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

Abstract

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.

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

“…Although study areas and design differ, this is comparable to the number of vertebrates detected in iDNA studies targeting specific invertebrate taxa such as carrion flies in Côte d'Ivoire and Madagascar , carrion flies in Panama (Rodgers et al, 2017), leeches in Borneo (Schnell et al, 2018), blowflies in Malaysia (Lee et al, 2016), leeches in Vietnam (Schnell et al, 2012), and even higher than when targeting ticks in Canada (Gariepy et al, 2012). Thirty-two vertebrate taxa were detected in the study sites in Brazil and Tanzania.…”

iDNA at Sea: Recovery of Whale Shark (Rhincodon typus) Mitochondrial DNA Sequences from the Whale Shark Copepod (Pandarus rhincodonicus) Confirms Global Population Structure

“…We successfully amplified mitochondrial DNA fragments of whale sharks in the size range of ∼1,000 bp from a copepod, one of the largest host DNA fragments to be recovered by an iDNA study (Schnell et al, 2012(Schnell et al, , 2015Lee et al, 2016;Pérez-Flores et al, 2016;Rodgers et al, 2017). This suggests the presence of largely intact whale shark DNA in or on copepods, although the exact source could not be identified as copepods were analyzed whole.…”

“…Invertebrate-derived DNA (iDNA) is an offshoot of this approach that involves the extraction of genetic material of animals via the flesh-eating or haematophagous invertebrates that parasitise them (Schnell et al, 2015;Schubert et al, 2015;Lee et al, 2016). To date, most iDNA studies have focused on terrestrial vertebrates and have extracted host DNA from insects, ticks, or leeches.…”

DNA barcodes and morphology reveal unrecognized species in Chironomidae (Diptera)

“…Over the past decade, the use of short standardized genetic markers for species identification, so-called DNA barcoding (Hebert et al 2003a, b), has proven effective in biodiversity assessments (Hajibabaei et al 2016;Lee et al 2016) and taxonomic revisions Miller et al 2016). DNA barcoding has aided our understanding of species community compositions, food webs and genetic variation within species (Baker et al 2016;Littlefair & Clare 2016;Roslin & Majaneva 2016) and is an important and useful asset in biosecurity (Ashfaq & Hebert 2016;DOI 10.1163/1876312X-00002172 Hodgetts et al 2016) and biomonitoring of freshwater ecosystems (Brodin et al 2013;Carew et al 2013).…”