Genetic diversity, spatial connectivity, and population structure of Asian silurid catfish Wallago attu (Bloch and Schneider, 1801) in the Ganga River System: insights from mitochondrial DNA analysis.

BACKGROUND: The Ganga River System (GRS) is a biodiversity hotspot, its ecological richness is shaped by a complex geological history. In this study, we examined the genetic diversity, spatial connectivity, and population structure of the Asian Silurid catfish, Wallago attu, across seven tributaries of the GRS. METHODS AND RESULTS: We employed three mitochondrial DNA (mtDNA) regions: cytochrome c oxidase subunit I (COXI), cytochrome b (Cyt b), and control region (CR). Our comprehensive dataset encompassed 2420 bp of mtDNA, derived from 176 W. attu individuals across 19 sampling sites within the seven rivers of GRS. Our findings revealed high gene diversity (Hd:0.99) within W. attu populations. Analysis of Molecular Variance (AMOVA) highlighted that maximum genetic variations were attributed within the populations, and the observed genetic differentiation among the seven populations of W. attu ranged from low to moderate. Network analysis uncovered the presence of three distinct genetic clades, showing no specific association with seven studied rivers. Bayesian skyline plots provided insights into the demographic history of W. attu, suggesting a recent population expansion estimated to have occurred approximately 0.04 million years ago (mya) during the Pleistocene epoch. CONCLUSIONS: These results significantly enhance our understanding of the genetic diversity and spatial connectivity of W. attu, serving as a vital foundation for developing informed conservation strategies and the sustainable management of this economically valuable resource within the Ganga River System.

Unveiling the genetic structure of pig population in a Himalayan state Uttarakhand through microsatellite and mitochondrial DNA analyses.

This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world's youngest (geo-dynamically sensitive) mountain system, "the Himalayas". Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand's domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.

Himalayan upliftment and Shiwalik succession act as a cradle for divergence in Bengal monitor lizard Varanus bengalensis (Reptilia: Varanidae) in India.

The Himalayan foothills and associated environment are well-known for driving the rapid diversification of many species and the formation of biodiversity hotspots. The effects of environmental change since the Miocene have accelerated species diversification, and hence are useful for studying population genetic structure, and evolutionary relationships via genetic approaches. To date, the effects of climatic fluctuations on the biogeography of large-bodied lizards have not been assessed comprehensively. Herein, we examine the diversification of Varanus bengalensis, focusing on its genetic structure to provide insights into how landscape structure and climatic fluctuations have shaped species differentiation. We confirm the existence of two distinct lineages within V. bengalensis distributed across the Himalayan foothills and the remainder of mainland India. Divergence analyses revealed the split between the Himalayan foothills and the remainder of the mainland lineages of V. bengalensis in the mid-Pliocene ~3.06 Ma, potentially as a consequence of the Siwalik broadening and climatic fluctuations across the Himalayan foothills. The results suggest recognition of a new lineage of V. bengalensis from the Himalayan foothills as a distinctive evolutionarily significant unit.

Unraveling the mystery of confiscated "jackal horns" in India using wildlife forensic tools.

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.

Genetic Analysis Reveals a Distinct Lineage of Hog Deer (Axis porcinus) in Kratie Province, Cambodia.

The hog deer (Axis porcinus) is an endangered cervid with drastic population declines. There are 2 recognized subspecies of hog deer: A. p. porcinus, ranging from Punjab Province in Pakistan, Nepal, and the Northern part of India to Myanmar, and A. p. annamiticus found in Indo-China, Thailand, Laos, Cambodia, and Vietnam. The current geographic range of A. p. annamiticus is still ambiguous. We analyzed variation in the mitochondrial DNA control region (mtDNA CR) to investigate the intra-species structure, differentiation, and demographic history of hog deer from Cambodia (Kratie Province), which we compared with the populations from India and Thailand. We also generated divergence time estimates using a concatenated dataset of complete Cyt b and partial CR. The CR data showed that Cambodian hog deer are genetically differentiated from the mainland Indian and Thai populations, forming a distinct basal clade. The time of divergence indicates that the Cambodian lineage split from the other 2 hog deer lineages around 0.51 Mya, during the Late Pleistocene. The results also suggest strong phylogeographic structure among hog deer: lineage A extends from Terai Arc (foothills of the Himalayas) to Assam, India (A. p. porcinus), lineage B from Manipur, India to Thailand (A. p. annamiticus), and lineage C is only known from Kratie Province, Cambodia. Lineage A exhibited a higher level of genetic diversity than lineages B and C, with recent demographic stability. Thus, the hog deer population in Kratie Province appears to be a distinct lineage that should be treated as an evolutionarily significant unit.

Complete mitogenome of Ganges river dolphin, Platanista gangetica gangetica and its phylogenetic relationship with other cetaceans.

The Ganges river dolphin, Platanista gangetica gangetica is one of the endangered cetaceans. Due to increasing anthropogenic activities, it has faced a significant reduction in distribution range since the late 1800s and has even gone extinct from most of the early localities. The investigation of complete mitogenome holds significant relevance for identifying evolutionary relationships and monitoring the endangered species. Herein, we report and characterize for the first time the 16,319 bp complete mitochondrial genome of P. g. gangetica. It comprises 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region (CR). The genome composition was A + T biased (59.6%) and exhibited a positive AT-skew (0.104) and negative GC-skew (- 0.384). All the genes were encoded on the heavy strand, except eight tRNAs and the ND6 gene. In the CR, an 18 bp tandem repeat sequence was observed. Our Bayesian Inference (BI) and Maximum Likelihood (ML) based phylogenetic analysis indicated that studied river dolphins were polyphyletic and the placement of Platanista was to be more basal than other river dolphins (Lipotes, Inia and Pontoporia). The pairwise genetic distance of Platanista with other cetaceans was varied, with an overall close affinity with whales. The model-based BI and ML phylogenetic analysis indicated that Platanista clustering with Ziphiidae with high to moderate supportive values (PP/BP = 98/68). The results of this study provide insights important for the conservation genetics and further evolutionary studies of the freshwater river dolphins.

Detection of 40 bp tandem repeat motif and associated insertions and deletions (INDEL) in the mitochondrial DNA control region of Sambar deer (Rusa unicolor).

Sambar (Rusa unicolor) is the largest oriental deer and has a wide distribution across South and Southeast Asia. Despite its wide distribution range, little information on the genetics of this species is available to date. We examined the genetic variability of Sambar populations using a partial fragment of the mtDNA control region and reconstructed the phylogeographic association of Sambar populations across India. We detected 56 haplotypes with an overall haplotype diversity, Hd = 0.939 ± 0.012 and nucleotide diversity, Pi = 0.029 ± 0.002 in Sambar populations across India. The Sambar populations of Northeast India exhibits 30 localized mtDNA control region haplotypes with no haplotype sharing with other populations of India. We identified a 40 bp tandem repeat motif in the mtDNA control region with variable copy numbers ranging between three to six duplications. The Sambar populations across India exhibited phylogeographic differentiation based on the observed insertion and deletion patterns in the mtDNA control region. The 40 bp tandem repeat motif was associated with patterns of insertions and deletions among different populations of Sambar in India. The findings of this study provide baseline information on the mtDNA genetic variability of Sambar populations across India, which is crucial for future population genetic studies.

Molecular and morphometric divergence of four species of butterflies (Nymphalidae and Pieridae) from the Western Himalaya, India.

Morphometric and molecular divergence among four butterfly species of the families Nymphalidae and Pieridae from the western Himalaya region were investigated using molecular tools, traditional morphometric measures and a truss network system. The considered species were Danaus chrysippus, Vanessa cardui, Pieris brassicae and Pieris canidia. Traditional taxonomy is sometimes unable to discriminate cryptic species or species that have close morphological features. Although taxonomists carefully examine external body features to differentiate the species; however, there is a risk for misidentification during a visual assessment of cryptic species. Therefore, we aimed to use the truss network system of 14 morphological landmarks interconnected to yield 90 variables about molecular taxonomy. Principal component analysis (PCA), discriminant function analysis (DFA) and cluster analysis (CA) were employed to determine morphometric variations. In the traditional analysis, 79, 68, 16 and 5 characters out of 90 were found significant (p < 0.05) for D. chrysippus, V. cardui, P. brassicae and P. canidia, respectively. One to seven principal components were extracted through PCA; they explained 87.5-100% of the total variance in samples. Notably, DFA correctly classified 100% of the original grouped cases and 100% of the cross-validated grouped cases. However, the variations were not the same for the two different methods (truss and traditional) employed for the analysis. We correctly identified all the species; the interspecies sequence divergence was between 0.1034 and 0.1398, and the intra-species sequence divergence range was 0.0001 to 0.0128 using the Cytochrome c oxidase subunit-I (COI) gene. The present study provides useful information about the application and complementary role of traditional with truss morphometric analysis for the precise identification and classification of the selected species.

Complete mitogenome of Kashmir musk deer (Moschus cupreus) and its comparative phylogenetic relationships.

Kashmir musk deer, Moschus cupreus (KMD) is one the most threatened species endemic to the Himalayan region of Kashmir, Pakistan and Afghanistan. Herein, we have sequenced, annotated and characterized the complete mitogenome of M. cupreus. The investigation and comparison of the mitogenome provide crucial information for phylogenetic analysis to understand the evolutionary relationships. The mitogenome of KMD was 16,354 bp long, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and non-coding control region. Its composition was highly A+T biased 68.42%, and exhibited a positive AT-skew (0.082) and negative GC-skew (- 0.307). The phylogenetic analysis suggested that KMD was a primitive and extant species in the genus Moschus, whereas Alpine musk deer (M. chrysogaster) and Himalayan musk deer (M. leucogaster) were the closest relatives. It indicated the placement of M. cupreus within the monotypic family Moschidae of musk deer. Hence, it provides a better understanding of lineage identification and musk deer evolution for further research.

Online selling of wildlife part with spurious name: a serious challenge for wildlife crime enforcement.

We examined an online sold product "Hatha Jodi" synonym of "paired arm" for the confirmation of its biological source. It was declared as a plant root. The morphological features of these samples were matched with the "intromittent organs" or "hemi penis" of the monitor lizard. For further confirmation, we used sequencing of a partial fragment of mitochondrial DNA cytochrome b gene. Sequence comparison indicated that these claimed plant products were actually biological samples of a common monitor lizard, Varanus bengalensis. Hence, it exhibited the ongoing illegal trade of the intromittent organ of a prohibited species with a misleading name using low risk and widely adopted modern trading method that imposes a severe challenge for combating against the wildlife crime.

Complete mitochondrial genome of northern Indian red muntjac (Muntiacus vaginalis) and its phylogenetic analysis.

We report complete mitochondrial genome of Northern Indian red muntjac, Muntiacus vaginalis, and its phylogenetic inferences. Mitogenome composition was 16,352 bp in length and its overall base composition in the circular genome was A = 33.2%, T = 29.0%, C = 24.50% and G = 13.30%. It exhibited a typical mitogenome structure, including 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a major non-coding control region (D-loop region). All the genes except ND6 and eight tRNA's were encoded on the heavy strand. Phylogenetic analyses showed that M. vaginalis is closely related to M. muntjak and formed a sister relationship with Elaphodus cephalophus. In view of the unclear distribution range and escalating habitat loss, it is important to identify its population genetic status. The complete mitogenome described in this study can be used in further phylogenetics, identification of extant maternal lineage, evolutionary significance unit and its genetic conservation.

Molecular identification of victim species and its sex from the ash: a case of burning alive leopard (Panthera pardus).

In a case of negative human-leopard (Panthera pardus) interaction, an animal was burnt alive in South Rajasthan, India. We identified the species and sex of the victim animal from the ash using forensic DNA analysis. We recovered three objects (half burnt clot, stone, and shrub twig) from the ash having suspected blood stains. We extracted DNA from these items and amplified a partial fragment of mitochondrial DNA cytochrome b and 12S RNA genes. The sequence generated from these amplicons suggested that the victim animal was a leopard. Furthermore, amplification of a fragment of SRY (224 bp) and ZFX/Y (442 bp) genes indicated that the blood clot was of a male leopard. Although attempts have been made to remove every possible evidence from the crime scene, the species and sex of the victim animal were determined from the challenging and invisible blood stains wrapped in the ash.

Complex Structural Landscape of Titanium Organophosphonates: Isolation of Structurally Related Ti4, Ti5, and Ti6 Species and Mechanistic Insights.

[Ti(acac)2(OiPr)2] reacts with tert-butylphosphonic acid to yield a series of titanium organophosphonates such as tetranuclear [Ti4(acac)4(µ-O)2(µ-tBuPO3)2(µ-tBuPO3H)4]·2CH3CN (1), pentanuclear [Ti5(acac)5(µ-O)2(OiPr)(µ-tBuPO3)4(µ-tBuPO3H)2] (2), hexanuclear [Ti6(acac)6(µ-O)2(OiPr)2(µ-tBuPO3)6] (3), or [Ti6(acac)6(µ-O)3(OiPr)(µ-tBuPO3)5(µ-tBuPO3H)]·2CH3CN (4). The isolation of each of these products in pure form depends on the molar ratio of the reactants or the solvent medium. Among these, 3 is obtained as the only product when the reaction is conducted in CH2Cl2. The structural analysis reveals that a simple cluster growth route relates the clusters 1-4 to each other and that a reactive cyclic single-4-ring titanophosphonate [Ti(acac)(OiPr)2(tBuPO3H)]2 is the fundamental building block. While the tetranuclear 1 has structural resemblance to the D4R building block of zeolites, the hexanuclear clusters 3 and 4 have the shape of zeolitic D6R building blocks. The presence of adventitious water in the phosphonic acid (arising from small quantities of hydrogen-bonded water) results in the formation of µ-O2- bridges across an adjacent pair of titanium centers in clusters 1-4. To further verify the stability of the hexanuclear cluster over other structural forms, the reaction of tBuPO3H2 was performed with [Ti(acac)2(O)], instead of Ti(acac)2(OiPr)2, in CH3CN to yield [Ti6(acac)6(µ-O)4(µ-tBuPO3)4(µ-tBuPO3H)2]·2CH3CN (5). Compound 5 exhibits a core structure similar to those of 3 and 4 with small variations in the intracluster Ti-O-Ti linkage. Compound 3 is an efficient and selective catalyst for olefin epoxidation under both homogeneous and heterogeneous conditions.

Antibacterial Activity of Indian Borage (Plectranthus amboinicus Benth) Leaf Extracts in Food Systems andAgainst Natural Microflora in Chicken Meat.

The ability of acetone and ethyl acetate extracts of the leaves of a traditional Indian medicinal plant, Indian borage (Plectranthus amboinicus Benth) to prevent spoilage of artificially inoculated model food systems (cabbage and papaya) and natural microflora of chicken meat was evaluated. These extracts were able to reduce the bacterial counts in all food systems; however, the effective concentration varied with the complexity of the system (cabbage

Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India.

The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani . Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.

Population genetics of the critically endangered three-striped turtle, Batagur dhongoka, from the Ganga river system using mitochondrial DNA and microsatellite analysis.

The three-striped roofed (Batagur dhongoka) is a semi-aquatic turtle that belongs to family Geoemydidae. Due to anthropogenic pressure, it has been facing an intense decline of over 80% in its distribution range in the past 50 years. It is considered as 'Critically Endangered' so effective conservation strategies are needed to protect the species by determining their genetic diversity and population genetic structure. This study investigates the genetic diversity, population structure and demographic pattern of B. dhongoka from two Turtle Rescue and Rehabilitation Centre established near Ganga river using mitochondrial cytochrome b (Cyt b: 1140 bp) ; control region (CR: 451 bp) and ten nuclear microsatellite loci. mtDNA results show low levels of nucleotide diversity (π = 0.0022) in B. dhongoka haplotypes and provide evidence for a low substitution rate. The demographic pattern estimated by the Bayesian skyline plot (BSP) analysis indicates historical stability followed by growth in the effective population size, with a recent reduction in population size from ~ 2 thousand years ago. The microsatellite findings show a moderate level of observed heterozygosity (Ho: 0.49). Bayesian-based clustering analysis revealed weak genetic structures in B. dhongoka and presence of admixed assignations suggesting close genetic relationships. These findings shed light on B. dhongoka's genetic status and underline the necessity of comprehensive rehabilitation and relocation programs and conservation and management techniques to ensure the species' long-term survival. In order to ensure the effective protection and conservation of B. dhongoka, the Government of India has taken a proactive measure by incorporating it into Schedule I of the Wildlife (Protection) Act, 1972, as amended in 2022.

Cytochrome b based genetic differentiation of Indian wild pig (Sus scrofa cristatus) and domestic pig (Sus scrofa domestica) and its use in wildlife forensics.

The Indian wild pig (Sus scrofa cristatus) is a protected species and listed in the Indian Wildlife (Protection) Act, 1972. The wild pig is often hunted illegally and sold in market as meat warranting punishment under law. To avoid confusion in identification of these two subspecies during wildlife forensic examinations, we describe genetic differentiation of Indian wild and domestic pigs using a molecular technique. Analysis of sequence generated from the partial fragment (421bp) of mitochondrial DNA (mtDNA) cytochrome b (Cyt b) gene exhibited unambiguous (>3%) genetic variation between Indian wild and domestic pigs. We observed nine forensically informative nucleotide sequence (FINS) variations between Indian wild and domestic pigs. The overall genetic variation described in this study is helpful in forensic identification of the biological samples of wild and domestic pigs. It also helped in differentiating the Indian wild pig from other wild pig races. This study indicates that domestic pigs in India are not descendent of the Indian wild pig, however; they are closer to the other wild pig races found in Asia and Europe.

Review: Single attribute and multi attribute facial gender and age estimation.

Facial age and gender recognition have vital applications as consumer profile prediction, social media advertisement, human-computer interaction, image retrieval system, demographic profiling, customized advertisement systems, security and surveillance. This paper presents a study on Single Attribute (Attribute: either Gender or Age) and Multi-Attribute (both Gender and Age) prediction model. We present a review for facial age estimation and gender classification methods based on conventional as well as deep learning approaches developed so far with analysis of their pros, cons and insights for future research. Moreover, this study also enlists the databases used for benchmarking results with their properties for both constrained and unconstrained environment.

Visiting Ladakh Himalaya for a better knowledge of butterflies: new faunistic data with annotations (Lepidoptera, Papilionoidea).

The present study enumerates 65 species of Papilionoidea from the Ladakh Himalaya with the geographical locations and adult flight data. All the species are documented by museum vouchers. Most of the species recorded, have restricted distribution or they are endemic to the Pamir-NW Himalaya region. Sixteen species are protected in the Indian Wildlife (Protection) Act, 1972; three species highly protected under schedule I: Baltia butleri, Pieris krueperi, Lasiommata menava; and others under schedule II: Papilio machaon, Parnassius charltonius, Parnassius epaphus, Colias ladakensis, Colias eogene, Colias stoliczkana, Pieris deota, Pontia chloridice, Alpherakya devanica, Pamiria metallica, Paralasa mani, Paralasa kalinda and Polygonia c-album. We report lower occurrences for the endemic Pieris deota, where the migrant Pontia chloridice is reported to fly at more than 600 m higher than earlier records indicated. Lastly, the male and female genitalia of some endemic and rare species are illustrated, including Euchloe daphalis.

Mean Bone Density in Interadicular Areas of Maxilla among Patients Visiting Dental Unit of a Tertiary Care Centre: A Descriptive Cross-sectional Study.

Introduction: A close relationship occurs between the type of bone density and the success of orthodontic mini-implant. The aim of this study was to find out the mean bone density in interradicular areas of the maxilla among patients visiting dental unit of a tertiary care centre. Methods: A descriptive cross-sectional study was performed at the Department of Orthodontics and Dentofacial Orthopedics at a tertiary care centre from 15 January 2022 to 28 June 2022 after taking ethical approval from the Institutional Review Committee (Reference number: UCMS/IRC/175/21). Data was collected from scan reports obtained with a computed tomography scanner. Bone density was measured at 6 mm height from the alveolar crest. Convenience sampling was done. Point estimate and 95% Confidence Interval were calculated. Results: Out of 70 patients, mean bone density at interradicular areas of maxilla was 992.31±204.20 HU (944.46-1040.13, 95% Confidence Interval). Between central and lateral incisor 50 (71.44%) had D2 type of bone density. Conclusions: The mean bone density in inter radicular areas of the maxilla among patients visiting the dental outpatient department was similar to other studies done in similar settings. Keywords: bone density; prevalence; prostheses and implants.