This document is downloaded from DR‑NTU (https://dr.ntu.edu.sg) Nanyang Technological University, Singapore. Leech blood‑meal invertebrate‑derived DNA reveals differences in Bornean mammal diversity across habitats Drinkwater, Rosie; Jucker, Tommaso; Potter, Joshua H. T.; Swinfield, Tom; Coomes, David A.; Slade, Eleanor M.; Gilbert, M. Thomas P.; Lewis, Owen T.; Bernard, Henry; Struebig, Matthew J.; Clare, Elizabeth L.; Rossiter, Stephen J. 2020 Drinkwater, R., Jucker, T., Potter, J. H. T., Swinfield, T., Coomes, D. A., Slade, E. M., Gilbert, M. T. P., Lewis, O. T., Bernard, H., Struebig, M. J., Clare, E. L. & Rossiter, S. J. (2020). Leech blood‑meal invertebrate‑derived DNA reveals differences in Bornean mammal diversity across habitats. Molecular Ecology, 30(13), 3299‑3312. https://dx.doi.org/10.1111/mec.15724 https://hdl.handle.net/10356/152420 https://doi.org/10.1111/mec.15724 © 2020 The Authors. Molecular Ecology published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Downloaded on 25 Sep 2021 14:15:17 SGT Received: 27 February 2020 | Revised: 26 October 2020 | Accepted: 2 November 2020 DOI: 10.1111/mec.15724 SPECIAL ISSUE Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats Rosie Drinkwater1 | Tommaso Jucker2 | Joshua H. T. Potter1 | Tom Swinfield3 | David A. Coomes3 | Eleanor M. Slade4,5 | M. Thomas P. Gilbert6,7 | Owen T. Lewis4 | Henry Bernard8 | Matthew J. Struebig9 | Elizabeth L. Clare1 | Stephen J. Rossiter1 1School of Biological and Chemical Sciences, Queen Mary University of London, London, Abstract UK The application of metabarcoding to environmental and invertebrate-derived DNA 2 School of Biological Sciences, University of (eDNA and iDNA) is a new and increasingly applied method for monitoring biodi- Bristol, Bristol, UK 3Department of Plant Sciences, Forest and versity across a diverse range of habitats. This approach is particularly promising for Ecology Conservation Group, University of sampling in the biodiverse humid tropics, where rapid land-use change for agriculture Cambridge, Cambridge, UK means there is a growing need to understand the conservation value of the remain- 4Department of Zoology, University of Oxford, Oxford, UK ing mosaic and degraded landscapes. Here we use iDNA from blood-feeding leeches 5Asian School of the Environment, Nanyang (Haemadipsa picta) to assess differences in mammalian diversity across a gradient of Technological University, Singapore City, forest degradation in Sabah, Malaysian Borneo. We screened 557 individual leeches Singapore 6Department of Biology, University of for mammal DNA by targeting fragments of the 16S rRNA gene and detected 14 Copenhagen, Copenhagen, Denmark mammalian genera. We recorded lower mammal diversity in the most heavily de- 7 University Museum, NTNU, Trondheim, graded forest compared to higher quality twice logged forest. Although the accu- Norway 8Institute for Tropical Biology and mulation curves of diversity estimates were comparable across these habitat types, Conservation, Universiti Malaysia Sabah, diversity was higher in twice logged forest, with more taxa of conservation concern. Sabah, Malaysia In addition, our analysis revealed differences between the community recorded in 9Durrell Institute of Conservation and Ecology (DICE), School of Anthropology the heavily logged forest and that of the twice logged forest. By revealing differences and Conservation, University of Kent, in mammal diversity across a human-modified tropical landscape, our study demon- Canterbury, UK strates the value of iDNA as a noninvasive biomonitoring approach in conservation Correspondence assessments. Rosie Drinkwater, Stephen Rossiter, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. KEYWORDS Emails: [email protected] (R.D.); biodiversity, Borneo, Haemadipsidae, invertebrate-derived DNA, land-use change, molecular [email protected] (S.R.) biomonitoring Funding information Natural Environment Research Council, Grant/Award Number: NE/K016148/1 and NE/S01537X/1 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2020 The Authors. Molecular Ecology published by John Wiley & Sons Ltd Molecular Ecology. 2021;30:3299–3312. wileyonlinelibrary.com/journal/mec | 3299 3300 | DRINKWATER et AL. 1 | INTRODUCTION allow genetic confirmation of species presence without the need for actual observations, it can also complement more conventional Tropical ecosystems are under pressure from deforestation (Hansen monitoring based on, for example, camera trap surveys, with associ- et al., 2013) and other anthropogenic activities driving forest degra- ated savings in fieldwork costs (e.g. Leempoel et al., 2020; Weiskopf dation (Lewis et al., 2015). The removal of trees, and the associated et al., 2017). Abrams et al. (2019) have extended this further by an- damage from timber extraction, causes lasting changes to vegetation alysing data from spatially matched iDNA and camera traps using an structure and microclimate, with knock-on consequence for species occupancy modelling framework and found that while both methods diversity (Blonder et al., 2018). For example, microclimatic extremes resulted in similar accumulation rates, the latter gave higher abso- are more frequent in logged forests than in older growth forests lute species richness values. These authors also demonstrated that (Blonder et al., 2018; Hardwick et al., 2015; Jucker et al., 2018). estimates of occupancy and detection probability varied depending In addition to altering floral and faunal community composition on host species but also depended on leech type, with tiger leech (Laurance et al., 2018; Wilkinson et al., 2018), logged forests can (Haemadipsa picta) samples resulting in higher detection and occu- show changes in diverse ecosystem functions, including litter de- pancy probabilities compared to brown leeches (Haemadipsa zeylan- composition, predation and seed dispersal (Bovo et al., 2018; Robert ica) (Abrams et al., 2019). M. Ewers et al., 2015). As a result, such forests show lower resilience A further consideration of using iDNA is whether habitat has an to numerous local and climatic stressors (Struebig et al., 2015) and effect on the efficacy of the invertebrate used for sampling (the so- are at greater risk of conversion to commodity agriculture (Edwards called “invertebrate sampler”). This may be particularly pertinent in et al., 2011). the context of land-use change, where small-bodied invertebrates Despite the well-known negative effects of forest degradation may be more sensitive to local conditions than the vertebrates for on ecosystem processes, there is evidence that these degraded which they are being used to assay. It is not known, for example, habitats can still support biodiversity and have considerably greater whether local microclimate conditions will alter the foraging be- conservation value than alternative agricultural landscapes (Deere haviour of invertebrate samplers, and thus their utility for comparing et al., 2017; Gibson et al., 2011). Even within highly degraded vertebrate diversity across habitats. Among the popular samplers forest, animal community composition tends to be more simi- are terrestrial leeches of the family Haemadipsidae, which are re- lar to forest than it is to agricultural plantations (Gray et al., 2014; stricted to humid habitats and are adversely impacted by the drier Wearn et al., 2017). Within heavily logged forest, for example, for- conditions arising from forest degradation (Hardwick et al., 2015; est remnants have been shown to be important for birds (Mitchell Jucker et al., 2018). Previously we showed that forest structure af- et al., 2018) and invertebrates (Gray et al., 2014). These and other fects the distributions of two congeneric haemadipsid leech species studies of how land-use change relates to biodiversity have increas- in logged forest (Drinkwater et al., 2019), yet it is not known whether ingly utilized data generated by LiDAR, an approach that allows new such habitat preferences have additional implications for the detec- and improved opportunities to quantify forest structure and micro- tion of mammals. climatic variables across spatial scales (Asner et al., 2018; Deere Here we apply iDNA to assess the impact of habitat degradation et al., 2020; Seaman et al., 2019). on mammal diversity across a tropical landscape. Additionally, we In recent years, the toolkit for biodiversity monitoring has ex- test whether landscape-scale variation in mammal diversity can be panded from solely field-based methods to also encompass molec- explained by temperature and humidity, which could suggest that ular techniques. In particular, advances in sequencing now allow for detected patterns are mediated by leech responses to microclimate. the routine metabarcoding of environmental DNA (eDNA) samples, To achieve this, we combined repeated surveys with a standard- thereby revolutionizing molecular ecology. One such area that has ized collection protocol for tiger leeches across a degraded forest seen rapid progress is the use of animal-feeding invertebrate spe- landscape in Malaysian Borneo. In this region, unsustainable logging