Molecular Systematics Division

Background: Catfishes are globally demanded as human food, angling sport and aquariums keeping thus are highly exploited all over the world. North-East India possess high abundance of catfishes and are equally exploited through decades. The strategies for conservation necessitate understanding the actual species composition, which is hampered due to sporadic descriptions of the species through traditional taxonomy. Therefore, actual catfish diversity in this region is important to be studied through the combined approach of morphological and molecular technique of DNA barcoding.

Background: The taxonomic validity of Northeast Indian endemic Mahseer species, Tor progeneius and Neolissochilus hexastichus, has been argued repeatedly. This is mainly due to disagreements in recognizing the species based on morphological characters. Consequently, both the species have been concealed for many decades. DNA barcoding has become a promising and an independent technique for accurate species level identification. Therefore, utilization of such technique in association with the traditional morphotaxonomic description can resolve the species dilemma of this important group of sport fishes.

One hundred thirty eight fish species were collected during a systematic survey of 35 rivers in Arunachal Pradesh state, India, in March 2004 to March 2008. Based on this survey and on literature review we developed a checklist with 213 fish species for the state. We have added 43 species to the previous record of 170 species. This study confirmed the occurrence of five new species described by previous investigations and encompasses the discovery of two new species, although the taxonomic status of 27 species is uncertain and requires additional study.

The Digital Elevation Model (DEM) can precisely represent hydro-geomorphological parameters for fish habitat inventory. The GIS technique equipped by Spatial Multi-Criteria Evaluation (SMCE) model helps in processing the selected parameters for fish habitat suitability mapping. In the present work DEM of the Shuttle Radar Topographic Mission (SRTM) using Interferometric Synthetic Aperture Radar (InSAR) technique is used for parameter inventory of the fish habitat in lotic system. Arunachal Pradesh (Eastern Himalaya) in the North-East region of India has been selected for this exercise. Information like stream network, stream slope, stream elevation and stream length are derived from SRTM DEM. The stream lengths under each category of stream slope and stream elevation are analysed. The state Arunachal Pradesh with total area of 83743 km 2 has 29003.23 km of river length, distributed in the range of 0˚ to 40˚ gradients and 107 m to 5699 m elevations. Since the studied parameters fluctuate between wide ranges, there is high variation in habitat characters as well as probability of species speciation and thereby diversification. The total stream length under suitable category is 62.69%, moderately suitable 21.42% and less suitable 15.89%. This study of fish habitat using geomorphological and hydrological parameters may be termed as ICHTHYOGEOMORPHOLOGY.

Understanding the sexual dimorphism in fish is an uphill task and is paradoxical in different species. In general, the studies on the biometrics of fish form the basis of fishery investigations particularly in the management and exploitation of fishery resources. The present study was carried in order to obtain characteristic relationship of various morphological parameters between the sexes of Neolissochilus hexagonolepis (McClelland). Considerable differences in the percentage of some morphometric characters on standard length have been observed between males and females. The males were found to have greater head width at operculum, snout length, predorsal length and preanal length than the females. On the other hand, the females had greater body depth at dorsal fin insertion, pectoral fin length, anal fin height and ventral fin height than the males. The males were found to have greater value of biometric index for body depth at dorsal fin insertion, pectoral fin length, anal fin height and height of ventral fin than the females; while the females had greater values for head width at operculum, snout length, predorsal length and preanal length. The variation in the biometric index and percentage of anal fin height on standard length was highly significant between males and females. Together the values of correlation coefficient 'r' between the variable characters and the standard length were found positive, with the highest value of regression coefficient 'b' in case of total length (b=1.3082) and lowest in case of head height at eye (b=0.0366).

DNA barcoding has become a popular method of choice for identification of specimen based on molecular techniques. Here, we present preliminary findings on generating robust DNA barcode library of Cervids of India. The dataset comprising the DNA barcode library of seven deer species included in the genus Cervus, Axis and Muntiacus classified under family Cervidae. Mitochondrial Cytochrome C Oxidase subunit I gene of ca. 710 bp accepted widely as DNA barcode region, was used for generating species specific signature from 31 known samples of seven Indian deer species. Expectedly, the NJ tree clustered three genera i.e. Cervus, Axis and Muntiacus of Cervids of India into three clades. Further, the intra-and interspecies distances based on Kimura 2 parameter model also supported the results. The average intra-and interspecies sequence divergence were 0.011 (±0.09) and 0.65 (±0.14), respectively. The present study has exhibited that DNA barcoding has discriminating power to delineate boundaries among the closely related species. The data generated are of high importance to the law enforcement agencies in effective identification of species in wildlife offence cases. The similar approach can be utilized for generating DNA barcodes for other Indian mammals for making effective management and conservation action decisions.

Across the world, hunting is one of the main causes of the decline in populations of wild vertebrates. This activity has serious effects not only on the specific, target populations but also on the dynamics and structures of other animal populations. Often the only evidence available for successful prosecution of poachers is in the form of small pieces of skin, bone, and meat. In such cases, forensic investigations can irrefutably establish the identity of the species involved in the illegal hunting by using genetic technologies. This articles describes an investigative study in a suspected wildlife hunting incident in which molecular biology techniques were employed to identify the species involved. Using fragments of cytochrome b (Cyt b) and 12S ribosomal RNA (12S rRNA) mitochondrial markers, the samples were confirmed to be from an IUCN Red List species, the Indian porcupine (Hystrix indica).This is the first genetic record of an Indian porcupine from the Uttarakhand population. The genetic analysis in this study was suitable for diagnosing the species and concluding a criminal investigation. Molecular forensic techniques can, therefore, provide an important tool that enables local law enforcement agencies to apprehend poachers. Meanwhile the present study represents a small step in reducing the hunting of porcupine in Uttarakhand as well as other adjoining states, with the aim of conserving biodiversity.

The Hangul (Cervus elaphus hanglu) is a ''Least Concern'' deer species, and it is the only survivor of the Red Deer group in the Indian subcontinent. The phylogenetic status of the Hangul relative to the other members of the family Cervidae is not known because sequence data are not available in public databases. Therefore, this study was carried out to determine the phylogenetic status and delineate the genetic boundaries of the Hangul with respect to the other Red Deer subspecies on the basis of cytochrome b gene sequence data (ca 421 bp). There are three major monophyletic groups of the Red Deer in the phylogenetic tree, which are referred to as the western (Hap-01 to Hap-10), eastern (Hap-11 to Hap-20) and tarim (Hap-21 to Hap-25) groups. The overall haplotype diversity and per-site nucleotide diversity were 0.9771 (±0.0523) and 0.0388 (±0.00261), respectively. In the phylogenetic tree, the Hangul clustered with the tarim group (Yarkand and Bactrian Red Deer) with a strong bootstrap support (92%) and was found to be genetically closer to the Bactrian Red Deer than to the Yarkand Red Deer. Our molecular analysis supported the idea that the Hangul diverged from the Bactrian Red Deer and migrated to India from Tajikistan approximately 1.2 MYA.

Indian Pangolin (Manis crassicaudata), an endangered mammalian species under IUCN red list. In India, small population of Chines Pangolin (Manis pentadactyla) are also present in the eastern part and protected under the Wildlife (Protection) Act, 1972 as a schedule I species along with Indian Pangolin. In national and international market the Indian Pangolin are highly in trade principally for its meat and scales. In curbing illegal wildlife, trade of Indian Pangolin on national and international level wildlife DNA forensics plays an important role in the identification of species from the seized material. We received n = 15 wildlife seizures assumed to be the scales of Pangolin from different state forest and the custom department for molecular analysis. The seizures sequenced for two mitochondrial genes i.e. Cyt b and 16S rRNA, which are often used in wildlife DNA forensic to species identification. The sequences thus generated from these seizures compared to the NCBI database through blast search tool and our laboratory-generated references, yielding 100% similarity with Indian Pangolin. We identified twelve (n = 12) Cyt b and five (n = 5) 16S rRNA species specific SNPs, fixed in Indian Pangolin. This study shows, the importance of authenticated references, DNA sequence data availability, highlighting the application of DNA forensics in identifying species from scales.

Skinks are present under the Scincidae family, widely distributed species in Indian subcontinent. Uttarakhand is one of the hotspot where number of identified and unidentified skink species reported. Herein, we first time provided the 12S rRNA genetic reference database of four skink species, i.e. Eutropis macularia, Eutropis carinata, Asymblepharus himalayanus and Lygosoma punctata, in Rajaji Tiger Reserve (RTR), Uttarakhand (India). The identified four species belong to three different genera, where Eutropis carinata and Asymblepharus himalayanus listed Least Concern and Vulnerable in IUCN, respectively. Here, we collected tissue samples of four different skink species from Rajaji Tiger Reserve during field survey. After successful laboratory procedure, we compared obtained sequences with publically available genetic database and we observed four sequences matched with respective species. Furthermore, the evolutionary sequence divergence result revealed that the Eutropis carinata and Eutropis macularia are close to each other with 0.11 genetic distance. The present study indicates that the exact number and population distribution of skink species are unidentified; therefore, herein we suggest the proper screening of Uttarakhand population around should be investigated, further genetic study in combination with a good sampling strategy to investigate species biology and status for conservation program.

Pangolins are a group of eight endangered mammalian species included in the family Manidae (Order Pholidota) and divided into four each African (Arboreal species; Phataginus tetradactyla, Phataginus tricuspis, Ground dwelling species; Smutsia gigantea and Smutsia temminckii) and Asian (Ground dwelling; Manis crassicaudata, Manis pentadactyla, Manis javanica and Manis culionensis) species. The taxonomy of all the eight extant pangolin species based on molecular genetics studies, remains unresolved and poorly examined. The present study is to address this lacuna by studying the phylogenetic, taxonomic status and molecular dating of Indian pangolin with other six out of eight extant pangolins (Sunda pangolin possibly extinct) based on complete coding region of mitochondrial cytochrome b gene. Overall sequences divergence among pangolins ranged between 0.01 ± 0.01 and 0.26 ± 0.03, where within 'Manis' it ranged between 0.01 ± 0.01 and 0.14 ± 0.03. Cytochrome b sequences based ph...

Pangolins are the worlds most trafficked mammalian species classified under family Manidae and face severe threat of extinction, largely due to the illicit trade of its parts and products, especially scales, in international markets. Pangolin scales are believed to be used in Traditional Chinese Medicines (TCM) and meat is used as delicacies in restaurants. Of the eight extant species of pangolin, morphological discrimination is easy but the situation becomes precarious once the scales and meat samples are seized and it is difficult to identify species based on morphology in such cases. However, wildlife DNA forensics has played an instrumental role in the identification of species from such type of materials. The present study investigated that three mitochondrial genes (Cyt b, 16S rRNA, and 12S rRNA) clearly showed the variation among seven extant pangolin species (Manis culionensis; possibly extinct), whereas, maximum variation was obtained in cytochrome b when compared to another two mitochondrial genes. The present study revealed that obtained SNPs based on short sequence length (Intervals) within the three mitochondrial genes will be helpful to design the short molecular marker and species-specific probe that is used in wildlife forensic for identifying pangolin species from the degraded sample. We also advocate using more than one molecular marker for species discrimination so as to minimize any false identification of the mammal's species reported in the trade. Furthermore, data generated from the study would help in strengthening the DNA database of Indian pangolin species.

Certain articles of worship are commonly sold in Uttarakhand, India by the name Hatha Jodi, a root of a rare plant found only in a few parts of central India. The present work provides genetic proof that the Hatha Jodi sold in three local markets of Uttarakhand contained material from the Varanus species, species protected under the Indian Wildlife (Protection) Act, 1972. A total of eight samples were bought, two each from the local markets in Haridwar and Rishikesh, three from Dehradun and one from an online source (Amazon). The initial inspection confirmed that two of the samples were made of plastic material. Therefore only the other six samples were subjected to DNA analysis. DNA sequences were successfully obtained and matched with reference sequences available in NCBI Genbank database through BLAST search tool for species identification. All the six samples matched 100% with the Indian monitor lizard. The findings indicate how commercialization and the wildlife trade are playing a role in decline of the population of the Indian monitor lizard. If strong protection measures are not taken as soon as possible, the Indian monitor lizards will go Extinct very soon. Therefore, we suggest that the Government and Wildlife enforcement agencies take serious action against the illegal articles available in the local markets of Uttarakhand under the name Hatha Jodi. Further, the government needs to take legal action against offenders in other states in which the product is available for sale.

Please cite this article as: Rajpoot A, Bahuguna A, Kumar VP, Molecular study of globally threatened turtle species (families Trionychidae and Geoemydidae) of Uttarakhand and their relationships with other Indian populations: A wildlife forensic and conservation genetic approach,

In the present study, we summarize the status (seizures number, quantity, hotspot, trade rout & mode of transportation) of illegal trade of pangolin with seizures reported from 2009 to 2018 in India using available data from print and electronic media. Over the last decade ca.119 pangolin seizures were recorded and it is estimated that ca.7500 individuals perished in a decade. It is concluded that in India its northeastern part is the hub of trade of pangolins. From, here it moves into China and Myanmar though road and postal services.

Species identification from the samples obtained in wildlife crime cases usually presents a difficult challenge for forensic science investigators. The present paper describes a short study where a blood stain sample was recovered from an area outside the protected area network and used to determine a species identity. The mitochondrial DNA region of the questioned sample was amplified and sequenced using universal primers of cytochrome b gene (Cyt b) and 16S ribosomal RNA (16S rRNA) for species identity. The obtained sequencing results were compared with the most homologous sequences extracted from the NCBI-GenBank database. A phylogenetic tree was prepared with the aligned sequences to determine the species identity with strong bootstrap support. The mean distance and species score generated revealed that the grade of sequence similarity showed maximum homology (100 %) with the sequence obtained from the database. Based on the genetic analysis, the collected sample related to Indi...

Non-invasive sampling is one of the most authentic techniques for the genetic study of endangered and rare animal species. In the present study based on non-invasive samples, we give the preliminary genetic documentation of snake species by using cytochrome b (Cyt b) and cytochrome c oxidase subunit I (COI) universal mitochondrial primers from Uttarakhand (UK), India. We sampled n=11 shed skin of unknown snake species from four different locations in Uttarakhand, India. The success rate of genomic DNA isolation, PCR amplification, and sequencing from collected samples was 100%. Afterward, in the genetics analysis, 8 out of 11 samples matched with Least Concern ver3.1 Rat snake species, two samples paired with Checkered keelback snake, and one sample matched with Indian cobra. Subsequently, 149 (Cyt b) and 207 (COI) species-specific fixed SNPs were observed. The obtained interspecific sequences divergences based on two mitochondrial loci among three snake species also show the high v...

The research paper is an outcome of the fieldwork conducted in a small village of Sitarganj block; district UdhamSingh Nagar (Uttarakhand) among Tharu tribal community. The Tharu Tribe is indigenous people living in Tarai plain on the border of India and Nepal. The Tharu tribe is one of the most populous tribes of India and mostly populations (approximately 80%) of India are living in Khatima and Sitarganj tehsil of UdhamSingh Nagar district (Uttarakhand). Tharu is recognised as a scheduled tribe by the Government of India. The aim of this study to see the health status of Tharu population on the basis of blood parameters i.e. RBC, WBC, Hemoglobin (Hb), Platelet, Hematocrit, MCV, Rh factors etc and find out the factors affecting their health. Most of the populations were found to be suffering from Anaemia and Malnutrition. The percentage of Anaemia is more in women compared to men in Tharu population. These results indicate a lack of health awareness on healthy lifestyle and also they have no any idea about healthy nutritious diet etc. They are inadequate to take nutritious substances (vitamins, proteins, minerals etc) because health status of this community is directly proportional to economic (financial) and Socio-cultural conditions of these peoples. Therefore the present study provides important data, to the government and other agencies so is to control health problem of Tharu tribes in Sitarganj block, UdhamSingh Nagar District in Uttarakhand, India. This step will be helpful for improve their health status and development. This study also helpful to apply on other tribles community present in India and another part of the world.

Species identification and assign the geographic origin from processed products based on morphological traits is a challenging task in wildlife forensics due to lack of the reference specimens. Here, we report species identification and assign the geographical origin of a fully tanned animal skin using complete mtDNA cytochrome b gene. A nucleotide sequence of 1140 bp cytochrome b was generated from the DNA extracted from the small piece of skin from the inner ear (IEP-01). GenBank BLAST search of the unknown Cyt b (1140bp) sequence against the full range of published Rangifer tarandus has facilitated in identification of species and ascertaining the species of origin with high meta probability (100%). We determined that the seized unknown skin is wild reindeer (R.t. groenlandicus) and has been originated from Canada, where this Least Concern species under the IUCN red list. We propose to establish genetic database across the range of the species threatened due to illegal trade to determine hotspots of poaching.

Etymologically derived from Anglo-French vultur, Old French voutoir, voutre from Latin vultur, earlier voltur, and perhaps related to vellere- "to pluck, to tear"-the generic name ‘vulture’ does little justice to the immense ecological role that vultures play in maintaining the life support system of mother Earth. Given the wide range of topo-geographical features present in the State of Uttarakhand, all the 9 species of vultures of the Indian sub-continent are found here. However, the rapid and alarming decline in vulture population is a matter of great concern for all concerned. And therefore, there is an urgent need to identify the causes of decline and other threats that plague the vulture population in the country, especially in the State of Uttarakhand.