The question of subspecies identity matters far more than a taxonomic technicality. Globally, the brown bear is listed as Least Concern by the IUCN, but that sweeping label conceals sharp regional declines. In Nepal, the species is classified as Critically Endangered, with fewer than 20 mature individuals estimated nationwide and a distribution restricted to the northern high Himalayas. The species enjoys full legal protection under Nepal’s National Parks and Wildlife Conservation Act of 1973, yet conservation planning has been hampered by a fundamental problem: nobody knew for certain which bear they were protecting. Historical records relied on indirect signs, local reports, and photographs, none of which could reliably distinguish the Tibetan brown bear from its Himalayan relative, whose range is centered on northern Pakistan and northwestern India.

Previous mitochondrial DNA studies had shown that the two subspecies represent genetically distinct evolutionary lineages despite their geographic proximity. The Tibetan brown bear occupies the Tibetan Plateau and adjoining high-altitude regions, while the Himalayan brown bear is largely confined to the northwestern Himalaya. But no genetic study of brown bears had ever been conducted within Nepal itself. The new research, led by Rishi Baral of Hokkaido University and colleagues, set out to close that gap by sampling two key landscapes: Mustang District within the Annapurna Conservation Area and Dolpa District within Shey-Phoksundo National Park, both characterized by cold arid climates, rugged terrain, and alpine steppe vegetation.

Between 2022 and 2024, field teams working with experienced local personnel collected ten non-invasive samples putatively attributed to brown bears, seven fecal samples and three hair samples, located using associated field signs such as tracks, digging marks, and feeding sites. The researchers swabbed the outer mucosal layer of feces with sterile swabs preserved in buffer, collected hair with sterilized forceps, and geo-referenced every sample with handheld GPS units before storage at minus 20 degrees Celsius. In the laboratory, DNA was extracted under sterile conditions with negative controls to monitor contamination, and a short fragment of the mitochondrial control region, the D-loop, was amplified using bear-specific primers designed for subspecies discrimination.

The genetic results were strikingly clear. Seven of the ten samples yielded successful mitochondrial sequences, and every one of them carried the same haplotype, one that phylogenetic analysis placed firmly within the Tibetan brown bear lineage. The Nepalese sequences formed a well-supported clade with reference samples from the Tibetan Plateau, while the Himalayan brown bear emerged as a distinct sister lineage, clearly separate. Bootstrap support values for the major nodes exceeded 70 percent, and the sloth bear served as a divergent outgroup. Haplotype diversity and nucleotide diversity were both zero, meaning no mitochondrial variation was detectable among the samples analyzed, a pattern consistent with historical bottlenecks, long-term isolation, and restricted female dispersal reported for Tibetan brown bears across their core range.

Microsatellite genotyping, though successful in only 40 percent of samples, a common limitation with degraded non-invasive material, identified two unique individuals, both male. One was detected in Upper Mustang from a single hair sample, and the other from three fecal samples collected in Dolpa. The male-only detection pattern fits a well-documented trend in bear genetics: males disperse farther and hold larger home ranges, so they are more frequently encountered in surveys, while females tend to remain near their birthplaces. That sex bias raises the possibility that female-mediated gene flow into Nepal is particularly limited, potentially deepening the genetic isolation of any resident bears or linking them only through seasonal movement across the Tibetan border.

The camera-trap data provided independent ecological corroboration. As part of a broader mammalian community survey, the team deployed 96 motion-triggered infrared camera stations, 64 in Mustang and 32 in Dolpa, arranged on a systematic 4-by-4-kilometer grid across elevations of roughly 3,500 to 5,600 meters, with stations separated by at least 2 kilometers and no bait or scent lures used. Over 9,336 camera-trap nights of effort, the traps recorded four independent brown bear capture events at three stations in Upper Mustang between April 2023 and June 2024, at elevations from 3,834 to 4,816 meters across alpine steppe, shrubland, and grassland. One bear was photographed twice in a single day at Lomanthang, moving upslope at dawn and downslope in the evening, apparently after concealing itself from five feral dogs detected nearby. Another individual spent the night of June 5, 2023 playing and jumping in front of a camera at Damodar Kunda. In Dolpa, cameras set for long-term snow leopard monitoring captured four additional brown bear detections in 2023 and 2024, including one animal that paused to inspect the lens at nearly 5,000 meters.

Independent experts from the IUCN Species Survival Commission’s Bear Specialist Group reviewed the photographs and consistently judged the recorded animals consistent with the Tibetan brown bear, citing pale to dark brown pelage, prominent shoulder humps, and concave facial profiles. The study also compiled a verified photograph of a live bear taken by a local horse owner above Samdo village in the Manaslu Conservation Area, showing an individual feeding on a carcass, evidence of either scavenging or predation. Synthesizing these records with published reports spanning 2008 to 2025, the authors mapped confirmed brown bear occurrence across several Trans-Himalayan landscapes, including Humla, Dolpa, Mustang, Manaslu, and the Kanchenjunga Conservation Area, all along the southern periphery of the species’ global range.

The authors are careful to note the limits of their data. With only two genetically confirmed individuals and no detectable mitochondrial variation, the study cannot yet demonstrate a resident breeding population in Nepal. Some detected animals may be dispersing or transient males from larger populations on the Tibetan Plateau. Whether Nepal supports permanent residents, seasonal migrants, or a movement corridor connecting Himalayan and Plateau populations remains an open question that will require expanded non-invasive sampling targeting females, nuclear genomic markers to assess connectivity and effective population size, and long-term monitoring across the fragmented alpine habitat.

Still, the repeated detections across multiple years and locations suggest that Nepal’s Trans-Himalayan landscapes are regularly used by brown bears rather than visited by accident. For a nationally Critically Endangered carnivore at the edge of its range, that distinction carries real weight. Peripheral populations often show reduced genetic diversity and heightened vulnerability to environmental change, infrastructure development, livestock grazing, and human-bear conflict, but they can also serve as stepping stones or refugia under future climate scenarios. The researchers argue that maintaining landscape connectivity across Trans-Himalayan corridors and mitigating conflict in pastoral communities should be immediate priorities, alongside transboundary collaboration with counterparts in China. The study establishes the first molecular baseline for Tibetan brown bears in Nepal and demonstrates how genetics, camera trapping, and local ecological knowledge can be woven together to illuminate the lives of species that dwell where few observers can follow.

Subject of Research: Genetic and camera-trap confirmation of the Tibetan brown bear (Ursus arctos pruinosus) in central Nepal

Article Title: Confirmation of the Tibetan Brown Bear (Ursus arctos pruinosus) in Central Nepal Based on Genetic and Camera‐Trap Evidence

Article References: Baral, R., Gurung, R. B., Sapkota, A., Subedi, N., Giordano, A. J., Paudel, R. P., Kadariya, R., Khanal, G., Kodzue, K., Tsubota, T., & Shimozuru, M. (2026). Confirmation of the Tibetan Brown Bear ( Ursus arctos pruinosus ) in Central Nepal Based on Genetic and Camera‐Trap Evidence. Ecology and Evolution, 16(10), Article e74400. https://doi.org/10.1002/ece3.74400

Image Credits: AI Generated

DOI: 10.1002/ece3.74400

Keywords: Tibetan brown bear, Ursus arctos pruinosus, Nepal, mitochondrial DNA, camera trapping, non-invasive genetics, Trans-Himalaya, conservation, phylogeography, Annapurna Conservation Area, critically endangered, wildlife monitoring

The technical achievement at the heart of the study is considerable. Building a truly complete genome has long been one of genomics’ most stubborn challenges, because repetitive DNA sequences near the centers and ends of chromosomes resist standard sequencing methods. The research team overcame this by combining PacBio HiFi long-read sequencing, which produces highly accurate reads spanning tens of thousands of DNA letters, with Hi-C technology, which captures the physical contacts between distant stretches of chromosomes and allows the sequences to be anchored into their correct chromosomal positions. The final assembly spans 2.42 gigabases, with a scaffold N50 of 72.35 megabases and a contig N50 of 66.56 megabases, meaning that half of the assembled genome resides in stretches longer than those figures. The guanine-cytosine content of the assembly sits at 42.36 percent. In practical terms, the contiguity of this assembly approaches the ideal of a single gap-free sequence per chromosome, giving researchers an unprecedented view of the bear’s genome architecture.

With that high-resolution reference in hand, the team turned to comparative genomics, aligning the Tibetan brown bear’s chromosomes against those of its closest living relative, the polar bear. The analysis revealed high chromosomal synteny between the two species, meaning that large blocks of genes retain the same order and orientation across both genomes despite millions of years of separate evolution. This structural conservation is scientifically valuable for two reasons. It confirms that the assembly is accurate, since genuine chromosome-scale structure should be preserved between closely related ursids, and it provides a stable framework for pinpointing the regions that have instead diverged, which are precisely the locations where adaptation to very different environments, Arctic sea ice versus high-altitude steppe, is most likely to leave its mark.

The genomic record also preserves a vivid portrait of the species’ demographic turbulence. By reconstructing changes in effective population size through time, the researchers found that the Tibetan brown bear expanded during the early Pleistocene, a period of dynamic climate and habitat change. That expansion, however, was followed by two severe population bottlenecks. The first occurred approximately two million years ago, coinciding with the pre-Poyang Glaciation, and the second struck around one hundred thousand years ago during the Last Glacial Period. Together, these crashes reduced the bear’s cumulative effective population size by nearly eighty percent. For a species that today persists only on the Qinghai-Xizang Plateau, this history of repeated near-collapses carries a sobering message about the genetic fragility that may still lurk beneath its wild, unbroken landscape.

Yet survival through those bottlenecks suggests the species carries more than vulnerability. Enduring glacial cycles on a plateau whose average elevation exceeds 4,000 meters demands a physiology unlike that of lowland relatives, and the most striking discovery of the study concerns exactly that. When the researchers examined candidate hibernation-related pathways, they found that the Tibetan brown bear displays a distinctly carbohydrate-dominated metabolic signature. This stands in sharp contrast to the hibernation strategy documented in North American brown bears, which rely primarily on lipid, or fat-based, metabolism to fuel their long winter dormancy. In other words, two populations of the same widespread species appear to have evolved fundamentally different biochemical approaches to the same survival problem.

The implications of that finding extend well beyond bears. Fat is the standard fuel of hibernation across most studied mammals, because it stores more energy per gram and spares blood sugar during months of fasting. A sugar-first strategy on the Tibetan Plateau hints at selective pressures unique to that environment, where the short growing season, the composition of available foods, and the metabolic demands of life at low oxygen levels may have favored a different balance of carbohydrate and lipid pathways. The authors emphasize that this distinct metabolic adaptation highlights the bear’s unique mechanisms for surviving the extreme plateau environment, and it gives physiologists a natural experiment in alternative hibernation biochemistry encoded within a single species.

For conservation biologists, the new genome arrives at a critical moment. The Tibetan brown bear sits at the top of the plateau’s food web, playing a crucial ecological role, yet high-quality genomic resources for the species have been scarce until now. A chromosome-level reference genome transforms what conservation managers can do: it enables accurate estimates of genetic diversity and inbreeding, allows the tracking of gene flow between populations, and provides the resolution needed to identify locally adapted lineages that deserve special protection. Given the roughly eighty percent historical reduction in effective population size documented in the study, such tools are not a luxury. They are the baseline data upon which any serious plan for the species’ long-term management on the plateau must rest.

The study also strengthens the broader evolutionary picture of the bear family. Ursids have long fascinated evolutionary biologists because the family contains species with radically different ecologies, from the omnivorous brown bear to the hypercarnivorous, ice-bound polar bear. A near telomere-to-telomere assembly for the Tibetan brown bear adds a critical high-quality data point for reconstructing the phylogenomic relationships within Ursus and for dating the divergences that produced today’s brown bear lineages. Because structural variants, gene duplications, and regulatory regions can now be examined in their full chromosomal context rather than through fragmented assemblies, questions about how bears colonized and adapted to some of Earth’s harshest habitats can be addressed with far greater precision than before.

The research was carried out by Muran Zhao, Anmin Wang, Hai Liu, Chenxing Yu, Yanlin Liu, Nan Sun, and Guogang Li of Qinghai Normal University, with fieldwork, sample collection, and laboratory analysis conducted under permits granted by the university. The work was supported by the National Natural Science Foundation of China. The team notes that the new assembly is intended as a resource for the wider community, facilitating future studies of ursid evolutionary history and supporting conservation and management of the plateau’s wildlife. Because the genome is derived from a female bear, it also enables improved analysis of the sex chromosomes, an area where earlier fragmented assemblies often fell short.

What began as a technical sequencing project has ended with a discovery that may echo well beyond the Qinghai-Xizang Plateau. If a close relative of the brown bears studied across North America and Eurasia can hibernate on a carbohydrate-dominated metabolic program, then hibernation is not a single fixed solution that evolution produced once and reused everywhere. It is a flexible toolkit, and different populations have assembled it from different parts. As climate change alters the length and severity of winters across the world’s mountains, understanding that flexibility, and the genes that underpin it, could prove essential not only for protecting the Tibetan brown bear but for predicting which hibernating species can adjust and which cannot. The near-complete genome of this high-altitude survivor is now available as the roadmap for answering those questions.

Subject of Research: Chromosome-level genome assembly and hibernation-related evolution of the Tibetan brown bear (Ursus arctos pruinosus)

Article Title: Near telomere-to-telomere genome reveals the phylogenomics and hibernation-related evolution in Tibetan brown bear (Ursus arctos pruinosus)

Article References: Zhao, M., Wang, A., Liu, H., Yu, C., Liu, Y., Sun, N., & Li, G. (2026). Near telomere-to-telomere genome reveals the phylogenomics and hibernation-related evolution in Tibetan brown bear (Ursus arctos pruinosus). BMC Genomics. https://doi.org/10.1186/s12864-026-13324-3

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13324-3

Keywords: Tibetan brown bear, telomere-to-telomere genome, genomics, hibernation, Qinghai-Xizang Plateau, population bottlenecks, PacBio HiFi, Hi-C sequencing, phylogenomics, conservation genomics, carbohydrate metabolism, Ursidae evolution