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 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 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 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.

Abstract P311: Effect of Non-Invasive Imaging on Cardiovascular Risk Factors and Downstream Testing: A Meta-Analysis of Randomized Controlled Trials

Circulation ◽  
2012 ◽  
Vol 125 (suppl_10) ◽  
Author(s):  
Seamus P Whelton ◽  
Khurram Nasir ◽  
Michael J Blaha ◽  
Daniel S Berman ◽  
Roger S Blumenthal
Keyword(s):  
Risk Factors ◽  
Risk Factor ◽  
Statistical Power ◽  
Controlled Trial ◽  
Meta Analysis ◽  
Cardiovascular Imaging ◽  
Significant Trend ◽  
Inclusion Criteria ◽  
Non Invasive ◽  
Randomized Controlled

Introduction: Non-invasive cardiovascular imaging has been proposed as a method to improve risk stratification and motivate improved patient and physician risk factor modification. Despite increasing use of these technologies there remains limited evidence documenting its effect on downstream testing and improvement in risk factor control. Hypothesis: Addition of the EISNER study to a prior meta-analysis will improve statistical power to demonstrate the downstream consequences of non-invasive cardiovascular imaging. Methods: A comprehensive literature search of the MEDLINE database (1966 through July 2011) was conducted. Major inclusion criteria required: 1) randomized controlled trial design, 2) participants with no known history of coronary heart disease or stroke, and 3) comparison of a group provided with results of a non-invasive imaging scan versus those without results. A total of eight trials with 4,084 participants met the inclusion criteria for this analysis. We analyzed the data using a random effects model to allow for heterogeneity. Results: Among imaging groups there was a significant increase in prescribing for statins (RR, 1.15; 95% CI, 1.01–1.32) and a non-significant trend for increased prescription of aspirin (RR, 1.15; 95% CI, 0.97–1.35), ACE/ARB (RR, 1.12; 95% CI, 0.96–1.31), and insulin (RR, 1.54; 95% CI, 0.75–3.18). There was a non-significant trend towards increased smoking cessation (RR, 1.35; 95% CI, 0.88–2.08). For downstream outcomes there was a non-significant increase in coronary angiography (RR, 1.20; 95% CI, 0.92–1.57), but not for revascularization (RR, 0.92; 95% CI, 0.55–1.53). There was no significant effect of imaging on the change in traditional risk factors. Limitations: There remains a limited number of trials in this important area. Therefore, trials included in this analysis use a variety of different imaging modalities and we were not able to pool the results based on appropriate clinical action (intensification at high risk and reduction at low risk). Conclusions: Non-invasive cardiovascular imaging leads to increased statin use, but associations with other downstream treatments and change in risk factors are not statistically significant. Our results highlight the limited amount of data for describing the downstream consequences after CAC testing.

scholarly journals Optical coherence tomography imaging of oral mucosa bullous diseases: a preliminary study

2020 ◽  
Vol 49 (2) ◽  
pp. 20190071
Author(s):  
Dario Di Stasio ◽  
Dorina Lauritano ◽  
Francesca Loffredo ◽  
Enrica Gentile ◽  
Fedora Della Vella ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Oral Mucosa ◽  
Statistical Power ◽  
Pemphigus Vulgaris ◽  
Invasive Technique ◽  
Optical Coherence ◽  
Non Invasive ◽  
Bullous Diseases ◽  
Subepithelial Layer

Objectives: Optical coherence tomography (OCT) is a non-invasive technique based on optical imaging with a micrometre resolution. The purpose of this study is to investigate the potential role of OCT in evaluating oral mucosa bullous diseases. Methods: two patients with bullous pemphigoid (BP) and one patient with pemphigus vulgaris (PV) were examined and images of their oral lesions were performed using OCT. Results: In OCT images, the BP blister has a clearly different morphology from the PV one compared to the blistering level. Conclusion: This exploratory study suggests that the OCT is able to distinguish epithelial and subepithelial layer in vivo images of healthy oral mucosa from those with bullous diseases, assisting the clinicians in differential diagnosis.The presented data are in accordance with the scientific literature, although a wider pool of cases is needed to increase statistical power. Histological examination and immunofluorescence methods remain the gold standard for the diagnosis of oral bullous diseases. In this context, the OCT can provide the clinician with a valuable aid both as an additional diagnostic tool and in the follow up of the disease.

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.

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.

scholarly journals Fragmented Integration: The Nova Scotia Steel and Coal Company and the Anatomy of an Urban-Industrial Landscape, c. 1912

2013 ◽  
Vol 22 (2) ◽  
pp. 139-158
Author(s):  
L. D. McCann
Keyword(s):  
Nova Scotia ◽  
Population Decline ◽  
Urban System ◽  
Poor Quality ◽  
Iron And Steel ◽  
Spatial Strategies ◽  
Industrial Landscape ◽  
Long Run ◽  
Regional Markets ◽  
And Control

This paper examines how forces of fragmentation within the Maritimes contribute a partial but important explanation of the urban-industrial collapse that marked the region in the early 20th century. Specifically, weaknesses that affected the spatial strategies of the vertically-integrated industrial giant, the Nova Scotia Steel and Coal Company, provide evidence of limited interaction within the Maritime urban system. Profits from exporting staples, pig iron, and steel products to foreign and national markets, although initially aided by tidewater location and control over all phases of production, were not sufficient to overcome, in the long-run, such forces of fragmentation as dispersed and limited regional markets, increased costs of producing poor quality resources, or the minimal presence of external economies. With "Scotia's" eventual demise, towns like Sydney Mines, Trenton, and New Glasgow suffered economic and population decline.

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