Biology subjects

Ramakrishnan, U.

Publications and source records attributed to Ramakrishnan, U..

At least 19 recordsLinked to original sources

bioRxiv2026

Rationalizing the application of spatial capture-recapture versus space-to-event models for monitoring populations of an endangered social carnivore

Reliable estimates of population size are fundamental to understanding wildlife population status and informing conservation. Obtaining such estimates remains challenging for unmarked species, particularly in tropical countries where logistical and financial constraints limit intensive monitoring. The endangered dhole (Cuon alpinus), a highly social canid without natural markings, is one such species for which robust population estimates remain scarce. We estimated dhole density in the Valparai plateau, a human-dominated agroforest-forest mosaic in India's Western Ghats. We compared Spatially Explicit Capture-Recapture (SECR) models based on individual identification from fecal DNA and Space-to-Event (STE) models based on camera-trap detections. We additionally applied both approaches to individually identifiable leopards (Panthera pardus) to cross-validate STE versus SECR estimates. SECR estimated dhole density at 22 individuals per 100 sq.km, with STE estimates varying substantially depending on how the camera viewshed area was defined. STE estimates based on post hoc viewshed measurements, particularly after reducing the viewshed by 10%, were comparable to SECR estimates. In contrast, STE underestimated leopard density relative to SECR (7 versus 12 per 100 sq.km), although uncertainty intervals overlapped. Ecologically, our results indicate that human-use agroforest mosaics can support dhole densities comparable to, or exceeding, those reported from several Protected Areas, highlighting their potential importance for dhole conservation. More broadly, we argue that STE models may offer a practical and relatively inexpensive approach for baseline monitoring of dholes from camera-trap surveys, but their reliability depends strongly on accurate characterization of the effective viewshed and may vary across species and landscapes.

ecology↗

bioRxiv2026

Leveraging collaborations between researchers, wildlife managers and citizen-volunteers to monitor endangered carnivore populations across space and time

Monitoring populations is fundamental for conserving threatened carnivores, but can be difficult to sustain in the long term across large landscapes. We present a collaborative framework for monitoring dholes (Cuon alpinus) in India's Western Ghats, combining fecal DNA-based individual identification, Spatially Explicit Capture-Recapture (SECR) models, state Forest Department participation, and trained citizen-volunteers. We surveyed across six sites between 2019-2023, encompassing three Protected Areas (Wayanad, Parambikulam, Periyar) and their adjacent Territorial Divisions. Fecal samples were genotyped using a panel of 96 Single Nucleotide Polymorphisms, and detections were analyzed using SECR models to estimate densities. In Wayanad Sanctuary, densities remained stable across 2019, 2022 and 2023, increasing marginally from 15.67 to 19.01 individuals per 100 sq.km. In 2023, densities varied substantially among six sites, from 9.73/100 sq.km in Parambikulam to 29.23 in Nemmara Territorial Division. Field implementation involved an average of 46 Forest Department personnel co-collecting data per site-year. Among former citizen-volunteers who were surveyed for project feedback (N=29), 83% went on to either work or pursue higher education in wildlife-related or -adjacent fields. We demonstrate that molecular individual identification coupled with SECR can provide a practical basis for dhole population assessments while enabling multi-stakeholder participation in field monitoring. Sustained engagement with wildlife managers and locally recruited volunteers can strengthen institutional capacity, facilitate knowledge exchange, and improve continuity of monitoring programs. We argue that integrating molecular ecology with collaborative governance and democratizing field-science offers a scalable pathway for landscape-level monitoring required to guide dhole conservation.

ecology↗

bioRxiv2026

There is no silver bullet: Tiger corridors do not ensure multispecies carnivore connectivity

Connectivity is critical to sustaining endangered carnivores in speciose yet fragmented landscapes such as in the global south. Corridors to mitigate fragmentation are designed based on charismatic species or habitat-based approaches, but their multispecies effectiveness for maintaining functional connectivity remains poorly tested. We combined landscape genetic analyses across five sympatric carnivores - Panthera tigris, Panthera pardus, Prionailurus viverrinus, Felis chaus, and Melursus ursinus, to evaluate how landscape features shape functional connectivity in a globally important felid landscape. We then assessed the efficiency of existing tiger corridors and single-species surrogates for maintaining multispecies functional connectivity. Species exhibited contrasting responses to landscape variables, producing distinct resistance surfaces and connectivity corridors. Spatial similarity of connectivity between species pairs was highly variable (r = 0.14-0.93), but no single species effectively captured connectivity patterns of the broader carnivore community (maximum mean overlap of <0.7 across species). Moreover, genetically optimized corridors were over 70% more efficient in capturing connectivity compared to existing tiger corridors, demonstrating mismatches between structural and functional connectivity. Our results highlight limitations of surrogate-based corridor planning and demonstrate that integrating multispecies functional connectivity can substantially improve conservation planning in human-dominated landscapes.

ecology↗

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↗

bioRxiv2026

Resource abundance and dietary specialization predict elevational migration in a hyperdiverse montane bird community

Migration is a well-described behavioural strategy that allows species to track variation in resources and climatic conditions by moving in response to seasonality. A common form is elevational migration, an annual short-distance movement undertaken by many mountain bird species globally. While studies show that the timing of migration may relate to food availability, the mechanisms determining which species migrate remain unclear. Our study investigated if the degree of dietary specialization explains why some high-elevation bird species in seasonal environments migrate downslope for the winter while others remain resident at high altitudes despite the apparent scarcity of their preferred food resources. We mist-netted birds along a 2300-m elevational gradient in the Eastern Himalaya and collected blood and faecal samples from 261 individual birds belonging to 18 species of high-elevation residents (ten) and elevational migrants (eight) in their breeding and wintering ranges. Using stable isotope ratios of carbon and nitrogen in whole blood and faecal DNA metabarcoding, we compared their seasonal trophic levels and dietary niches. Nitrogen isotope ratios showed that residents had a substantially lower trophic position in the winter compared to summer (-0.35 [-0.52, -0.17]), whereas migrants had a slightly higher trophic position in the winter (0.15 [-0.02, 0.32]). This trophic shift in residents was likely due to a decrease in insectivory and an increase in frugivory in the winter. The frequency of key insect orders (Lepidoptera, Hemiptera, and Coleoptera) declined by 20-35% in their winter diets alongside an increase in fruit, particularly from the family Polygonaceae (0.33 [0.18, 0.46]). Additionally, compared with residents, migrants showed greater overlap in their dietary niches between summer and winter (98% vs 80%). Because arthropod abundances in the Himalayas peak at high elevations in the summer and decline in the winter, we suggest that elevational migrants are likely dietary specialists that track resources, while high-elevation residents are dietary generalists that supplement their winter diet with fruit and nectar because of the scarcity of arthropods. These findings indicate that a species dietary specialization is linked to its migratory behaviour, providing a potential mechanistic explanation for how different species solve the challenge of seasonal resource limitation.

ecology↗

bioRxiv2026

Predominant tetraploidy and lack of ploidy-associated genetic structure across invasive Lantana camara populations in India

Polyploidization is widely recognised as a major driver of plant diversification, with many species persisting as mixed-ploidy systems where multiple cytotypes co-exist. Polyploids are disproportionately represented among invasive species, yet their role in facilitating biological invasions remains poorly understood. Lantana camara, one of the worlds most successful invasive plants, exhibits remarkable cytotype diversity, but the distribution and evolutionary relationships of these cytotypes in its native and invasive ranges have remained unclear. Here, we characterise ploidy variation and assess genetic differentiation among cytotypes in invasive L. camara populations across India. Flow cytometry of more than a thousand individuals reveals that tetraploids overwhelmingly dominate the invasive range, accounting for more than 95% of individuals, while triploids and hexaploids occur at much lower frequencies. Using genome-wide ddRAD-derived SNP markers from diploids, triploids, tetraploids, and hexaploids, we find no genetic differentiation among cytotypes. Instead, individuals of different ploidy levels cluster together across multiple genetic clusters, consistent with recurrent and potentially independent origins of polyploids. These patterns further suggest that L. camara polyploids likely arise via autopolyploid formation. Together, our results establish tetraploidy as the predominant cytotype in Indias invasive populations and reveal a lack of cytotype-specific genetic structure. These findings highlight the need to investigate the ecological advantages of tetraploids and the mechanisms that generate cytotype diversity, key steps toward understanding how polyploidy contributes to the invasive success of this globally important species.

evolutionary biology↗

bioRxiv2026

Spotted fever Rickettsia and relapsing fever Borrelia in rodents from southern India

Bacterial zoonoses constitute a substantial fraction of emerging infectious diseases. In this study, we investigated the presence of pathogenic bacterial genera--Rickettsia, Borrelia, Orientia, Leptospira, and Coxiella--in rodents from southern India. We detected low circulation of Rickettsia (7.26%), Borrelia (6.45%), and Leptospira (0.8%), whereas Orientia and Coxiella were not detected in the rodents sampled. Notably, we observed contrasting patterns of tissue association, with rickettsiae detected exclusively in pooled organ tissues and borreliae detected only in blood, suggesting the influence of pathogen biology in detection probabilities. Our phylogenetic analyses further revealed spotted fever group rickettsiae and relapsing fever group borreliae in both synanthropic and forest-associated rats, highlighting a potential transmission risk to people and livestock in the region. By revealing the circulation of zoonotic bacteria in new host species, this study underscores the need for systematic surveillance of wildlife to better characterize bacterial diversity and its public health implications.

ecology↗

bioRxiv2025

Anthropogenic habitats shape gut microbiome composition in Southern Indian bats

BackgroundAnthropogenic habitat modification and associated resources can exert selection pressures on wildlife and their microbiomes, altering their diversity, resulting in homogenization and making them resemble the human microbiome. Diet is an important predictor of the microbiomes of volant vertebrates, mainly for birds, but for bats, results remain inconclusive. In spite of Indias exceptional bat diversity, there is little understanding of how their microbiomes respond to anthropogenic habitats. Therefore, we investigated the trends of taxonomic and functional diversity and their relationships with host feeding-guild and phylogeny for six wide-ranging bat species across six anthropogenically modified sites in Southern India by generating 16S barcode sequences from their fecal samples. ResultsEubacteria dominated samples with diet-specific taxonomic composition. Frugivore microbiomes contained large proportions of Cyanobacteria, possibly sourced from consumed plant matter or polluted drinking-water sources, and Lactobacillales dominated insectivore microbiomes, while Gammaproteobacteria were abundant regardless of host feeding guild. We found human pathogens in our samples possibly transferred from polluted water to the guts of bats foraging in nearby areas. We observed diet-specific taxonomic, phylogenetic, and functional composition. However, functional composition incorporating abundances displayed a high degree of overlap across feeding-guilds, suggesting functional homogenisation of microbiomes across feeding guilds, possibly due to anthropogenicity. Sample-wise diversity indices were significantly different with respect to diet only when samples from the same roost were not pooled together. However, in all cases, microbiomes from the same diet types displayed significant taxonomic and phylogenetic similarity to each other. Lastly, we observed limited concordance of microbiome diversity with chiropteran phylogeny. ConclusionsBecause of these potential signatures of pollution on bat microbiomes such as pathogens, we recommend their monitoring, especially because Cyanobacteria play a known role in bat and human disease. Our study is one of the first to study microbiome composition and function from bat species common around human inhabitation in South India, and establishes baselines in this region.

evolutionary biology↗

bioRxiv2025

Genetic Erosion at the Edge: Landscape fragmentation and connectivity in sloth bears of the Indian terai

Habitat fragmentation is a major global threat to biodiversity, particularly for species at the periphery of their range where populations are smaller and historically more isolated. Fragmented landscapes reduce connectivity, erode genetic diversity, and elevate inbreeding risk, potentially leading to local extinction. Landscape genetics offers a powerful framework to assess how land-use patterns influence gene flow and population viability. We investigated the endemic sloth bear (Melursus ursinus) populations in the Indian Central Terai landscape, a multi-use, high human density region exemplifying fragmentation and range-edge pressures. Using a ddRAD-seq based approach on non-invasively collected faecal samples (n=209), we generated genomic data, and identified 66 individuals using 964 SNP markers. Despite weak spatial genetic structure, with Dudhwa populations showing the highest differentiation (FST = 0.30). The populations exhibited extremely low heterozygosity (HO = 0.073) and high fixation index (FIS = 0.45), indicating recent bottlenecks and isolation. Landscape genetic analyses revealed agriculture density as the primary barrier to gene flow, followed by road density. Compared to sloth bear populations in Central India and Nepal Terai, CTL bears exhibit markedly reduced genetic variation, likely driven by historic fragmentation and peripheral range effects. This study provides the first genomic baseline for sloth bears in the CTL and underscores the urgency of integrating genetic monitoring with habitat management to prevent further erosion of genetic diversity and ensure long-term population persistence.

ecology↗

bioRxiv2025

Landscape matters: Deriving a generalizable understanding of population connectivity using empirical data and graph theory

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/674386v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1226384org.highwire.dtl.DTLVardef@b3949eorg.highwire.dtl.DTLVardef@1e24ae0org.highwire.dtl.DTLVardef@1a1c773_HPS_FORMAT_FIGEXP M_FIG C_FIG Human impacts on ecosystems have accelerated globally, driving a 10% decline in terrestrial biodiversity and a 70% decline in wildlife populations over the past five decades. These losses are closely linked to habitat modification and fragmentation, highlighting the urgent need for management strategies grounded in a clear understanding of how wildlife use landscapes and navigate human-altered areas. Connectivity between populations is critical for species persistence and is shaped by the interplay between landscape features and species movement. Most connectivity studies pursue application-focused goals, such as designing corridors or assessing land-use effects, often targeting single species within specific landscapes. While these approaches provide depth, they limit the development of general principles that apply across species and regions. Graph theory offers a powerful framework to distill complex connectivity patterns into comparable metrics, creating opportunities to identify such generalities. In this study, we examined connectivity patterns for 11 Indian carnivore species distributed across heterogeneous landscapes. Using secondary data, we developed habitat networks from species distribution models that incorporated both habitat quality and matrix resistance. We then applied graph theory to generate networks based on connectivity between identified habitat nodes, enabling comparisons across species and landscapes. Our results show that while connectivity patterns differ markedly among species, broad trends emerge. Larger-bodied species like tigers, which in our study are often threatened species, can overcome the effects of fragmentation better than smaller bodied species, however their connectivity is dependent on the existence of high-quality patches. Fragmented and heterogenous landscapes were always associated with modular, less efficient networks irrespective of the species. Importantly, landscape characteristics had greater influence on network-level connectivity properties, while species traits more strongly determined node-level structural complexity of the network. By integrating network theory with multispecies analyses across diverse landscapes, our work moves beyond single-species case studies to identify general drivers of connectivity. In terms of conservation, our approach allows us to generate broad insights into drivers of population connectivity informing strategies for lesser-known species and guide more effective, landscape-scale management in an era of rapid environmental change.

ecology↗

bioRxiv2025

Ancient bridges, modern threat: Conserving landscape heterogeneity ensures sustenance of living root-bridges in Meghalaya

The Anthropocene, marked by rapid biodiversity loss, has renewed attention on natures contributions to people, which include ecological, cultural, and spiritual values. A striking example of such nature-culture interactions are the living root-bridges of Meghalaya, India, where Khasi people ingeniously train the aerial roots of Ficus elastica across river valleys to form natural bridges. These structures, currently under consideration for UNESCO World Heritage recognition, exemplify sustainable resource use in one of the wettest and most landslide-prone regions of the world. However, increasing tourism and unregulated construction is threatening to this nature culture relationship in a biodiversity hotspot. In such situations, understanding the factors governing the geneflow is vital to the preservation of interactions between the pollinating fig wasps, the fig tree and its seed dispersers. Despite its ecological and cultural significance, little is known about the population biology or dispersal potential of F. elastica. Here, we investigated dispersal potential of natural populations of F. elastica across Meghalaya. Using ddRAD-SNP genotyping ([~]12K SNPs from 308 individuals), we detected four genetic clusters corresponding to E. Khasi, W. Khasi, W. Jaintia, and Ribhoi hills. Redundancy analysis and resistance modelling revealed that wind regimes and topography jointly structure these populations, enabling gene flow within but not across river valleys. Analysis of spatial distribution of related individuals indicates short dispersal distance of 1-4km varying across different populations. Given F. elasticas association with riparian ecosystems, and with UNESCO recognition pending, our study underscores the need for strict guidelines to curb habitat destruction and ensure the long-term survival of both the species and its cultural legacy.

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

The population structure of invasive Lantana camara is shaped by its mating system

Over the last century, invasive species have emerged as an important driver of global biodiversity loss. Many invasive species have low genetic diversity in the invaded habitats, owing to the demographic bottleneck during introduction. Lantana camara is one of the hundred most problematic invasive species globally. Despite its ecological importance in many countries, our understanding of the genetic diversity patterns of this plant remains poor. Previous studies hypothesize that invasive L. camara is a species complex with a hybrid origin, though this has never been tested. We investigated the population genetic patterns of L. camara by sampling 359 plants that represented a spectrum of flower colour variants across 36 locations, spanning most of the biogeographic regions across India. Analyses of the population structure using 19,008 SNPs revealed that L. camara in India exhibits a strong genetic structure. Interestingly, the structuring pattern does not exhibit a strong correlation with geography. In the structure analysis, individuals with similar flower colours clustered together regardless of their location of origin. The genetic distance between most of the individuals was low, indicating the absence of multiple species. A high inbreeding coefficient and a low proportion of heterozygous sites observed suggested that the strong structure could be due to self-fertilization. This was further confirmed by bagging experiments, which demonstrated that L. camara is self-compatible in India. Thus, we infer that L. camara exists as homozygous inbred lines formed by self-fertilization and that these inbred lines could be associated with distinct flower colours. Together, this would explain the correlation between flower colour and genetic structure, and the lack of geographic structure. These results refute the argument that L. camara is a species complex and emphasize the importance of the mating system in shaping the patterns of diversity in this invasive species. Our findings highlight a hitherto unknown role for mating systems in invasive species, furthering our understanding of evolution in invasive species.

evolutionary biology↗

bioRxiv2024

From single species to communities: microsatellite amplicon sequencing to monitor felids using Feliplex

O_LIThe current biodiversity crisis demands a shift from single-species to multispecies approaches in conservation, particularly for rare and endangered species. However, this transition requires tools optimised for multispecies research, which are currently limited. C_LIO_LIRecent advances in high-throughput sequencing (HTS) technologies and bioinformatics have enabled efficient and robust acquisition of genetic data. Amplicon sequencing approaches, in particular, have demonstrated potential for enhancing non-invasive genetic studies of endangered species, but their application has been mostly limited to single species. C_LIO_LITo enable multispecies genetic research, we introduce a cost-effective and robust HTS-based amplicon sequencing approach for genotyping multiple species simultaneously, designed for population monitoring, including individual identification and ascertaining patterns of population structure. C_LIO_LIWe developed Feliplex, a multiplex panel of 85 co-amplifying tetranucleotide microsatellite markers for cross-genotyping Felidae species, to demonstrate the utility of our approach. Feliplex was validated on known samples from nine Indian felid species across the genera Panthera, Prionailurus, and Felis. We applied it to invasive (blood and tissue) and non-invasive (hair and faeces) DNA extracts from 173 wild individuals obtaining respectively 70% and 56% multilocus genotyping success rates. The panel accurately identified known population clusters in tigers (Panthera tigris, n=19) and revealed hitherto unknown genetic structure in fishing cats (Prionailurus viverrinus, n=40). C_LIO_LIFeliplexs wide applicability across Felidae allows reliable multispecies genotyping from low-quality/quantity samples, while supporting cost-effective genetic studies and conservation monitoring of lesser-known species like small cats. Our approach has a broad applicability and can be adapted to develop similar multispecies panels for closely related species groups. C_LI

ecology↗

bioRxiv2024

Beyond neutral loci: Examining immune gene variation in tigers (Panthera tigris)

Assessing genetic diversity at loci putatively involved in fitness, such as immune genes, could provide important insights into the survival and vulnerability of endangered species. Research on immune genes in wild species has traditionally focussed on the Major Histocompatibility Complex (MHC) genes, which represent a small proportion of the immune gene repertoire and limits our understanding of immunity in non-model species. Here, we investigate five families of non-MHC immune genes - Tumor Necrosis Factors, interleukins, Toll-like Receptors, Leukocyte Immunoglobulin-Like Receptors, and chemokines - involved in adaptive and innate immunity in tiger Panthera tigris, an endangered carnivore known to have experienced historical bottlenecks and inbreeding. By leveraging 107 publicly available whole genomes, this study provides a comparative, multi-subspecific assessment of non-MHC immunogenetic diversity in tigers and identifies populations of conservation concern. We found higher genetic variation at immune receptor genes compared to neutral regions and immune signaling genes. Site frequency spectra suggest balancing selection on Toll-like receptor genes. Further, tiger populations with histories of bottlenecks and inbreeding, such as South China tigers and North western Indian tigers exhibit reduced genetic diversity and higher mutation load at immune genes, compared to large and connected tiger populations. Overall, we find that genetic drift is likely the predominant evolutionary force shaping genetic variation in tigers at both neutral and immune loci. However, some immune polymorphisms persist despite drift, thereby maintaining elevated variation, indicating that tigers have not been entirely stripped of their immunogenetic resilience. Such immunogenetic resilience may prove vital as spillover threats intensify. Significance statementUnderstanding immune gene diversity beyond the MHC genes is essential for accurately assessing the adaptive potential of endangered species. Here, we leverage whole-genome sequencing across multiple tiger subspecies to show that non-MHC immune receptor genes harbour greater variation than neutral loci, and that balancing selection might maintain diversity at Toll-like receptor genes. Even in bottlenecked populations, some immune polymorphisms are retained, indicating that tigers possess broader immunogenetic resilience than previously thought.

evolutionary biology↗

bioRxiv2024

Unbounding fish: Assessing vulnerability to overexploitation for transboundary fish populations

SummeryGlobally coastal fisheries are managed according to political jurisdictions of nations and their provinces. This practice often results in multiple states/provinces managing a single genetically distinct fish population autonomously and without coordination. In multi-species, decentralized and data poor fisheries such management lead to poor assessment and eventually overharvest of fish. To assess overexploitation risk for such interjurisdictional populations, we propose a risk indicator IRIIS which incorporates 1) species-specific vulnerability 2) distribution of genetically-distinct populations with respect to jurisdictional boundaries and 3) differences in management practices across jurisdictions. As a case study we evaluated overexploitation risk for individual populations of nine commonly caught fish species spanning across multiple jurisdictions along Indias west coast. Our results indicate that interjurisdictional differences in management alters innate biological susceptibility. IRIIS is also sensitive to population-level differences and policy changes. Our analyses emphasize the need for population-level assessments and interjurisdictional cooperation to achieve sustainable fisheries. Science and society statementCoastal fisheries worldwide are managed through politically defined maritime jurisdictions, while fish populations are structured by biological processes such as dispersal, ocean currents, and natural barriers. This fundamental mismatch between biological population boundaries and jurisdictional management boundaries often results in the same population being exploited under multiple, uncoordinated governance regimes. In the context of the global overfishing crisis, such governance fragmentation can lead to inaccurate stock assessments and heightened risk of local population collapse. This challenge is particularly acute in developing and tropical countries, where fisheries are multispecies, data-limited, and increasingly decentralized to support community-based governance. While decentralization promotes social justice, it can inadvertently intensify the misalignment between biological and administrative boundaries, complicating sustainable management. In this manuscript, we introduce a robust framework -- the Integrative Risk Indicator for Interjurisdictional Stocks (IRIIS) -- which has a high applicability for multispecies, data-poor, and decentralized fisheries. Building on, and extending beyond, species-level Productivity Susceptibility Analysis (PSA), IRIIS integrates population genomics to delineate biologically meaningful population boundaries and combines these with fisheries policies and regulations across jurisdictions to quantify management-associated risks of overexploitation at the population level. We apply IRIIS to case studies of nine commercially important fish species harvested along the west coast of India. Our results demonstrate that the framework can (i) distinguish differential vulnerability among populations of the same species, (ii) explicitly capture management disparities across jurisdictions exploiting shared populations, and (iii) detect sensitivity to temporal changes in fisheries policies. By linking genomics, governance, and risk assessment, IRIIS provides a practical framework for identifying interjurisdictional management gaps and actionable entry points for policy coordination. This approach is particularly relevant for the Global South, where reconciling social equity objectives with ecological sustainability is both essential and challenging.

ecology↗

bioRxiv2024

Identification of distinct rodent-associated adenovirus lineages from a mixed-use landscape in the Western Ghats biodiversity hotspot

Shifts in land-use patterns and increased human-livestock-wildlife interactions have generated numerous possibilities for pathogen spillover. This demands increased efforts of pathogen surveillance in wildlife, especially in changing landscapes with high biodiversity. We investigated adenovirus diversity in small mammals, an understudied host taxon, from a forest-plantation mosaic in the Western Ghats biodiversity hotspot. Using PCR-based screening followed by Sanger sequencing and phylogenetic analyses, we attempted to detect and characterize adenovirus diversity in seven species of small mammals. We observed high prevalence (up to 38.8%) and identified five lineages of adenoviruses with unique mutations in the endemic and dominant small mammal species, Rattus satarae. These lineages significantly differed from other known Murine adenoviruses (p-distance > 25%), indicating the likelihood of novel adenovirus diversity in this endemic small mammal. Collectively, our results highlight the potential for unexplored diversity of DNA viruses like adenovirus in poorly explored host taxa inhabiting human-used landscapes and its zoonotic implications.

evolutionary biology↗

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↗