barcodes to test their ability to discriminate between studied taxonomic groups. In our study, we used a total of 42 specimens, excluding the outgroup, of 14 species belonging to 5 genera representing 4 subfamilies were used. 11 specimens were collected from the lower Gangetic Plains of West Bengal, India, including the vulnerable Sagar Islands, each showing a very high AT content (average = 69%), especially in the 1st codon position. Cox1 barcodes were able to distinguish between species with very high interspecific genetic divergence. The percentage of intraspecific genetic divergences ranges from 0% to 2.2% for the studied dataset, with the interspecific range being very high, from 0.58% to 28.8%. 1000 bootstrapped Maximum likelihood (ML) with Kimura-2-parameter phylogenetic tree and similar bootstrap-based IQ-Tree was constructed based on cox1 gene, for clarity. The ML tree is used to understand the delimitation of the species using Poisson Tree Process (PTP) analysis. The phylogenetic and delimitation study determined that most of the genus level clusters are monophyletic. The subfamily Muscinae showed non-monophyletic lineage as seen by the separation of genera Musca from genera Haematobia in both ML and IQ-Tree. [ABSTRACT FROM AUTHOR]

Owing to its high copy number and its small size, mtDNA analysis is the most reliable choice when biological materials from crime scenes are degraded or have mixed STR profiles. To examine the occurrence of heteroplasmy along with its frequency and pattern in both HV1 and HV2 regions of the mtDNA among unrelated individuals from India. Mitochondrial DNA control region [hypervariable region one (HV1) and hypervariable region two (HV2)] were analysed in blood and buccal tissues of 104 unrelated individuals from the Indian state of Gujarat. A high frequency of point heteroplasmy (PH) and length heteroplasmy (LH) was revealed. PH was detected in 7.69% of the population, with a higher frequency observed in blood than in buccal samples. However, there were no statistically significant differences in PH between the two tissues (Chi-square = 0.552, p ≥ 0.05). A total of six PH positions were detected: three at HV1, and another three at HV2. The studied population showed 46.15% LH in the HV1 and HV2 regions of both tissues. The LH positions observed in the Gujarat population were the same as those previously reported at HV1 np16184–16193 and HV2 np303–315. Our findings suggest that differences in the pattern of heteroplasmy found in different tissues can complicate the forensic analysis, on the other hand, the probability of a match between the questioned and reference samples increases when the heteroplasmy is identical in both tissues. Variability of PH among persons and even within tissues recommends analysing multiple tissue samples before drawing a conclusion in forensic mtDNA analyses. [ABSTRACT FROM AUTHOR]

Cow, Bos taurus , and female buffalo, Bubalus bubalis, are considered sacred animals that are a part of rural livelihood in India. The purity of products from these bovine species has significant sentimental implications in the dairy and meat industry. Therefore, the mitochondrial DNA and the sex origin, targeting the X and Y chromosomes from these bovine species, were selected to design three multiplex real-time probe PCR assays: Hi-PCR® Cow Detection Kit (MBPCR184), Hi-PCR® Buffalo Detection Kit (MBPCR185) and Hi-PCR® Cattle Sex Determination Kit (MBPCR186). Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines were followed to perform different studies using reference control DNAs. An Internal Reagent Control (IRC) was part of every assay, thus ensuring a successful reaction. The assays were 100% specific, with no cross-amplification of the two bovine species. The amplification of the X chromosomal target was observed for male and female DNAs, whereas Y chromosome amplification was observed only for the male DNA. The assays were 100% specific to the target genes in these organisms with no non-specificity towards any other targets or organisms. The limit of detection for sex determination was 0.01 ng/µl, whereas the differential capability of the assay was 3 copies/µl and 30 copies/µl for Bos taurus and Bubalus bubalis , respectively. The assays were reproducible at 1 ng/µl genomic DNA with 95% CI. The assays are open and compatible with other brands of Real-Time PCR systems used in forensic labs. The experiments presented here verify that the developed real-time PCR assays are robust, produce reliable and reproducible results for detection and differentiation of Bos taurus and Bubalus bubalis and their sex even at low DNA concentrations. [ABSTRACT FROM AUTHOR]

The paper presents the record of the poorly known endemic species of wood roach from India after a gap of almost 40 years. In India, discernible work has been done on the DNA barcode of cockroaches including the genus Salganea. This work forms the first mitochondrial DNA barcode for the species Salganea rehni Roth, 1979. [ABSTRACT FROM AUTHOR]

Internationally, illegal wildlife trade involves highly prized and charismatic species and their derivatives. At the same time, common or less known species and their parts are also encountered but receive less attention than charismatic species. Given the increasing demand for wildlife products in many parts of the world, profit, and short supply, many fake articles derived from domestic or wild animals are frequently encountered in the wildlife trade. Jackal horn (locally known as "Siyar or Gidar singhi") is one such fake item widely used in sorcery and other occult practices available through offline and online trading platforms within India. We used a combination of morphological, microscopic hair, and molecular approaches (Cyt b and 16 s rRNA genes) to reveal the true identity of confiscated "jackal horns" (n = 342). Detailed morphological study of the jackal horns showed that it varied in size, shape, color of hair, attachment material, and filling material. The microscopic hair and molecular approaches revealed that all the items sold as jackal horns were fake and made up of protected wild species and domestic animals. Our results confirm the use of the biological samples from few wild species protected under the Wild Life (Protection) Act, 1972, of India. Therefore, the law enforcement agencies are cautioned to get forensic opinions while dealing with such counterfeit items. [ABSTRACT FROM AUTHOR]

Labeo fimbriatus is a medium carp species found throughout India's peninsular river basins and is regarded as a valuable aquaculture resource alongside Indian major carps due to its taste and nutritional value. This species has recently declined dramatically due to habitat degradation and overfishing. Because of its enormous economic importance, a selective breeding programme is likely to be in place to improve performance traits. Knowledge of genetic variation among the base population from which the broodstock will be selected is an important step in this process. A diverse genetic base of broodstock is required to achieve the best response to selection for long-term aquaculture management practices. Consequently, using mitochondrial DNA (ATPase 6 and Control region) and microsatellite markers, we have made the first step toward estimating the level of genetic variation and how it is distributed among the four populations of L. fimbriatus found in peninsular rivers in India. The ATPase 6 gene analysis in four populations revealed 15 haplotypes and 51 variable sites, in contrast to the Control region, which had 60 haplotypes together with 73 variable sites and a haplotype diversity of 0.941. Twelve microsatellite loci displayed estimated allele numbers (NA) ranging from 3 to 19, observed heterozygosity (HO), and expected heterozygosity (HE), respectively, of 0.705 to 0.753 and 0.657 to 0.914. Each marker type showed a significant FST value, indicating the presence of low to moderate genetic differentiation across entire wild populations. The Godavari, Kaveri, and Mahanadi populations formed one cluster according to the UPGMA, which was based on genetic distance matrix, while the Krishna population formed a separate cluster. The comparative genetic analysis of data from different markers utilized in the current study would enable the identification of the genetic stocks of L. fimbriatus and facilitate conservation measures and selective breeding. [ABSTRACT FROM AUTHOR]

The new genus Kudratoviella for the former Caloplaca zeorina group having the highest level of bootstrap support in the phylogenetic tree of the Teloschistaceae, based on combined dataset of nrITS, 28S nrLSU DNA and 12S SSU mtDNA sequences, which does not belong to any other earlier proposed genera of the subfamily Xanthorioideae, is described. The genus Oceanoplaca Arup, Søchting et Bungartz found to be a new synonym of the genus Loekoeslaszloa S. Y. Kondr., Kärnefelt, A. Thell et Hur, and Villophora onas Søchting, Søgaard et Arup appeared to be new synonym of Raesaeneniana maulensis (S. Y. Kondr. et Hur) S. Y. Kondr., Elix, Kärnefelt et A. Thell. Sixteen new combinations are proposed, i.e. Honeggeria leoncita (for Xanthomendoza leoncita Bungartz et Søchting), Honeggeria wetmorei (for Xanthoria wetmorei S. Y. Kondr. et Kärnefelt), Kudratoviella anularis (for Caloplaca anularis Clauzade et Poelt), Kudratoviella bohlinii (for Caloplaca bohlinii H. Magn.), Kudratoviella rajasthanica (for Caloplaca rajasthanica S. Y. Kondr., Upreti et G. P. Sinha), Kudratoviella scrobiculata (for Caloplaca scrobiculata H. Magn.), and Kudratoviella zeorina (for Caloplaca zeorina B. G. Lee et Hur), Loekoeslaszloa caesioisidiata (for Caloplaca caesioisidiata Arup et van den Boom), Loekoeslaszloa caesiosorediata (for Caloplaca caesiosorediata Arup et van den Boom), Loekoeslaszloa chemoisidiosa (for Oceanoplaca chemoisidiosa Søchting et Bungartz), Loekoeslaszloa isidiosa (for Placodium isidiosum Vain.), Loekoeslaszloa sideritoides (for Oceanoplaca sideritoides Søchting et Bungartz), Raesaeneniana darwiniana (for Villophora darwiniana Søchting, Søgaard et Arup), Raesaeneniana patagonica (for Villophora patagonica Søchting et Søgaard), Raesaeneniana rimicola (for Villophora rimicola Søchting), and Raesaeneniana wallaceana (for Villophora wallaceana Søchting et Søgaard). Iqbalia kashmirensis is for the first time confirmed from South Korea and India on the basis of 'extraneous mycobiont DNA' (sensu Kondratyuk et al. 2019 b). [ABSTRACT FROM AUTHOR]

Mitochondrial disorders are a class of heterogeneous disorders caused by genetic variations in the mitochondrial genome (mtDNA) as well as the nuclear genome. The spectrum of mtDNA variants remains unexplored in the Indian population. In the present study, we have cataloged 2689 high confidence single nucleotide variants, small insertions and deletions in mtDNA in 1029 healthy Indian individuals. We found a major proportion (76.5 %) of the variants being rare (AF<=0.005) in the studied population. Intriguingly, we found two 'confirmed' pathogenic variants (m.1555 A>G and m.14484 T>C) with a frequency of ∼1 in 250 individuals in our dataset. The high carrier frequency underscores the need for screening of the mtDNA pathogenic mutations in newborns in India. Interestingly, our analysis also revealed 202 variants in our dataset which have been 'reported' in disease cases as per the MITOMAP database. Additionally, we found the frequency of haplogroup M (52.2 %) to be the highest among all the 18 top-level haplogroups found in our dataset. In comparison to the global population datasets, 20 unique mtDNA variants are found in the Indian population. We hope the whole genome sequencing based compendium of mtDNA variants along with their allele frequencies and heteroplasmy levels in the Indian population will drive additional genome scale studies for mtDNA. Furthermore, the identification of clinically relevant variants in our dataset will aid in better clinical interpretation of the variants in mitochondrial disorders., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time. [ABSTRACT FROM AUTHOR]

Taenia solium cysticercosis is a potentially eradicable neglected zoonotic disease with public health importance. The genetic lineages of T. solium in Asia and Africa/America are distinct and the genetic composition of the parasite was found to influence the clinical symptoms in patients with cysticercosis. In the present study, the Cysticerci collected from pigs of two southern states of India (Karnataka and Andhra Pradesh) were genetically characterized based on mitochondrial (COX 1 and Cyt b) and ribosomal (ITS‐1 and TBR) DNA markers. The study confirms the existence of two mitochondrial lineages of the parasite as Asian and African/American. Cytochrome oxidase 1 (COX 1) based analysis revealed the existence of two sub‐lineages of the parasite within the Asian lineage based on the polymorphism at 994 position as 994A/G. In India, both the sub‐lineages were identified and genetic divergence among different Indian isolates was evident. Further, the sequence analysis of Cytochrome B (Cyt b) revealed the existence of six sub‐lineages of T. solium in India as 69T/69G, 97A/97G as well as 264T/264C. The analysis of nucleotide sequence of large subunit ribosomal DNA (TBR) revealed the existence of two sub‐lineages in India based on the deletion of a nucleotide at 624th position. The cysts collected in the present study were more closely related to those of China and Indonesia than with other Indian isolates. Further, the sequence analysis did not indicate the presence of Taenia asiatica in the examined pigs and African/American lineages of T. solium. The results of the present study help to better understand the genetic diversity of T. solium in India. [ABSTRACT FROM AUTHOR]

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue ‘Celebrating 50 years since Lewontin’s apportionment of human diversity’. [ABSTRACT FROM AUTHOR]

Two new species and a new record of blood sucking biting midges of the subgenus Lasiohelea Kieffer, 1921 of the genus Forcipomyia Meigen, 1818 are described after the morphological and molecular data. The new species. Forcipomyia (Lasiohelea) peditata and F. (L.) falcata were fetched from the Sub-Himalayan region, and F. (L.) parvitas (Liu and Yu, 1996) from both the Gangetic plain and western plateau regions of West Bengal. The DNA barcoding of Mitochondrial COX I gene has also been used as molecular evidence. [ABSTRACT FROM AUTHOR]

In 2014, 157 years after the Sepoy Mutiny of 1857, several unidentified human skeletons were discovered in an abandoned well at Ajnala, Punjab. The most prevailing hypothesis suggested them as Indian soldiers who mutinied during the Indian uprising of 1857. However, there is an intense debate on their geographic affinity. Therefore, to pinpoint their area of origin, we have successfully isolated DNA from cementum-rich material of 50 good-quality random teeth samples and analyzed mtDNA haplogroups. In addition to that, we analyzed 85 individuals for oxygen isotopes (δ18O values). The mtDNA haplogroup distribution and clustering pattern rejected the local ancestry and indicated their genetic link with the populations living east of Punjab. In addition, the oxygen isotope analysis (δ18O values) from archaeological skeletal remains corroborated the molecular data and suggested the closest possible geographical affinity of these skeletal remains toward the eastern part of India, largely covering the Gangetic plain region. The data generated from this study are expected to expand our understanding of the ancestry and population affinity of martyr soldiers. [ABSTRACT FROM AUTHOR]

Horseshoe crab (Tachypleus gigas) is an archaic group of marine species which plays a vital role in the saline ecosystem. We attempted to develop a baseline database about the ecology, phylogeography, and genetic variation among the horseshoe crab population from Odisha, India. We collected 152 samples of horseshoe crab from the coastal area of the Bay of Bengal. The generated cytochrome c oxidase subunit I gene (COI) sequences of T. gigas were compared with the GenBank sequences of five populations from Bangladesh, Thailand, Singapore, South China, and Malaysia. A total of 33 unique haplotypes were observed in six populations of T. gigas. Pairwise F‐statistic distance (FST) between South China‐India, Malaysia‐India, Singapore‐India, Thailand‐India, and Bangladesh‐India were 0.021, 0.020, 0.017, 0.015, and 0.008, respectively. It indicated that the Indian and Bangladesh populations were genetically close and distinct from the other four populations. Furthermore, the migrant per generation (Nm) was 0.16, which indicated a low gene flow among T. gigas populations. The haplotype diversity (Hd) and nucleotide diversity (π) were 0.7482 and 0.00313, respectively. It signifies the ecological importance of the Indian population that would help in formulating the future strategy for the conservation of horseshoe crab. [ABSTRACT FROM AUTHOR]

The tribal and generic-level phylogeny of Scarabaeinae (Coleoptera: Scarabaeidae) dung beetles have been often debated globally. However, fauna from India have not been a part of these analyses due to lack of data. We used partial sequences of 16S mtDNA gene of dung beetles collected from different parts of the Western Ghats, India, to examine (i) the tribal positions of Onthophagini, Onitini and Oniticellini, and (ii) the phylogenetic position of different genera of Onthophagini. We found that Oniticellini nested within Onthophagini, suggesting the invalid position of Oniticellini. The nonOnthophagus genera of Onthophagini – Caccobius, Cleptocaccobius, Milichus – nested within Onthophagus, suggesting that these three genera might be invalid and could be subgenera of Onthophagus. Onitini formed a separate clade in the phylogenetic tree. The results suggest for tribal-level reclassification of dung beetles, as noted in previous studies. The present study may enrich the molecular data of the Indian dung beetles, which are currently lacking. [ABSTRACT FROM AUTHOR]

Vermileonidae (wormlions) comprises 61 described species in 12 genera and is one of the oddest and most rarely collected dipteran families. Larvae of Vermileonidae are famous for their pitfall prey behaviour, whereas the adults are rarely seen. Here we report, for the first time, the complete mitochondrial genome from members of Vermileonidae. Phylogenetic reconstruction based on a representative sampling of the order reveals new insights into relationships between the Vermileonidae and other members of lower brachyceran flies. A sister-group relationship between Vermileonidae and Xylophagidae is supported, and the higher-level clade relationships are Tabanomorpha + (Muscomorpha + (Xylophagomorpha + Stratiomyomorpha)). Combining mitochondrial genome data with a morphological phylogeny, geographical distribution and geological history, we propose that the Vermileonidae originated in India during the Middle Jurassic, spreading to Africa via land bridges during the Late Jurassic, to the Palaearctic after the collision of India with Laurasia in the Late Oligocene, and to the Nearctic in the Early Miocene, via either North Atlantic or Beringian land bridges. Wet forested regions have proved to be barriers to their dispersal, explaining their absence from Central Africa, South America and eastern North America. [ABSTRACT FROM AUTHOR]

The snow leopard (Panthera uncia), one of the most threatened felids distributed along the high-altitude mountains in the Himalayas, has experienced a steady population decline in most of its distribution range due to the loss of suitable habitats, anthropogenic activities, and retaliatory killings. We undertook the genetic assessment of the snow leopard in the Western Himalaya, India, and identified 18 unique individuals. The snow leopard populations exhibited moderate genetic variability, i.e., effective number of alleles = 3.96 ± 0.004, observed heterozygosity = 0.539 ± 0.038 and no variation at mtDNA. We found the snow leopard populations under panmixia, possibly due to the long-ranging behavior and dispersal patterns. We present the first population genetic account of the snow leopard from the Western Himalayas and discuss the importance of non-invasive genetics in monitoring the snow leopard population in the tough terrain of the trans-Himalayan region of India. [ABSTRACT FROM AUTHOR]

Gastric carcinoma, in India, is the second most prevalent cause of cancer-related deaths since most patients are asymptomatic until the disease progresses to advanced stages. Hence, there is a need for non-invasive and specific biomarkers for early screening and diagnosis. Human mitochondrial DNA (mtDNA) has 37 genes involved in oxidative phosphorylation pathway (OxPhos). There are several 100 to 1000 mitochondria in a human cell and each mitochondrion has two to 10 copies of mtDNA. There is a significant association between the mtDNA copy number and an increase in risk of various cancers. There is also a relation between the changes in the sequence of mtDNA in genes, such as MT-CYB, MT-ATP6 and gastric cancer, according to which the tumor cells switch to aerobic glycolysis for ATP production even in the presence of oxygen due to Warburg effect. Multiple factors have an adverse effect on mitochondrial gene expression and impairs the OxPhos pathway due to lack of sophisticated DNA repair mechanism in mitochondria. Techniques, such as Next Generation Sequencing and Whole Genome Sequencing, are capable of early detection of copy number variants and mtDNA mutations in blood sample essential for better prognosis of gastric cancer. Through the course of this study, various reports of a correlation between mtDNA damage and gastric cancer were analyzed and it was found that the increasing evidence of the role of mtDNA and its copy number in cancer indicates its significance as a potential biomarker for gastric cancer. [ABSTRACT FROM AUTHOR]

India ranks the second in the world in terms of its sheep population with approximately 74.26 million represented by 44 well-described breeds in addition to several non-descript populations. Genetic diversity and phylogeography of Indian sheep breeds remain poorly understood, particularly for south Indian breeds. To have a comprehensive view of the domestication history of Indian sheep, we sequenced the mitochondrial DNA (mtDNA) control region (D-loop) and cytochrome b gene (CYTB) of 16 Indian domestic sheep breeds, most of them (13) from the south India. We analysed these sequences along with published data of domestic and wild sheep from different countries, including India. The haplotype diversity was relatively high in Indian sheep, which were classified into the three known mtDNA lineages, namely A, B and C. Lineage A was predominant among Indian sheep whereas lineages B and C were observed at low frequencies but C was restricted to the breeds of north and east India. The median joining network showed five major expanding haplogroups of lineage A (A1–A5). Out of which, A2, A4 and A5 were more frequent in Indian sheep in contrast to breeds from other parts of the world. Among the 27 Indian sheep breeds analysed, Mandya and Sonadi breeds were significantly different from other Indian breeds in the MDS analyses. This was explained by a very high contribution of lineage B into these two breeds. The Approximate Bayesian Computation (ABC) provided evidence for the domestication of lineage A sheep in the Indian subcontinent. Contrary to the current knowledge, we also found strong support for the introduction of lineage B into Indian subcontinent through sea route rather than from the Mongolian Plateau. The neighbour-joining tree of domestic and wild sheep revealed the close genetic relationship of Indian domestic sheep with Pakistani wild sheep O. vignei blanfordi. Based on our analyses and archaeological evidences, we suggest the Indian subcontinent as one of the domestication centres of the lineage A sheep, while lineage B sheep might have arrived into India from elsewhere via Arabian sea route. To the best of our knowledge, this is the first comprehensive study on Indian sheep where we have analysed more than 740 animals belonging to 27 sheep breeds raised in various regions of India. Our study provides insight into the understanding of the origin and migratory history of Indian sheep. [ABSTRACT FROM AUTHOR]

Badis kaladanensis, a new percoid fish is described from the Kaladan basin of Mizoram, northeast India. It belongs to the Badis badis species group but can be easily distinguished from its congeners, except from B. kanabos and B. tuivaiei, in having a dark blotch on the dorsal fin between the base of 3rd to 5th spines. It is further distinguished from B. kanabos in having more scales in lateral row (27–30 vs. 25–26), more circumpeduncular scale rows (18–20 vs. 16–17) and smaller eye (7.5–8.9% SL vs. 9.5–12.7); and from B. tuivaiei in having fewer vertebrae (28–29 vs. 30–31) and more rakers on the first gill arch (9 vs. 6–8). The analysis of the mitochondrial DNA (coi and cytb) revealed the distinctness of B. kaladanensis from all other Badis species with the interspecific distance ranges from 5.4–20.4%. (coi) and 5.1–26.3% (cytb). [ABSTRACT FROM AUTHOR]

Background: Adulteration of meat with their cheaper or inferior counterparts has become a common practice in the meat industry which threatens the feelings as well as the health of the people. Meat adulteration has issues relating to social, religious, economic, and public health. Therefore, it is important to develop simple and reliable techniques for the authentication of species of meat. Mitochondrial markers have been widely used in species identification and authentication as PCR of species-specific markers of mitochondrial origin is relatively rapid, accurate, sensitive and cost-effective as compared to other PCR based assays. The present study was carried out for authentication of raw and cooked meat from different species using PCR amplification of species-specific Cytb and D-loop markers of mitochondrial origin. Methods: In this study, detection of different raw meat viz. beef, carabeef, mutton, chevon, chicken, duck meat and dog meat as well as meat samples subjected to different processing temperatures was done using PCR of species-specific mitochondrial Cytb and Dloop markers. Samples of beef, carabeef, mutton, chevon, chicken, duck meat and dog meat were collected randomly from different locations of the North-Eastern region of India. The meat samples were subjected to heat treatment in hot water (80°C) to have 75°C core temperature. They were also cooked in steam to have the core temperature of 95°C. The samples were also subjected to autoclaving at a temperature of 121°C and 15 lb pressure. Result: The markers used in this study successfully amplified unique fragments for beef, carabeef, mutton, chevon, chicken, duck meat and dog meat. The sizes of the amplified products were 126 bp for beef, 226 bp for carabeef, 254 bp for mutton, 453 bp for chevon, 256 bp for chicken, 292 bp for duck meat and 100 bp for dog meat. The results were consistent in the meat samples which were subjected to different cooking temperatures ranging from 75-121°C. Consequently, these markers were validated for crossamplification by checking them with other meat samples and no amplifications were observed in non-target species. The results suggested that all the markers were highly specific for the target species. The simplicity, sensitivity and stability of the assay indicated that this method could be very useful for meat authentication and thereby to detect adulteration. [ABSTRACT FROM AUTHOR]

Dung beetles are diverse, cosmopolitan, and endemic to different biogeographic zones. But, their taxonomy and phylogeny is currently not well understood in the old-world tropics. Within the subfamily Scarabaeinae, Onthophagus is the most species rich and complex genus with 2189 species worldwide. India has approximately 400 species of dung beetles belonging to 30 genera. Based on morphology, the dung beetles of certain genera in Oriental and Afrotropical regions have been classified into Species Groups. Presently the genetic information of dung beetles of India is poorly represented in the databases, thus limiting knowledge on the phylogenetic relationships of the Indian fauna. In this study, we aimed to provide barcodes of 27 species belonging to Onthophagus and one species of Onitis and to examine whether the resulting phylogenetic tree complies with the Species Groups. Kimura 2 parameter model was used to measure genetic distance and Neighbour Joining method was used for the tree construction. The tree topology did not fully support the Species Groups of Onthophagus as other studies from the African region have noted. The DNA barcodes generated from this study can serve as a reference for future phylogenetic studies. [ABSTRACT FROM AUTHOR]

Nematodes of the genus Physaloptera are globally distributed and infect a multitude of hosts. Their life cycle involves orthopterans and coleopterans as intermediate hosts. The morphological characters alone are inadequate to detect and differentiate Physaloptera spp. from its congeners. Moreover, molecular studies are limited to compare them precisely. The present communication reports the first molecular phylogenetic characterization of feline Physaloptera spp. from India based on mitochondrial cytochrome c oxidase subunit 1 (COX1) and small subunit ribosomal DNA (18S rDNA). The nematodes were first isolated from the stomach of adult stray cats during necropsy examination. Based on the gross and microscopic characters, the worms were identified as P. praeputialis. Morphological identification was further confirmed through PCR targeting the barcode region of the mitochondrial cytochrome c oxidase subunit I (MT-COI) gene, using nematode-specific primers cocktail followed by species specific primers targeting partial COX1 and 18S rRNA genes. Generated sequences were submitted in NCBI GenBank (MW517846, MW410927, MW411349), and phylogenetic trees were constructed using the maximum likelihood method. When compared with other sequences of Physaloptera species across the globe, the present isolates showed 85.6–97.7% and 97.3–99% nucleotide homology based on COX1 and 18S rRNA gene, respectively. BLASTn analysis revealed a strong identity to other Physaloptera spp., and the phylogenetic tree placed all Physaloptera spp. in the same cluster. This study again indicates the usefulness of molecular techniques to substantiate the identity of species that may lack adequate descriptions and impart new insight for the potentially overlooked significance of P. praeputialis infections in felines. [ABSTRACT FROM AUTHOR]

The present study is the first comprehensive report on diversity, population structure, genetic admixture and mitochondrial DNA variation in South Indian draught type zebu cattle. The diversity of South Indian cattle was moderately high. A significantly strong negative correlation coefficient of -0.674 (P<0.05) was observed between the effective population size of different breeds and their estimated FIS. The genetic structure analysis revealed the distinctness of Kangayam, Vechur and Punganur cattle from the rest of the zebu breeds. The results showed the influence of Hallikar breed in the development of most Mysore type cattle breeds of South India with the exception of Kangayam. Bayesian clustering analysis was performed to assess the taurine admixture in South Indian zebu cattle using purebred Jersey and Holstein-Friesian as reference genotypes. Relatively high levels of taurine admixture (>6.25%) was observed in Punganur, Vechur, Umblachery and Pulikulam cattle breeds. Two major maternal haplogroups, I1 and I2, typical of zebu cattle were observed, with the former being predominant than the later. The pairwise differences among the I2 haplotypes of South Indian cattle were relatively higher than West Indian (Indus valley site) zebu cattle. The results indicated the need for additional sampling and comprehensive analysis of mtDNA control region variations to unravel the probable location of origin and domestication of I2 zebu lineage. The present study also revealed major concerns on South Indian zebu cattle (i) risk of endangerment due to small effective population size and high rate of inbreeding (ii) lack of sufficient purebred zebu bulls for breeding and (iii) increasing level of taurine admixture in zebu cattle. Availability of purebred semen for artificial insemination, incorporation of genomic/molecular information to identify purebred animals and increased awareness among farmers will help to maintain breed purity, conserve and improve these important draught cattle germplasms of South India. [ABSTRACT FROM AUTHOR]

Background and Aim: India has large varieties (recognized, unrecognized) of native chickens (Desi) scattered throughout the country, managed under scavenging system different from commercial chicken breeds. However, they are less investigated for genetic diversity they harbor. The present study was planned to evaluate genetic diversity among two native chicken populations of North Gujarat (proposed Aravali breed) and South Gujarat (Ankleshwar breed). Aravali chicken, a distinct population with unique characters different from the registered chicken breeds of India is under process to be registered as a new chicken breed of Gujarat, India. Materials and Methods: Two mitochondrial markers, namely, cytochrome c oxidase subunit I (COX I) and cytochrome b (Cyt b) genes were studied across 10 birds from each population. Methodology included sample collection (blood), DNA isolation (manual), polymerase chain reaction amplification of mitochondrial genes, Sanger sequencing, and purification followed by data analysis using various softwares. Results: Haplotype analysis of the COX I gene unveiled a total eight and three haplotypes from the Aravali and Ankleshwar populations, respectively, with haplotype diversity (Hd) of 92.70 % for the Aravali and 34.50% for the Ankleshwar breed. Haplotype analysis of the Cyt b gene revealed a total of four haplotypes from the Aravali population with 60% Hd and no polymorphism in Ankleshwar breed. The phylogenetic analysis uncovered Red Jungle Fowl and Gray Jungle Fowl as prime roots for both populations and all domestic chicken breeds. Conclusion: Study findings indicated high genetic variability in Aravali chicken populations with COX I mitochondrial marker being more informative for evaluating genetic diversity in chickens. [ABSTRACT FROM AUTHOR]

India plays a significant role in dugong conservation by having the largest population within South Asia. The status of dugongs in India is largely unknown due to a paucity of reliable ecological data. This study generated mitochondrial control region sequences from ~10% of dugong individuals from existing populations within India. Furthermore, data generated in this study were compared with the global data to assess genetic lineages, population structure, and genetic diversity of Indian populations.Multiple analyses suggest that the Indian dugong populations are part of a single genetic cluster, comprising South Asia, North‐west Indian Ocean, and South‐west Indian Ocean populations. Despite small population size, they retain high genetic diversity with unique mitochondrial DNA haplotypes within South Asia. Within India, novel haplotypes are observed from all dugong habitats sampled, with overall high haplotype diversity (0.85 ± 0.04) but low nucleotide diversity (0.005 ± 0.001). Indian populations exhibit genetic differentiation with higher within‐population variance (63.41%) than among populations (36.59%). Two of the haplotypes observed in India are shared with Sri Lanka, implying genetic connectivity between these populations.The genetic data from Indian dugong populations provide critical insights into the identification of dugong corridors and important dugong conservation zones in India. We suggest site‐specific interventions, including the creation of new marine protected areas and boundary reorganization and expansion of other existing protected areas, to ensure population connectivity. In addition, simultaneous efforts towards seagrass meadow restoration, reduction of dugong mortalities, and community participation in dugong conservation are recommended for population recovery of this threatened marine herbivore. [ABSTRACT FROM AUTHOR]

Background: Parkinson's disease (PD) is a multifaceted illness affecting ~ 0.3% of the world population. The genetic complexity of PD has not been, fully elucidated. Several studies suggest that mitochondrial DNA variants are associated with PD.Objective: Here, we have explored the possibility of genetic association between mitochondrial haplogroups as well as three independent SNPs with PD in a representative east Indian population.Methods and Material: The Asian mtDNA haplogroups: M, N, R, B, D, M7, and 3 other SNPs: 4336 T/C, 9055 G/A, 13708 G/A were genotyped in 100 sporadic PD patients and 100 matched controls via conventional PCR-RFLP-sequencing approach.Results: The distribution of mtDNA haplogroups, as well as 3 single polymorphisms, did not show any significant differences (P > 0.05) between patients and controls.Conclusion: This is the first of its kind of study from India that suggests no association of selected mitochondrial DNA variations with PD. [ABSTRACT FROM AUTHOR]

Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin's theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed. [ABSTRACT FROM AUTHOR]

The Greater Lizardfish, Saurida tumbil, forms a significant fishery in the demersal trawls along the west coast of India. But, the information regarding the stock structure of this species is scarce. In the present study, the morphology of fish, otolith shape, meristic traits and mt-DNA D-loop region were used to delineate the stocks collected from the west coast of India. Samples were collected between October to November 2018 from three major fish landing centres namely Mumbai, Mormugao and Kochi. Truss network analysis and otolith shape indices revealed the morphological divergence for body and otolith shape among the sampling regions. However, meristic traits and D-loop sequences of mitochondrial DNA could not show variation among the stocks, suggesting the existence of a single panmictic population of S. tumbil. The results of the present study are useful to formulate the stock-specific management measures for S. tumbil along the west coast of India. [ABSTRACT FROM AUTHOR]

The DNA barcode data of Asian Glass Lizard, Dopasia gracilis, is limited in the global database, especially from India. The present study aimed to generate a barcode sequence of morphologically identified D. gracilis from the Mizoram state in northeast India and compared with other Anguidae species. The studied species showed monophyletic clustering in the Bayesian analysis (BA) phylogeny with strong posterior probability support and also discriminated sufficient Kimura 2 parameter genetic distances. The barcode data of D. gracilis revealed high intra-species genetic variability and formed two clusters in BA phylogeny. The Templeton, Crandall, and Sing network also depicted four different haplotypes within the barcode sequences of D. gracilis. The DNA sequences generated from northeast India showed 6.5-6.6% and 7.3% genetic distances with the sequences generated from Yunnan Province and Tibetan Plateau, respectively. Considering the high genetic distances, multiple clustering, and distinct haplotypes, the present study assumed the presence of possible cryptic diversity of D. gracilis in the Indochina sub-region and a distinct population in northeast India. We recommended the generation of more DNA information from different localities to elucidate the actual diversity of D. gracilis within the known range distribution. [ABSTRACT FROM AUTHOR]

The molecular information of lesser-known bullfrog, Hoplobatrachus litoralis is restricted from Bangladesh (type locality) and Myanmar. The morphological observation further evidenced the rangeextension of this species from India and Myanmar. Here, we collected the H. litoralis specimen from the Dampa Tiger Reserve, Mizoram state and provides a new altitude record (268 m) and range-extension in northeast India. The DNA barcoding with mitochondrial Cytochrome b gene discriminates H. litoralis from other congeners with sufficient genetic distance (13.9% to 27.8%). The Bayesian phylogeny revealed monophyletic clustering of all five Hoplobatrachus species and showed the sister relationship of H. litoralis and H. tigerinus. The generated sequences of H. litoralis from northeast India depicted shallow divergence (1.5%) from the sequences generated from Bangladesh, indicates the possible genetic variability due to the alteration of the ecological niche. We suggested further physiological and molecular study with extensive sampling of this species to confirm their actual range distribution, high-altitude adaptation, and gene flow. [ABSTRACT FROM AUTHOR]

Bos gaurus gaurus commonly called as gaur is a wild bovid species inhabiting South and Southeast Asia and attained vulnerable status in India. In this study, we typed 62 extant free-ranging wild gaur individuals for mitochondrial partial displacement loop (D-loop) and cytochrome b gene (Cyt b) from the Melghat Tiger Reserve (MTR). Two historical DNA samples originating from museums and two Tectona grandis bark fibers samples browsed by wild gaur were also used as a source of environmental DNA. Both D-loop and Cyt b loci show the occurrence of a single haplotype in the contemporary wild gaur population. While D-loop fragment sequencing of two historical museum samples reveals two unique haplotypes, virtually absent in the present wild gaur population of MTR. Amplifications of the similar haplotypes in gaur DNA samples obtained through chewed T. grandis bark fibers have proved the efficacy of eDNA. Bayesian Skyline Plot (BSP) analysis using extant and historical D-loop sequences illustrate population decline starting from upper Mesolithic. Also, the BSP graph indicates accelerated effective population size decline (Ne), a time period coinciding with the different phases of the ∼5000 years old Indus civilization. The plot shows an overall declining trend in the wild gaur population, a probable outcome of ever-shrinking habitat in the central Indian landscape caused by prehistoric, medieval and colonial hunting practices. [ABSTRACT FROM AUTHOR]

The giant black tiger shrimp, Penaeus monodon, is one of the most economically important marine shrimp species, and it has a huge global economic impact. In this study, population diversity of P. monodon along the nine distinct coastal regions of India was determined by the molecular data of the mitochondrial control region (D‐Loop) and five mitochondrial genes (12SrRNA, 16SrRNA, COX1, Cytb and ND1). The mitochondrial DNA regions were highly AT‐rich, and demographic events suggested a recent population expansion. The results revealed a high level of genetic diversity, and we observed an increment of rare mutations and haplotypes within all populations. Chennai and Port Blair population showed the highest number of unique haplotypes. A significant level of population differentiation existed within all populations. A high level of genetic variations was observed within all populations. Neutral point mutations (silent or missense) were observed within all mitochondrial protein‐coding genes. The mitochondrial control region (D‐Loop), 16S ribosomal RNA and cytochrome b gene should be the potential marker for P. monodon. The 16S ribosomal RNA region would be the best mitochondrial marker for biogeographical phylogenetic studies in P. monodon. This study might have a great significance for the establishment of selective breeding strategies to develop genetically improved broodstock and to maintain wild stock diversity. [ABSTRACT FROM AUTHOR]

Fuel filling attendants are constantly exposed to the complex mixture of gasoline and all refinery environments are probably carcinogenic for humans. These workers are considered as an unorganized group in India and unaware of the risk. The present study was focused to monitor workplace pollutants (particulate matter size 10 [PM10 μm], total volatile organic compound [VOC], and carbon monoxide [CO]), benzene exposure (phenol), and to evaluate their genotoxicity effect with reference to relative mitochondrial DNA copy number (MtDNAcn), 8‐OHdG (8‐hydroxy‐2′‐deoxyguanosine), and micronuclei (MN) frequency (%) among fuel filling attendants. This study recorded 318 ± 134 and 1,050 ± 260 μg/m3 time‐weighted average concentration of PM10 and CO, respectively. However, total VOC levels recorded were below the detectable level (BDL) to 290 ± 50 μg/m3. A total of 53 subjects (26 exposed and 27 control) participated in this study with similar sociodemographic information. It was noticed that fuel filling attendants were not using proper personal protective equipment (PPE) and are younger generation. The significantly (p = <.001) higher level of phenol, a metabolite of benzene, was detected in the exposed group. The significantly elevated level of urinary 8‐OHdG (p =.01), MN frequency (p =.001), and relative MtDNAcn (p =.001) was observed in exposed group as compared to the control group. The study exemplify that workers were exposed to the benzene, workplace pollutant, and observed genotoxicity suggest malignancy risk. This study highlights the importance of biomonitoring in occupational settings to avoid malignancies. The possible engineering controls, frequent health check‐ups, awareness about the risks, and PPE use can reduce health hazards. [ABSTRACT FROM AUTHOR]