# Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study

> How reliable is a scat found beside a snow leopard scrape? In 2-day surveys in India, China and Mongolia, DNA showed that up to 54% of scats identified in the field were wrong, with red fox scats the most common mix-up. The same scats revealed individual snow leopards and their sex, showing how DNA from scat could help monitor this elusive cat.

Summary by Kersey Lawrence, Original Wisdom. Updated 9 November 2026. Page: https://www.originalwisdom.com/tracking-literature/2008-janecka-jackson-population-monitoring-snow-leopards/

## Citation and access

- **Authors:** J. E. Janečka, R. Jackson, Z. Yuquang, L. Diqiang, B. Munkhtsog, V. Buckley-Beason and W. J. Murphy
- **Year published:** 2008
- **Journal or source:** Animal Conservation
- **Full citation:** Janečka, J. E., Jackson, R., Yuquang, Z., Diqiang, L., Munkhtsog, B., Buckley-Beason, V. and Murphy, W. J. 2008. Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study. Animal Conservation 11(5): 401–411.
- **DOI:** 10.1111/j.1469-1795.2008.00195.x
- **Access status:** Publisher link only
- **Where to find it:** https://doi.org/10.1111/j.1469-1795.2008.00195.x

## Tags

- **Species:** Mammals > Eurasian lynx; Mammals > Grey wolf; Mammals > Red fox; Mammals > Snow leopard
- **Region:** Asia > China; Asia > India; Asia > Mongolia
- **Tracking:** Paths; Scat; Sign surveys; Tracking; Tracks; Tracks and signs identification
- **Methods and technology:** DNA; Observer reliability; Population estimation
- **Data type:** New field data
- **Observer qualification:** Not reported
- **Discipline:** Wildlife tracking
- **Year published:** 2008

## Detailed keywords

- **Species:** Studied: snow leopard (Panthera uncia). Other species identified from the collected scats by DNA: red fox (Vulpes vulpes), lynx (Eurasian lynx, Lynx lynx, in the species tree) and wolf or domestic dog (Canis lupus or Canis familiaris; the short DNA segment could not separate them). Reference species used to build the species tree include tigers (Panthera tigris), domestic cat (Felis silvestris catus), wildcat (Felis silvestris), leopard cat (Prionailurus bengalensis), Corsac fox (Vulpes corsac), Tibetan fox (Vulpes ferrilata), sable (Martes zibellina), badger (Meles meles) and mountain weasel (Mustela altaica). The short segment could not separate domestic cat from wildcat, and Tibetan fox and Corsac fox were barely distinguishable. Iberian lynx (Lynx pardinus) is mentioned as a comparison. Captive snow leopard DNA (one male, one female) from the Zoological Society of San Diego served as controls.
- **Location and habitat:** Three regions of Central Asia: one site in Ladakh, north-western India; two sites in Dulan County, Qinghai, central China; three sites in South Gobi, southern Mongolia. Rugged, high-altitude snow leopard habitat; transects along ridgelines, saddles, outcrops and wildlife trails. Red fox scats were found up to 3930 m in Qinghai. Qinghai is described as having more human disturbance.
- **Topics:** noninvasive genetic sampling; scat surveys; field identification of scat versus DNA identification; species misidentification (snow leopard scats mistaken for red fox); sign surveys likely overestimating snow leopard abundance; individual identification from scat; sex identification from scat; microsatellite primer design avoiding repetitive DNA elements; genotyping errors (allele dropout, false alleles); genetic diversity; population structure; snow leopard scrapes and marking sites; comparison with camera trapping.
- **Statistics or models:** Student’s t-test (comparing a genotype quality index, Q, between the original domestic cat primers and the new snow leopard primers); Hardy–Weinberg equilibrium tests with sequential Bonferroni correction; probability of identity (PID and PID-sibs); haplotype and nucleotide diversity (DNASP); neighbour-joining species tree (Kimura two-parameter model, bootstrap support). Software: GENEALEX, DNASP, REPEATMASKER, BLAT, BLAST. Inconsistencies in the paper: (1) the text says all seven markers were variable “in both Ladakh and Qinghai”, but Table 5 gives Ladakh and South Gobi (Qinghai produced no complete genotypes); (2) control region nucleotide diversity is given as 0.0017 in the Results and 0.0021 in the Discussion; (3) the Methods list seven snow leopards sequenced for mitochondrial DNA (three Ladakh, three South Gobi, one Qinghai), the Results say eight; (4) the text cites Table 1 for the Qinghai genotyping result, which is in Table 2; (5) the field identification error for Ladakh is given as 35%, while 8 of the 25 DNA-identified Ladakh scats (32%) were not snow leopard.
- **Data type:** New field data: brief 2-day scat surveys in each region (5.4 km in Ladakh, 11.1 km in Qinghai, 9.7 km in South Gobi). Survey dates are not given. A camera-trapping survey in the Mongolian site (April to May 2007) is cited as personal observation for comparison.

## Synopsis

### 1. What they did

Snow leopards live at low densities in rugged, high mountains across Central Asia, and most surveys of them have relied on signs such as pugmarks (footprints), scrapes and scats, plus interviews with local people. Camera trapping gives better counts but needs long periods in the field and is costly in remote areas. The authors ran a pilot study to see whether DNA from scat could be used to monitor snow leopards.

- Collecting scats. Field teams, guided to snow leopard areas by local wildlife biologists and knowledgeable residents (such as herders and former hunters), searched ridgelines and outcrops for scrapes and tracks. Transects followed wildlife trails along saddles, ridgelines and outcrops that snow leopards often use. Each region was surveyed for only 2 days: Ladakh (India), Qinghai (China) and South Gobi (Mongolia).

- Field identification. Each scat was given a likely species in the field, based on its shape and how close it was to other snow leopard signs. In Ladakh and South Gobi the teams mainly collected scats they thought were from snow leopards; in Qinghai they collected every intact carnivore scat.

- DNA species identification. A short piece of mitochondrial DNA was read from each scat and compared with known species.

- Better genetic markers. The usual markers for telling individual snow leopards apart were designed for the domestic cat. The authors redesigned primers (the short DNA sequences that start each test) for seven markers to match snow leopard DNA exactly, to read shorter pieces, and to avoid repetitive stretches of DNA that cause errors. They compared old and new primers on 17 confirmed snow leopard scats.

- Individuals, sex and diversity. They used the new markers to identify individual snow leopards, a male-only (Y chromosome) marker to identify sex, and a set of mitochondrial markers to look at genetic diversity across the three regions.

### 2. What they found

What the scats really were

- 109 scats were collected (32 in Ladakh, 50 in Qinghai, 27 in South Gobi). DNA identified the species for 78% of them.

- Ladakh: 17 snow leopard, 6 red fox and 2 wolf or dog.

- Qinghai: 3 snow leopard, 10 lynx, 21 red fox and 2 wolf or dog.

- South Gobi: 11 snow leopard and 13 red fox.

- Field identification was often wrong: 35% of scats in Ladakh and 54% in South Gobi were misidentified. Many scats thought to be from snow leopards were from red foxes, and fox scats were regularly found on snow leopard scrape sites in South Gobi.

Better markers

- The new snow leopard primers gave usable genotypes 72.6% of the time, against 46.1% for the original domestic cat primers, with less allele dropout, fewer false readings and cleaner results. The genotype quality index was significantly higher (0.43 versus 0.22).

- Over half of the domestic cat markers examined had repetitive DNA beside them, which helps explain the errors.

Individual snow leopards

- Complete genotypes were obtained for 71% of snow leopard scats in Ladakh and 73% in South Gobi, but none of the three from Qinghai.

- Four snow leopards (2 males, 2 females) were detected in Ladakh, one male in Qinghai, and five (3 males, 2 females) in South Gobi, all within 2-day surveys.

- Ladakh and South Gobi gave similar numbers of individuals even though far fewer scrapes were seen in Ladakh (2 versus 23).

- In Ladakh, a camera survey 45 km away had found six individuals in 135 km². In the Mongolian site, a 2-month camera survey over 145 km² (April to May 2007) found four adults and three cubs, compared with the three males and two females found from scat.

Genetic diversity

- Genetic diversity was lower in South Gobi than in Ladakh. Mitochondrial DNA varied very little across the three regions, despite more than 1000 km and major barriers between them.

### 3. What they concluded

- DNA from scat is an effective way to monitor snow leopards and other carnivores: brief surveys confirmed snow leopards even where they are scarce, and detected several individuals where they are more common.

- Because so many scats are misidentified in the field, earlier sign surveys that counted scats likely overestimated snow leopard numbers and produced unreliable density indices. The authors suggest that scat-based snow leopard surveys should at least include genetic species identification.

- Primers designed for the target species, avoiding repetitive DNA, reduce genotyping errors that could bias population estimates.

- Scat surveys are probably less affected by behaviour, environment and season than sign surveys, and could cover large areas where long camera surveys are not feasible. Where camera trapping is practical, scat DNA can add information on connectivity and relatedness.

- Consistent sampling strategies and marker panels across studies are needed, and survey designs and estimation methods still need to be developed.

### 4. How tracking was or was not used

The study is a test of tracks and signs work. Field teams searched for snow leopard scrapes and tracks, walked transects along wildlife trails and landscape features snow leopards are known to use, and identified scats in the field by their shape and by how close they were to other snow leopard signs. DNA then checked those field identifications, showing that up to about half were wrong, with red fox scats the most common mistake. No trailing was reported.

### 5. Tracker or observer certification

Not reported. The paper does not say who identified the scats in the field or how experienced they were. Local wildlife biologists and knowledgeable residents (such as herders and former hunters) guided the teams to snow leopard areas. This matters because the main tracking finding, the high rate of field misidentification, rests on observers whose skill is not described.

### 6. Other technologies, skills or innovations

- Scats were stored in tubes with silica desiccant, and DNA was extracted with a stool DNA kit.

- Species identification from a short piece of the cytochrome b gene, using carnivore-specific primers first designed for South American carnivores.

- Seven redesigned snow leopard microsatellite markers (named “PUN”) for identifying individuals, each test run three times to reduce errors.

- A male-specific (Y chromosome) marker for sexing scats.

- Control region primers that react only with snow leopard DNA, which the authors describe as an inexpensive test to confirm snow leopard scat with a simple laboratory method.

- Global Positioning System (GPS) locations of sites are given in the supplementary material.

### 7. Implications for conservation (from the paper)

- Little is known about snow leopard status in much of their range, and better information is needed for conservation plans.

- Sign surveys based on scat probably overestimate snow leopard abundance; genetic species identification should be part of scat-based surveys.

- Scat DNA allows large-scale studies of snow leopard numbers, sex, relatedness and population structure without capturing animals, which will inform conservation across the range.

### 8. Implications for tracking (Original Wisdom's observations)

_These are Original Wisdom's observations, not the authors'._

- Snow leopard and red fox scats were often confused in the field, and fox scats were found on snow leopard scrape sites, so being close to other snow leopard signs did not guarantee a snow leopard scat.

- Because the paper does not describe who identified the scats or how experienced they were, it shows how often scats were misidentified in this study, not how accurate skilled trackers would be.

## Cite this summary

Lawrence, K. 2026. Summary of: Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study (Janečka and Jackson et al., 2008). Original Wisdom, Tracking Literature. https://www.originalwisdom.com/tracking-literature/2008-janecka-jackson-population-monitoring-snow-leopards/