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DNA barcoding of bird species in Cyprus: a tool for conservation purposes


DNA barcoding has become a widely used and valuable tool in taxonomic research during the past three decades and its application is expanding to fields such as wildlife forensics (e.g. anti-poaching actions). One of the major advantages of DNA barcoding is that it allows for species identification from largely incomplete, deformed or cooked samples and even from traces of biological material. Cyprus is a well-known biodiversity hotspot, the island avifauna comprising around 400 species, 117 of which are listed in Annex I of the Birds Directive (2009/147/EC). Each year on average, 2.3 million individuals (mainly small migratory birds) are trapped illegally on the island and often served at restaurants. Consequently, reliable identification of specimens from processed tissues can be crucial for undertaking legal actions. Herein DNA barcoding of the large majority of bird species resident in Cyprus plus several migrants that were illegally captured was carried out to support local authorities in their anti-poaching actions. In this study, tissue from 103 specimens representing 81 bird taxa were sampled and a 648-bp long fragment of the Cytochrome Oxidase subunit Ι (COI) gene was targeted using a combination of standard, nested and semi-nested PCR depending on the condition of the tissue at hand. Sequences were obtained from all investigated samples and a total of 92 haplotypes was recovered. Phylogenetic reconstructions returned a pattern of relationships among taxa largely compatible with known avian phylogeny. Furthermore, diagnostic polymorphisms within the genus including one of the main targeted species, Sylvia atricapilla, were found. In conclusion, an avian genetic dataset is now available for the law enforcement authorities to identify specimens either confiscated (even when morphologically deformed or cooked) during raids in restaurants and in other premises suspected of serving illegally protected bird species or from trappers.

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H. Abe , A. Hayano and M Inoue-Murayama . (2012) Forensic species identification of large macaws using DNA barcodes and microsatellite profiles. Mol. Biol. Reports 39: 693699.

H Akaike . (1974) New look at the statistical model identification. IEEE Transactions on Automatic Control AC-19: 716723.

F. Barbanera , M. Guerrini , C. Beccani , G. Forcina , P. Anayiotos and P Panayides . (2012) Conservation of endemic and threatened wildlife: Molecular forensic DNA against poaching of the Cypriot mouflon (Ovis orientalis ophion, Bovidae). Forensic Sci. Internatn: Genet. 6: 671675.

A.-L. Brochet , W. Van Den Bossche , S. Jbour , P. K. Ndang’Ang’a , V. R. Jones , W. A. L. I. Abdou , A. R. Al-Hmoud , N. G. Asswad , J. C. Atienza , I. Atrash , N. Barbara , K. Bensusan , T. Bino , C. Celada , S. I. Cherkaoui , J. Costa , B. Deceuninck , K. S. Etayeb , K. Feltrup-Azafzaf , J. Figelj , M. Gustin , P. Kmecl , V. Kocevski , M. Korbeti , D. Kotrošan , J. M. Laguna , M. Lattuada , D. Leităo , P. Lopes , N. López-Jiménez , V. Lucić , T. Micol , A. Moali , Y. Perlman , N. Piludu , D. Portolou , K. Putilin , G. Quaintenne , G. Ramadan-Jaradi , M. Ružić , A. Sandor , N. Sarajli , D. Saveljić , R. D. Sheldon , T. Shialis , N. Tsiopelas , F. Vargas , C. Thompson , A. Brunner , R. Grimmett and S. H. M Butchart . (2016) Preliminary assessment of the scope and scale of illegal killing and taking of birds in the Mediterranean. Bird Conserv. Internatn. 26: 128.

Y. Cai , B. Yue , W. Jiang , S. Xie , J. Li and M Zhou . (2010) DNA barcoding on subsets of three families in Aves. Mitochondrial DNA 21: 132137.

M. L. Coghlan , N. E. White , L. Parkinson , J. Haile , P. B. S. Spencer and M Bunce . (2011) Egg forensics: An appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs. Forensic Sci. Internatn: Genetics 6: 268273.

D. L. Dalton and A Kotze . (2011) DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa. Forensic Sci. Internatn. 207: 5154.

D. Darriba , G. L. Taboada , R. Doallo and D Posada . (2012) JModelTest 2: More models, new heuristics and parallel computing. Nature Methods. 9: 772.

R. DeSalle , M. G. Egan and M Siddall . (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Phil. Trans. R. Soc. Series B, Biol. Sci. 360: 19051916.

P. Doukakis , E. K. Pikitch , A. Rothschild , R. DeSalle , G. Amato and S.-O Kolokotronis . (2012) Testing the effectiveness of an international conservation agreement: Marketplace forensics and CITES caviar trade regulation. PLoS ONE 7: e40907.

C. J. Dove , N. C. Rotzel , M. Heacker and L Weigt . (2008) Using DNA barcodes to identify bird species involved in birdstrikes. J. Wildl. Manage. 72: 12311236.

M. J. Eaton , G. L. Meyers , S.-O. Kolokotronis , M. S. Leslie , A. P. Martin and G Amato . (2010) Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates. Conserv. Genet. 11: 13891404.

J Felsenstein . (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783791.

L. Filonzi , S. Chiesa , M. Vaghi and F Nonnis Marzano . (2010) Molecular barcoding reveals mislabelling of commercial fish products in Italy. Food Res. Internatn. 43: 13831388.

C. M. Francis , A. V. Borisenko , N. V. Ivanova , J. L. Eger , B. K. Lim , A. Guillén-Servent , S. V. Kruskop , I. Mackie and P. D. N Hebert . (2010) The role of DNA barcodes in understanding and conservation of mammal diversity in Southeast Asia. PLoS ONE 5: 112.

L. Frézal and R Leblois . (2008) Four years of DNA barcoding: Current advances and prospects. Infection, Genet. Evol. 8: 727736.

A. Gaur , C. S. Singh , A. Sreenivas and L Singh . (2012) DNA-based identification of a snake in a wine bottle using universal primers: A case of mistaken identity. Forensic Sci. Internatn. 214: e51e53.

M. Guerrini and F Barbanera . (2009) Noninvasive genotyping of the red-legged partridge (Alectoris rufa, Phasianidae): Semi-nested PCR of mitochondrial DNA from feces. Biochem. Genet. 47: 873883.

S. Guindon , J.-F. Dufayard , V. Lefort , M. Anisimova , W. Hordijk and O Gascuel . (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Systematic Biol. 59: 307321.

P. D. Hebert , A. Cywinska and S. L Ball . (2003) Biological identifications through DNA barcodes. Proc. R. Soc. London B: Biol. Sci. 270: 313321.

P. D. Hebert , M. Y. Stoeckle , T. S. Zemlak and C. M Francis . (2004) Identification of birds through DNA barcodes. PLoS Biology 2: e312.

M. J. Hickerson , C. P. Meyer and C Moritz . (2006) DNA barcoding will often fail to discover new animal species over broad parameter space. Systematic Biol. 55: 729739.

R. Inger , R. Gregory , J. P. Duffy , I. Stott , P. Voříšek and K. J Gaston . (2015) Common European birds are declining rapidly while less abundant species’ numbers are rising. Ecol. Lett. 18: 2836.

A Iyengar . (2014) Forensic DNA analysis for animal protection and biodiversity conservation: A review. J. Nat. Conserv. 22: 195205.

W. Jetz , G. H. Thomas , J. B. Joy , K. Hartmann and A. O Mooers . (2012) The global diversity of birds in space and time. Nature 491: 444448.

K. C. R. Kerr , D. A. Lijtmaer , A. S. Barreira , P. D. N. Hebert and P. L Tubaro . (2009) Probing evolutionary patterns in neotropical birds through DNA barcodes. PloS ONE 4: e4379.

P. Librado and J Rozas . (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 14511452.

C. P. Meyer and G Paulay . (2005) DNA barcoding: Error rates based on comprehensive sampling. PLoS Biology 3: 110.

C. Moritz and C Cicero . (2004) DNA barcoding: Promise and pitfalls. PLoS Biology 2: 15291531.

M. Nishibori , M. Hanazono , Y. Yamamoto , M. Tsudzuki and H Yasue . (2003) Complete nucleotide sequence of mitochondrial DNA in White Leghorn and White Plymouth Rock chickens. Anim. Sci. J. 74: 437439.

F. Rodríguez , J. L. Oliver , A. Marín and J. R Medina . (1990) The general stochastic model of nucleotide substitution. J. Theoret. Biol. 142: 485501.

F. Ronquist and J. P Huelsenbeck . (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 15721574.

D Rubinoff . (2006) Utility of mitochondrial DNA barcodes in species conservation. Conserv. Biol. 20: 10261033.

F. H. Sheldon , C. E. Jones and K. G McCracken . (2000) Relative patterns and rates of evolution in heron nuclear and mitochondrial DNA. Molec. Biol. Evol. 17: 437450.

M. D. Sorenson and T. W Quinn . (1998) Numts: a challenge for avian systematics and population biology. The Auk 115: 214221.

M. D. Sorenson , J. C. Ast , D. E. Dimcheff , T. Yuri and D. P Mindell . (1999) Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molec. Phylogenet. Evol. 12: 105–14.

K. Tamura , G. Stecher , D. Peterson , A. Filipski and S Kumar . (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Molec. Biol. Evol. 30: 27252729.

E. S. Tavares and A. J Baker . (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol. Biol. 8: 81.

E. S. Tavares , P. Gonçalves , C. Y. Miyaki and A. J Baker . (2011) DNA barcode detects high genetic structure within neotropical bird species. PLoS ONE. 6: e28543.

J. D. Thompson , T. J. Gibson , F. Plewniak , F. Jeanmougin and D. G Higgins . (1997) The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 48764882.

R. D Ward . (2009) DNA barcode divergence among species and genera of birds and fishes. Molec. Ecol. Resources 9: 10771085.

D. A. Weese and S. R Santos . (2008) Genetic identification of source populations for an aquarium-traded invertebrate. Anim. Conserv. 12: 1319.

L. J. Welton , C. D. Siler , C. W. Linkem , A. C. Diesmos , M. L. Diesmos , E. Sy and R. M Brown . (2013) Dragons in our midst: Phyloforensics of illegally traded Southeast Asian monitor lizards. Biol. Conserv. 159: 715.

M. Wiemers and K Fiedler . (2007) Does the DNA barcoding gap exist? - a case study in blue butterflies (Lepidoptera: Lycaenidae). Front. Zool. 4: 116.

K. W. Will , B. D. Mishler and Q. D Wheeler . (2005) The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biol. 54: 844851.

X Xia . (2013) DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution. Molec. Biol. Evol. 30: 17201728.

X. Xia , Z. Xie , M. Salemi , L. Chen and Y Wang . (2003) An index of substitution saturation and its application. Molec. Phylogenet. Evol. 26: 17.

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Bird Conservation International
  • ISSN: 0959-2709
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