Incorporating DNA barcodes into a multi-year inventory of the fishes of the hyperdiverse Lower Congo River, with a multi-gene performance assessment of the genus Labeo as a case study

Mitochondrial DNA

Volumn 22, Issue SUPPL. 1, 2011, Pages 52-70

  Lowenstein, Jacob H ^a,b   Osmundson, Todd W ^c   Becker, Sven ^d   Hanner, Robert ^d   Stiassny, Melanie L J ^a  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF GUELPH   (Canada)

Author keywords

Africa; Congo; Cytochrome c oxidase subunit I; DNA barcoding; Fish; RAG1

Indexed keywords

CYTOCHROME C OXIDASE;

ARTICLE; BIODIVERSITY; DNA BARCODING; DNA LIBRARY; ENZYME SUBUNIT; FISH; GENUS; HABITAT; MOLECULAR LIBRARY; MORPHOLOGY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RIVER; RIVER BASIN; SPECIES IDENTIFICATION;

ANIMALS; BASE SEQUENCE; CONGO; CYPRINIDAE; DEMOCRATIC REPUBLIC OF THE CONGO; DNA BARCODING, TAXONOMIC; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; FISH PROTEINS; FISHES; HOMEODOMAIN PROTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; RIVERS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

CYPRINIDAE; LABEO; PISCES;

EID: 80052306198     PISSN: 19401736     EISSN: 19401744     Source Type: Journal    
DOI: 10.3109/19401736.2010.537748     Document Type: Article

References (58)

1. Agosti D. 2006. Biodiversity data are out of local taxonomists' reach. Nature 439:392. (Pubitemid 43152813)
2. Amato G, Egan MG, Rabinowitz A. 1999. A new species of muntjac, Muntiacus putaoensis (Artiodactyla: Cervidae) from northern Myanmar. Anim Conserv 2:1-7. (Pubitemid 129500953)
3. Boulenger GA. 1901. Les poissons du bassin du Congo. Bruxelles: ́Etat Indépendant du Congo. p 532.
4. Boulenger GA. 1909. Catalogue of the fresh-water fishes of Africa in the British Museum of Natural History. London: Taylor and Francis, p 373.
5. Chapman L, Chapman C. 2001. Fishes of the African rain forests. In: Weber W, White LJT, Vedder A, Naughton-Treves L, editors. African rain forest ecology and conservation: An interdisciplinary perspective. New Haven, CT: Yale University Press. p 263-290.
6. Clark JF. 2002. The African Stakes of the Congo War. New York: Pellgrave MacMillan. p 266.
7. Davis JI, Nixon KC. 1992. Populations, genetic variation, and the delimitation of phylogenetic species. Syst Biol 41:421-435.
8. DeSalle R. 2006. What's in a character? J Biomed Inform 39:6-17.
9. DeSalle R, Egan M, Siddall M. 2005. The unholy trinity: Taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc London Ser B Biol Sci 360:1905-1916. (Pubitemid 44365051)
10. Gilles A, Lecointre G, Miquelis A, Loerstcher M, Chappaz R, Brun G. 2001. Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region. Mol Phylogenet Evol 19:22-33. (Pubitemid 32996697)
11. Gordon D. 2006. Nachituti's gift: Economy, society, and environment in Central Africa. Madison, WI: University of Wisconsin Press.
12. Hanner R, Gregory T. 2007. Genomic Diversity Research and the Role of Biorepositories. Cell Preservation Technology 5:10.
13. Hubert N, Hanner R, Holm E, Mandrak N, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P. 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3:e2490. Doi: 2410.1371/journal.pone.0002490.
14. Ivanova NV, Zemlak TS, Hanner RH, Hebert PDN. 2007. Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes 7:544-548. (Pubitemid 47035520)
15. Janzen D, Hallwachs W, Blandin P, Burns J, Cadiou J, Chacon I, Dapkey T, Deans A, Epstein M, Espinoza B. 2009. Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Molecular Ecology Resources 9:1-26.
16. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298. (Pubitemid 351890825)
17. Klopper R, Smith G, Chikuni A. 2002. The global taxonomy initiative in Africa. Taxon 51:159-165. (Pubitemid 34475846)
18. Lanave C, Preparata G, Saccone C, Serio G. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93. (Pubitemid 14116237)
19. La Salle J, Wheeler Q, Jackway P, Winterton S, Hobern D, Lovell D. 2009. Accelerating taxonomic discovery through automated character extraction. Zootaxa 2217:43-55.
20. Lévêque C. 1997. Biodiversity dynamics and conservation: The freshwater fish of Tropical Africa. Cambridge: Cambridge University Press. p 452.
21. Locke S, Mclaughlin J, Marcogliese D. 2010. DNA barcodes show cryptic diversity and a potential physiological basis for host specificity among Diplostomoidea (Platyhelminthes: Digenea) parasitizing freshwater fishes in the St. Lawrence River, Canada. Mol Ecol 19:2813-2827.
22. López J, Chen W, Ort́ G. 2004. Esociform phylogeny. Copeia 2004: 449-469.
23. Lowenstein J, Amato G, Kolokotronis S. 2009. The real maccoyii: Identifying tuna sushi with DNA barcodes-contrasting characteristic attributes and genetic distances. PLoS ONE 4:e7866.
24. Markert J, Schelly R, Stiassny M. 2010. Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids. BMC Evol Biol 10: 149.
25. Miller S. 2007. DNA barcoding and the renaissance of taxonomy. P Natl Acad Sci USA 104:4775-4776. (Pubitemid 47186125)
26. Miller M, Holder M, Vos R, Midford P, Liebowitz T, Chan L, Hoover P, Warnow T. 2009. The CIPRES Portal [Online]. Available at http://www.phylo.org [Accessed 3 June 2010].
27. Nickum JG. 2004. Guidelines for the use of fishes in research. Bethesda, MD: American Fisheries Society.
28. PAFFA. 2008. Workshop report. In The First African Fish Barcode of Life initiative (FISH-BOL) Regional Working Group Workshop. Addis Ababa: Addis Ababa University, Ethiopia.
29. Padial J, Miralles A, De la Riva I, Vences M. 2010. The integrative future of taxonomy. Front Zool 7:16.
30. Paugy D, Guégan J, Agnèse J. 1990. Three simultaneous and independent approaches to the characterization of a new species of Labeo (Teleostei, Cyprinidae) from West Africa. Can J Zool 68:1124-1131.
31. Prunier G. 2009. Africa's World War: Congo, the Rwandan Genocide, and the Making of a Continental Catastrophe. Oxford: Oxford University Press.
32. Rambaut A. 2010. FigTree v1.3.1 [Online]. Available at http://tree. bio.ed.ac.uk [Accessed 30 October 2010].
33. Ratnasingham S, Hebert PDN. 2007. BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol Ecol Notes 7: 355-364. (Pubitemid 46714172)
34. Reader J. 1999. Africa: A biography of the continent. New York: Vintage. p 816.
35. Reid GM. 1985. A revision of African species of Labeo (Pisces: Cyprinidae) and a re-definition of the genus. Braunschweig: Verlag van J. Crammer. p 322.
36. Reyntjens F. 2009. The Great African War: Congo and Regional Geopolitics, 1996-2006. Cambridge: Cambridge University Press. p 340.
37. Roberts T. 1986. Review: A revision of African species of Labeo (Pisces: Cyprinidae) and a re-definition of the genus. G.M. Reid 1985. Copeia 847-848.
38. Roberts T, Stewart D. 1976. An ecological and systematic survey of fishes in the rapids of the Lower Zaire or Congo River. Bull Mus Comp Zool Harvard Coll 147:239-317.
39. Rozen S, SkaletskyH. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
40. Runge J. 2007. The Congo River, Central Africa. In: Gupta A, editor. Large rivers: Geomorphology and management. New York: Wiley. p 293-309.
41. Sarkar IN, Thornton JW, Planet PJ, Figurski DH, Schierwater B, DeSalle R. 2002. An automated phylogenetic key for classifying homeoboxes. Mol Phylogenet Evol 24:388-399.
42. Skelton P. 1994. Diversity and distribution of freshwater fishes in East and Southern Africa. In: Teugels GG, Guégan JF, Albaret JJ, editors. Biological diversity of African fresh and brackish water fishes. Tervuren: Musee Royal de l'Afrique Centrale. p 95-131.
43. Skelton P, Tweddle D, Jackson P. 1991. Cyprinids of Africa. In: Winfield I, Nelson J, editors. Cyprinid fishes, systematics, biology and exploitation. London: Chapman and Hall. p 211-233.
44. Stamatakis A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688.
45. Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57:758-771.
46. Stiassny MLJ. 2002. Conservation of freshwater fish biodiversity: The knowledge impediment. Verh Gesellsch Ichthyol 3:7-18.
47. Stiassny MLJ, Getahun A. 2007. An overview of Labeonin relationships and the phylogenetic placement of the Afro-Asian genus Garra Hamilton, 1922 (Teleostei: Cyprinidae), with the description of five new species of Garra from Ethiopia, and a key to all African species. Zool J Linnean Soc 150:41-83. (Pubitemid 46645609)
48. Swartz ER, Mwale M, Hanner R. 2008. A role for barcoding in the study of African fish diversity and conservation. S Afr J Sci 104: 293-298.
49. Thieme ML, Abell R, Stiassny MLJ, Skelton PH. 2005. Freshwater ecoregions of Africa and Madagascar: A conservation assessment. Washington, DC: Island Press. p 431.
50. Thys van den Audenaerde D. 1987. Review of Reid GM 1985, a revision of African species of Labeo (Pisces, Cyprinidae). Rev Zool Afr 100:487-492.
51. Tshibwabwa SM. 1997. Systématique des espéces africaines du genre Labeo (Teleostei, Cyprinidae) dans les régions ichtyogéo-graphiques de Basse-Guinée et du Congo. Vol I et II. Faculté des Sciences, Facultés Universitaires Notre-Dame de la Paix de Namur, Belgium. Namur: Presses Universitaires de Namur. p 530.
52. Tshibwabwa SM, Teugels G. 1995. Contribution to the systematic revision of the African cyprinid fish genus Labeo: Species from the Lower Zaire river system. J Nat Hist 29:1543-1579. (Pubitemid 26454379)
53. Tshibwabwa SM, Stiassny MLJ, Schelly R. 2006. Description of a new species of Labeo (Teleostei: Cyprinidae) from the Lower Congo River. Zootaxa 1224:33-44. (Pubitemid 43965641)
54. Victor B. 2007. Coryphopterus kuna, a new goby (Perciformes: Gobiidae: Gobiinae) from the western Caribbean, with the identification of the late larval stage and an estimate of the pelagic larval duration. Zootaxa 1526:51-61. (Pubitemid 47094512)
55. Ward RD, Woodwark M, Skibinski DOF. 1994. A comparison of genetic diversity levels in marine, freshwater, and anadromous fishes. J Fish Biol 44:213-232. (Pubitemid 2049041)
56. Ward RD, Hanner R, Hebert P. 2009. The campaign to DNA barcode all fishes, FISH-BOL. J Fish Biol 74:329-356.
57. Wong E, Shivji H, Hanner R. 2009. Identifying sharks with DNA barcodes: Assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resources 9:243-256.
58. Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J Mol Evol 39:306-314. (Pubitemid 24283346)