Deciphering amphibian diversity through DNA barcoding: Chances and challenges

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 360, Issue 1462, 2005, Pages 1859-1868

  Vences, Miguel ^a   Thomas, Meike ^b   Bonett, Ronald M ^c   Vieites, David R ^c  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b UNIVERSITY OF COLOGNE   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

16S rRNA; Amphibia; Aneides; cox1; DNA barcoding; Mantellidae

Indexed keywords

AMPHIBIAN; CALLING BEHAVIOR; CELL ORGANELLE; DNA; GENE EXPRESSION; POPULATION STRUCTURE; SPECIES DIVERSITY; TAXONOMY;

AMPHIBIA; ANURA; MANTELLINAE; SALAMANDROIDEA;

CYTOCHROME C OXIDASE; DNA; PRIMER DNA; RNA 16S;

AMPHIBIA; ANIMAL; ARTICLE; BIODIVERSITY; COMPARATIVE STUDY; DIAGNOSTIC PROCEDURE; DNA SEQUENCE; GENETICS; GEOGRAPHY; INFORMATION PROCESSING; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE;

AMPHIBIA; ANIMALS; AUTOMATIC DATA PROCESSING; BASE SEQUENCE; BIODIVERSITY; DNA; DNA PRIMERS; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION, MOLECULAR; GEOGRAPHY; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR SEQUENCE DATA; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 33645772986     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2005.1717     Document Type: Article

References (78)

1. Alford, R. A. & Richards, S. J. 1999 Global amphibian declines: a problem in applied ecology. Annu. Rev. Ecol. Syst. 30, 133-165. (doi:10.1146/annurev.ecolsys.30.1.133.)
2. Altig, R. & McDiarmid, R. W. 1999 Body plan: development and morphology. In Tadpole: the biology of anuran larvae (ed. R. W. McDiarmid & R. Altig), pp. 24-51. Chicago: University of Chicago Press.
3. Altschul, S. R., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. 1990 Basic local alignment search tool. J. Mol. Biol. 215, 403-410. (doi:10.1006/jmbi.1990.9999.)
4. Alvarado Bremer, J. R., Vinas, J., Mejuto, J., Ely, B. & Pla, C. 2005 Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined effects of vicariance, secondary contact, introgression, and population expansion on the regional phylogenies of two highly migratory pelagic fishes. Mol. Phylogenet. Evol. 36, 169-187.
5. Arntzen, J. W. 1989 The identification of eggs of some species of palaearctic newts (genus Trititrus) by starch gel electrophoresis. Isozyme Bull. 22, 69.
6. Avise, J. C. 2000 Phylogeography: the history and formation of species, p. 447. Cambridge, MA: Harvard University Press.
7. Babik, W., Szymura, J. M. & Rafinski, J. 2003 Nuclear markers, mitochondrial DNA, and male secondary sexual traits variation in a newt hybrid zone (Triturus vulgaris X T. montandoni). Mol. Ecol. 12, 1913-1930. (doi:10.1046/j.1365-294X.2003.01880.x.)
8. Babik, W., Branicki, W., Crnobrnja-Isailovic, J., Cogalniceanu, D., Sas, I., Olgun, K., Poyarkov, N. A., Garcia-Paris, M. & Arntzen, J. W. 2005 Phylogeography of two European newt species-discordance between mtDNA and morphology. Mol. Ecol. 14, 2475-2491.
9. Balinsky, J. B. 1981 Adaptation of nitrogen metabolism to hyperosmotic environment in Amphibia. J. Exp. Zool. 215, 335-350. (doi:10.1002/jez. 1402150311.)
10. Berger, L. et al. 1998 Chytridomycosis causes amphibian mortality associated with population declines in the rainforests of Australia and central America. Proc. Natl Acad. Sci. USA 95, 9031-9036. (doi:10.1073/pnas.95.15.9031.)
11. Blaustein, A. R., Wake, D. B. & Sousa, W. P. 1994 Amphibian declines: judging stability, persistence, and susceptibility of populations to local and global extinctions. Conserv. Biol. 8, 60-71. (doi:10.1046/j.l523-1739.1994. 08010060.x.)
12. Bossuyt, F. & Milinkovitch, M. C. 2000 Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits. Proc. Natl Acad. Sci. USA 97, 6585-6590. (doi:10.1073/pnas.97.12.6585.)
13. Bradley, R. D. & Baker, R. J. 2001 A test of the genetic species concept: cytochrome b sequences and mammals. J. Mammal 82, 960-973. (doi:10.1644/1545-1542(2001) 082<0960:ATOTGS>2.0.CO;2.)
14. Chase, M. W., Salamin, N., Wilkinson, M., Dunwell, J. M., Kesanakurthi, R. P., Haidar, N. & Savolainen, V. 2005 Land plants and DNA barcodes: short-term and longterm goals. Phil. Trans. R. Soc. B 360, 1889-1895. (doi:10.1098/rstb.2005.1720.)
15. Chiari, Y., Vences, M., Vieites, D. R., Rabemananjara, F., Bora, P., Ramilijaona Ravoahangimalala, O. & Meyer, A. 2004 New evidence for parallel evolution of color patterns in Malagasy poison frogs (Mantella). Mol. Ecol. 13, 3763-3774. (doi:10.1111/j.1365-294X.2004.02367.x.)
16. Daszak, P., Cunningham, A. A. & Hyatt, A. D. 2003 Infectious disease and amphibian population declines. Div. Distrib. 9, 141-150. (doi:10.1046/j.1472-4642.2003. 00016.x.)
17. Davic, R. D. & Welsh, H. H. 2004 On the ecological role of salamanders. Annu. Rev. Ecol. Syst. 35, 405-434. (doi:10.1146/annurev.ecolsys. 35.112202.130116.)
18. Emerson, S. B. 1986 Convergence and morphological constraint in frogs: variation in postcranial morphology. Fieldiana Zool. 43, 1-19.
19. Funk, D. J. & Omland, K. E. 2003 Species-level paraphyly and polyphyly: frequency, causes and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Syst. 34, 397-423. (doi:10.1146/annurev. ecolsys.34.011802.132421.)
20. Garćia-París, M., Alcobendas, M., Buckley, D. & Wake, D. B. 2003 Dispersal of viviparity across contact zones in Iberian populations of fire salamanders (Salamandra) inferred from discordance of genetic and morphological traits. Evolution 52, 129-143.
21. Glaw, F. & Köhler, J. 1998 Amphibian species diversity exceeds that of mammals. Herpetol. Rev. 29, 11-12.
22. Goldberg, C. S., Sullivan, B. K., Malone, J. H. & Schwalbe, C. R. 2004 Divergence among barking frogs (Eleuther-odactylus augusti) in the southwestern United States. Herpetologica 60, 312-320.
23. Haas, A. 2003 Phylogeny of frogs as inferred from primarily larval characters. Cladistics 19, 23-89.
24. Hanken, J. 1999 Why are there so many new amphibian species when amphibians are declining? Trends Ecol. Evol. 14, 7-8. (doi:10.1016/S0169- 5347(98)01534-1.)
25. Harris, D. J., Batista, V., Lymberakis, P. & Carretero, M. A. 2004 Complex estimates of evolutionary relationships in Tarentola mauritanica (Reptilia: Gekkonidae) derived from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 30, 855-859. (doi:10.1016/S1055-7903(03)00260-4.)
26. Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. 2003 Biological identification through DNA barcodes. Proc. R. Soc. B 270, 313-321. (doi:10.1098/rspb.2002.2218.)
27. Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. & Hallwachs, W. 2004a Ten species in one: DNA barcoding reveals cryptic species in the Neotropical skipper butterfly Astraptes fulgerator. Proc. Natl Acad. Sci. USA 101, 14812-14817. (doi:10.1073/pnas.0406166101.)
28. Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S. & Francis, C. M. 2004b Identification of birds through COI DNA barcodes. PLOS Biol. 2, 1-7. (doi:10.1371/journal.pbio.0020312.)
29. Highton, R. 1998 Is Ensatina eschscholtzii a ring species? Herpetologica 54, 254-278.
30. Highton, R. 2000 Detecting cryptic species using allozyme data. In The biology of plethodontid salamanders (ed. R. C. Bruce, R. G. Jaeger & L. D. Houck), pp. 215-241. New York: Kluwer Academic/Plenum Publishers.
31. Hoegg, S., Vences, M., Brinkmann, H. & Meyer, A. 2004 Phylogeny and comparative substitution rates of frogs inferred from three nuclear genes. Mol. Biol. Evol. 21, 1188-1200. (doi:10.1093/molbev/msh081.)
32. Jackman, T. R. 1993 Evolutionary and historical analyses within and among members of the salamander tribe Plethodontini (Amphibia: Plethodontidae). Ph.D. dissertation, University of California, Berkeley.
33. James, C. H. & Moritz, C. 2000 Intraspecific phylogeography in the sedge frog Litoria fallax (Hylidae) indicates pre-Pleistocence vicariance of an open forest species from eastern Australia. Mol. Ecol. 9, 349-358. (doi:10.1046/j.1365-294x.2000.00885.x.)
34. Kasapidis, P., Magoulas, A., Mylonas, M. & Zouros, E. 2005 The phylogeography of the gecko Cynopodion kotschyi (Reptilia: Gekkonidae) in the Aegean archipelago. Mol. Phylogenet. Evol. 35, 612-623. (doi:10.1016/j.ympev. 2005.02.005.)
35. Kimura, M. 1980 A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120. (doi:10.1007/BF01731581.)
36. Köhler, J., Vieites, D. R., Bonett, R. M., Hita Garcia, F., Glaw, F., Steinke, D. & Vences, M. 2005 Boost in species discoveries in a highly endangered vertebrate group: new amphibians and global conservation. BioScience 55, 693-696.
37. Kuchta, S. R. & Tan, A.-M. 2005 Isolation by distance and post-glacial range expansion in the rough-skinned newt, Taricha granulosa. Mol. Ecol. 14, 225-244. (doi:10.1111/j.1365-294X.2004.02388.x.)
38. Larson, A. & Chippindale, P. T. 1993 Molecular approaches to the evolutionary biology of plethodontid salamanders. Herpetologica 49, 204-215.
39. Larson, A., Wake, D. B., Maxson, L. R. & Highton, R. 1981 A molecular phylogenetic perspective on the origins of morphological novelties in the salamanders of the tribe Plethodontini (Amphibia, Plethodontidae). Evolution 35, 405-422.
40. Mahoney, M. J. 2001 Molecular systematics of Plethodon and Amides (Caudata: Plethodontidae: Plethodontini): phylogenetic analysis of an old and rapid radiation. Mol. Phylogenet. Evol. 18, 174-188. (doi:10.1006/mpev.2000. 0880.)
41. Malkmus, R. & Kosuch, J. 2000 Description of a new Ansonia larva (Ansonia guibei) from Borneo. Salamandra 36, 121-124.
42. Markmann, M. & Tautz, D. 2005 Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Phil. Trans. R. Soc. B 360, 1917-1924. (doi:10.1098/rstb. 2005.1723.)
43. Masta, S. E., Sullivan, B. K., Lamb, T. & Routman, E. J. 2002 Molecular systematics, hybridization, and phylogeography of the Bufo americanus complex in eastern North America. Mol. Phylogenet. Evol. 24, 302-314. (doi:10. 1016/51055-7903(02)00216-6.)
44. Monaghan, M. T., Balke, M., Gregory, T. R. & Vogler, A. P. 2005 DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Phil. Trans. R. Soc. B 360, 1925-1933. (doi:10.1098/rstb.2005. 1724.)
45. Monsen, K. J. & Blouin, M. S. 2003 Genetic structure in a montane ranid frog: restricted gene flow and nuclear-mitochondrial discordance. Mol. Ecol. 12, 3275-3286. (doi:10.1046/j.1365-294X.2003.02001.x.)
46. Moritz, C., Schneider, C. J. & Wake, D. B. 1992 Evolutionary relationships within the Ensatina eschschohzii complex confirm the ring species interpretation. Syst. Biol. 41, 273-291.
47. Mueller, R. L., Macey, J. R., Jaekel, M., Wake, D. B. & Boore, J. L. 2004 Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc. Natl Acad. Sci. USA 101, 13820-13825. (doi:10.1073/pnas. 0405785101.)
48. Palumbi, S., Martin, A., Romano, S., McMillan, W. O., Slice, L. & Grabowski, G. 1991 The simple fool's guide to PCR, ver. 2, p. 46. Honolulu: University of Hawaii.
49. Parmelee, J. R., Knutson, M. G., Lyon, J. E. 2002 A field guide to amphibian larvae and eggs of Minnesota, Wisconsin, and Iowa. US Geological Survey. Biological Resources Division, Information and Technology Report USGS/BRD/ITR-2002-0004, Washington, DC.
50. Parra-Olea, G. & Wake, D. B. 2001 Extreme morphological and ecological homoplasy in tropical salamanders. Proc. Natl Acad. Sci. USA 98, 7888-7891. (doi:10.1073/pnas.131203598.)
51. Ranvestel, A. W., Lips, K. R., Pringle, C. M., Whiles, M. R. & Bixby, R. J. 2004 Neotropical tadpoles influence stream benthos: evidence for the ecological consequences of decline in amphibian populations. Freshw. Biol. 49, 274-285. (doi:10.1111/j.1365-2427.2004.01184.x.)
52. Rissler, L. J. & Taylor, D. R. 2001 The phylogenetics of desmognathine salamander populations across the southern Appalachians. Mol. Phylogenet. Evol 27, 197-211.(doi:10.1016/S1055-7903(02)00405-0.)
53. Saccone, C., DeCarla, G., Gissi, C., Pesole, G. & Reynes, A. 1999 Evolutionary genomics in the Metazoa: the mitochondrial DNA as a model system. Gene 238, 195-210. (doi:10.1016/S0378-1119(99)00270-X.)
54. Sequeira, F., Alexandrine, J., Rocha, S., Arntzen, J. W. & Ferrand, N. 2005 Genetic exchange across a hybrid zone within the Iberian endemic golden-striped salamander, Chioglossa lusitanica. Mol. Ecol 14, 245-254. (doi:10.1111/j.1365-294X.2004.02390.x.)
55. Steinke, D., Vences, M., Salzburger, W. & Meyer, A. 2005 Taxi-a software for DNA barcoding using distance methods. Phil. Trans. R. Soc. 360, 1975-1980. (doi:10.1098/rstb.2005.1729.)
56. Stuart, S. N., Chanson, J. S., Cox, N. A., Young, B. E., Rodrigues, A.S. L., Fischman, D. L. & Waller, R. W. 2004 Status and trends of amphibian declines and extinctions worldwide. Science 306,1783-1786. (doi:10.1126/science. 1103538.)
57. Swofford, D. L. 2002 PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods), v. 4beta10. Sunderland, MA: Sinauer.
58. Symula, R., Schulte, R. & Summers, K. 2001 Molecular phylogenetic evidence for a mimetic radiation in Peruvian poison frogs supports a Mullerian mimicry hypothesis. Proc. R. Soc. B 268, 2415-2421. (doi:10.1098/rspb.2001.1812. )
59. Symula, R., Schulte, R. & Summers, K. 2003 Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates. Mol. Phylogenet. Evol. 26, 452-475. (doi:10.1016/S1055-7903(02)00367-6.)
60. Tautz, D., Arctander, P., Minelli, A., Thomas, R. H. & Vogler, A. P. 2003 A plea for DNA taxonomy. Trends Ecol. Evol. 18, 70-74. (doi:10.1016/S0169- 5347(02)00041-1.)
61. Thomas, M., Raharivololoniaina, L., Glaw, F., Vences, M. & Vieites, D. R. 2005 Montane tadpoles in Madagascar: molecular identification and description of the larval stages of Mantidactylus elegans, Mantidactylus madecassus, and Boophis lanrenti from the Andringitra Massif. Copeia 2005, 174-183.
62. Thomaz, D., Guiller, A. & Clarke, B. 1996 Extreme divergence of mitochondrial DNA within species of pulmonate land snails. Proc. R. Soc. B 263, 363-368.
63. Van der Meijden, A., Vences, M., Hoegg, S., Meyer, A. In press. Nuclear and mitochondria! phylogenies reveal a previously unrecognised radiation of ranid frogs from southern Africa. Mol. Phylogenet. Evol.
64. Veith, M., Kosuch, J., Feldmann, R., Martens, H. & Seitz, A. 2000 A test for correct species declaration of frog legs imports from Indonesia into the European Union. Biodivers. Conserv. 9, 333-341. (doi:10.1023/A: 1008906918236.)
65. Vences, M., Vieites, D. R., Glaw, F., Brinkmann, H., Kosuch, J., Veith, M. & Meyer, A. 2003 Multiple overseas dispersal in amphibians. Proc. R. Soc. B 270, 2435-2442. (doi:10.1098/rspb.2003.2516.)
66. Vences, M., Thomas, M., van der Meijden, A., Chiari, Y. & Vieites, D. R. 2005 Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front. Zool. 2, 5. (doi:10.1186/1742-9994-2-5.)
67. Wake, D. B. 1963 Comparative osteology of the plethodontid salamander genus Aneides. J. Morphol. 113, 77-118. (doi:10.1002/jmor.1051130106.)
68. Wake, D. B. 1966 Comparative osteology and evolution of the lungless salamanders, family Plethodontidae. Mem. So. Cal. Acad. Sci. 4, 1-11.
69. Wake, D. B. 1991 Homoplasy: the result of natural selection or evidence of design limitations? Am. Nat. 138, 543-567. (doi:10.1086/285234.)
70. Wake, D. B. 1997 Incipient species formation in salamanders of the Ensatina complex. Proc. Natl Acad. Sci. USA 94, 7761-7767. (doi:10.1073/pnas.94. 15.7761.)
71. Wake, D. B. & Jockusch, E. L. 2000 Detecting species borders using diverse data sets. In The biology of plethodontid salamanders (ed. R. C. Bruce, R. G. Jaeger & L. D. Houck), pp. 95-119. New York: Kluwer Academic/Plenum Publishers.
72. Weisrock, D. W., Kozak, K. H. & Larson, A. 2005 Phylogeographical analysis of mitochondrial gene flow and introgression in the salamander, Plethodon shermani. Mol. Ecol. 14, 1457-1472. (doi:10.1111/j.1365-294X.2005. 02524.x.)
73. Welsh, H. H. & Droege, S. 2001 A case for using plethodontid salamanders for monitoring biodiversity and ecosystem integrity of North American forests. Conserv. Biol. 15, 558-569. (doi:10.1046/j.1523-1739. 2001.015003558.x.)
74. Welsh, H. H. & Ollivier, L. M. 1998 Stream amphibians as indicators of ecosystem stress: a case study from California's redwoods. Ecol. Appl. 8, 1118-1132.
75. Wiens, J. J0 Chippindale, P. T. & Hillis, D. M. 2003 When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders. Syst. Biol. 52, 501-514.
76. Wilbur, H. M. 1980 Complex life cycles. Annu. Rev. Ecol. Syst. 11, 67-93. (doi:10.1146/annurev.es.11.110180.000435.)
77. Ziegler, T. 2002 Die Amphibien und Reptilien eines Tieflandfeuchtwald- Schutzgebietes in Vietnam, p. 342. Münster: Natur und Tier-Verlag.
78. Ziegler, T. & Vences, M. 2002 The tadpole of Rhacophorus verrucosus Boulenger, 1893 from Vietnam (Amphibia: Anura: Rhacophoridae). Faunistische Abhandlungen Staatliches Museum für Naturkunde Dresden 22, 319-327.