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Evaluating DNA barcoding criteria using African duiker antelope (Cephalophinae) as a test case

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Abstract

African duikers in the subfamily Cephalophinae (genera Cephalophus, Philantomba and Sylvicapra) constitute an important target for DNA barcoding efforts because of their importance to the bushmeat trade and protection under the Convention for International Trade in Endangered Species (CITES). Duikers also make a challenging test case of barcoding methods due to their recent diversification, substantial intra-specific genetic variation and high species richness. However, no study to date has evaluated how well DNA barcoding methods can be used to delineate all of the taxa within this group. To address this question, cytochrome c oxidase subunit 1 (COX1) sequences from all eighteen species within this subfamily and an outgroup taxon (genus Tragelaphus) were used to build a neighbor-joining tree, identify species-specific diagnostic synapomorphies, and determine whether species exceed a given pair-wise genetic distance threshold commonly employed in DNA barcoding studies. Tree-based analyses of the data indicate that several species within two clusters of closely related taxa consistently failed to form reciprocally monophyletic clades and similarly lack species-specific synapomorphies. Furthermore, one additional taxon failed to constitute a diagnosable clade and another occupied an unresolved position in the tree. Of the two genetic distance criteria evaluated, the 3% threshold was far more effective in delimiting species than a threshold level based on the ratio of inter- to intra-specific distances. However, neither approach could effectively delineate all sister species. While the taxonomy of this group might be open to question, the fact that barcodes consistently failed to differentiate several currently recognized sister taxa challenges the routine application of this approach in forensic studies of duiker species. Future barcoding work of this group should always include a complete taxonomic sampling and strive to include a broader geographic sampling of sequence diversity than has been carried out to date. Lastly, this work highlights the need to re-examine the taxonomy of this group, which may illuminate why some barcoding criteria fail to reliably differentiate species.

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References

  • Abdo Z, Golding GB (2007) A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups. Syst Biol 56:44–56

    Article  PubMed  CAS  Google Scholar 

  • Ansell WFH (1972) Order Artiodactyla. In: Meester J, Setzer HW (eds) The mammals of Africa: an identification manual. Smithsonian Institution Press, Washington, DC, pp 1–84

    Google Scholar 

  • Barnes RFW (2002) The bushmeat boom and bust in West and Central Africa. ORYX 36:236–242

    Article  Google Scholar 

  • Bennett EL, Blencowe E, Brandon K et al (2007) Hunting for consensus: reconciling bushmeat harvest, conservation and development policy in west and central Africa. Conserv Biol 21:884–887

    Article  PubMed  Google Scholar 

  • Bowkett AE, Plowman AB, Stevens JR, Davenport TRB, van Vuuren BJ (2009) Genetic testing of dung identification for antelope surveys in the Udzungwa Mountains, Tanzania. Conserv Genet 10:251–255

    Article  CAS  Google Scholar 

  • Carstens BC, Dewey TA (2010) Species delimitation using a combined coalescent and information- theoretic approach: an example from North American Myotis bats. Syst Biol 59:400–414

    Article  PubMed  Google Scholar 

  • Crandall KA, Fitzpatrick JF Jr (1996) Crayfish molecular systematics: using a combination of procedures to estimate phylogeny. Syst Biol 45:1–26

    Article  Google Scholar 

  • Davalos LM, Porzecanski AL (2009) Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria. Mol Phylogenet Evol 53:234–248

    Article  PubMed  CAS  Google Scholar 

  • DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B Biol Sci 360:1905–1916

    Article  CAS  Google Scholar 

  • Dorst J, Danderlot P (1970) A filed guide to the larger mammals of Africa. Collins, London

    Google Scholar 

  • Drummond AJ, Rambaut A (2007) TRACER v1.4. Available at http://beast.bio.ed.ac.uk/Tracer

  • East R, Grubb P, Wilson VJ (1988) Classification of antelopes adopted for the antelope survey. In: East R (compiler) Antelopes: global survey and regional action plans Part 1: East & Northeast Africa. IUCN, Gland, pp 3–4

  • East R, Grubb P, Wilson VJ (1990) Classification of antelopes adopted for the antelope survey. In: East R (compiler) Antelopes: global survey and regional action plans Part 1: West & Central Africa, Gland, IUCN, pp 4–5

  • Eaton MJ, Myers GL, Kolokotronis SO et al (2010) Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates. Conserv Genet 11:1389–1404

    Article  Google Scholar 

  • Folmer O, Black M, Hoeh W et al (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol 3:294–299

    PubMed  CAS  Google Scholar 

  • Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu Rev Ecol Evol Syst 34:387–423

    Article  Google Scholar 

  • Glenn TC, Schable NA (2005) Isolating microsatellite DNA loci. In: Zimmer EA, Roalson EH (eds) Molecular evolution: producing the biochemical data, part B. Elsevier Academic Press Inc, San Diego, pp 202–222

    Chapter  Google Scholar 

  • Goodacre SL, Wade CM (2001) Patterns of genetic variation in Pacific island land snails: the distribution of cytochrome b lineages among Society Island Partula. Biol J Linn Soc 73:131–138

    Article  Google Scholar 

  • Grubb P (2005) Order Artiodactyla. In: Wilson DE, Reeder DM (eds) Mammal species of the world: a taxonomic and geographic reference, 3rd edn. Johns Hopkins University Press, Baltimore, pp 637–722

    Google Scholar 

  • Haltenorth T (1963) Klassifikation der Säugetiere: Artiodactyla. Handb Zool 8(32):1–167

    Google Scholar 

  • Haltenorth T, Diller H (1977) The collins field guide to the mammals of Africa including Madagascar. The Stephen Green Press, Massachusetts

    Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270:313–321

    Article  CAS  Google Scholar 

  • Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biol 2:1657–1663

    Article  CAS  Google Scholar 

  • Heyden K (1969) Studien zur Systematik von Cephalophinae Brooke, 1879; Reducini Simpson, 1945 und Peleini Sokolov, 1953 (-Antilopinae Baird, 1857). Z Wiss Zool 178:348–441

    Google Scholar 

  • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755

    Article  PubMed  CAS  Google Scholar 

  • Jansen van Vuuren B, Robinson TJ (2001) Retrieval of four adaptive lineages in duiker antelope: evidence from mitochondrial DNA sequences and fluorescence in situ hybridization. Mol Phylogenet Evol 20:409–425

    Article  Google Scholar 

  • Kerr KCR, Birks SM, Kalyakin MV et al (2009) Filling the gap—COI barcode resolution in eastern Palearctic birds. Front Zool 6:29

    Article  PubMed  Google Scholar 

  • Kingdon J (1997) The Kingdon field guide to African mammals. Academic Press, London

    Google Scholar 

  • Knowles LL, Carstens BC (2007) Delimiting species without monophyletic gene trees. Syst Biol 56:887–895

    Article  PubMed  Google Scholar 

  • Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163

    Article  PubMed  CAS  Google Scholar 

  • Linares MC, Soto-Calderon ID, Lees DC, Anthony NM (2009) High mitochondrial diversity in geographically widespread butterflies of Madagascar: a test of the DNA barcoding approach. Mol Phylogenet Evol 50:485–495

    Article  PubMed  CAS  Google Scholar 

  • Lopez JV, Yuhki N, Masuda R et al (1994) NUMT, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39:174–190

    PubMed  CAS  Google Scholar 

  • Monaghan MT, Wild R, Elliot M et al (2009) Accelerated species inventory on Madagascar using coalescent-based models of species delineation. Syst Biol 58:298–311

    Article  PubMed  CAS  Google Scholar 

  • Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLoS Biol 2:1529–1531

    Article  CAS  Google Scholar 

  • Newing H (2001) Bushmeat hunting and management: implications of duiker ecology and interspecific competition. Biodivers Conserv 10:99–118

    Article  Google Scholar 

  • Ntie S, Johnston AR et al (2010) A molecular diagnostic for identifying central African forest artiodactyls from faecal pellets. Anim Conserv 13:80–93

    Article  Google Scholar 

  • O’Meara BC (2010) New heuristic methods for joint species delimitation and species tree inference. Syst Biol 59:59–73

    Article  PubMed  Google Scholar 

  • Pons J, Barraclough TG, Gomez-Zurita J et al (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst Biol 55:595–609

    Article  PubMed  Google Scholar 

  • Poulsen JR, Clark CJ, Mavah G et al (2009) Bushmeat supply and consumption in a tropical logging concession in northern Congo. Conserv Biol 23:1597–1608

    Article  PubMed  CAS  Google Scholar 

  • Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system. Mol Ecol Notes 7:355–364

    Article  PubMed  CAS  Google Scholar 

  • Renoult JP, Geniez P, Bacquet P et al (2009) Morphology and nuclear markers reveal extensive mitochondrial introgressions in the Iberian Wall Lizard species complex. Mol Ecol 18:4298–4315

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Springs Harbor

    Google Scholar 

  • Sarkar IN, Planet PJ, Desalle R (2008) CAOS software for use in character-based DNA barcoding. Mol Ecol Resour 8:1256–1259

    Article  PubMed  CAS  Google Scholar 

  • Swofford D (2000) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland

    Google Scholar 

  • Tavares ES, Baker AJ (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evol Biol 8:81

    Article  PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  PubMed  CAS  Google Scholar 

  • van Vliet N, Nasi R (2008) Hunting for livelihood in Northeast Gabon: patterns, evolution, and sustainability. Ecol Soc. http://www.ecologyandsociety.org/vol13/iss2/art33/. Accessed 27 September 2009

  • van Vliet N, Zundel S, Miquel C, Taberlet P, Nasi R (2008) Distinguishing dung from blue, red and yellow-backed duikers through noninvasive genetic techniques. Afr J Ecol 46:411–417

    Article  Google Scholar 

  • Vrba ES (1995) The fossil record of African antelopes (Mammalia, Bovidae) in relation to human evolution and paleoclimate. In: Vrba ES, Denton GD, Partrige TC, Burckle LH (eds) Paleoclimate and evolution, with emphasis on human origins. Yale University Press, New Haven, pp 385–424

    Google Scholar 

  • Wilkie DS, Carpenter JF (1999) Bushmeat hunting in the Congo Basin: an assessment of impacts and options for mitigation. Biodivers Conserv 8:927–995

    Article  Google Scholar 

  • Yang ZH, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA 107:9264–9269

    Article  PubMed  CAS  Google Scholar 

  • Yassin A, Markow TA, Narechania A et al (2010) The genus Drosophila as a model for testing tree- and character-based methods for species identification using DNA barcodes. Mol Phylogenet Evol 57:509–517

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Stevens Touladjan, The San Diego Zoo, The Gladys Porter Zoo, Bettine Jansen van Vuuren, Andrew Bowkett, Emma Stokes, Fiona Maisels, Deb Pires, Mitch Eaton, Patrick Mickala, Nathalie van Vliet, Rostan Aba’a, Joseph Dew, and Bryan Curran for collecting or donating samples. This study was funded by The National Science Foundation grant DEB 0516425.

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Authors and Affiliations

  1. Department of Biological Sciences, 2000 Lakeshore Drive, University of New Orleans, New Orleans, LA, 70148, USA

    Anne R. Johnston, Stephan Ntie & Nicola M. Anthony

  2. Trinity College of Arts & Sciences, Duke University, Box 97981, Durham, NC, 27708, USA

    Megan K. Morikawa

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  1. Anne R. Johnston
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  2. Megan K. Morikawa
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  4. Nicola M. Anthony
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Correspondence to Nicola M. Anthony.

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Johnston, A.R., Morikawa, M.K., Ntie, S. et al. Evaluating DNA barcoding criteria using African duiker antelope (Cephalophinae) as a test case. Conserv Genet 12, 1173–1182 (2011). https://doi.org/10.1007/s10592-011-0220-2

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