Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: evidence from a known tropical mammal community

Rodgers, Torrey W.; Xu, Charles C.Y.; Giacalone, Jacalyn; Kapheim, Karen M.; Saltonstall, Kristin; Vargas, Marta; Yu, Douglas W.; Somervuo, Panu; McMillan, W. Owen; Jansen, Patrick A.

doi:10.1101/133405

Cited by 24 publications

(45 citation statements)

References 35 publications

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“…To conclude, our results suggest that urban fly‐based mammal biodiversity assessment may become a very time‐ and cost‐effective monitoring tool, especially if coupled to the many ongoing urban citizen science initiatives (Silvertown, ). Further investigations of the relative performance of this and other methods would, however, be very welcome, as recent reports have shown that fly‐ and camera trap‐based biodiversity assessments only provide partially overlapping results and can sometimes fail at detecting relatively abundant wildlife species (Lee et al., ; Rodgers et al., ).…”

Section: Discussionmentioning

confidence: 99%

“…Recently, the use of invertebrate-derived DNA (iDNA) was put forward as a promising strategy to assess mammalian biodiversity (summarized in: Calvignac-Spencer, Leendertz, Gilbert, & Schubert, 2013;Schnell et al, 2015). Leeches as well as blow and flesh flies (families Calliphoridae and Sarcophagidae; later on flies) were, for example, used as wildlife DNA samplers in pristine tropical areas (Calvignac-Spencer, Merkel, et al, 2013;Lee, Gan, Clements, Wilson, & Adamowicz, 2016;Rodgers et al, 2017;Schnell et al, 2012;Schubert et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…All adults feed on faeces and carcasses if available and females are especially attracted to carcasses where they can obtain the proteins necessary to the maturation of their reproductive system and oviposit (Gennard, 2012;Mart ın-Vega & Baz, 2013). Fly seem to feed opportunistically, exploiting faeces and carrion from a broad range of mammals (Calvignac-Spencer, Merkel, et al, 2013;Lee et al, 2016;Rodgers et al, 2017). As they are also abundant worldwide in nearly all habitats, including most cities, they could in principle be used to characterize wild mammal communities in urban settings.…”

Section: Introductionmentioning

confidence: 99%

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Blow flies as urban wildlife sensors

Hoffmann

Merkel

Sachse

et al. 2018

Molecular Ecology Resources

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Wildlife detection in urban areas is very challenging. Conventional monitoring techniques such as direct observation are faced with the limitation that urban wildlife is extremely elusive. It was recently shown that invertebrate-derived DNA (iDNA) can be used to assess wildlife diversity in tropical rainforests. Flies, which are ubiquitous and very abundant in most cities, may also be used to detect wildlife in urban areas. In urban ecosystems, however, overwhelming quantities of domestic mammal DNA could completely mask the presence of wild mammal DNA. To test whether urban wild mammals can be detected using fly iDNA, we performed DNA metabarcoding of pools of flies captured in Berlin, Germany, using three combinations of blocking primers. Our results show that domestic animal sequences are, as expected, very dominant in urban environments. Nevertheless, wild mammal sequences can often be retrieved, although they usually only represent a minor fraction of the sequence reads. Fly iDNA metabarcoding is therefore a viable approach for quick scans of urban wildlife diversity. Interestingly, our study also shows that blocking primers can interact with each other in ways that affect the outcome of metabarcoding. We conclude that the use of complex combinations of blocking primers, although potentially powerful, should be carefully planned when designing experiments.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Blow flies as urban wildlife sensors

Hoffmann

Merkel

Sachse

et al. 2018

Molecular Ecology Resources

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“…To address these risks, it employs different levels of replication (i.e. extraction, PCRs), a curated reference database, and the probabilistic taxonomic assignment method PROTAX (Somervuo, Koskela, Pennanen, Henrik Nilsson, & Ovaskainen, ) that has been shown to be robust even when reference databases are incomplete (Richardson, Bengtsson‐Palme, & Johnson, ; Rodgers et al, ). Leech samples were digested, DNA was extracted, and then mitochondrial target DNA of host species was amplified with PCR and sequenced using Illumina high‐throughput sequencing.…”

Section: Methodsmentioning

confidence: 99%

Identifying conservation priorities in a defaunated tropical biodiversity hotspot

Tilker

Abrams

Nguyen

et al. 2020

Diversity and Distributions

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

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“…Remarkable articles published as Molecular Advances included evaluation of individual barcoding for whole‐genome resequencing (Overgaard‐Therkildsen & Palumbi, ), ancient DNA analyses that identify mollusc shells as historical metagenomic archives (Der Sarkissian et al., ) and development of metabarcoding in carrion flies as a powerful tool for biological surveys of terrestrial mammals (Rodgers et al., ). Additionally, a study by Nazareno, Bemmels, Dick, and Lohmann () provides insight on minimal samples sizes needed for population genomic studies.…”

Section: State Of the Journalmentioning

confidence: 99%