Using terrestrial haematophagous leeches to enhance tropical biodiversity monitoring programmes in Bangladesh

Weiskopf, Sarah R.; McCarthy, Kyle P.; Tessler, Michael; Rahman, Hasan A.; McCarthy, Jennifer L.; Hersch, Rebecca; Faisal, Mohammad Muzaffar; Siddall, Mark E.

doi:10.1111/1365-2664.13111

Cited by 45 publications

(77 citation statements)

References 37 publications

(63 reference statements)

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“…Our analysis did reveal a difference in mammal detection success between the two types of leeches. It is possible that the larger size of tiger leeches leads to a higher chance to amplify mammalian DNA (see also Weiskopf et al , 2018). We also found a slightly stronger bias in tiger leeches towards larger bodied mammals.…”

Section: Discussionsupporting

confidence: 54%

“…Recent methodological advances, namely amplicon-based high-throughput sequencing or 'metabarcoding', now also allow the reliable reading of such DNA sources (Abrego et al , 2018). Invertebrate-derived DNA (iDNA) is an offshoot of eDNA, where terrestrial vertebrates can be detected via their DNA that was ingested by invertebrates (Schnell et al , 2012(Schnell et al , , 2015Calvignac-Spencer et al , 2013a, 2013bTessler et al , 2018;Weiskopf et al , 2018).…”

Section: Introductionmentioning

confidence: 99%

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Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Abrams

Hoerig

Brozovic

et al. 2018

Preprint

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1. Invertebrate-derived DNA (iDNA), in combination with high throughput sequencing, has been proposed as a cost-efficient and powerful tool to survey vertebrate species. Previous studies, however, have only provided evidence that vertebrates can be detected using iDNA, but have not taken the next step of placing these detection events within a statistical framework that allows for robust biodiversity assessments.2. Here, we compare concurrent iDNA and camera-trap surveys. Leeches were repeatedly collected in close vicinity to 64 camera-trap stations in Sabah, Malaysian Borneo. We analyze iDNA-derived mammalian detection events in a modern occupancy model that accounts for imperfect detection and compare the results with those from occupancy models parameterized with camera-trap-derived detection events. We also combine leech-iDNA and camera-trap data in a single occupancy model.3. We found consistent estimates of occupancy probabilities produced by our camera-trap and leech datasets. This indicates that the metabarcoding of leech-iDNA method provides reasonable estimates of occupancy and can be a suitable method for studying and monitoring mammal species in tropical rainforests. However, we also show that a more extensive collection of leeches would be needed to assess mammal biodiversity with a similar robustness as with camera traps. As certain taxa were only detected in leeches, we see great potential in complementing camera-trap studies with the iDNA approach, as long as the collection of leeches follows a similar robust and standardized sampling scheme. 4. Synthesis and applications. The approach we describe here is not restricted to the processing of leech samples, but can be used for the analysis of other iDNA and environmental DNA (eDNA) data. Our study is the first step to shift the application of e/iDNA studies from opportunistic ad-hoc collections to systematic surveys required for long-term wildlife populations and biodiversity monitoring programs.

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Section: Discussionsupporting

confidence: 54%

Section: Introductionmentioning

confidence: 99%

Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Abrams

Hoerig

Brozovic

et al. 2018

Preprint

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“…Since the field of iDNA originated, targeted collection followed by iDNA analyses of gut contents has been carried out on different invertebrate taxa such as leeches (Drinkwater et al, 2019;Pérez-Flores, Rueda-Calderon, Kvist, Siddall, & Oceguera-Figueroa, 2016;Schnell et al, 2018;Weiskopf et al, 2018), sand flies (Kocher, De Thoisy, et al, 2017), blow and flesh flies Hoffmann et al, 2018;Lee, Gan, Clements, & Wilson, 2016;Lee, Sing, & Wilson, 2015;Rodgers et al, 2017;Schubert et al, 2015), mosquitoes (Kocher, De Thoisy, et al, 2017), ticks (Gariepy et al, 2012), marine copepods (Meekan et al, 2017), and shrimps (Siegenthaler et al, 2019). This has offered a new and promising tool to complement traditional vertebrate monitoring methods, something of great value in the ongoing biodiversity monitoring efforts (Bohmann et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests

et al. 2019

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Background: Thousands of bulk arthropod samples are collected globally every year for monitoring programs, conservation efforts, and ecosystem assessments. The taxonomic contents of these samples can be assessed either morphologically or molecularly using DNA metabarcoding coupled with high-throughput sequencing, the latter of which has gained popularity in recent years. In a related field, only vertebrateingesting invertebrates, such as carrion flies and blood-feeding leeches, are targeted for collection, and metabarcoding is carried out on the vertebrate DNA in their gut contents to provide information on vertebrate diversity (invertebrate-derived DNA, iDNA). Aims:Here, we show that the two approaches can be combined, that is, that vertebrate DNA can be detected through metabarcoding of bulk arthropod samples.Materials and Methods: Two metabarcoding primer sets were used to PCR amplify mammal and vertebrate DNA in DNA extracted from bulk arthropod samples collected with pitfall and Malaise traps in tropical forests in Brazil and Tanzania. Results:In total, 32 vertebrate taxa were detected representing mammals, amphibians, and birds. Detected taxa were within, or close to, their known geographical distributions. Conclusion:This study demonstrates that with a relatively small additional investment, information on vertebrate diversity can be obtained from bulk arthropod samples. This is of particular interest in projects where bulk arthropod samples are collected and extracted with the aim to use metabarcoding to assess arthropod taxa.In such studies, the additional information on vertebrates can further inform ecological assessments and monitoring programs and function as a supplement to traditional survey methods of vertebrates.

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“…The use of eDNA is relatively new but shows considerable promise. Invertebrate-derived DNA (iDNA) approaches using terrestrial hematophagous leeches, in particular, have proven adept at detecting tropical mammals (Schnell et al, 2012; Schnell et al, 2018; Weiskopf et al, 2018). Recently, Abrams et al (2019) showed that combining camera-trapping and iDNA leech data has the potential to improve detection probabilities for tropical mammal species beyond what would be provided by each method independently.…”

Section: Introductionmentioning

confidence: 99%

Identifying conservation priorities in a defaunated tropical biodiversity hotspot

Tilker

Abrams

Nguyen

et al. 2019

Preprint

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Aim: Unsustainable hunting is leading to widespread defaunation across the tropics. To 21 mitigate against this threat with limited conservation resources, stakeholders must 22 make decisions on where to focus anti-poaching activities. Identifying priority areas in a 23 robust way allows decision-makers to target areas of conservation importance, 24 therefore maximizing the impact of conservation interventions. 25 Location: Annamite mountains, Vietnam and Laos.26 2 Methods: We conducted systematic landscape-scale surveys across five study sites (four 27 protected areas, one unprotected area) using camera-trapping and leech-derived 28 environmental DNA. We analyzed detections within a Bayesian multi-species occupancy 29 framework to evaluate species responses to environmental and anthropogenic 30 influences. Species responses were then used to predict occurrence to unsampled 31 regions. We used predicted species richness maps and occurrence of endemic species to 32 identify areas of conservation importance for targeted conservation interventions.33 Results: Analyses showed that habitat-based covariates were uninformative. Our final 34 model therefore incorporated three anthropogenic covariates as well as elevation, which 35 reflects both ecological and anthropogenic factors. Conservation-priority species tended 36to found in areas that are more remote now or have been less accessible in the past, and 37 at higher elevations. Predicted species richness was low and broadly similar across the 38 sites, but slightly higher in the more remote site. Occupancy of the three endemic species 39 showed a similar trend. 40Main conclusion: Identifying spatial patterns of biodiversity in heavily-defaunated 41 landscapes may require novel methodological and analytical approaches. Our results 42 indicate to build robust prediction maps it is beneficial to sample over large spatial 43 scales, use multiple detection methods to increase detections for rare species, include 44 anthropogenic covariates that capture different aspects of hunting pressure, and analyze 45 data within a Bayesian multi-species framework. Our models further suggest that more 46 remote areas should be prioritized for anti-poaching efforts to prevent the loss of rare 47 and endemic species. 48

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Using terrestrial haematophagous leeches to enhance tropical biodiversity monitoring programmes in Bangladesh

Cited by 45 publications

References 37 publications

Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Shifting up a gear with iDNA: from mammal detection events to standardized surveys

Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests

Identifying conservation priorities in a defaunated tropical biodiversity hotspot

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