Wildlife genetics and its applications for snow leopard conservation in Nepal

By Dibesh Karmacharya

As they gracefully navigate through the high Himalayan mountain landscape, the elusive and endangered snow leopards exemplify nature’s greatest gift to all of us. Snow leopards are found throughout the Himalayan region. These magnificent creatures are the quintessential top carnivore, often the main balancing factor for all the downstream preys; sustaining the fine ecological balance.

Nepal’s high Himalaya region provides excellent refuse to snow leopards. It is estimated that there are close to 400 snow leopards in Nepal spread throughout pockets of various conservation areas. But the exact number of this species in Nepal remains to be studied. There are various reasons why experts believe the exact number of snow leopard found in Nepal could be much lower than the estimated number. Snow leopard’s long-term viability has continuously been threatened by conflict with locals because of livestock depredation-sometimes resulting in retaliatory killings. Loss of habitat and declining prey numbers due to their preferred grazing areas being encroached for livestock usage are also some of the major contributing factors for snow leopard’s declining numbers.

Furthermore, there is active illicit trans-border market for wildlife animal parts in the northern frontiers of Nepal and Tibet; as a result poaching has become widespread. As substitute to tiger bones and other tissue parts, Asian traditional medicine market has an increasing demand for bones and other tissue parts of endangered felids such as snow leopard. This has exacerbated the threat of snow leopards in Nepal.

Prior to any effective conservation strategy being designed and implemented, it is crucial to gather reasonable data on estimation of existing abundance and distribution of snow leopard in Nepal. However because of elusive, solitary nature of snow leopard and its rugged rocky terrain habitat, information available is sparse and inadequate on their actual distribution and population status.

Majority of snow leopard studies have consisted of surveys that relied upon sign (e.g. pugmarks, scrapes and scats), interviews with local inhabitants, and camera trapping. However, these approaches have several disadvantages including the need for extended time in the field (>40–50 days), the difficulty of setting camera traps in snow leopard habitat, and the high cost of field work in remote areas. Hence additional methods to supplement sign surveys and camera trapping therefore become essential for effective monitoring of snow leopards.

Genetic analysis has become an effective and popular method and is used in all aspects of wildlife biology and conservation. Since portions of genome of every individual is unique; use of genetic tools yield highly specific information which in turn can be used in various aspects of wildlife biology such as migration rates, population size, bottlenecks and kinship. Genetic analysis can also be utilised to identify species, sex and individuals; and provide insight on its population trend as well as to gather other taxonomic level information. Since it is infeasible to enumerate populations of low density, wide-ranging and elusive species like snow leopards, non-invasive methods of detecting snow leopards by using scat or fecal sample have been frequently employed to infer estimations on the number of individuals in a certain area; moreover, this method has also been favoured for eliminating the need for direct interactions (invasive) that could potentially have adverse effects on animal welfare.

Most of the non-invasive wildlife genetics methods involve extracting genetic material (DNA) from the fecal matter, and then subjecting that DNA for species and sex identification molecular assay-mainly Polymerase Chain Reaction (PCR). Same DNA can also be subjected to DNA fingerprinting assay to derive individual identification and characterisation. Phylogenetics can also be carried out to draw evolutionary relatedness among populations found at different areas, thereby helping us draw “genetic movement map” and figure out whether there is any gene flow between separate populations. So with the molecular or genetic technique, not only we will be able to tell whether fecal matter or any biological sample belongs to certain species, say snow leopard, but also we will be able to tell whether it is male or female and also whether two samples are from the same individual or are coming from different individuals.

The applications and utilisation of such information are not only confined to population estimation and trend analysis, but they can also be used to draw complete genetic relationship maps between various populations and thereby help us comprehend wildlife habit and habitat of endangered species like snow leopards in landscape level- this whole new field of wildlife biology is also known as Landscape genomics. Molecular based wildlife forensics can be a very effective tool to fight against poaching. DNA fingerprinting as it is commonly known can be used to identify an unknown tissue or any animal part and see if it belongs to any endangered species.

Currently, efforts are underway to initiate genetic based wildlife research in Nepal. The Center for Molecular Dynamics Nepal, based in Kathmandu, has embarked into this field in collaboration with various wildlife conservation related governmental and non-governmental organisations. It is very important that our policy makers, academicians and conservation enthusiasts are all on board to review our current conservation efforts more closely and utilise new upcoming technologies to gather accurate information, which in turn will help us in designing effective conservation strategies. In that context, the currently available wildlife genetics tools can be polished to fit Nepal’s needs in her conservation efforts.

(Dibesh Karmacharya is the International Director of the Center for Molecular Dynamics Nepal and can be reached at dibesh@cmdn.org This e-mail address is being protected from spambots. You need JavaScript enabled to view it )


The first snow leopard was successfully photographed in Tuva, Russia

RIA Novosti, translated by Heda Jindrak
March 12, 2010

permanent link: http://en.tuvaonline.ru/2010/03/12/5400_snowleopard.html

The participants in the first Russian-Mongolian expedition for the study of groupings of irbis (snow leopard), which took place from February 20 to March 7 on the Tsagan-Shibetu ridge (western Tuva), made the first photos of this rare predator in the republic, as announced by the World Wildlife Fund (WWF) of Russia.

During the field research the members of the expedition, which included specialists from the “Uvsu-Nur depression” nature reserve (Russia), from the administration of especially protected natural territories of the Ubsu-Nuur lake basin (Mongolia), and from the Institute of Biology of Mongolian Academy of Sciences, searched practically the entire Russian part of the Tsagan-Shibetu ridge, discovered 14 tracks of snow leopard and collected fecal specimens of irbis for clarification of their numbers by DNA analysis.

The scientists successfully tracked some irbises and discovered areas of active range of the predators. The members of the expedition also discovered a family group of three irbises, apparently a female with two older kittens; they also were successful in photographing the animals for the first time in Tuva.

“In the future, it is planned to set up photo-traps in these locations, to study the spatial structure of the groupings of this species on Tsagan-Shibetu,” the report notes. After preliminary evaluation of these new data, the population of snow leopard on the Russian part of the ridge is estimated at 8-9 individuals. The scientists hope to get a more accurate picture of the numbers of sex-age composition of the population after DNA analysis of the predators’ fecal samples at the IPEE RAN laboratory.

As a result of DNA analysis of biomaterials collected on the Mongolian part of the ridge Tsagan-Shibetu in 2009, the numbers of the population of this species on this territory is estimated at 9 individuals. In this way, the total numbers of the trans-border population in this center of distribution is no fewer than 17-20 individuals. In April 2010, the work on the study of trans-border groupings of irbis on Tsagan-Shibetu will be continued on Mongolian territory. The obtained data will allow not just to estimate the condition of this group, but also to offer soundly-based suggestions for its protection. The development of eco-tourism in the irbis ranges based on reports by local people in Western Tuva with support of WWF should have a positive impact on the protection and development of the population of this predator. The action is planned to start already in May of this year.

The snow leopard, or irbis, lives in the mountainous heights of the Himalayas, Hindukush, Pamir, Tian-Shan, Altai and Western Sayans, Greater Caucasus and adjacent mountains. In the summer the animals prefer not to descent below the border where trees begin to grow, and live in the high rocky regions and mountain meadows, ascending all the way to six thousand meters. In winter the snow leopard find shelter in the forests located at the elevation of two thousand meters above sea level.

Illegal but lucrative hunting for snow leopard furs has substantially reduced the population. A snow leopard skin can bring in about sixty thousand dollars on the black markets of Asia. Snow leopard is under government protection in all the countries of its range, but poaching threatens its numbers just like before. Lately the number of the snow leopard has increased somewhat, and currently there are about six thousand individuals in existence.

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DNA could offer captive-breeding alternative to snow leopard studbook

Oct 16, 2009 11:03 AM in Scientific AmericanBy John PlattCaptive breeding of endangered snow leopards (Panthera uncia) has relied since 1976 on an international studbook that matches animals at zoos around the world for purposes of keeping the big cats from becoming too inbred.

Breeding via studbook, however, is a slow process that does not offer many benefits to an endangered species with small populations, such as the snow leopard. Now a team from the College of Veterinary Medicine at Western University of Health Sciences in Pomona, Calif., hopes to come up with an alternative breeding program that will rely on DNA instead of family trees.

Principal investigators Margaret Barr, Kristopher Irizarry and Janis Joslin have received a $100,000 grant from the Institute of Museum and Library Services to develop a strategy for using genetic analysis to maximize the breeding of snow leopards to enhance species diversity and robustness.

The existing snow leopard studbook is “slow and cumbersome,” Barr says. “It relies on demographic information and traditional observational genetics in deciding on which animals might be assets to the breeding program. The individual animals are bred and observed to see if the offspring survive, thrive and successfully reproduce free of diseases of concern. Zoos need a faster way to determine that they are correctly identifying the best individual animals for breeding for the long-term success of the program.”

According to the IUCN Red List of Threatened Species, worldwide populations for the cats are estimated at 4,000 to 6,000 animals. About 550 live in captivity in zoos. The species’s limited genetic range has weakened the animals’ immune systems and left them susceptible to a variety of diseases, such as pneumonia, enteritis from salmonella, and two different papillomaviruses, “which cause them to develop squamous cell carcinomas on their skin and in their mouths,” Barr says. The big cats also have problems similar to those in overbred domesticated animals, like hip dysplasia and colobomas (eye lesions).

As part of its research, the team will collect and store DNA samples from up to 100 snow leopards from North American captive populations. “Some of these samples will be used to generate a sequence of the snow leopard genome and to begin to identify genes that might play a role in the snow leopard’s increased susceptibility to some diseases,” Barr says.

Before that, the team plans to organize a workshop for several groups interested in snow leopard conservation, including “zoo curators and veterinarians involved in the Association of Zoos and Aquariums‘ Snow Leopard Species Survival Plan (SSP); key members of some SSPs for other endangered animals; geneticists and experts in genomics; immunologists; and reproductive physiologists,” Barr says. The team will use the workshop to come up with a “comprehensive strategy for applying functional genomics to animal conservation issues.”

The team hopes its results will also be applicable to other endangered species. “There are many other species of endangered cats such as the cheetah, Pallas’s cats, sand cats and Asiatic lions that have medical problems that could be evaluated using this same process, and breeding programs could be managed using the approach developed in this research,” Barr says.

The team’s yearlong project begins this month. http://www.scientificamerican.com/blog/post.cfm?id=dna-could-offer-captive-breeding-al-2009-10-16 

The Power of Genetics in Snow Leopard Conservation

The October 2008 issue of Animal Conservation features the first results of the genetic work conducted by Jan Janecka, Texas A&M University, in partnership with the Snow Leopard Conservancy and others.

Animal Conservation: Vol 11(5):pages 401-411. Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study. 2008. J. E. Janečka, R. Jackson, Z. Yuquang, L. Diqiang, B. Munkhtsog, V. Buckley-Beason, W. J. Murphy

An abstract is available at: http://www3.interscience.wiley.com/journal/121356219/abstract

This pioneering genetic study was also featured in the October 15 issue of New Scientist Online

The full story, paraphrased below, is available at:
The article describes how snow leopard numbers can be read in their scat. A genetic test specific to endangered snow leopards can reveal vital information on their numbers and diversity from a sample of feces. What is more, a pilot study has found that some feces thought to come from snow leopards were actually from red foxes or lynx – a disturbing sign that previous estimates of snow leopard numbers may be far too high.
Genetic testing of feces is more precise than field observations, but efforts to date have been limited because the costs were high. But now, these genetic approaches have become reasonably priced, allowing for large-scale studies. In addition, standard molecular primers based on domestic cats were not reliable when testing the degraded DNA in snow leopard feces. This led co-author Jan Janecka of Texas A&M University to develop tests specific for snow leopard DNA in scat.

Trials using the new approach in China, India and Mongolia show it is much more reliable and can effectively identify individual snow leopards.

That information is crucial for conservation, says co-author Rodney Jackson, director of the Snow Leopard Conservancy of Sonoma, California, which has plans for expanding the genetic test-based survey program.

Animal Conservation is a publication of the Zoological Society of London. The journal provides a forum for rapid and timely publication of novel scientific studies of past, present and future factors influencing the conservation of animal species and their habitats. The focus is on rigorous studies of an empirical or theoretical nature, relating to species and population biology. A central theme is to publish important new ideas and findings from evolutionary biology and ecology that contribute towards the scientific basis of conservation biology.

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