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Large-scale Quantification of Vertebrate Biodiversity in Ailaoshan Nature Reserve from Leech iDNA

By Yinqiu Ji, Christopher CM Baker, Yuanheng Li, Viorel D Popescu, Zhengyang Wang, Jiaxin Wang, Lin Wang, Chunying Wu, Chaolang Hua, Zhongxing Yang, Chunyan Yang, Charles C.Y. Xu, Qingzhong Wen, Naomi E Pierce, Douglas W Yu

Posted 11 Feb 2020
bioRxiv DOI: 10.1101/2020.02.10.941336

Environmental DNA (eDNA) has great potential to complement visual surveys, camera trapping, and bioacoustics in measuring biodiversity. We report here a large-scale attempt to use DNA from leech-ingested bloodmeals to estimate vertebrate occupancy at the scale of an entire protected area: the 677 km2 Ailaoshan national-level nature reserve in Yunnan province, southwest China. We contracted 163 park rangers to collect leeches in 172 patrol areas, resulting in 30,468 total leeches, divided over 893 replicate samples. Replicate sampling from each patrol area was achieved by providing rangers with preservative-filled tubes in separate, self-sealing bags, inducing them to distribute collected leeches over multiple bags, which we could sequence separately. We show that combining leech-derived DNA data with Bayesian site-occupancy modeling can produce detailed and useful biodiversity inferences for a wide range of vertebrates in a reasonable timeframe. For example, in Ailaoshan, sites at lower elevations and closer to the reserve edge have higher occupancy of domestic species (cows, sheep, goats) compared to sites at higher elevations and closer to the reserve interior. Muntjak deer show similar occupancy patterns to the domesticated species, but otherwise, most species of large mammal wildlife (e.g. sambar, black bear, serow, tufted deer) show the opposite pattern: greater occupancy at higher elevations and closer to the reserve interior. We conclude that leech-derived eDNA can be used to efficiently measure the effectiveness of protected areas in terms of vertebrate biodiversity outcomes and to help us optimize the deployment of management resources within reserves, by providing valuable information on the spatial distributions of vertebrate species and on the environmental and anthropogenic correlates of those distributions.

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