Noninvasive DNA-based species and sex identification of Asiatic wild dog (
                
                  
                
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Modi, Shrushti; Mondol, Samrat; Ghaskadbi, Pallavi; Hussain, Zehidul; Nigam, Parag; Habib, Bilal

doi:10.1007/s12041-018-1017-6

Cited by 12 publications

(11 citation statements)

References 12 publications

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“…We got a male biased sex-ratio (4:1) in this pilot study. While there is no conclusive information on dhole sex ratio across its range, our earlier study (Modi et al, 2018) in the same landscape has shown a male biased (M:F ratio of 3:1) sex ratio, and ecological study in southern India by Venkataraman (1998) suggested male biased packs. Future studies with extensive genetic sampling across this landscape would potentially provide more accurate sex ratio for dholes.…”

Section: Discussionmentioning

confidence: 57%

“…Once the initial temperature and multiplexing standardisations were performed using reference blood DNA samples, final standardisation was conducted with dhole faecal DNA. Species identification was performed for all field-collected faeces using specific mtDNA primers described in Modi et al (2018). PCR reactions were performed with four μl of hotstart taq mix (QIAGEN Inc., Hilden, Germany), four μM BSA, 0.5 μM of primer mix and three μl of DNA extract with conditions including initial denaturation (95 °C for 15 min); 50 cycles of denaturation (94 °C for 30 s), annealing (50 °C for 30 s) and extension (72 °C for 35 s); followed by a final extension (72 °C for 10 min).…”

Section: Methodsmentioning

confidence: 99%

“…Molecular sexing of the identified individuals was conducted using already developed multiplex sexing approach (Modi et al, 2018), where three sex chromosome specific markers (DBY, AHT-X40 and SRY) were combined to generate a three-band pattern for males and a single band for females. This approach reduces identification of ‘false negatives’ of males due to allelic dropout from the Y chromosome from poor quality samples.…”

Section: Methodsmentioning

confidence: 99%

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

Modi¹,

Habib²,

Ghaskadbi³

et al. 2019

PeerJ

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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.

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Section: Discussionmentioning

confidence: 57%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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

Modi¹,

Habib²,

Ghaskadbi³

et al. 2019

PeerJ

Self Cite

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“…A total of 623 samples were collected from six protected areas during the study period (2016–2019). We identified 590 dhole faeces through species-specific molecular assay 27 , attaining an amplification success of 94%. Using a panel of 12 microsatellite markers 26 , we generated a dataset of 349 genotypes attaining a success rate of 59.1%.…”

Section: Resultsmentioning

confidence: 99%

Genetic analyses reveal demographic decline and population differentiation in an endangered social carnivore, Asiatic wild dog

Modi

Mondol

Nigam

et al. 2021

Sci Rep

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Deforestation and agricultural intensification have resulted in an alarming change in the global land cover over the past 300 years, posing a threat to species conservation. Dhole is a monophyletic, social canid and, being an endangered and highly forest-dependent species, is more prone to the loss of favorable habitat in the Anthropocene. We determined the genetic differentiation and demographic history of dhole across the tiger reserves of Maharashtra using the microsatellite data of 305 individuals. Simulation-based analyses revealed a 77–85% decline in the major dhole sub-populations. Protected areas have provided refuge to the historically declining dhole population resulting in clustering with strong genetic structure in the remnant dhole population. The historical population decline coincides with the extreme events in the landscape over the past 300 years. The study highlights the pattern of genetic differentiation and diversity of a highly forest-dependent species which can be associated with the loss of forest cover outside tiger reserves. It also warrants attention to develop conservation plans for the remnant surviving population of dholes in India.

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“…Fecal molecular biotechnology provides a rapid and dependable way of sampling endangered animals [11–14]. In addition, with the development of molecular biology technology, fecal DNA is extensively used in genetic biology studies for species identification [15–17], individual identification [18–20], sex identification [21–25], population genetic structure [26–28], and genetic diversity evaluation [29]. However, fecal sampling has some problems, such as poor fecal DNA isolation quality and low success rate of PCR amplification [30].…”

Section: Introductionmentioning

confidence: 99%

Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

Zhang¹,

Wei²,

Dong³

et al. 2019

BMC Biotechnol

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BackgroundTo avoid destructive sampling for conservation and genetic assessment, we isolated the DNA of clam Cyclina sinensis from their feces. DNA electrophoresis and PCR amplification were used to determine the quality of fecal DNA. And we analyzed the effects of different conditions on the degradation of feces and fecal DNA.ResultsThe clear fecal DNA bands were detected by electrophoresis, and PCR amplification using clam fecal DNA as template was effective and reliable, suggesting that clam feces can be used as an ideal material for noninvasive DNA isolation. In addition, by analyzing the effects of different environmental temperatures and soaking times on the degradation of feces and fecal DNA, we found that the optimum temperature was 4 °C. In 15 days, the feces maintained good texture, and the quality of fecal DNA was good. At 28 °C, the feces degraded in 5 days, and the quality of fecal DNA was poor.ConclusionsThe clam feces can be used as an ideal material for noninvasive DNA isolation. Moreover, the quality of fecal DNA is negatively correlated with environmental temperature and soaking time.

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Noninvasive DNA-based species and sex identification of Asiatic wild dog ( $${\varvec{Cuon~alpinus}}$$ C u o n a l p i n u

Cited by 12 publications

References 12 publications

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

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

Genetic analyses reveal demographic decline and population differentiation in an endangered social carnivore, Asiatic wild dog

Fecal DNA isolation and degradation in clam Cyclina sinensis: noninvasive DNA isolation for conservation and genetic assessment

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