Applying DNA barcoding to conservation practice: a case study of endangered birds and large mammals in China

Abstract

Owning to advantages over traditional species identification methods, DNA barcoding is suggested to be a promising tool in conservation research. However, the use of DNA barcoding to accurately identify unknown samples in conservation practices has not been well documented in the literature. To illustrate this issue, we implemented a survey of endangered birds and mammals in China based on mitochondrial Cytochrome c Oxidase subunit I (COI) gene. We included mostly confiscated specimens and non-invasive samples while concealing species information to simulate real-world scenarios of identification. In total, 47 avian and 39 mammalian specimen were re-identified by sequential analyses of online species assignment, genetic distances, phylogenetic reconstruction, and diagnostic nucleotide method. With this multiple analyses approach, 82 individuals were accurately assigned to the species level and four individuals to the genus level. 78.72% of the avian specimen and 87.18% of mammalian specimen identifications were consistent with morphological classification. Among those inconsistent with morphological classification, we Communicated by Anurag chaurasia.This article belongs to the Topical Collection: Biodiversity protection and reserves.Electronic supplementary material The online version of this article (identified several potential errors including misidentification based on morphology and mislabelling that may have occurred while combining results from different analytical methods. Our case study not only enriches the barcode database, but also reports a successful application of DNA barcoding identification to conservation practices, which could effectively facilitate species identification of unknown samples in conservation practices in the future.

A continental-wide molecular approach unraveling mtDNA diversity and geographic distribution of the Neotropical genus Hoplias

“…Indeed, some authors have already detected cryptic species and described new ones using an integrative approach combining DNA Barcoding and traditional taxonomy [ 13 – 20 ]. Application of DNA barcoding has also effectively facilitated species identification of unknown samples for conservation purposes [ 21 ].…”

Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region

“…The same herbal medicine is often associated with different plant species in different national pharmacopoeias, which sometimes leads to adulteration and misidentification of herbal remedies [ 6 , 7 ]. Identifying the botanical origins of herbal medicines can be challenging, particularly where herbal medicines are distributed in highly processed forms such as powders or slices [ 7 , 14 ]. Morphological and genetic features are the main characteristics used for discrimination of herbal medicine species [ 11 , 14 , 20 ].…”

“…Identifying the botanical origins of herbal medicines can be challenging, particularly where herbal medicines are distributed in highly processed forms such as powders or slices [ 7 , 14 ]. Morphological and genetic features are the main characteristics used for discrimination of herbal medicine species [ 11 , 14 , 20 ]. Morphological identification of processed herbal medicines requires professional expertise and taxonomic keys that accurately identify features such as color, size and shape of the sliced and whole plant parts [ 29 ].…”

“…Another advantage of DNA-based approaches is that they do not require years of taxonomic training as for plant taxonomist for morphologically accurate identification. DNA barcoding based on short nuclear or organellar DNA sequences is used for the identification of a broad spectrum of organisms including plants, animals, microorganisms and fungi [ 14 , 15 , 16 , 17 ]. Several genetic markers, including rbc L, mat K, psb A- trn H, trn L-F and rps 16 in the chloroplast genome and ribosomal DNA internal transcribed spacers (rDNA-ITS) in the nuclear genome, are widely used as representative DNA barcode regions for identification of plant species and/or botanical origins of herbaceous medicinal materials [ 17 , 18 , 19 ].…”

Blood, sweat and tears: a review of non-invasive DNA sampling

“…Whether they were legally hunted or poached and confiscated (e.g. [59]), this type of sampling does not qualify as non-invasive due to the disturbance and/or death of the animal through human activity. Often, a better term for such sampling is "non-destructive", which does not damage the specimen [60,61] (Table 1).…”