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

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.