Document Type : Original Article

Authors

1 Maaty Biodiversity Conservation & Societal Research Organization, Kaulagarh, Dehradun- 248003 Uttarakhand, India

2 Molecular Systematics laboratory, Zoological Survey of India, NRC, 218, Kaulagarh Road, Dehradun-248195, Uttarakhand, India

3 Uttarakhand Biodiversity Board, 423, Indira Nagar Colony, Dehradun-248006 Uttarakhand, India

Abstract

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 variability in the Uttarakhand snake population. The current study based on the non-invasive genetic sampling approach showed its importance in biodiversity conservation, especially those species which are under the endangered and critically endangered category. The genetic reference database of snake species helpful in species management, population, evolutionary-based study, and wildlife forensic in the future.

Keywords

Preliminary genetic documentation of snake species through shed skin from Uttarakhand, India: A non-invasive genetic sampling approach

 

Ankita Rajpoot1, Ved Prakash Kumar1*, Archana Bahuguna2, Sargam Singh Rasaily3

1Maaty Biodiversity Conservation & Societal Research Organization, Kaulagarh, Dehradun- 248003 Uttarakhand, India

2Molecular Systematic laboratory, Zoological Survey of India, NRC, 218, Kaulagarh Road, Dehradun-248195, Uttarakhand, India

3Uttarakhand Biodiversity Board, 423, Indira Nagar Colony, Dehradun-248006 Uttarakhand, India

‎*Email:tiwaryved@gmail.com

Received: 6 May 2020 / Revised: 24 June 2020 / Accepted: 5 August 2020 / Published online: 5 August 2020. Ministry of Sciences, Research and Technology, Arak University, Iran.

How to cite: Rajpoot A., Kumar V.P., Bahuguna A., Rasaily S.S. (2021).Preliminary genetic documentation of snake species through shed skin from Uttarakhand, India: A non-invasive genetic sampling approach, 5(1), 81-91. https://doi.org/10.22120/jwb.2020.127147.1138

 

Abstract

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 variability in the Uttarakhand snake population. The current study based on the non-invasive genetic sampling approach showed its importance in biodiversity conservation, especially those species which are under the endangered and critically endangered category. The genetic reference database of snake species helpful in species management, population, evolutionary-based study, and wildlife forensic in the future.

 Keywords: Mitochondrial DNA and conservation, non-invasive genetic sampling, snakes, shed skin

 

Introduction

Non-invasive genetic sampling is a proportionately new approach for data-collection, has a great opportunity to explore the fauna in the wild. Through this approach, biologists can collect critical data of different wildlife animals without handling, capturing, or even observing individual animals (Mills et al., 2000; Carroll et al., 2018). Molecular techniques have proven to be crucial for identifying morphologically conservative species by extracting genetic material from hair, shed skin, feces, or other DNA source from non-invasive samples. The first time non-invasive genetic sampling was introduced as a method to obtain genetic samples from rare and elusive brown bears (Ursus arctos) in Europe in 1992 (Hoss et al., 1992; Taberlet & Bouvet, 1992) to study social structure in chimpanzees (Pan troglodytes) (Morin & Woodruff, 1992). According to a previous study, non-invasive samples do not require capture and handling of animals (Taberlet et al., 1999). This sampling has even greater value when the threatened and rare species are the objects of study.

Today DNA can be successfully recovered from diverse animal sources such as hair, feathers, shed skins, etc. Non-invasive genetic sampling is used as an essential tool in the study of large carnivore species and reptiles species such as snakes because it is difficult to handle for sample collection. It used in the detection of rare species to forensic applications (Waits, 2004); conservation management of rare or cryptic species (Piggott & Taylor, 2003), population estimation (Boulanger et al., 2004; McKelvey & Schwartz 2010; Caroline et al., 2019), accurate data collection (Paetkau, 2003) and addressing genotyping errors (Bonin et al., 2004).

Nonetheless, snakes are a group of reptiles with many derived morphological characters related to their peculiar behavior and lifestyle. Snakes belong to the squamate reptiles, characterized by the regular shedding of the epidermis' outer layers, also known as ecdysis (Landmann, 1986; Maderson et al., 1998). In snakes, the epidermis' superficial layers are detached as a single, coherent sheet, whereas other Squamates (lizards and geckos) shed multiple smaller flakes. Most living reptiles are covered by scales of different sizes, thickness, variety, and color, and these characterize other species (Maderson, 1985a & b; Landm

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