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Assessment of bias in morphological identification of carnivore scats confirmed with molecular scatology in north-eastern Himalayan region of Pakistan.

ABSTRACT: Scats are often used to study ecological parameters of carnivore species. However, field identification of carnivore scats, based on their morphological characteristics, becomes difficult if many carnivore species are distributed in the same area. We assessed error rates in morphological identification of five sympatric carnivores' scats in north-eastern Himalayan region of Pakistan during 2013-2017. A sample of 149 scats were subjected to molecular identification using fecal DNA. We used a confusion matrix to assess different types of errors associated with carnivore scat identification. We were able to amplify DNA from 96.6% (n = 144) of scats. Based on field identification of carnivore scats, we had predicted that out of 144 scats: 11 (7.6%) scats were from common leopard, 38 (26.4%) from red fox, 29 (20.1%) from Asiatic jackal, 37 (25.7%) from yellow throated martin, 14 (9.7%) from Asian palm civet and 15 (10.4%) from small Indian civet. However, molecular identification revealed and confirmed nine were scats (6.24%) from common leopard, 40 (27.8 %) from red fox, 21 (14.6%) from Asiatic jackal, 45 (31.25%) from Asian palm civet, 12 (8.3%) scats from small Indian civet, while 11 scats (7.6%) were found from Canis lupus Spp., three (2%) from dog, one (0.7 %) scat sample from porcupine, and two (1.4%) from rhesus monkey. Misidentification rate was highest for Asian palm civet (25.7%), followed by red fox (11.1%) and Asiatic jackal (9.7%) but least for common leopard scats (4.2%). The results specific to our study area concur with previous studies that have recommended that carnivore monitoring programs utilize molecular identification of predator scats. Using only morphological identification of scats can be misleading and may result in wrong management decisions.

SUBMITTER: Akrim F

PROVIDER: S-EPMC6052849 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Assessment of bias in morphological identification of carnivore scats confirmed with molecular scatology in north-eastern Himalayan region of Pakistan.

Akrim Faraz F Mahmood Tariq T Max Tamara T Nadeem Muhammad Sajid MS Qasim Siddiqa S Andleeb Shaista S

PeerJ 20180716

Scats are often used to study ecological parameters of carnivore species. However, field identification of carnivore scats, based on their morphological characteristics, becomes difficult if many carnivore species are distributed in the same area. We assessed error rates in morphological identification of five sympatric carnivores' scats in north-eastern Himalayan region of Pakistan during 2013-2017. A sample of 149 scats were subjected to molecular identification using fecal DNA. We used a conf ...[more]

PMID: 30038872

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Project description:BACKGROUND:Spirometra erinaceieuropaei is a diphylobothriid tapeworm with a complex life-cycle including definitive, intermediate and paratenic (transport) hosts. Multiple routes of parasite transmission often make it impossible to determine what type of host a specific infected animal is considered to be. Spargana larvae cause sparganosis, a severe food- and water-borne disease mainly found in Asia. In Poland, Spirometra sp. was reported in large carnivores in Bia?owie?a Primeval Forest for the first time in the 1940s and was recently confirmed as S. erinaceieuropaei in several mammals and snakes using molecular methods. METHODS:In total, 583 carcasses of 9 carnivore species were necropsied between 2013 and 2019 in north-eastern (NE) Poland. The larvae of S. erinaceieuropaei (spargana) were isolated from subcutaneous tissue, counted, and preserved for genetic analyses. We calculated the prevalence and intensity of infection. To assess spatial variation in S. erinaceieuropaei infection probability in NE Poland, we applied a generalized additive model (GAM) with binomial error distribution. To confirm the species affiliation of isolated larvae, we amplified a partial fragment of the 18S rRNA gene (240 bp in length). RESULTS:Spirometra larvae were found in the subcutaneous tissue of 172 animals of 7 species and confirmed genetically as S. erinaceieuropaei. The overall prevalence in all studied hosts was 29.5% with a mean infection intensity of 14.1 ± 33.8 larvae per individual. Native European badgers and invasive raccoon dogs were characterized by the highest prevalence. An analysis of parasite spread showed a spatially diversified probability of infection with the highest values occurring in the biodiversity hot spot, Bia?owie?a Primeval Forest. CONCLUSIONS:Our study revealed that various mammal species (both native and non-native) can serve as S. erinaceieuropaei reservoirs. The frequency and level of infection may differ between selected hosts and likely depend on host diversity and habitat structure in a given area. Further studies are needed to assess the distribution of the parasite throughout Europe and the environmental and biological factors influencing infection severity in wild mammals.

Project description:The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5 agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85 alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596) types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties (0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice germplasm in NE India should consider saving rice varieties representing different types with specific emphasis given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice varieties in NE India is crucial for maintaining future food security in the changing world.

Dataset Information

Assessment of bias in morphological identification of carnivore scats confirmed with molecular scatology in north-eastern Himalayan region of Pakistan.

Publications

Assessment of bias in morphological identification of carnivore scats confirmed with molecular scatology in north-eastern Himalayan region of Pakistan.

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