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.

doi:10.1111/mec.15724

Cited by 30 publications

(44 citation statements)

References 105 publications

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“…2015). The presence of all these species have been confirmed in the area using leech-based iDNA sampling (Drinkwater et al . 2020).…”

Section: Discussionmentioning

confidence: 87%

“…Now the focus is moving towards the development of standardised invertebrate collection methods and biodiversity analyses (Abrams et al . 2019, Drinkwater et al . 2020) allowing for greater integration of the two techniques (Tilker et al .…”

Section: Discussionmentioning

confidence: 99%

“…2012) or, in more recent studies, by hand-searching within fixed areas (Abrams et al . 2019, Drinkwater et al . 2020).…”

Section: Introductionmentioning

confidence: 99%

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Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

Drinkwater

Clare

Chung

et al. 2021

Preprint

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The application of environmental DNA (eDNA) sampling in biodiversity surveys has gained widespread acceptance, especially in aquatic systems where free eDNA can be readily collected by filtering water. In terrestrial systems, eDNA-based approaches for assaying vertebrate biodiversity have tended to rely on blood-feeding invertebrates, including leeches and mosquitoes (termed invertebrate-derived DNA or iDNA). However, a key limitation of using blood-feeding taxa as samplers is that they are difficult to trap, and, in the case of leeches, are highly restricted to humid forest ecosystems. Dung beetles (superfamily Scarabaeoidea) feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps; are globally distributed; and also occur in a wide range of biomes, allowing mammal diversity to be compared across habitats. In this exploratory study, we test the potential utility of dung beetles as vertebrate samplers by sequencing the mammal DNA contained within their guts. First, using a controlled feeding experiment, we show that mammalian DNA can be retrieved from the guts of large dung beetles (Catharsius renaudpauliani) for up to 10 hours after feeding. Second, by combining high-throughput sequencing of a multi-species assemblage of dung beetles with PCR replicates, we show that multiple mammal taxa can be identified with high confidence. By providing preliminary evidence that dung beetles can be used as a source of mammal DNA, our study highlights the potential for this widespread group to be used in future biodiversity monitoring surveys.

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“…2015). The presence of all these species have been confirmed in the area using leech-based iDNA sampling (Drinkwater et al . 2020).…”

Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

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Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

Drinkwater

Clare

Chung

et al. 2021

Preprint

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“…For example, aquatic vertebrate or invertebrate communities can be detected with eDNA metabarcoding of water samples (Shaw et al, 2016;Stat et al, 2017;Valentini et al, 2016), animal diets can be detected from eDNA metabarcoding of feces (De Barba et al, 2014;Massey et al, in press;Roffler et al, 2021), and plants and fungi can be detected by eDNA metabarcoding of pollen or ice core samples (Bell et al, 2019;Kraaijeveld et al, 2015;Varotto et al, 2021). Similarly, an emerging technique to monitor the diversity of terrestrial vertebrates uses animalfeeding invertebrates (whether feeding upon blood, flesh, or scat) as direct sources of species' DNA and is called invertebrate-derived DNA (iDNA) (Batovska et al, 2018;Calvignac-Spencer et al, 2013;Drinkwater et al, 2019Drinkwater et al, , 2020Gogarten et al, 2020;Kocher et al, 2017; P. S. Lee et al, 2016;Schnell et al, 2012;van der Heyde et al, 2020;D. W. Yu et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…Leeches (Drinkwater et al, 2019;Schnell et al, 2012Schnell et al, , 2018Weiskopf et al, 2018) and carrion flies (Calvignac-Spencer et al, 2013; P. S. Lee et al, 2016;Lynggaard et al, 2019;Rodgers et al, 2017) have been the primary sources of validating iDNA metabarcoding for monitoring vertebrate biodiversity. The limited number of studies utilizing metabarcoding with leeches or carrion flies as iDNA samplers have shown that both taxa effectively profile biodiversity in remote or difficult to access environments such as tropical forests (Drinkwater et al, 2020;Gogarten et al, 2020; P. S. Lee et al, 2016;Weiskopf et al, 2018). There is a growing literature of comparing carrion flies as iDNA sources for metabarcoding to camera trapping (Gogarten et al, 2020; P. S. Lee et al, 2016;Rodgers et al, 2017) but even with their utility for profiling animal diversity, neither leeches nor carrions flies are widely collected for other research purposes.…”

Section: Introductionmentioning

confidence: 99%

Invertebrates for vertebrate biodiversity monitoring: comparisons using three insect taxa as iDNA samplers

Massey

Bronzoni

Silva

et al. 2021

Preprint

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Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or feces. Here, we use metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) to profile gamma and alpha diversity in a dry, tropical forest in the southern Amazon. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. Carrion flies were the most effective sampler, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, in describing vertebrate biodiversity followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.

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Creating genetic reference datasets: Indirect sampling of target species using terrestrial leeches as sample “collectors”

et al. 2021

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Sampling genetic material from rare and often secretive mammals can be difficult in challenging environments such as tropical rainforests. Large-scale sampling is important however for resolving species' taxonomic uncertainties, as well as to help provide genetic material for reference databases that can be used with DNA forensics to combat the illegal wildlife trade. Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) offer a promising way to overcome this sampling bottleneck, though to date e/iDNA studies have been primarily used to obtain information about species presence using barcoding or metabarcoding approaches. In this study, we collected 4,710 terrestrial leeches across six protected areas in the Annamite Mountains of Viet Nam and Laos and sequenced fragments (223-694 bp) of mt-Cytb and/or mt-Dcr of the mitogenomes from six species that are frequently found in the illegal wildlife trade. Although amplification success was generally low (<50%) because DNA was highly degraded, we showed that e/iDNA samples can be an important source of genetic material for difficult to sample species and show promise as a way to fill existing sampling gaps. Because e/iDNA sampling has the potential to generate much-needed genetic data to improve taxonomic assessments, this approach can be used to support conservation management by contributing to genetic databases that are necessary to determine the origin of wildlife products or to inform the reintroduction of confiscated animals.

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Leech blood‐meal invertebrate‐derived DNA reveals differences in Bornean mammal diversity across habitats

Abstract: 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.

Cited by 30 publications

References 105 publications

Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

Dung beetles as vertebrate samplers – a test of high throughput analysis of dung beetle iDNA

Invertebrates for vertebrate biodiversity monitoring: comparisons using three insect taxa as iDNA samplers

Creating genetic reference datasets: Indirect sampling of target species using terrestrial leeches as sample “collectors”

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