scholarly journals Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus): implications in population estimation and dynamics

2018 ◽  
Author(s):  
Shrushti Modi ◽  
Bilal Habib ◽  
Pallavi Ghaskadbi ◽  
Parag Nigam ◽  
Samrat Mondol
Keyword(s):  
Population Structure ◽  
Population Decline ◽  
Poor Quality ◽  
Individual Identification ◽  
Cumulative Probability ◽  
Cuon Alpinus ◽  
Non Invasive ◽  
Species Markers ◽  
Wild Dog ◽  
Physical Features

AbstractBackgroundThe Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information and landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on field-collected dhole faeces in four tiger reserves of the central Indian landscape in the state of Maharashtra, India. Further, we conducted preliminary analyses of dhole population structure and demography in the study area.ResultsWe tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63) and produced a cumulative probability of identity (unbiased) and probability of identity (sibs) value of 4.7×10−10 and 1.5×10−4, respectively. Our preliminary analyses of population structure indicated four genetic subpopulations in dholes. Qualitative analyses of population demography show signal of population decline.ConclusionOur results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. Our methods can be used to estimate dhole populations and assess population trends for this elusive, social carnivore.

scholarly journals Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7453
Author(s):  
Shrushti Modi ◽  
Bilal Habib ◽  
Pallavi Ghaskadbi ◽  
Parag Nigam ◽  
Samrat Mondol
Keyword(s):  
Statistical Power ◽  
Population Decline ◽  
Poor Quality ◽  
Individual Identification ◽  
Cuon Alpinus ◽  
Non Invasive ◽  
Individual Discrimination ◽  
Species Markers ◽  
Wild Dog ◽  
Physical Features

Background The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India. Results We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples. Conclusion Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

scholarly journals Identifying unknown Indian wolves by their distinctive howls: its potential as a non-invasive survey method

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sougata Sadhukhan ◽  
Holly Root-Gutteridge ◽  
Bilal Habib
Keyword(s):  
Reproductive Behaviour ◽  
Identification Accuracy ◽  
Individual Identification ◽  
Survey Method ◽  
Reliable Estimate ◽  
Mark Recapture ◽  
Test Dataset ◽  
Individual Level ◽  
Non Invasive ◽  
Supervised Classification Methods

AbstractPrevious studies have posited the use of acoustics-based surveys to monitor population size and estimate their density. However, decreasing the bias in population estimations, such as by using Capture–Mark–Recapture, requires the identification of individuals using supervised classification methods, especially for sparsely populated species like the wolf which may otherwise be counted repeatedly. The cryptic behaviour of Indian wolf (Canis lupus pallipes) poses serious challenges to survey efforts, and thus, there is no reliable estimate of their population despite a prominent role in the ecosystem. Like other wolves, Indian wolves produce howls that can be detected over distances of more than 6 km, making them ideal candidates for acoustic surveys. Here, we explore the use of a supervised classifier to identify unknown individuals. We trained a supervised Agglomerative Nesting hierarchical clustering (AGNES) model using 49 howls from five Indian wolves and achieved 98% individual identification accuracy. We tested our model’s predictive power using 20 novel howls from a further four individuals (test dataset) and resulted in 75% accuracy in classifying howls to individuals. The model can reduce bias in population estimations using Capture-Mark-Recapture and track individual wolves non-invasively by their howls. This has potential for studies of wolves’ territory use, pack composition, and reproductive behaviour. Our method can potentially be adapted for other species with individually distinctive vocalisations, representing an advanced tool for individual-level monitoring.

scholarly journals Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor‐quality samples

2021 ◽  
Vol 30 (6) ◽  
pp. 1457-1476
Author(s):  
Phillip A. Morin ◽  
Brenna R. Forester ◽  
Karin A. Forney ◽  
Carla A. Crossman ◽  
Brittany L. Hancock‐Hanser ◽  
...  
Keyword(s):  
Population Structure ◽  
Marine Species ◽  
Poor Quality ◽  
Harbor Porpoise ◽  
Coastal Marine

scholarly journals Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 144
Author(s):  
Ulrike H. Taron ◽  
Johanna L. A. Paijmans ◽  
Axel Barlow ◽  
Michaela Preick ◽  
Arati Iyengar ◽  
...  
Keyword(s):  
Genetic Data ◽  
Mitochondrial Genomes ◽  
Morphological Similarity ◽  
Cuon Alpinus ◽  
Extensive Analysis ◽  
Wild Dog ◽  
Canid Species ◽  
Reference Genomes ◽  
Lines Of Evidence ◽  
Complete Mitochondrial Genomes

The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.

scholarly journals Empowering conservation practice with efficient and economical genotyping from poor quality samples

2018 ◽  
Author(s):  
Meghana Natesh ◽  
Ryan W. Taylor ◽  
Nathan Truelove ◽  
Elizabeth A. Hadly ◽  
Stephen Palumbi ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Material ◽  
Cost Effective ◽  
Poor Quality ◽  
Wildlife Trade ◽  
List Type ◽  
High Quality ◽  
Conservation Practice ◽  
Queen Conch ◽  
Close Relatives

AbstractModerate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations.However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from labor medical settings. As a result, most genetic data from market or field settings is limited to easily amplified mitochondrial DNA or a few microsatellites.To enable genotyping in conservation contexts, we used next-generation sequencing of multiplex PCR products from very low-quality DNA extracted from feces, hair, and cooked samples. We demonstrated utility and wide-ranging potential application in endangered wild tigers and tracking commercial trade in Caribbean queen conch.We genotyped 100 SNPs from degraded tiger samples to identify individuals, discern close relatives, and detect population differentiation. Co-occurring carnivores do not amplify (e.g. Indian wild dog/Dhole) or are monomorphic (e.g. leopard). 62 SNPs from conch fritters and field-collected samples were used to test relatedness and detect population structure.We provide proof-of-concept for a rapid, simple, cost-effective, and scalable method (for both samples and number of loci), a framework that can be applied to other conservation scenarios previously limited by low quality DNA samples. These approaches provide a critical advance for wildlife monitoring and forensics, open the door to field-ready testing, and will strengthen the use of science in policy decisions and wildlife trade.

scholarly journals A set informative multiple autosomal markers for human identification: forensic research and population genetics analysis in a Chinese Xinjiang Hui group

2017 ◽  
Author(s):  
Tong Xie ◽  
Yuxin Guo ◽  
Ling Chen ◽  
Yating Fang ◽  
Yunchun Tai ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Genetic Relationships ◽  
Statistical Parameter ◽  
Strong Support ◽  
Personal Identification ◽  
Forensic Identification ◽  
Parameter Analysis ◽  
Individual Identification ◽  
Cumulative Probability ◽  
Discrimination Power

AbstractIn recent years, insertion/deletion (InDel) markers became a promising and useful supporting tool in forensic identification cases and biogeographic research field. In this study, 30 InDel loci were explored to reveal the genetic diversities and genetic relationships between Chinese Xinjiang Hui group and the 24 previously studied populations using varies methods such as forensic statistical parameter analysis, phylogenetic reconstruction, STRUCTURE analysis, multi-dimensional scaling, and principal component analysis. The observed heterozygosity and expected heterozygosity ranged from 0.1971 (HLD118) to 0.5092 (HLD 92), 0.2222 (HLD 114) to 0.5000 (HLD 6), respectively. Besides, after Bonferroni correction, no deviations from Hardy-Weinberg equilibrium tests were found at all 30 loci in Xinjiang Hui group. The cumulative probability of exclusion and combined discrimination power were 0.988849 and 0.99999999999378, respectively, which indicated that the 30 loci could be used as complementary genetic markers for paternity test and be qualified for personal identification in forensic cases. In this study, we found that Xinjiang Hui group had close relationships with most Chinese groups, especially Han populations, and all the results based on different genetic methods we used had a strong support for this finding. The 30 InDel loci has important significance in forensic identification research, in spite of this, for a better understanding of genetic background of the Chinese Xinjiang Hui group, molecular genetic genotyping at various genetic markers is necessary in future studies.Summary StatementWe report here, a promising Individual identification and population differentiation maker which could be used in forensic cases.

scholarly journals Validation of a noninvasive technique to quantify stress in northern bobwhite (Colinus virginianus)

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Jessica L Mohlman ◽  
Kristen J Navara ◽  
Michael J Sheriff ◽  
Theron M Terhune ◽  
James A Martin
Keyword(s):  
Colinus Virginianus ◽  
Population Decline ◽  
Endocrine System ◽  
Northern Bobwhite ◽  
Noninvasive Technique ◽  
Acth Challenge ◽  
Non Invasive ◽  
Management Actions ◽  
Hunting Dog ◽  
Corticosterone Metabolites

Abstract Examination of the endocrine system through non-invasive fecal sampling may improve population management more than using demographic indicators alone. By addressing the physiological mechanisms that are influencing fitness, management actions can be proactively developed to alleviate stressors. Proactive determination of vulnerable populations is critical for species of concern, such as the Northern Bobwhite (Colinus virginianus), which have suffered decades of population decline. We validated an assay to noninvasively measure the adrenocortical response of captive reared bobwhite through fecal corticosterone metabolites (FCM). All individuals received three sequential 48-hour treatments in which samples were collected every 4 hours, including a reference period, an adrenocorticotropic hormone (ACTH) challenge and a biological stressor (exposure to a hunting dog). Reference FCM values had a mean concentration of 16.75 pg/mg (95% CrI: 13.68, 19.91) with adrenocortical activity increasing by 73% for the duration of the ACTH challenge (29.00 pg/mg; CrI: 25.01, 33.78). FCM concentrations remained similar to that of the reference levels during the biological stressor (16.56 pg/mg; CrI: 13.33, 19.92). Our study validates the use of feces to detect changes in FCM levels in our subject species but also demonstrates the complexity of FCM and the importance of both physiological and biological validation prior to field implementation.

scholarly journals Population structure and spatial distribution of porbeagles (Lamna nasus) in Irish waters

2019 ◽  
Vol 76 (6) ◽  
pp. 1581-1590 ◽  
Author(s):  
Luke W J Cameron ◽  
William K Roche ◽  
Jonathan D R Houghton ◽  
Paul J Mensink
Keyword(s):  
Population Structure ◽  
Spatial Distribution ◽  
North Atlantic ◽  
Population Decline ◽  
The North ◽  
Aggregation Site ◽  
Show Evidence ◽  
Long Term Trends ◽  
Almost All

Abstract Porbeagles throughout the North Atlantic have experienced severe population decline through overfishing, with the northeastern population listed as critically endangered. Management of this population is constrained by the paucity of data on porbeagle population structure, distribution and behaviour in this region. Here we use a long-term (47 year) Irish capture-mark-recapture dataset to investigate the population structure, spatial distribution and seasonal movements of this species. From 1970–2017, a total of 268 sharks (9 recaptures) were ID tagged, with most individuals likely being juvenile based on length at maturity estimates (mean total length = 143.9 cm, SD = 35.4). Almost all captures were recorded at three distinct locations near angling hubs along the south, west and north coasts with catches peaking in August. Long-term trends in capture date indicated a shift towards earlier capture dates in the northern site (n = 153). Our findings suggest Irish waters may act as a persistent summer aggregation site for juveniles, which show evidence for seasonal site fidelity, returning to nearby locations between years. These findings demonstrate the utility of such programmes, which can be implemented, with minimal expense by engaging with the angling sector, to elucidate the population structure and distribution of wide-ranging fish species.

Recent records of dhole (Cuon alpinus, Pallas 1811) in Uttarakhand, Western Himalaya, India

Mammalia ◽  
2018 ◽  
Vol 82 (6) ◽  
pp. 614-617
Author(s):  
Ranjana Pal ◽  
Shagun Thakur ◽  
Shashank Arya ◽  
Tapajit Bhattacharya ◽  
Sambandam Sathyakumar
Keyword(s):  
Small Area ◽  
Western Himalaya ◽  
Camera Trap ◽  
Himalayan Region ◽  
Cuon Alpinus ◽  
Local Stakeholders ◽  
Ecological Parameters ◽  
Wild Dog

Abstract Camera trap photographs of solitary individuals of Asiatic wild dog or dholes (Cuon alpinus, Pallas 1811) have been recorded from Kheda Tal area in Uttarkashi district of Uttarakhand. This is the first photographic confirmation of the presence of this species in the Himalayan habitats of Uttarakhand. The presence of dholes here seems to be confined to a relatively small area of unprotected habitats affected by various anthropogenic uses. The population of endangered dhole is rapidly declining especially in Himalayan region. Thus, it is imperative that local stakeholders are aware of their presence, and it is highly recommended that investigations of the ecological parameters of this population are continued.

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