s. K. Gupta

Wildlife Institute of India | WII · Head of the Department of Animal Ecology and Conservation Biology

We describe a protocol for identifying wild versus domestic bovid horns using multidisciplinary approaches for implementing applicable wildlife laws. We used DNA and morphometry methods to identify four wild and two domestic bovid species from horn trophies. It helped in testing a horn trophy suspected from a wild buffalo that was seized by authori...

Purpose Avian haemosporidian may affect the host from body damage to the extinction of a population. Knowledge of their status may help in future avifauna conservation plans. Hence, their status in two bird groups of India and their phylogenetic relationships with other known lineages of the world were examined. Methods Cytochrome b gene sequences...

We describe the applicability of the cementum annuli analysis technique for estimating the age of Tiger Panthera tigris and Asiatic Lion Panthera leo using incisor teeth. We used I2 and I3 incisor teeth from the right mandible of Tiger and I2 and I3 from the left premaxilla of the Lion. The longitudinal sections of the teeth were prepared using an...

Background: Human activities have resulted in a rapid increase of modified habitats in proximity to wildlife habitats in the Himalaya. However, it is crucial to understand the extent to which human habitat modification affects wildlife. Mesocarnivores generally possess broader niches than large carnivores and adapt quickly to human activities. Here...

A known haven of amphibian diversity, South Asia is also a hotspot of taxonomic confusions. Vastly distributed from Saudi Arabia to Myanmar, the dicroglossid genus Euphlyctis (“skittering” or “skipper” frogs) is a representative example. Combining phylogenetic analyses with 16S barcoding and genome size variation of 403 frogs from 136 localities, w...

Hair from the Tibetan antelope (Pantholops hogdsonii), or Chiru, is used to create one of the world’s finest wool, hence termed ’Shahtoosh’. Chiru is a protected species and is illegally hunted for the mass-scale collection of its wool. Another fine quality wool hair derived from Pashmina goat (Capra hircus) is farmed in and around Ladakh, Jammu an...

The Psyra Walker, 1860, is a typical Sino-Himalayan genus of the subfamily Ennominae, currently known by 18 species/4 subspecies globally and 9 species from India. This study aims to revise the taxonomy and ecology of Indian Psyra by providing a morphology-based diagnostic key, highlighting their altitudinal, habitat and seasonal preferences, and m...

Pig farming has a profound caste-based and cultural association in India. In Uttarakhand, pigs are raised predominantly by the specific community contributing to their livelihood. Unlike other livestock species in the State, the piggery sector is unorganised and the pig farming is not sufficient to meet the increasing demand for pork. The study aim...

The hog deer (Axis porcinus) is an endangered cervid with drastic population declines. There are two 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 ran...

Hair from the Tibetan antelope (Pantholops hogdsonii), or Chiru, is used to create one of the world's finest wool, hence termed 'Shahtoosh'. Chiru is a protected species and is illegally hunted for the mass-scale collection of its wool. Another fine quality wool hair derived from Pashmina goat (Capra hircus) is farmed in and around Ladakh, Jammu an...

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...

The genus Xenortholitha Inoue, 1944 is mainly distributed in the Sino-Japanese and Indian Himalayan Region (IHR). The current communication reports the first distributional record of Xenortholitha falcata Yazaki, 1993 from western Himalaya, India extending its range far westwards from its previously known range in Eastern Nepal. We provide a brief...

The Endangered Kashmir musk deer Moschus cupreus occurs in the western Himalayan region from Nepal to Afghanistan, but there is a lack of comprehensive and reliable information on its range. The region also harbours the Endangered Himalayan musk deer Moschus leucogaster , and this range overlap may have led to misidentification of the two musk deer...

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,...

Understanding the population genetic structure and species boundaries in the complex river system has been challenging. The genus Sperata , a commercially important and widely distributed freshwater catfishes of India, belongs to Bagridae. The taxonomy of the Sperata genus is complex and still under revision. Recently, five valid species of Sperata...

The freshwater turtles of the iconic Ganga river system are one such group of vulnerable turtles. Despite common knowledge of the severity of turtle trade in the region, Gangetic turtles continue being poached in large volume, evident from the numerous and extensive seizures across the Gangetic belt. The intensive wildlife trade in Gangetic turtles...

Understanding population genetics, genetic diversity and the migration pattern of ecologically important species is crucial for effective conservation plans. We studied mitochondrial cytochrome c oxidase subunit-I (COI) gene variation in painted lady butterfly (Vanessa cardui) from different altitudinal gradients of Uttarakhand (Western Himalayas),...

The illegal wildlife trade has threatened the existence of many extant wild animal species throughout the world. While dealing with the illegal wildlife trade of horns, we face problems of not having a proper protocol and lack of reference database to assign the species for proper implementation of wildlife laws. In one such condition, a horn troph...

Age estimation methods, through cementum analysis, for wild animals are rarely developed in Southeast Asian Countries. In the present study, we describe the applicability of the cementum analysis technique for developing a fast (plus minus 1, 19 hours) and cost-effective age estimation method for Bengal tiger (Panthera tigris tigris) and Asiatic li...

We examined the Avian haemosporidians (Plasmodium and Haemoproteus) status in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India and their phylogenetic relationships with other known lineages of the world. The use of common genetic markers with information on the geographic distribution of parasite and host samp...

We report molecular identification of the confiscated body fat suspected of Himalayan black bear, Ursus thibetanus, seized by the forest department of a Himalayan State of India. We successfully extracted DNA, amplified, and sequenced 254 bp of cytochrome b (cyt b) and 439 bp of 16S rRNA genes from the fat samples.

The Red-crowned roofed turtle ( Batagur kachuga ) and Three-striped roofed turtle ( B. dhongoka ) are ‘critically endangered’ turtles in the Geoemydidae family. Herein, we generated the novel mitochondrial genome sequence of B. kachuga (16,155) and B. dhongoka (15,620) and compared it with other turtles species. Batagur mitogenome has 22 transfer R...

Horseshoe crab ( Tachypleus gigas ) is an archaic group of marine creature which plays a vital role in the saline ecosystem. Many researchers emphasize and enhance the knowledge about the horseshoe crab's basic biology, morphology, and ecology, whereas very little information is available about its population genetics. We attempted to develop a bas...

Lycodon mackinnoni is a poorly known Himalayan endemic snake known from Western Himalaya. Since the original description of L. mackinnoni almost 112 years ago, this species was not reported from its type locality and its phylogenetic position remain unknown. We herein, provide detail morphological description, comparison with type material, phyloge...

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 reconstructe...

Background: Hangul (Cervus hanglu hanglu) or Kashmiri stag belongs to the family Cervidae and is only surviving red deer in the Indian subcontinent. Its complete mitogenome sequence is lacking in the open database for further phylogenetic inferences. Methods and results: We sequenced and characterized the first complete mitogenome of Hangul, which...

Background: Hangul (Cervus hanglu hanglu) or Kashmiri stag belongs to the family Cervidae and is the only surviving red deer in the Indian subcontinent. Its complete mitogenome sequence is lacking in the open database for further phylogenetic inferences. Methods and results: We sequenced and characterized the first complete mitogenome of Hangul, wh...

Background: Identifying factors shaping population genetic structure across continuous landscapes in the context of biogeographic boundaries for lineage diversification has been a challenging goal. The red muntjacs cover a wide range across multiple vegetation types, making the group an excellent model to study South and Southeast Asian biogeograph...

We report a case study, wherein we established the putative cause of the death of three leopards by identifying the species and number of individual prey species from the gut contents using molecular tools. In a National Park within Northern part of India, the suspicious death of three leopards ( Panthera pardus) was reported from different localit...

The gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated...

DNA barcodes in species tagging have become a popular tool for taking inventories of species from different groups worldwide. The present study aimed to generate DNA barcodes of butterfly species from the Western Himalayas in Uttarakhand, India. The Indian Western Himalayan region (IWHR) has been explored to a limited extent about butterfly species...

Testudinoidea represents an evolutionarily unique taxon comprising both turtles and tortoises. The contrasting habitats that turtles and tortoises inhabit are associated with unique physio-ecological challenges hence enable distinct adaptive evolutionary strategies. To comparatively understand the pattern and strength of Darwinian selection and phy...

Swamp deer (Rucervus duvaucelii) is a large cervid confined to isolated patches in the wet grasslands of Himalayan foothills and dry grasslands of central India. There are currently three accepted subspecies of swamp deer: R. duvaucelii duvaucelii, R. duvaucelii branderi and R. duvaucelii ranjitsinhi, based on their distribution range, habitat pref...

First reporting of albino five striped palm squirrel in Dehradun, Uttarakhand

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...

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Sperata seenghala (Giant river-catfish) and Sperata aor (Long-whiskered catfish) are commercially important freshwater catfishes of India, belongs to family Bagridae. Due to high nutritional significance and the low number of intramuscular bones, both fishes have considerable demand in South Asian countries. Both of the Sperata species are morpholo...

Morphometric and molecular divergence among four butterfy 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. Tradi...

Background We investigated the phylogeographic pattern of red muntjac across its distribution range, intending to address the presence of distinct lineages from Northwest India. The Complete mitogenome analysis revealed that India holds three mitochondrial lineages of red muntjac, whereas four were identified from its entire distribution range: Him...

A decline in the numbers of threatened species is often reversed by reintroduction with the aim of repopulating or strengthening the population to reduce the risk of extinction. The success of reintroduction programs is associated with demographic and genetic monitoring of the reintroduced populations. We undertook a genetic assessment of the Criti...

The endangered Kashmir musk deer (Moschus cupreus) is native to the high altitudinal region of the Himalayas. In this study, we sequenced, annotated and characterized the complete mitogenome of M. cupreus to gain insight into the molecular phylogeny and evolution of musk deer. The mitogenome of M. cupreus, which is 16,354 bp long comprised 13 prote...

Kashmir musk deer, KMD (Moschus cupreus) is one the most threatened species reported from the Himalayan region of Kashmir, Pakistan and Afghanistan. A comprehensive and reliable distribution range of musk deer is still lacking. Recently, a molecular study confirmed the presence of KMD in Mustang in Nepal, west of Annapurna Himalayas. Here, we inves...

We investigated the phylogeographic pattern of red muntjac across its distribution range, intending to address the presence of distinct lineages from Northwest India. The Complete mitogenome analysis revealed that India holds three mitochondrial lineages of red muntjac, whereas four were identified from its entire distribution range: Himalayan red...

We present a comprehensive inventory of amphibians from Panna Tiger Reserve in Madhya Pradesh based on morphological, molecular and bioacoustic data. Representatives of 15 anuran species were collected, corresponding to roughly four fifths of the known amphibian species of Madhya Pradesh. The main results of this study are: (1) Description of adver...

In many aquatic species, alteration of habitats and human-induced barriers shape the population’s genetic structure in rivers with longitudinal connectivity. The golden mahseer, Tor putitora (GM) is an endangered and sensitive cyprinid species. It is considered an indicator of a healthy freshwater ecosystem and is found in cold-water habitats. Ther...

We describe the identification of the leopard cat (Prionailurus bengalensis), jungle cat (Felis chaus) fishing cat (Prionailurus viverrinusis), wild cat (Felis silvestris) and caracal (Caracal caracal) using combined approach of morphological and molecular based analysis. Three mitochondrial genes [12S rRNA, 16S rRNA and cytochrome b (Cyt b)] and h...

The populations of the butterfly Danaus chrysippus, Vanessa cardui, Pieris canidia and Pieris brassicae (Lepidoptera: Nymphalidae and Pieridae) occurs in erratic habitat in Western Himalayas of Uttarakhand. In the present study, RAPD (random amplified polymorphic DNA) markers were used to assess the results of habitat loss and fragmentation on the...

This study aimed to find out the research gap in terms of total area covered, species diversity, taxonomic and phylo-geographic/biogeographic shortfall in Indian Himalayan region (IHR~60,000 km2). Study area consists of Bhagirathi River Basin (IHR~60,000 km2), Uttarakhand from Indus River System under biogeographic province 2B and Teesta River Basi...

Mishmi takin (Budorcas taxicolor taxicolor) is an endangered and least studies species. We sequenced and annotated a 16,584 bp long complete mitogenome of Mishmi takin (B. t. taxicolor). It was encoded by 37 genes: 13 Protein-Coding Genes (PCGs), two ribosomal RNA genes, 22 transfer RNA, and non-coding control region. All tRNA genes show a typical...

Taxa classified as subspecies may in fact be cryptic species. We assessed the taxonomic status of the Blue‐throated Flycatcher Cyornis rubeculoides complex in India, which consists of several forms with similar plumages and song. We used mitochondrial and nuclear DNA, plumage traits, and detailed song analysis to ascertain the taxonomic status of t...

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 m...

We developed a protocol which determines age in spotted deer, Axis axis (Erxleben, 1777) through cementum layers in the tooth which is economical and requires lesser time (±19 hours). The permanent frst incisor teeth from mandibles of known estimated ages (2, 4, 5, 8 and 9 years) were ground longitudinally on median plane on a set of sandpapers wit...

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 R...

The hog deer (Axis porcinus) is threatened by habitat alteration, fragmentation, and poaching, which have led to a drastic decline of its wild population. Two subspecies of A. porcinus have been described from its distribution range. A. p. porcinus is reported to occur from Pakistan along the Himalayan foothills through Nepal, India and Myanmar, an...

Illegal wildlife trade has been detected as a global threat to the sustainability of biodiversity and the security of society. It invited the strict wildlife protection laws. In the past two decades, forensic science has evolved rapidly with its emerging branch “wildlife forensics” with great success. Investigation of wildlife crime is increasingly...

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...

The Eld’s deer or brow-antlered deer (Rucervus eldii) is one of the most endangered cervids of Southeast Asia. Geographically, it has three distinct subspecies; Sangai or Manipur's brow-antlered deer (R. e. eldii), Siamese brow-antlered deer (R. e. siamensis) and Thamin or Myanmar’s brow antlered deer (R. e. thamin). We examined the genetic diversi...

We describe six sets of primers for amplifying the mitochondrial control region (CR) of various bird species belonging to nine families of the order Passeriformes. These overlapping primers, with both short and long fragments, yielded an approximately 1 kb fragment of the CR. The short length of the amplified product makes the primers suitable for...

The swamp deer (Rucervus duvaucelii) occurs, primarily, in the wet grasslands of the Himalayan foothills as well as the dry grasslands of central India. Three subspecies have been identified, namely R. duvaucelii duvaucelii, R. duvaucelii branderi and R. duvaucelii ranjitsinhi. Degradation of grassland habitats led to a drastic decline in the total...

We describe six novel ungulate-specific conserved primers for sequencing the complete mitochondrial cytochrome c oxidase I (COI) gene of selected threatened species from degraded samples for effective conservation planning. These primers amplified 301–1599 bp DNA fragments in various combinations. The method described may assist in the sequencing o...

Objective: To investigate the authenticity of infant Rhino horn sample from morphometric, microscopic, genetic and phylogenetic studies. Methods: A suspected rhino horn sample (11 cm × 13 cm) was sent to the laboratory for identification. Relevant morphometric data of sample were taken. Similarly, established methods for microscopic examination of...

The mitochondrial DNA (mtDNA) control region is extensively used in the phylogeography of species. We examined sequence variations in the mtDNA control region of sambar (Rusa unicolor) populations from the South, Central and North India. Most of the samples collected from the south India exhibited a 40 bp insertion in the mtDNA control region. This...

We describe a protocol for the identification of two endangered cervids from decomposed and degraded samples based on the mitochondrial DNA cytochrome b (cyt b) gene and control region (D-loop) analysis. The identification of the species was achieved using DNA extracted from 16 unknown carcasses and two references samples of Eld’s deer (Rucervus el...