Biology subjects

Harihar, A.

Publications and source records attributed to Harihar, A..

5 recordsLinked to original sources

bioRxiv2026

Demographic history, geographic distance, and landscape features shape the genetic divergence of wild tigers in northeast India

Habitat fragmentation creates small, isolated populations vulnerable to inbreeding, genetic drift, and high genetic load. For conservation management, it is essential to distinguish contemporary landscape resistance from historical demographic processes as drivers of these genetic patterns, especially for conservation priority regions such as northeast India which intersects two major tiger conservation landscapes. We studied the genetic structure and landscape connectivity of tigers across four protected areas in northeast India: Kaziranga, Manas, Orang, and Nameri, using faecal samples. From 741 samples collected over two field seasons, we identified 654 confirmed tiger specimens. Using methylation-based enrichment and ddRAD-seq of 176 samples, we generated a high-quality dataset of 3091 SNPs across 44 individuals. Population structure analyses identified three genetically distinct clusters: Kaziranga-Nameri, Manas, and Orang. Isolation-by-distance and landscape resistance explained 13% and 17% of the observed genetic divergence, respectively, with human settlements influencing gene flow. Orangs pronounced divergence from Kaziranga, despite geographic proximity and corridors, suggests a post-bottleneck founder effect, as evidenced by reduced heterozygosity (Ho = 0.24), nucleotide diversity (pi = 0.24), and effective population size (Ne = 1.3). These findings reveal that demographic and genetic recovery can decouple: Orangs population has recently grown, yet genome-wide evidence shows ongoing genetic erosion that monitoring has not detected. Similar patterns have been reported in other Indian tiger populations, indicating that such decoupling may be systemic. Target 4 of the Kunming-Montreal Global Biodiversity Framework requires explicit genetic diversity monitoring; this study demonstrates that non-invasive genomics can operationalise that mandate at a conservation-relevant scale.

evolutionary biology↗

bioRxiv2025

Synthetic Substitutes as a Conservation Tool: Evaluating Synthetic Leopard Fur for Demand Reduction and Species Recovery

Providing synthetic substitutes is a widely promoted strategy to shift consumer demand away from wildlife products derived from threatened species. Yet, there is little evidence on whether such product substitution interventions effectively prevent illegal or unsustainable harvesting and contribute to the recovery of threatened populations. Drawing on the Furs For Life (FFL) Zambia initiative, which supplied synthetic furs known as "Heritage Furs" to replace leopard skins traditionally worn during Lozi royal ceremonies in Western Zambia, we present an evaluation designed to test both the effects and causal mechanisms of substitution. Guided by the EMMIE framework, commonly used in crime prevention evaluation, we triangulated data from semi-structured questionnaires, law enforcement patrols, court records, camera trap monitoring, and stakeholder interviews conducted between 2018 and 2024. Qualitative analysis using the General Elimination Method was employed to assess plausible alternative explanations for leopard recovery. By 2024, adoption of synthetic furs among leopard fur users exceeded 80 percent, while self-reported ownership of authentic leopard furs declined by 70 percent. At the same time, patrol detections of leopard poaching incidents decreased, and camera trap density estimates increased from an average of 2.7 to 3.8 leopards per 100 square kilometers across the focal landscape. An integrated mechanism of change, derived from stakeholder perspectives, indicates that while substitution reduced demand, concurrent and reinforcing effects of counter-poaching and counter-trafficking operations were critical to leopard recovery. This study provides the first empirical link between a demand reduction initiative based on synthetic substitutes and measurable species population recovery.

ecology↗

bioRxiv2025

Tiger diet in Ranthambore Tiger Reserve: how do metabarcoding and mechanical sorting compare?

Accurately describing large carnivore diets is critical for understanding trophic interactions and identifying targeted conservation strategies. Most studies have relied on traditional dietary analysis based on mechanical sorting and identification of undigested prey remains, a method known to be error-prone and ecologically biased. Here, we compare the diet of tigers using non-invasively collected scats from Ranthambore Tiger Reserve in India, analysed using mechanical sorting and DNA metabarcoding. We found that DNA metabarcoding outperformed mechanical sorting in detecting higher overall prey and rare prey species occurrences, uncovering higher prey diversity. The study revealed that tigers were subsisting mainly on wild prey such as sambar and chital. However, domestic cattle contributed the highest relative prey biomass to their diet. Our findings demonstrate that DNA metabarcoding is an efficient, effective and powerful approach that overcomes several of the previously identified biases of the mechanical sorting approach and provides an accessible and particularly useful tool for carnivore dietary studies based on non-invasive samples. The increased frequency of livestock depredation relative to previous studies highlights the need for active mitigation measures to secure this population.

ecology↗

bioRxiv2024

Trace DNA from kill sites identifies predating tigers

Predation ecology and evidence-based conflict management strategies require reliable and accurate identification of individual predators. Identifying predators is, however, complex, as they are secretive and individual identification is difficult. Trace DNA that predators leave behind at kill sites might provide an effective strategy to identify them but remains poorly evaluated at scale. We use non-invasive genetic samples from kill sites to assess their utility for predator identification. We systematically investigated 198 livestock kills in two critical source tiger populations in central India: Kanha and Bandhavgarh Tiger Reserves. We collected 342 salivary swabs from carcasses, 33 scat and 395 shed hair samples as potential sources of predator DNA, and individual tigers were identified using up to 123 SNP markers. All three sample sources identified predator species with high success (>95%). We identified individuals (with at least one sample per kill site, based on >40 SNPs) at 86% of all kill sites where tigers were detected. Shed hair samples were most effective for individual identification, followed by saliva and scat. Sample source and sampling season were the primary determinants of the number of SNPs typed per sample and the success of individual identification. Based on the site and type of sample collection, we classify species and individuals into three categories: true predator (high confidence as predator), circumstantial predator (medium confidence) and predator uncertain (low confidence). Individuals were classified as a true predator at 72 sites, circumstantial predator at 34 sites and predator uncertain at 49 sites. Our protocol allowed us to differentiate between predators and scavengers, even when multiple tigers were detected at the same kill site. Surprisingly, [~]40% of Bandhavgarhs tigers were identified at at least one kill site. We suggest that when paired with systematic kill site investigation and sample collection, these methods can be effectively used to understand predation ecology better and facilitate evidence-based conflict management.

genetics↗

bioRxiv2020

Estimating leopard (Panthera pardus) densities when populations comprise polymorphic phenotypes: an application of spatial mark-resight models

Melanism is a form of pigmentation polymorphism where individuals have darker colouration than what is considered the "wild" phenotype. In the case of leopards, Panthera pardus, melanism occurs at higher frequencies amongst populations in tropical and subtropical moist forests of south and southeast Asia, presenting a unique challenge in estimating and monitoring these populations. Unlike the wild phenotype that is readily recognizable by its rosette patterns, melanism results in individuals being unidentifiable or unmarked through photographic captures obtained using white flash cameras. Spatial mark-resight (SMR) models that require only a subset of the population to be marked offer the opportunity to estimate population density. In this study, we present an application of SMR models to estimate leopard densities using camera trap survey data from three sampling years at Manas National Park (MNP), India. By using an SMR model that allowed us to include captures of unidentified sightings of marked individuals, we were also able to incorporate captures where identity was either not confirmed or only known from a single flank. Following 18,674 trap-days of sampling across three years, we obtained 728 leopard photo-captures, of which 22.6% (165) were melanistic. We estimated leopard densities of 4.33, 2.61 and 3.37 individuals/100km2 across the three years. To our best knowledge, these represent the first known estimates of leopard densities from populations comprising both melanistic and wild phenotypes. Finally, we highlight that SMR models present an opportunity to revisit past camera trap survey data for leopards and other species such as Jaguars, P. onca, that exhibit phenotypic polymorphism towards generating valuable information on populations.

ecology↗