DOI: 10.5061/dryad.1j6v6
title: Data from: Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples

description: Rodentia is the most diverse order among mammals, with more than 2,000
 species currently described. Most of the time, species assignation is so
 difficult based on morphological data solely that identifying rodents at
 the specific level corresponds to a real challenge. In this study, we
 compared the applicability of 100 bp mini-barcodes from cytochrome b and
 cytochrome c oxidase 1 genes to enable rodent species identification.
 Based on GenBank sequence datasets of 115 rodent species, a 136 bp
 fragment of cytochrome b was selected as the most discriminatory
 mini-barcode, and rodent universal primers surrounding this fragment were
 designed. The efficacy of this new molecular tool was assessed on 946
 samples including rodent tissues, feces, museum samples and feces/pellets
 from predators known to ingest rodents. Utilizing next-generation
 sequencing technologies able to sequence mixes of DNA, 1,140 amplicons
 were tagged, multiplexed and sequenced together in one single 454 GS-FLX
 run. Our method was initially validated on a reference sample set
 including 265 clearly identified rodent tissues, corresponding to 103
 different species. Following validation, 85.6% of 555 rodent samples from
 Europe, Asia and Africa whose species identity was unknown were able to be
 identified using the BLASTN program and GenBank reference sequences. In
 addition, our method proved effective even on degraded rodent DNA samples:
 91.8% and 75.9% of samples from feces and museum specimens respectively
 were correctly identified. Finally, we succeeded in determining the diet
 of 66.7% of the investigated carnivores from their feces and 81.8% of owls
 from their pellets. Non-rodent species were also identified, suggesting
 that our method is sensitive enough to investigate complete predator
 diets. This study demonstrates how this molecular identification method
 combined with high-throughput sequencing can open new realms of
 possibilities in achieving fast, accurate and inexpensive species
 identification.
description: Fasta S1 COI115Species
 from GenBankAlignment of COI
 sequences from 115 rodent species from GenBankFasta S2 Cytb115Species
 from GenBankAlignment of cytb
 sequences from 115 rodent species from GenBankFasta S3 Design
 primersFasta S4 Reference
 SamplesAlignment of rodent
 haplotypes obtained from the 265 reference samplesFasta S5 Rodentia
 HaplotypesAlignment of the rodent
 haplotypes obtained for ethanol preserved samplesFasta S6 Prey
 HaplotypesAlignment of the prey
 haplotypes obtained from faecal and pellet samplesFasta S7 Museum Murinae
 True HaplotypesAlignment of the rodent
 haplotypes obtained from museum samplesFasta S8 Museum Human
 DNA contamination HaplotypesAlignment of the human
 haplotypes retrieved from rodent museum sample analysisFasta S9 Museum DNA
 contamination HaplotypesAlignment of the
 vertebrate haplotypes corresponding to contaminations detected in rodent
 museum samplesFasta S10 Predator
 HaplotypesAlignment of the
 predator haplotypes detected in faecal and pellet
 samplesFatsa S11
 Environnemental contamination HaplotypesAlignment of the
 bacterial and unknown haplotypes detected in faecal and pellet
 samples