Genetic assessment of captive breeding program of Indian Pangolin: implications for conservation and management.

BACKGROUND: Captive breeding programs play a vital role in conservation of threatened species, necessitating an understanding of genetic diversity among captive individuals to ensure long-term genetic viability, appropriate mate selection, and successful reintroduction to native habitats. METHODS AND RESULTS: We did not observe any recent genetic bottleneck, and population showed moderate genetic diversity. The estimated effective population size, representing individuals capable of contributing genetically to future generations, was estimated as 18.6 individuals (11.4-35.1 at 95% CI). Based on the genetic make-up and allelic diversity, we found seventeen pangolins (11 females and 6 males) were genetically unrelated and relatively more potent than others. CONCLUSION: In this study, we evaluated the captive breeding program of the Indian pangolin population at the Pangolin Conservation Breeding Centre in Nandankanan Zoological Park, Bhubaneswar, Odisha. We highlight the significance of genetic monitoring within the captive population of Indian pangolin for preserving genetic diversity and ensuring the long-term survival of the species. We established the genetic profiles of all 29 pangolins and identified 17 pangolins to be prioritized for enhanced breeding and future zoo exchange programs. We appreciate the zoo authorities for promoting genetic assessment of pangolin for better and more effective monitoring of the captive breeding of the endangered Indian pangolin.

Isotope Engineered Fluorinated Single and Bilayer Graphene: Insights into Fluorination Selectivity, Stability, and Defect Passivation.

Tailoring the physicochemical properties of graphene through functionalization remains a major interest for next-generation technological applications. However, defect formation due to functionalization greatly endangers the intrinsic properties of graphene, which remains a serious concern. Despite numerous attempts to address this issue, a comprehensive analysis has not been conducted. This work reports a two-step fluorination process to stabilize the fluorinated graphene and obtain control over the fluorination-induced defects in graphene layers. The structural, electronic and isotope-mass-sensitive spectroscopic characterization unveils several not-yet-resolved facts, such as fluorination sites and CF bond stability in partially-fluorinated graphene (F-SLG). The stability of fluorine has been correlated to fluorine co-shared between two graphene layers in fluorinated-bilayer-graphene (F-BLG). The desorption energy of co-shared fluorine is an order of magnitude higher than the CF bond energy in F-SLG due to the electrostatic interaction and the inhibition of defluorination in the F-BLG. Additionally, F-BLG exhibits enhanced light-matter interaction, which has been utilized to design a proof-of-concept field-effect phototransistor that produces high photocurrent response at a time <200 µs. Thus, the study paves a new avenue for the in-depth understanding and practical utilization of fluorinated graphenic carbon.

Free-ranging dogs are seriously threatening Himalayan environment: delineating the high-risk areas for curbing free-ranging dog infestation in the Trans-Himalayan region.

It is becoming more widely recognised that free-ranging dogs, which have a nearly global distribution, threatening native wildlife. Their increasing population and spread to new areas is of growing concern for the long-term viability of wildlife species. Hence, it is imperative to understand the factors responsible for their infestation and map areas where native species are most vulnerable. Using the random forests algorithm, we modelled the free-ranging dog infestation in the Trans-Himalayan region to pinpoint the high-risk areas where free-ranging dogs are threatening the native wildlife species. We found that the likelihood of free-ranging dog occurrence is most in valley regions and up to 4000 m, often in proximity to roads. Our results also indicated that free-ranging dog prefers areas with wildlife near to protected areas. The predictor variables, such as potential evapotranspiration of the coldest quarter, distance to protected areas, elevation, distance to roads, and potential evapotranspiration of the driest quarter, significantly influence the distribution of the free-ranging dogs. We found that within the Ladakh region of the Trans-Himalayan area, the high-risk zones for free-ranging dogs are located in and around Hemis National Park, Karakoram Wildlife Sanctuary, and Changthang Wildlife Sanctuary. While, in the Lahaul and Spiti region the high-risk areas encompass Pin Valley National Park, Inderkilla National Park, Khirganga National Park, Kugti Wildlife Sanctuary, and several other protected areas. We identified the potentially high-risk areas for implementing strategies to mitigate the possible impact of free-ranging dogs on native wildlife of the Himalayas. Hence, the identified high priority areas can be used for implementing actions for controlling the population growth and further preventing the infestation of the free-ranging dogs into the new areas.

The Sela macaque (Macaca selai) is a distinct phylogenetic species that evolved from the Arunachal macaque following allopatric speciation.

Arunachal macaque (M. munzala) is an endangered and recently discovered cercopithecine primate from Western Arunachal Pradesh, India. On genetic analyses of Arunachal macaques, we observed spatially distributed substantial inter-species genetic divergence among the samples collected from Arunachal Pradesh. The results suggested that Arunachal macaque evolved into two phylogenetic species about 1.96 mya following allopatric speciation by means of Sela mountain pass in Arunachal Pradesh, India. We describe - Sela macaque (M. selai) as a new macaque species that interestingly exhibited high intra-specific genetic variation and also harbors at least two conservation units. Further, we report the past demographic trajectories and quantify genetic variation required for taxonomic clarification. The present study also identifies gap areas for undertaking surveys to document the relic and unknown trans-boundary populations of macaques through multinational, multi-lateral cross border collaboration.

DNA matchmaking in captive facilities: a case study with tigers.

BACKGROUND: Genetics driven interventions if adopted in conservation breeding projects may enhance the overall success by prioritizing breeding among genetically most competent individuals and delaying or completely diminishing the ill effects of inbreeding. METHODS AND RESULTS: In the present study, we investigated genetic make-up of 15 tigers housed at five different captive facilities of West Bengal in India and report the moderate level of genetic variation. We identified five tigers based on individual genetic attributes that may be prioritized for future breeding or animal exchange programmes. The occurrence of first and second order related individuals in captivity require management attention and they should be paired considering their immediate genetic background. CONCLUSION: Considering tiger as a case study, we highlight the use of genetic assessment and necessity to validate the studbook records in formulating adaptive management strategies for long-term conservation and management of species of interest.

Population genetics of Sambar (Rusa unicolor) from the Western Himalayas: preliminary findings.

BACKGROUND: The sambar (Rusa unicolor) is one of the largest deer distributed across diverse habitats of India and threatened due to habitat loss, changes in the land-use patterns, illegal poaching, and anthropogenic disturbances. Here, we report the first population genetics account of sambar deer from the Western Himalayas. METHODS AND RESULTS: We observed relatively compromised genetic diversity (π = 0.0008 ± 0.0006 at mtDNA and Ho = 0.499 ± 0.056 at nDNA). We identified 60 unique individuals using a select panel of seven loci (PID sib cum 1.60E-03). Bayesian skyline plot showed a stable demographic history since the past 8 kyr with a decline in recent years. The population lacked genetic structuring, likely due to the contiguous distribution and large dispersal patterns of sambar. CONCLUSION: The preliminary findings are valuable in exploring the utility of genetic diversity in monitoring the sambar population, estimating density following capture-recapture analysis, and aid to the conservation planning of sambar in large landscapes.

Population genetic attributes of common leopard (Panthera pardus fusca) from Uttarkashi, Western Himalayas.

BACKGROUND: The common leopard (Panthera pardus fusca), which persists in most of its historic range, is experiencing steady population decline due to habitat loss, anthrophonic disturbances, illegal poaching for their body parts, and retaliatory killings in response to the leopard-human conflicts. METHODS AND RESULTS: We analysed 143 scats samples and identified 32 unique leopards following a selected panel of seven loci with cumulative PID sibs 5.30E-04. We observed moderate genetic diversity at nuclear (Ho = 0.600 ± 0.06) and mitochondrial markers (Hd = 0.569 ± 0.009; π = 0.001 ± 0.0002) and found sub-structuring in the leopard population at Uttarkashi, Western Himalayas. CONCLUSIONS: The present study exhibits the utility of non-invasive genetics in monitoring the leopard population and paves the path to investigate population genetic parameters in further studies.

Large-scale genomic analysis reveals the genetic cost of chicken domestication.

BACKGROUND: Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS: We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION: This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Evaluation of genetic polymorphisms at 21 autosomal STR loci in Ramgharia Sikh population of Punjab, India.

BACKGROUND: STR (Short Tandem Repeat) markers are highly polymorphic markers, which are widely used in forensics DNA analysis and aid to ascertain unique genotype profiles of individuals and determine the genetic diversity of the given population. AIM: In the present study, an attempt has been made to evaluate the population genetic diversity of the Ramgharia Sikh population of Punjab, India, using 21 autosomal STR loci (D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, and D2S1338) to augment the emerging forensic database related to the indigenous population of India. SUBJECTS AND METHODS: For generation of the database, 200 (blood on FTA card) samples were obtained from genetically unrelated Ramgharia Sikhs residing in the state of Punjab. Twenty-one autosomal STR markers were analysed using the Globalfiler® PCR amplification kit. RESULTS: With the help of various statistical tools, a total of 232 alleles were observed and 11.048 ± 1.284 (mean ± standard deviation) alleles per locus were recorded. No locus deviated from Hardy Weinberg Equilibrium. SE33 locus was found to be the most polymorphic and exhibited the highest discrimination power, that is, 0.99. Moreover, results further indicated that Ramgharia Sikhs of Punjab showed a high affinity with Bhils of Madhya Pradesh (India). Thus, the studied population showed genetic proximity with the geographically close populations of India and showed significant genetic variations with distant populations, which was evident from the UPGMA tree and Principal Component Analysis plot. CONCLUSION: Overall, the 21 autosomal STRs were found to be polymorphic in the Ramgharia population and suitable for forensic casework and studies on population genetics.

Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids.

Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.

Species identification from seized animal oil: a case study of suspected Gangetic dolphin (Platanista gangetica).

Poaching of South Asian river dolphins is considered one of the main reasons for the rapid decline of their natural populations. To curb the escalated rate of poaching, high numbers of oil and meat seizures are recovered with subsequent convictions by the law enforcement agencies. In this connection, we report a case where suspected animal oil was confiscated by the forest official of West Bengal. We extracted DNA and successfully amplified partial fragments of Cytb and 16S rRNA mitochondrial genes. The generated sequences identified that the seized oil belonged to the Ganges river dolphin (Platanista gangetica) which is protected as Schedule I under the Wildlife (Protection) Act, 1972 of India and listed as "Endangered" under IUCN and APPENDIX I in CITES. In routine case work analysis, oil samples are not preferred for forensic DNA investigation due to low DNA yield and presence of inhibitors or contaminants leading to high failure rate. However, the present study generates hope for identifying species from seized animal oil and supports law enforcement in successful prosecution of the case.

Key genetic and forensic attributes of Uttarakhand population of India.

The present study aimed to investigate the genetic and forensic attributes of Uttarakhand population based on 20 autosomal STR loci implemented in PowerPlex® 21 System. Results unveiled 219 alleles ranging from 6 (TH01, TPOX) to 20 (Penta E). Forensic analysis revealed locus Penta E as the most polymorphic and discriminative loci, whereas genetic analysis indicated presence of higher heterozygosity within population. Phylogenetic analysis indicated higher genetic affinity of Uttarakhand population with the neighbouring Himachal Pradesh population. Overall, the study indicates that the PowerPlex® 21 System is suitable for genetic and forensic analysis in Uttarakhand population.

Genetic monitoring of Himalayan goral (Naemorhedus goral) from Western Himalayas, India.

BACKGROUND: Himalayan goral (Naemorhedus goral), solitary cliff-dwelling species and are distributed throughout the Indian Himalayan region. Its populations across the range are facing severe threats due to habitat loss, fragmentation and changes in the land-use patterns by various anthropogenic activities. METHODS AND RESULTS: We carried out genetic analyses of Himalayan goral using the mitochondrial control regions and microsatellite loci (n = 10) in the Uttarkashi district of Uttarakhand. We reported a moderate genetic diversity at nuclear (Ho 0.602 ± 0.057) and mitochondrial markers (Hd-0.6931 ± 0.053; π-0.0048 ± 001). Bayesian skyline plot indicates a sharp decline in the goral population in the last 100 years. CONCLUSIONS: Our results indicate the population of Himalayan goral in Uttarkashi is under panmictic condition, plausibly due to long-ranging behaviour. The present study laid the foundation for future non-invasive genetics monitoring and detailed population genetic assessment of goral from the entire range in the Western Himalayas.

Highly sensitive broadband binary photoresponse in gateless epitaxial graphene on 4H-SiC.

Due to weak light-matter interaction, standard chemical vapor deposition (CVD)/exfoliated single-layer graphene-based photodetectors show low photoresponsivity (on the order of mA/W). However, epitaxial graphene (EG) offers a more viable approach for obtaining devices with good photoresponsivity. EG on 4H-SiC also hosts an interfacial buffer layer (IBL), which is the source of electron carriers applicable to quantum optoelectronic devices. We utilize these properties to demonstrate a gate-free, planar EG/4H-SiC-based device that enables us to observe the positive photoresponse for (405-532) nm and negative photoresponse for (632-980) nm laser excitation. The broadband binary photoresponse mainly originates from the energy band alignment of the IBL/EG interface and the highly sensitive work function of the EG. We find that the photoresponsivity of the device is > 10 A/W under 405 nm of power density 7.96 mW/cm2 at 1 V applied bias, which is three orders of magnitude greater than the obtained values of CVD/exfoliated graphene and higher than the required value for practical applications. These results path the way for selective light-triggered logic devices based on EG and can open a new window for broadband photodetection.

Evaluation of genetic polymorphism at 20 autosomal STR loci in Rajput population of Himachal Pradesh, India.

In the present study, genetic diversity indices and forensic parameters of Rajput population of Himachal Pradesh, India, were obtained at 20 autosomal short tandem repeat (STR) loci included in the PowerPlex® 21 System (Promega, USA). With 227 alleles and 11.35 ± 0.89 alleles per locus, none of the locus deviated from the Hardy-Weinberg equilibrium (HWE). The most polymorphic and discriminative locus was Penta E. Phylogenetic tree showed high genetic affinity of Rajput population of Himachal Pradesh with Rajputs of Madhya Pradesh and Yadav of Bihar. Overall, the tested 20 autosomal STRs were polymorphic in Rajput population and found suitable in forensic casework and population genetic studies.

Assessment of genetic polymorphism at 20 autosomal STR loci in scheduled caste population of Himachal Pradesh.

In this study, we evaluated the genetic diversity indices and forensic parameters of scheduled caste population of Himachal Pradesh, India, at 20 autosomal STR loci. Altogether, 233 alleles were observed with an average of 11.65 ± 0.88 alleles per locus. In exception of locus D13S317, no loci deviated from Hardy Weinberg equilibrium. Locus Penta E was found to be the most polymorphic and discriminative loci. The combined power of discrimination and the combined power of exclusion were 1 and 0.999. Further, we established the phylogenetic relationship between the scheduled caste population of Himachal Pradesh and 14 other populations of India. We found 20 autosomal STR loci used in the present study were polymorphic and can be used in population genetic studies and forensic related case works.

Pangolin Indexing System: implications in forensic surveillance of large seizures.

Demand for pangolin scales in East Asia has increased dramatically in the past two decades, raising concern to the pangolin survival and bringing them to the brink of local extinction. Enumerating the number of individuals from the seized pangolin scales primarily goes undocumented, mostly due to the unavailability of the appropriate methods. In this study, we developed a Pangolin Indexing System, a multi-locus STR panel of eight dinucleotide microsatellites that showed promising results in individualization and assignment of scales into Chinese and Indian pangolins. The combined power of exclusion was 0.83 and 0.99 for Chinese and Indian pangolin. The select panel of eight polymorphic STRs exhibited the cumulative probability of identity 3.7 × 10-9 for Indian pangolin and 3.6 × 10-7 for Chinese pangolin and identified 51 unique genotypes from the 74 scales selected from the four pangolin seizures. The study demonstrated the first report of cross-species validation of STRs developed from Malayan pangolin to Indian pangolin and showed the potential application of Pangolin Indexing System in screening of large seizures through DNA profiling from the scales of Indian and Chinese pangolin.

Genetic polymorphism of 20 autosomal short tandem repeats (STRs) in Himachal Pradesh population, India.

Genetic diversity indices and forensic parameters at 20 autosomal short tandem repeat (STR) loci were evaluated in 233 unrelated individuals of Himachal Pradesh, India. In total, 255 alleles were observed with an average of 11.25 ± 0.88 alleles per locus. None of the loci deviated from Hardy Weinberg Equilibrium. The most polymorphic and discriminative locus was Penta E. The combined power of exclusion and the combined power of discrimination were found to be 0.99 and 1. Additionally, the genetic relationship of the Himachal Pradesh population with the populations of the neighboring state was also investigated. All the STR loci were found polymorphic, and the select panel of STRs was found suitable for population genetic studies and forensic analysis.

Species dilemma of musk deer (Moschus spp) in India: molecular data on cytochrome c oxidase I suggests distinct genetic lineage in Uttarakhand compared to other Moschus species.

Musk deer are of high conservation priority owing to poaching pressure because of its musk pod. Representation of musk deer status using genetics is poorly documented in India, and it is not confirmed as to how many species of musk deer are present. We characterize for the first time, the genetic diversity of musk deer from Uttarakhand using Cytochrome Oxidase sub-unit (COI) gene (486 bp) and compared with the data available for other species. Results revealed the presence of six haplotypes in the Uttarakhand population amongst 17 sequences. Of these, 12 sequences shared the single haplotype. The intra-species sequences divergence was 0.003-0.017, whereas divergence with other species of musk deer was 0.071-0.081. Bayesian phylogenetic tree revealed that samples from Uttarakhand formed a separate clade with respect to other species of musk deer, whereas three species distributed in China clustered in the same clade and showed low sequences divergence, i.e., 0.002-0.061. Because of different ecomorph reported, we suggest using the barcoding based approach for inter and intra-species distinction and delineating species boundaries across the range for effective conservation. Besides, systematic classification, DNA barcoding would also help in dealing wildlife offence cases for disposal of the legal report in court.

Identifying the tick Amblyomma javanense (Acari: Ixodidae) from Chinese pangolin: generating species barcode, phylogenetic status and its implication in wildlife forensics.

Zoonotic diseases transmitted through ticks and other ectoparasites often travel across the globe with illegally traded wildlife parts and products. In this study, we analyzed a confiscated case of pangolin scales and observed a few dead ticks attached. On genetic analysis, the pangolin scales were identified to be originated from Chinese pangolin (Manis pentadactyla), an IUCN listed Critically Endangered species, and ticks were identified as Amblyomma javanense. Here, we provide the first authentic physical record of A. javanense from India as a parasite of Chinese pangolin and also generated its species DNA barcode that may be useful for biologists working on ticks in species validation and constructing phylogenies across the globe.