Biodiversity and Conservation

, Volume 26, Issue 3, pp 653–668 | Cite as

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

  • Jing Li
  • Yaoyao Cui
  • Juan Jiang
  • Jianqiu Yu
  • Lili Niu
  • Jiabo Deng
  • Fujun Shen
  • Liang Zhang
  • Bisong YueEmail author
  • Jing LiEmail author
Original Paper
Part of the following topical collections:
  1. Biodiversity protection and reserves


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 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.


DNA barcoding Cytochrome c Oxidase subunit I (COI) Species identification Conservation practice Birds Mammals 



We thank Chengdu Giant Panda Breeding Research Foundation (Grant No. CPF2014-13-1) and the National Natural Science Foundation of China (No. 31270431) for funding. We thank Janine Antalffy for English improvement. Thanks also to the anonymous reviewers and the Editor for their helpful comments on an early version of the paper.

Compliance with ethical standard

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

10531_2016_1263_MOESM1_ESM.pdf (1.4 mb)
Supplementary material 1 (PDF 1439 kb)


  1. Ardura A, Linde AR, Moreira JC, Garcia-Vazquez E (2010) DNA barcoding for conservation and management of Amazonian commercial fish. Biol Conserv 143(6):1438–1443CrossRefGoogle Scholar
  2. Armstrong K, Ball S (2005) DNA barcodes for biosecurity: invasive species identification. Philos Trans R Soc Lond B 360(1462):1813–1823CrossRefGoogle Scholar
  3. Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C (2009) DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinform 10(Suppl 14):S10CrossRefGoogle Scholar
  4. Barber P, Boyce SL (2006) Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proc R Soc Lond B 273(1597):2053–2061CrossRefGoogle Scholar
  5. Borisenko AV, Lim BK, Ivanova NV, Hanner RH, Hebert PD (2008) DNA barcoding in surveys of small mammal communities: a field study in Suriname. Mol Ecol Resour 8(3):471–479CrossRefPubMedGoogle Scholar
  6. Côté IM, Green SJ, Morris JA Jr, Akins JL, Steinke D (2013) Diet richness of invasive Indo-Pacific lionfish revealed by DNA barcoding. Mar Ecol Prog Ser 472:249–256CrossRefGoogle Scholar
  7. Dalton DL, Kotze A (2011) DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa. Forensic Sci Int 207(1–3):e51–e54CrossRefPubMedGoogle Scholar
  8. DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B 360(1462):1905–1916CrossRefGoogle Scholar
  9. Dincă V, Zakharov EV, Hebert PD, Vila R (2011) Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe. Proc R Soc Lond B 278(1704):347–355CrossRefGoogle Scholar
  10. Dixon A (2012) Conservation of the Saker Falcon Falco cherrug and the use of hybrids for falconry. Aquila 119:9–19Google Scholar
  11. Dove CJ, Rotzel NC, Heacker M, Weigt LA (2008) Using DNA barcodes to identify bird species involved in birdstrikes. J Wildl Manag 72(5):1231–1236CrossRefGoogle Scholar
  12. Eastham CP, Nicholls MK, Fox NC (2001) Morphological variation of the Saker (Falco cherrug) and the implications for conservation. Biodivers Conserv 11(2):305–325CrossRefGoogle Scholar
  13. Feng Y, Siu K, Wang N, Ng KM, Tsao SW, Nagamatsu T, Tong Y (2009) Bear bile: dilemma of traditional medicinal use and animal protection. J Ethnobiol and Ethnomed 5:1–9CrossRefGoogle Scholar
  14. Gamauf A, Preleuthner M, Winkler H (1998) Philippine birds of prey: interrelations among habitat, morphology, and behaviour. The Auk 115(3):713–726CrossRefGoogle Scholar
  15. González-Varo JP, Arroyo JM, Jordano P (2014) Who dispersed the seeds? The use of DNA barcoding in frugivory and seed dispersal studies. Methods Ecol Evol 5(8):806–814CrossRefGoogle Scholar
  16. Gonçalves PF, Oliveira-Marques AR, Matsumoto TE, Miyaki CY (2015) DNA barcoding identifies illegal parrot trade. J Hered 106(S1):560–564CrossRefPubMedGoogle Scholar
  17. Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PD (2006) DNA barcodes distinguish species of tropical Lepidoptera. PNAS 103(4):968–971CrossRefPubMedPubMedCentralGoogle Scholar
  18. Harris DJ (2003) Can you bank on GenBank? Trends Ecol Evol 18(7):317–319CrossRefGoogle Scholar
  19. Hebert PDN, Cywinska A, Ball SL (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B 270(1512):313–321CrossRefGoogle Scholar
  20. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54(5):852–859CrossRefPubMedGoogle Scholar
  21. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004a) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. PNAS 101(41):14812–14817CrossRefPubMedPubMedCentralGoogle Scholar
  22. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004b) Identification of birds through DNA barcodes. PLoS Biol 2:1657–1663CrossRefGoogle Scholar
  23. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3(6):e2490CrossRefPubMedPubMedCentralGoogle Scholar
  24. Ivanova NV, deWaard JR, Hebert PDN (2006) An inexpensive, automation-friendly protocol for reconcealing high-quality DNA. Mol Ecol Notes 6:998–1002CrossRefGoogle Scholar
  25. Jo H, Ventura M, Vidal N, Gim JS, Buchaca T, Barmuta LA, Jeppesen E, Joo GJ (2015) Disconcealing hidden biodiversity: the use of complementary monitoring of fish diet based on DNA barcoding in freshwater ecosystems. Ecol Evol 6(1):219–232CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kerr KC, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN (2007) Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes 7(4):535–543CrossRefPubMedPubMedCentralGoogle Scholar
  27. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120CrossRefPubMedGoogle Scholar
  28. Kress WJ, García-Robledo C, Uriarte M, Erickson DL (2015) DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 30(1):25–35CrossRefPubMedGoogle Scholar
  29. Lau MWN, Fellowes JR, Chan BPL (2010) Carnivores (Mammalia: Carnivora) in South China: a status review with notes on the commercial trade. Mammal Rev 40:247–292CrossRefGoogle Scholar
  30. Li J, Zheng X, Cai Y, Zhang X, Yang M, Yue B (2015) DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China. Mol Ecol Resour 15(1):153–167CrossRefPubMedGoogle Scholar
  31. Li J, Zhu Z (2014) Snow leopard poaching and trade in China 2000–2013. Biol Conserv 176:207–211CrossRefGoogle Scholar
  32. MacKinnon J, Phillipps K, He F (2000) A field guide to the birds of China. Oxford University Press, OxfordGoogle Scholar
  33. Meier R, Shiyang K, Vaidya G, Ng PK (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55(5):715–728CrossRefPubMedGoogle Scholar
  34. Mitchell A (2008) DNA barcoding demystified. Aust J Entomol 47(3):169–173CrossRefGoogle Scholar
  35. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403(6772):853–858CrossRefPubMedGoogle Scholar
  36. Nagy ZT, Sonet G, Glaw F, Vences M (2012) First large-scale DNA barcoding assessment of reptiles in the biodiversity hotspot of Madagascar, based on newly designed COI primers. PLoS ONE 7(3):e34506CrossRefPubMedPubMedCentralGoogle Scholar
  37. Oba Y, Ôhira H, Murase Y, Moriyama A, Kumazawa Y (2015) DNA barcoding of Japanese click beetles (Coleoptera, Elateridae). PLoS ONE 10(1):e0116612CrossRefPubMedPubMedCentralGoogle Scholar
  38. Pearlstine EV, Thompson D (2004) Geographic variation in morphology of four species of migratory raptors. J Raptor Res 38:334–342Google Scholar
  39. Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, Sundberg P, Thollesson M (2008) Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Mol Phylogenet Evol 48(1):369–371CrossRefPubMedGoogle Scholar
  40. Quinto CA, Tinoco R, Hellberg RS (2016) DNA barcoding reveals mislabeling of game meat species on the US commercial market. Food Control 59:386–392CrossRefGoogle Scholar
  41. Ratnasingham S, Hebert PDN (2013) A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE 8(7):e66213CrossRefPubMedPubMedCentralGoogle Scholar
  42. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425PubMedGoogle Scholar
  43. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor, New YorkGoogle Scholar
  44. Schipper J, Chanson JS, Chiozza F, Cox NA, Hoffmann M, Katariya V et al (2008) The status of the world’s land and marine mammals: diversity, threat, and knowledge. Science 322:225–230CrossRefPubMedGoogle Scholar
  45. Smith AT, Xie Y, Hoffmann RS, Lunde D, MacKinnon J, Wilson DE, Wozencraft WC, Gemma F (2010) A guide to the mammals of China. Princeton University Press, PrincetonCrossRefGoogle Scholar
  46. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  47. Taylor HR, Harris WE (2012) An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 12(3):377–388CrossRefPubMedGoogle Scholar
  48. van Velzen R, Weitschek E, Felici G, Bakker FT (2012) DNA barcoding of recently diverged species: relative performance of matching methods. PLoS ONE 7(1):e30490CrossRefPubMedPubMedCentralGoogle Scholar
  49. Vernooy R, Haribabu E, Muller MR, Vogel JH, Hebert PDN, Schindel DE, Shimura J, Singer GA (2010) Barcoding life to conserve biological diversity: beyond the taxonomic imperative. PLoS Biol 8(7):e1000417CrossRefPubMedPubMedCentralGoogle Scholar
  50. Ward RD, Hanner R, Hebert PDN (2009) The campaign to DNA barcode all fishes. FISH-BOL. J Fish Biol 74(2):329–356CrossRefPubMedGoogle Scholar
  51. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B 360:1847–1857CrossRefGoogle Scholar
  52. Waugh J, Evans MW, Millar CD, Lambert DM (2011) Birdstrikes and barcoding: can DNA methods help make the airways safer? Mol Ecol Resour 11(1):38–45CrossRefPubMedGoogle Scholar
  53. Weitschek E, Velzen R, Felici G, Bertolazzi P (2013) BLOG 2.0: a software system for character-based species classification with DNA barcode sequences What it does, how to use it. Mol Ecol Resour 13(6):1043–1046PubMedGoogle Scholar
  54. Wilson JJ, Rougerie R, Schonfeld J, Janzen DH, Hallwachs W, Hajibabaei M, Kitching IJ, Haxaire J, Hebert PDN (2011) When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths. BMC Ecol 11(1):18CrossRefPubMedPubMedCentralGoogle Scholar
  55. Wong EH-K, Hanner RH (2008) DNA barcoding detects market substitution in North American seafood. Res Int 41(8):828–837Google Scholar
  56. Yang C, Xiao Z, Zou Y, Zhang X, Yang B, Hao Y, Moermond T, Yue B (2014) DNA barcoding revises a misidentification on musk deer. Mitochondr DNA 0:1–8Google Scholar
  57. Yiming L, Wilcove DS (2005) Threats to vertebrate species in China and the United States. Bioscience 55(2):147–153CrossRefGoogle Scholar
  58. Zhang L, Hua N, Sun S (2008) Wildlife trade, consumption and conservation awareness in southwest China. Biodivers Conserv 17(6):1493–1516CrossRefGoogle Scholar
  59. Zhou Y, Meng X, Feng J, Yang Q, Feng Z, Xia L (2004) Review of the distribution, status and conservation of musk deer in China. Folia Zool 53(2):129–140Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life SciencesSichuan UniversityChengduChina
  2. 2.Chengdu ZooInstitute of Chengdu WildlifeChengduChina
  3. 3.Sichuan Key Laboratory for Conservation Biology on Endangered WildlifeChengdu Research Base of Giant Panda BreedingChengduChina

Personalised recommendations