Population genetics and conservation implications of the critically endangered Javan rhinoceros (Rhinoceros sondaicus) in Indonesia: a genomic and ecological assessment

Project Abstract

This study integrates genomic, ecological, and conservation data to assess the population genetics and long-term viability of the critically endangered Javan rhinoceros (Rhinoceros sondaicus) in Indonesia, with an emphasis on informing targeted management actions. We generated whole-genome sequencing data from all known living individuals across the national population, complemented by noninvasive samples from key habitat fragments to maximize coverage while minimizing disturbance. Population genomic analyses reveal extremely low genetic diversity (heterozygosity markedly below regional benchmarks for rhinoceroses) and strong signals of inbreeding within isolated subpopulations, consistent with a long-term demographic bottleneck. Principal component analyses and admixture tests indicate minimal contemporary gene flow between core habitat blocks, underscoring the genetic isolation of remnant groups. We detected several runs of homozygosity and elevated inbreeding coefficients, which correlate with reduced adaptive potential, particularly in genes linked to immune response and reproductive biology. Mitochondrial haplotype diversity is likewise limited, reinforcing concerns about historical population contraction and maternal lineage loss. Ecological assessments conducted through camera trap arrays, radio-telemetry (where feasible), and environmental DNA (eDNA) surveys provide granular insights into habitat use, ranging behavior, and temporal activity patterns. The results show strong fidelity to protected lowland swamp forest mosaics and riverine corridors, with seasonal shifts in resource availability driving movement corridors that currently intersect high-density human activity zones. Habitat suitability modeling highlights climate-vegetation interactions as critical determinants of carrying capacity, with projected habitat contraction under drought-augmented scenarios. Predator-prey dynamics appear stable, but demographic vulnerabilities due to skewed sex ratios and low juvenile recruitment threaten population growth. Our integrated model combines genomic diversity metrics with ecological connectivity indices to identify four priority management units (PMUs) that maximize genetic exchange potential while preserving existing habitat integrity. Conservation implications center on augmenting gene flow through carefully planned translocations, habitat restoration to re-create functional corridors, and the establishment of a robust, long-term monitoring framework incorporating genomics and eDNA. We propose a stepwise genetic rescue strategy beginning with the smallest, most isolated populations to avoid outbreeding depression while maximizing heterozygosity gains. Proactive anti-poaching measures, community-inclusive land-use planning, and cross-jurisdictional governance are recommended to sustain corridor connectivity and reduce human-rhino conflict. The study also contributes to methodological advancements by validating low-input sequencing pipelines for endangered wildlife and developing an integrated decision-support tool that couples genomic data with ecological and demographic indicators. Overall, the findings provide actionable, evidence-based guidance for reversing genetic erosion and stabilizing the population trajectory of the Javan rhinoceros in Indonesia, aligning conservation actions with both current realities and future climate-informed projections.

Project Overview

What This Project Is About

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A plain-language overview of the topic and what the project investigates.

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The Problem It Addresses

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What problem or gap this project tackles and why it matters to the field or society.

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Objectives of the Project

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1. Understand how genetics help explain population decline in Javan rhinos.
2. Describe how habitat and movement affect survival and reproduction.
3. Identify key conservation needs to maintain or enhance genetic diversity.

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What You Will Do Step by Step

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1. Review basic biology of the Javan rhinoceros and current conservation status.
2. Learn simple genetic concepts (genes, DNA, diversity) with non-technical explanations.
3. Collect or access existing non-invasive samples (e.g., dung) and ecological data.
4. Analyze data with straightforward methods to assess diversity and relatedness.
5. Interpret findings in the context of habitat, threats, and management options.
6. Draft practical conservation recommendations for policymakers and caretakers.

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Expected Outcome

Outcomes include a clear picture of genetic health, actionable conservation suggestions, and improved understanding for non-experts about how genetics and ecology intersect in wildlife protection.