DOI: 10.5061/dryad.57vg4
title: Data from: Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity

description: Large-scale monitoring schemes are essential in assessing global mammalian
 biodiversity, and in this framework leeches have recently been promoted as
 an indirect source of DNA from terrestrial mammal species. Carrion feeding
 flies are ubiquitous and can be expected to feed on many vertebrate
 carcasses. Hence, we tested whether fly-derived DNA analysis may also
 serve as a novel tool for mammalian diversity surveys. We screened DNA
 extracted from 201 carrion flies collected in tropical habitats of Côte
 d’Ivoire and Madagascar for mammal DNA using multiple PCR systems and
 retrieved DNA sequences from a diverse set of species (22 in Côte
 d’Ivoire, 4 in Madagascar) exploiting distinct forest strata and
 displaying a broad range of body sizes. Deep-sequencing of amplicons
 generated from pools of flies performed equally well as individual
 sequencing approaches. We conclude that the analysis of fly-derived DNA
 can be implemented in a very rapid and cost-effective manner and will give
 a relatively unbiased picture of local mammal diversity. Carrion flies
 therefore represent an extraordinary and thus far unexploited resource of
 mammal DNA, which will likely prove useful for future inventories of wild
 mammal communities.
description: Short PCR product - all
 cycles with fusion primersSequencing of this
 amplicon was performed on a Pico Titer Plate using a GS FLX platform,
 according to manufacturer’s instructions (Roche Applied Sciences,
 Penzberg, Germany). Reads still comprise fusion primer sequences (forward
 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse
 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCGCTGTTATCCCTAGGGTAACT-3').mam_2_Fusion.fastqShort PCR product - last 5 cycles with fusion primersSequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCGCTGTTATCCCTAGGGTAACT-3').mam_2_2.Rd_Fusion_5x.fastqLong PCR product - all cycles with fusion primersSequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCAGATAGAAACCGACCTGGAT-3').mam_4.fastqLong PCR product - last 5 cycles with fusion primersSequencing of this amplicon was performed on a Pico Titer Plate using a GS FLX platform, according to manufacturer’s instructions (Roche Applied Sciences, Penzberg, Germany). Reads still comprise fusion primer sequences (forward 5'-CGTATCGCCTCCCTCGCGCCATCAGAGACGCACTCCGGTTGGGGTGACCTCGGA-3, reverse 5'-CTATGCGCCTTGCCAGCCCGCTCAGAGACGCACTCAGATAGAAACCGACCTGGAT-3').mam_4_2.Rd_Fusion_5x.fastqSupporting Alignment S1All Sanger sequences generated for this study.Alignment_S1.fasta