Whole genome sequencing has revealed that snow leopards have low genetic diversity because they are rare, and probably always have been.
A recently published study finds that snow leopards, Panthera uncia, have the lowest genetic diversity of all the big cats, probably because they have always had a small population throughout their entire evolutionary history. Such low genetic diversity increases their risk of extinction in a rapidly changing environment.
Snow leopards are the top predator in their high altitude habitat, with some animals capable of hunting and killing prey that is three times their own body weight. Snow leopards commonly prey upon blue sheep, Argali wild sheep, ibex, and deer, as well as marmots, pikas, and other small mammals. Sadly, when their natural prey becomes harder to find, snow leopards sometimes kill livestock to survive, and this, in turn, often leads to retaliatory killings of snow leopards by local farmers or herders.
Snow leopards are a key indicator of the health of their high-altitude habitat. The loss of these animals would indicate the decline and collapse of their entire alpine ecosystem. These big cats are highly specialized to live in their remote habitat in the arid, mountainous regions of 12 northern and central Asian countries, including Russia, Afghanistan, Nepal, and Tibet (Figure 1). In the Himalaya mountains, snow leopards live in pristine high elevation areas, mostly above the tree line and up to 5500 meters (18,000 feet) in elevation.
“Snow leopards live in these really untouched areas, unlike other big cat species, which have suffered from human impact already,” said the study’s lead author, conservation geneticist Katie Solari, a research scientist in biology at Stanford University. Dr Solari is also the Associate Director of the Program for Conservation Genomics (PCG).
In their recently published genomics study, Dr Solari and collaborators estimated that these highly specialized big cats have a population size of less than 8,000 individuals (ref). (The Snow Leopard Trust, an organization devoted to the conservation of these rare big cats, relies on population census data and their estimates suggest there are between 3,920 and 6,390 snow leopards left in the wild.)
Snow leopard numbers are believed to be in decline due to a wide variety of anthropogenic threats, particularly poaching and farming. Additionally, snow leopards are under threat from increasing greenhouse gas emissions, which are expected to cause a shift of the Himalayan treeline and a shrinking of the alpine zone, thereby reducing snow leopard habitat by an estimated 30% (ref). Due to their small population size and to the growing effects of climate change, snow leopards are currently listed as ‘Vulnerable’ by the International Union for Conservation of Nature (IUCN).
“They don’t have many individuals,” Dr Solari told me in email. “They don’t have much genetic diversity.” This limited genetic diversity reduces the genetic tools these big cats have available to deal with the changing climate.
“Snow leopards are just not well situated to deal with changes that are likely coming their way.”
Dr Solari and collaborators came to this worrying conclusion after they analyzed whole-genome sequencing data extracted from snow leopard samples. Prior to this research, not much was known about snow leopard genetics because only four individuals had ever been fully sequenced. This study brings that number to 41, including 35 wild snow leopards and six individuals from zoos around the world.
Obtaining such a large number of samples required years of work and extensive collaboration with researchers and wildlife officials from 11 countries, all of whom contributed snow leopard blood and tissue samples for this research.
Dr Solari and collaborators did also uncover some good news: despite their low genetic diversity, snow leopards are not like some other big cat species that also have small populations. Cheetahs, for example, had very large populations historically before they experienced two sudden population crashes – creating a genetic “bottleneck” – that led to their restricted genetic diversity today. As a result, it is harder for cheetahs to thrive as negative mutations were passed down to fewer and fewer individuals. These negative mutations lowered their reproductive success and increased their susceptibility to disease.
In contrast to cheetahs, Dr Solari and colleagues found that, despite snow leopards’ low genetic diversity, they had a significantly lower “homozygous load” than cheetahs. Thus, snow leopards inherit fewer duplicate copies of potentially harmful genetic mutations from their parents. This suggests that the snow leopards’ persistent small, stable population size allowed these animals to purge such mutations. Basically, if a negative trait surfaced, affected individuals died before reproducing or their progeny were less successful. This genetic purging, facilitated by historic inbreeding, allowed the snow leopard population to remain relatively healthy even with small numbers.
But the situation is changing rapidly.
“Because their habitat is so inhospitable, human population growth didn’t really affect snow leopards very much, but climate change will,” pointed out the study’s senior author, evolutionary biologist Dmitri Petrov, a Michelle and Kevin Douglas Professor in the School of Humanities and Sciences at Stanford. Professor Petrov’s expertise lies in understanding the process of rapid adaptation to and newly arising mutations in a range of systems and ecological contexts.
“If their habitat starts degrading, then snow leopards might go extinct fairly easily, simply because there’s just not much ecological space for them and the total population is so small,” Professor Petrov said.
In a second study, also recently published, Dr Solari, Professor Petrov and collaborators report a genetic test they developed for testing snow leopard feces (ref). This test utilizes a single nucleotide polymorphism (SNP) panel method that is broadly usable for conservation projects in any country – cost effective, streamlined lab protocol and user-friendly open-source bioinformatics protocols for panel design and analysis. This SNP panel will provide valuable information to the snow leopard conservation community in their efforts to monitor local and global snow leopard population health and sizes by identifying individual snow leopards, assessing their diets, internal parasite load, microbiome diversity and hormonal milieu, as well as tracking population trends without having to stress them out by physically capturing them. This non-invasive SNP fecal test promises to be valuable to the snow leopards and their human guardians in the face of the changing climate.
“Humans don’t need to show up in their mountains to build or start agriculture. The climate changes, and it affects everyone and everything, even in such remote areas.”
Sources:
Katherine A. Solari, Simon Morgan, Andrey D. Poyarkov, Byron Weckworth, Gustaf Samelius, Koustubh Sharma, Stephane Ostrowski, Uma Ramakrishnan, Zairbek Kubanychbekov, Shannon Kachel, Örjan Johansson, Purevjav Lkhagvajav, Heather Hemmingmoore, Dmitry Y. Alexandrov, Munkhtsog Bayaraa, Alexey Grachev, Miroslav P. Korablev, Jose A. Hernandez-Blanco, Bariushaa Munkhtsog, Barry Rosenbaum, Viatcheslav V. Rozhnov, Ali Madad Rajabi, Hafizullah Noori, Kulbhushansingh R. Suryawanshi, Ellie E. Armstrong, and Dmitri A. Petrov (2025). Exceedingly low genetic diversity in snow leopards due to persistently small population size, Proceedings of the National Academy of Sciences 122(41):e2502584122 | doi:10.1073/pnas.2502584122
Katherine A. Solari, Shakeel Ahmad, Ellie E. Armstrong, Michael G. Campana, Hussain Ali, Shoaib Hameed, Jami Ullah, Barkat Ullah Khan, Muhammad A. Nawaz, and Dmitri A. Petrov (2025). Next-Generation Snow Leopard Population Assessment Tool: Multiplex-PCR SNP Panel for Individual Identification From Faeces, Molecular Ecology Resources 25(4):e14074 | doi:10.1111/1755-0998.14074
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