A minimalist barcode can identify a specimen whose DNA is degraded

Abstract

A DNA barcode based on 650 bp of mitochondrial gene cytochrome c oxidase I is proving to be highly functional in species identification for various animal groups. However, DNA degradation complicates the recovery of a full-length barcode from many museum specimens. Here we explore the use of shorter barcode sequences for identification of such specimens. We recovered short sequences -i.e. ∼ ∼ ∼ ∼ 100 bp -with a single PCR pass from more than 90% of the specimens in assemblages of moth and wasp museum specimens from which full barcode recovery was only 50%, and the latter were usually less than 8 years old. Short barcodes were effective in identifying specimens, confirming their utility in circumstances where full barcodes are too expensive to obtain and the identification comparisons are within a confined taxonomic group.

Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections

“…Membership in a provisional species was determined using sequences that contained at least 500 bp. This avoids the analytical complications (18) introduced by absentee base-pair information (or lack of sequence overlap). Incomplete barcodes may lack the characteristic 1-or 2-bp differences that may be used to separate species with very similar barcodes ( Fig.…”

“…1). The variable and diagnostic locus is not included in the 5Ј region from which many of the short barcode sequences have been generated, and this draws attention to the issue of species identification accuracy with respect to region selection and amplicon size, as has been noted previously within fishes (23), wasps (18), and Lepidoptera (24). Morphology and ecology expose this pair of species, giving us confidence that a single-bp difference in the barcodes can also reveal a real species-level difference.…”

DNA Barcoding Indonesian freshwater fishes: challenges and prospects

“…In contrast with DNA extracted from well-preserved organisms, environmental DNA (eDNA) consists of a mixture of potentially degraded DNA present in trace amounts from many different organisms [190]. Since the long size of the "universal" COI barcode target (658 bp long) is not suitable for a successful amplification of degraded DNA, some authors have introduced a universal "mini-barcode" of 130 bp [194][195][196][197] This mini-barcode approach was also recently implemented in a biosecurity perspective for freshwater fish species transiting in the international ornamental trade using eDNA from water of quarantine tanks [170]. In their study, the authors targeted a single species (Danio rerio) and COI was successfully detected at fish densities as low as 0.08 g/L, further illustrating the potential of this approach as a tool for monitoring quarantine facilities for a variety of invasive and/or endangered species, in the context of the international ornamental fish trade.…”

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

“…COI, or a mini-barcode internal to COI (e.g. Hajibabaei et al, 2006), is therefore the ideal candidate for the biodiversity capsule approach. Other possible sources of biodiversity overestimation include secondary prey detection where DNA adheres to or is retained within the gut-contents of the predated items (Sheppard et al, 2005) and amplification of nuclear mitochondrial pseudogenes (NUMTs) (Dunshea et al, 2008;Moulton et al, 2010;Zeale et al, 2011).…”