Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target

Lee, Ping-Shin; Sing, Kong-Wah; Wilson, John James

doi:10.1371/journal.pone.0123871

Cited by 42 publications

(69 citation statements)

References 50 publications

(75 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This may limit the detections to species with higher primer binding affinity, resulting in species diversity being underrepresented (Shokralla et al 2012). Lee et al (2015) found the primers used in this study exhibited no strong amplification bias across mammal species (from Peninsular Malaysia), but the test only included a limited number of species (n = 41).…”

Section: Discussionmentioning

confidence: 88%

“…Ten blowfly traps baited with rotten fish (see Lee et al 2015) were set per transect at 10 m intervals and 2 m above the ground. The traps were emptied every 24 h, and collected blowflies (Diptera: Calliphoridae) were frozen at -20°C within 5 h of trap emptying.…”

Section: Baited Blowfly Trapsmentioning

confidence: 99%

“…Frequently used methods include live trapping, such as cage traps (Hanif-Ridzuan et al 2010;Madinah et al 2011), mist nets, and harp traps (Kingston et al 2003;Sing et al 2013), camera traps (Clements 2013;Hedges et al 2015a), indirect signs such as tracks or scat (Daim 2002), interviews with local communities (Sharma et al 2005), direct observations by researchers (Syakirah et al 2000;Jayaraj et al 2013), and hair traps (Castro-Arellano et al 2008;Hedges et al 2015b). Recent additions to the toolbox are secondary sources of mammal DNA, for example, mammal DNA detected from owl-pellet bones (Rocha et al 2015) and invertebrate gut contents (Calvignac-Spencer et al 2013a, 2013bSchnell et al 2012Schnell et al , 2015Lee et al 2015). These methods can provide accurate identification of mammal species, are not stressful to the mammals themselves, require the least ecological and taxonomic expertise, and yet have the potential to detect rare and cryptic species (Calvignac-Spencer et al 2013a;Schnell et al 2012;Lee et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Recent additions to the toolbox are secondary sources of mammal DNA, for example, mammal DNA detected from owl-pellet bones (Rocha et al 2015) and invertebrate gut contents (Calvignac-Spencer et al 2013a, 2013bSchnell et al 2012Schnell et al , 2015Lee et al 2015). These methods can provide accurate identification of mammal species, are not stressful to the mammals themselves, require the least ecological and taxonomic expertise, and yet have the potential to detect rare and cryptic species (Calvignac-Spencer et al 2013a;Schnell et al 2012;Lee et al 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Blowflies (Diptera: Calliphoridae) have shown promising potential as sources of mammal DNA due to their presence in all habitats (Norris 1965) and broad host preferences as saprophagous and coprophagous generalists (Calvignac-Spencer et al 2013a, 2013bAzwandi et al 2013; Lee et al 2015;Schnell et al 2015). Chrysomya bezziana has been reported feeding on mammal species from the orders Artiodactyla (7 spp.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Lee

Gan

Clements

et al. 2016

Genome

Self Cite

View full text Add to dashboard Cite

Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowflyderived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.

show abstract

Section: Discussionmentioning

confidence: 88%

Section: Baited Blowfly Trapsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Lee

Gan

Clements

et al. 2016

Genome

Self Cite

View full text Add to dashboard Cite

show abstract

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

et al. 2019

View full text Add to dashboard Cite

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.

show abstract

Comparison of mosquito and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

et al. 2023

View full text Add to dashboard Cite

The use of invertebrate-derived DNA (iDNA) is a promising non-invasive tool to monitor wildlife. While most studies have been carried out in dense tropical and subtropical forests and have focused on the use of a single category of invertebrates, this study compares the use of flies and mosquitoes-derived DNA to assess vertebrate diversity in semi-urban environments. We conducted our sampling in four different forest plots in Berlin, Germany. Pools of flies and non-bloodfed mosquitoes were metabarcoded using 108-bp vertebrate-specific 12 S rRNA (12 S-V5) and 94-bp mammal-specific 16 S rRNA (16Smam) mitochondrial markers, and individual bloodfed mosquitoes were sequenced using the 340-bp vertebrate-specific 12 S rRNA fragment (Mam-12 S-340). Most sequencing was only successful for mammal species.From the fly pools, we detected 10 mammal species using 16Smam, and six species using 12 S-V5. From the non-bloodfed mosquito pools, we only amplified putative contaminant DNA, indicating that mosquito females without visual signs of a blood meal carry no traces of vertebrate DNA. Finally, in the bloodfed mosquitoes, we identified four mammal species. We did not find significant differences in the proportion of mammal species detected regarding the total available number of species between sampling localities. Fly samples were easier to obtain and more abundant over the sampled localities compared to mosquito samples. We conclude that, while there are a few advantages in using mosquito blood meals, the use of flies in the detection of wildlife in a suburban environment is more effective in terms of collection of samples and detection of vertebrates, although this technique is limited to few mammal species in the urban environment.

show abstract

Reading Mammal Diversity from Flies: The Persistence Period of Amplifiable Mammal mtDNA in Blowfly Guts (Chrysomya megacephala) and a New DNA Mini-Barcode Target

Cited by 42 publications

References 50 publications

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

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

Comparison of mosquito and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

Contact Info

Product

Resources

About