Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent

Abstract

Background Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. Methods We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. Results Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. Conclusions Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.

Genetic analyses reveal demographic decline and population differentiation in an endangered social carnivore, Asiatic wild dog

“…Another important finding is the relatively old timing of decline for dholes. Our results suggest a median dhole decline timing of ~ 300 years in both NNTR and TATR, much older than tiger/leopard decline timing in central India (tiger- decline ~ 200 years ago 46 , leopard- decline ~ 125 years ago 45 ). This could be explained by a combination of habitat loss driven population decline in historical times followed by hunting during the British era 29 .…”

“…The magnitude of decline for dholes corroborates with other co-occurring large carnivores in this landscape. For example, earlier studies have shown a 90% and 98% decline in leopard and tiger population in the central Indian region, respectively 45 , 46 . The relatively less decline for dholes compared to other larger carnivores is possibly due to fewer demands of dholes as trophies/illegal wildlife trade.…”

Individual Identification of Large Felids in Field Studies: Common Methods, Challenges, and Implications for Conservation Science

“…Complementary to photographic survey methods, noninvasive genetic-capture sampling using faecal DNA has become commonplace for the individual identification of tigers (Mondol et al, 2009;Thapa et al, 2018), leopards (Busby et al, 2009;Bhatt et al, 2020), jaguars (Roques et al, 2014;Wultsch et al, 2014) and cheetahs (Busby et al, 2009). The faecal DNA obtained from these species are genotyped using genetic markers such as microsatellites or single nucleotide polymorphism (SNP) panels (Magliolo et al, 2021;Thuo, 2021).…”

Effects of faecal inorganic contents in accurate measures of stress and nutrition hormone in large felines: implications for physiological assessments in free-ranging animals

“…A team of experienced field personnel surveyed forest trails of aforementioned protected areas (see Bhatt et al, 2020) and collected fresh tiger faeces during winter seasons of 2016-2018.…”