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Abstract Information on geographic patterns of species genetic diversity is often needed to inform conservation strategies. Obtaining data over large geographic areas can be difficult, especially for rare or elusive species. Here, we explore the use of invertebrate‐derived DNA (iDNA) obtained from terrestrial leeches to assess genetic diversity of the Annamite striped rabbit Nesolagus timminsi, a little‐known and highly threatened lagomorph endemic to the Annamites ecoregion of Vietnam and Laos. We collected 4,877 leeches pooled into 651 leech bulk samples from eight study areas across the northern and central Annamites. Using metabarcoding, we detected Annamite striped rabbit DNA in 11 leech bulk samples from five of the study areas. We amplified up to 3,000 bp of six mitochondrial DNA loci of Annamite striped rabbit from nine of the 11 bulk samples. Haplotype network analyses showed five shared haplotypes among these samples. Phylogenetic trees constructed using maximum likelihood and Bayesian inference showed little geographic structuring among the Annamite striped rabbit populations across the five study areas. Our results provide information that can be directly used to inform planned ex situ conservation measures for the Annamite striped rabbit. We discuss our results within the context of using iDNA to noninvasively obtain data to assess species genetic diversity, and the potential of this approach to be applied to other species and systems.

Abstract The Annamite mountains of Vietnam and Laos are a global biodiversity hotspot harboring several threatened endemic species. Conservation efforts to protect these endemics are hampered by a lack of knowledge on their ecology and distribution. We conducted landscape scale camera‐trapping across six study areas in the Annamites to assess distribution patterns of two endemics: the Annamite dark muntjac species complex Muntiacus rooseveltorum/ truongsonensis and the Annamite striped rabbit Nesolagus timminsi. We used a Bayesian single‐species occupancy framework to estimate occupancy as a function of ecological and anthropogenic factors. Our study showed that Annamite dark muntjac was predominantly found at higher elevations (>1000 m) and in areas that were more inaccessible to people and had lower surrounding village density. Annamite striped rabbit exhibited both positive and negative responses to elevation among study areas, with no clear response to the anthropogenic covariates. Our results showed that covariate responses varied among the study areas when random effects were included on study areas. We discuss the application of random effects to investigate species occupancies across large spatial scales, and the risk of not accounting for variation among study areas. Our prediction maps provide the first comprehensive overview of the distribution of these endemic species across a substantial part of their range and can be used to help stakeholders focus conservation efforts on priority areas.