Underestimation of species richness in neotropical frogs revealed by mtDNA analyses

PLoS ONE

Volumn 2, Issue 10, 2007, Pages

  Fouquet, Antoine ^a,b   Gilles, André ^b   Vences, Miguel ^c   Marty, Christian ^d   Blanc, Michel ^d   Gemmell, Neil J ^a  

^a UNIVERSITY OF CANTERBURY   (New Zealand)

^b AIX MARSEILLE UNIVERSITY   (France)

^c TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^d Impasse Jean Galot ^*  (French Guiana)

Author keywords

[No Author keywords available]

Indexed keywords

DNA 16S; MITOCHONDRIAL DNA; DNA; RIBOSOME DNA; RNA 16S;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; FROG; GENETIC DISTANCE; GEOGRAPHIC DISTRIBUTION; MONOPHYLY; NONHUMAN; PARAPHYLY; PHYLOGENY; PREVALENCE; SEQUENCE ANALYSIS; SPECIES RICHNESS; STATISTICAL SIGNIFICANCE; ANIMAL; BIODIVERSITY; BIOLOGICAL MODEL; CHEMISTRY; GENETIC VARIABILITY; METABOLISM; MOLECULAR EVOLUTION; POPULATION GENETICS; SPECIES DIFFERENCE;

AMPHIBIA; ANURA; LEPTODACTYLIDAE;

ANIMALS; BIODIVERSITY; DNA; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; MODELS, BIOLOGICAL; MODELS, GENETIC; PHYLOGENY; RANIDAE; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 38549083165     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001109     Document Type: Article

References (93)

1. Collins JP, Halliday T (2005) Forecasting changes in amphibian biodiversity: aiming at a moving target. Philosophical Transactions of the Royal Society B-Biological Sciences 360: 309-314.
2. Houlahan JE, Findlay CS, Schmidt BR, Meyer AH, Kuzmin SL (2000) Quantitative evidence for global amphibian population declines. Nature 404: 752-755.
3. Pechmann JHK, Wilbur HM (1994) Putting declining amphibian populations in perspective-Natural fluctuations and human impacts. Herpetologica 50: 65-84.
4. Pounds JA, Fogden MPL, Campbell JH (1999) Biological response to climate change on a tropical mountain. Nature 398: 611-615.
5. Pounds JA, Puschendorf R (2004) Ecology-clouded futures. Nature 427: 107-109.
6. Roy D (2002) Amphibians as environmental sentinels. Journal of Biosciences 27: 187-188.
7. Stuart SN, Chanson JS, Cox NA, Young BE, Rodrigues ASL, Fischman DL, Waller RW (2004) Status and trends of amphibian declines and extinctions worldwide. Science 306: 1783-1786.
8. Dubois A (2005) Developmental pathway, speciation and supraspecific taxonomy in amphibians, 1: Why are so many frog species in Sri Lanka. Alytes 22: 19-37.
9. Glaw F, Köhler J (1998) Amphibian species diversity exceeds that of mammals. Herpetological Review 29: 11-12.
10. Harken J (1999) Why are there so many new amphibian species when amphibians are declining? Trends in Ecology and Evolution 14: 7-8.
11. Köhler J, Vieites DR, Bonett RM, Garcia FH, Glaw F, Steinke D, Vences M (2005) New amphibians and global conservation: A boost in species discoveries in a highly endangered vertebrate group. Bioscience 55: 693-696.
12. Campbell JA, Savage JM (2000) Taxonomic reconsideration of Middle American frogs of the Eleutherodactylus rugulosus group (Anura: Leptodactylidac): A reconnaissance of subtle nuances among frogs. Herpetological Monographs 14: 186-292.
13. Cherry LM, Case SM, Wilson AC (1977) Relative rates of morphological evolution in primates, carnivores and frogs. American Zoologist 17: 910-910.
14. Cherry IM, Case SM, Wilson AC (1978) Frog Perspective on Morphological Difference between Humans and Chimpanzees. Science 200: 209-211.
15. Emerson SB (1986) Convergence and morphological constraint in frogs: variation in postcranial morphology. Fieldiana Zoology 43: 1-19.
16. Shubin NH, Jenkins FA (1995) An Early Jurassic jumping frog. Nature 377: 49-52.
17. Bossuyt F, Milinkovitch MC (2000) Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits. Proceedings of the National Academy of Sciences of the United States of America 97: 6585-6590.
18. Parra-Olea G, Wake DB (2001) Extreme morphological and ecological homoplasy in tropical salamanders. Proceedings of the National Academy of Sciences of the United States of America 98: 7888-7891.
19. Wake DB (1991) Homoplasy-the result of natural-selection, or evidence of design, limitations. American Naturalist 138: 543-567.
20. Pfenninger M, Schwenk K (2007) Cryptic animal species are homogeneously distributed among taxa and biogeographical regions. BMC Evolutionary Biology 7: 121.
21. Duellman WE (1999) Patterns of distribution of amphibians: a global perspective. Johns Hopkins University Press.
22. Young BE, Stuart SN, Chanson JS, Cox NA, Boucher TM (2004) Disappearing jewels: The status of New World amphibians, NatureServe.
23. Duellman WE (2004) Cusco Amazónico: the lives of amphibians and reptiles in an Amazonian rainforest. Cornell University Press.
24. Berven KA, Grudzien TA (1990) Dispersal in the wood frog (Rana sylvatica)- implications for genetic population structure. Evolution 44: 2047-2056.
25. Blaustein AR, Wake DB, Sousa WP (1994) Amphibian declines-judging stability, persistence, and susceptibility of populations to local and global extinctions. Conservation Biology 8: 60-71.
26. Duellman WE (1982) Quaternary climatic-ecological fluctuations in the lowland tropics: frogs and forests. In: Prance CT, ed. Biological diversification in the tropics Columbia Univ. Press. pp 389-402.
27. Gascon C, Lougheed SC, Bogart JP (1998) Patterns of genetic population differentiation in four species of Amazonian frogs: A test of the riverine barrier hypothesis. Biotropica 30: 104-119.
28. Kusano T, Maruyama K, Kanenko, S (1999) Breeding site fidelity in the Japanese toad, Bufo japonicus formosus. Herpetological Journal 9: 9-13.
29. Reading CJ, Loman J, Madsen T (1991) Breeding pond fidelity in the common toad, Bufo bufo. Journal of Zoology 225: 201-211.
30. Bush MB (1994) Amazonian speciation-a necessarily complex model. Journal of Biogeography 21: 5-17.
31. Frailey CD, Lavina, EL, Rancy A, Filho JPS (1989) A proposed Pleistocene/ Holocene lake in the Amazonas basin and its significance to Amazonian geology and biogeography. Acta Amazonica 18: 119-143.
32. Haffer J (1969) Speciation in amazonian forest birds. Science 165: 131-137.
33. Haffer J (1990) Geoscientific aspects of allopatric speciation. In: Peters G, Hutterer R, eds. Vertebrates in the tropics Museum A. Koenig. pp 45-60.
34. Haffer J (1997) Alternative models of vertebrate speciation in Amazonia: An overview. Biodiversity and Conservation 6: 451-476.
35. Moritz C. Patton JL, Schneider CJ, Smith TB (2000) Diversification of rainforest faunas: An integrated molecular approach. Annual Review of Ecology and Systematics 31: 533-563.
36. Noonan BP, Gaucher P (2005) Phylogeography and demography of Guianan harlequin toads (Atelopus): diversification within a refuge. Molecular Ecology 14: 3017-3031.
37. Nores M (1999) An alternative hypothesis for the origin of Amazonian bird diversity. Journal of Biogeography 26: 475-485.
38. Lynch JD (1979) The amphibians of the lowland tropical forests. In: Duellman WE, ed. The South American herpetofauna: Its origin, evolution and dispersal Monograph of the Museum of Natural History, University of Kansas. pp. 189-215.
39. Wynn A, Heyer WR (2001) Do geographically widespread species of tropical amphibians exist? An estimate of genetic relatedness within the Neotropical frog Leptodactylus fuscus (Schneider 1799) (Anura, Leptodactylidae). Tropical Zoology 14: 255-285.
40. Chek AA, Lougheed SC, Bogart JP, Boag PT (2001) Perception and history: molecular phylogeny of a diverse group of Neotropical frogs, the 30-chromosome Hyla (Anura: Hylidae). Molecular Phylogenetics and Evolution 18: 370-85.
41. Grant T, Frost DR, Caldwell JP, Gagliardo R, Haddad CFB, Kok PJR, Means DB, Noonan BP, Schargel WE, Wheeler WC (2006) Phylogenetic systematics of dart-poison frogs and their relatives (Amphibia: Athesphatanura: Dendrobatidae). Bulletin of the American Museum of Natural History 299(1): 262.
42. Noonan BP. Wray KP (2006) Neotropical diversification: the effects of a complex history on diversity within the poison frog genus Dendrobates. Journal of Biogeography 33: 1007-1020.
43. Roberts JL, Brown JL, May RV, Arizabal W, Schulte R, Summers K (2006) Genetic divergence and speciation in lowland and montane Peruvian poison frogs. Molecular Phytogenetics and Evolution 41: 149-164.
44. Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proceedings of the National Academy of Sciences of the United States of America 101: 14812-14817.
45. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biology 2: 1657-1663.
46. Vences M, Thomas M, Bonett RM, Vieites DR (2005) Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philosophical Transactions of the Royal Society B-Biological Sciences 360: 1859-1868.
47. Vences M, Thomas M, Van der Meijden AY, Chiari Y, Vieites DR (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology 2.
48. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology Evolution and Systematics 34: 397-423.
49. Avise JC (2000) Phylogeography: The history and formation of species. Cambridge, Massachusetts. Harvard University Press. 447 p.
50. de Queiroz K (1999) The general lineage concept of species and the defining properties of the species category. In: Wilson R, ed. Species: new interdisciplinary essays. Cambridge, Massachusetts, U.S.A.: MIT Press. pp 49-89.
51. Meyer CP, Paulay G (2005) DNA barcoding: Error rates based on comprehensive sampling. PLoS Biology 3: 2229-2238.
52. Ekrem T, Willassen E, Stur E (2007) A comprehensive DNA sequence library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution 43: 530-542.
53. Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium. populations. Evolution 47: 264-279.
54. Vences M, Wake D (2007) Speciation, species boundaries and phylogeography of amphibians. In: Heatwole H, Tyler M, eds. Amphibian Biology, vol. 7. Amphibian Systematics. Chipping Norton, Australia: Surrey Beatty and Sons.
55. Suatoni E, Vicario S, Rice S, Snell T, Caccone A (2006) An analysis of species boundaries and biogeographic patterns in a cryptic species complex: The rotifer-Brachionus plicatilis. Molecular Phylogenetics and Evolution 41: 86-98.
56. Fouquet A, Vences M, Salducci M-D, Meyer A, Marty C, Blanc M, Gilles A (2007) Revealing cryptic diversity using molecular phylogenetics and phylogeography in frogs of the Scinax ruber and Rhinella margaritifera species groups. Molecular Phylogenetics and Evolution 43: 567-582.
57. Vences M, Köhler J (2006) The current status of genetic exploration in amphibians: taxonomic and geographic disparities. In: Vences M, Köhler J, Ziegler T, Böhme W, eds. Herpetologia Bonnensis II. Proceedings of the 13th Congress of the Societas Europaea Herpetologica. Bonn, Zoologisches Forschungsmuseum A. Koenig and Societas Europaea Herpetologica. pp 193-195.
58. Garda AA, Cannatella DC (2007) Phylogeny and biogeography of paradoxical frogs (Anura, Hylidae, Pseudae) inferred from 12S and 16S mitochondrial DNA. Molecular Phylogenetics and Evolution 44: 104-114.
59. Mulcahy DG, Morrill BH, Mendelson JR (2006) Historical biogeography of lowland species of toads (Bufo) across the trans-Mexican neovolcanic belt and the Isthmus of Tehuantepec. Journal of Biogeography 33: 1889-1904.
60. Crawford AJ, Smith EN (2005) Cenozoic biogeography and evolution in direct-developing frogs of Central America (Leptodactylidae: Eleutherodactylus) as inferred from a phylogenetic analysis of nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 35: 536-555.
61. Meegaskumbura M, Bossuyt F, Pethiyagoda R, Manamendra-Arachchi K, Bahir M, Milinkovitch MC, Schneider CJ (2002) Sri Lanka: an amphibian hot spot. Science 298: 379.
62. Stuart BL, Inger RF, Voris HK (20D6) High level of cryptic species diversity revealed by sympatric lineages of Southeast Asian forest frogs. Biology Letters 2: 470-474.
63. Lougheed SC, Austin JD, Bogart JP, Boag PT, Chek AA (2006) Multi-character perspectives on the evolution of intraspecific differentiation in a Neotropical hylid frog. BMC Evolutionary Biology 6:
64. Collins AC, Dubach JM (2000) Biogeographic and ecological forces responsible for speciation in Ateles. International Journal of Primatology 21: 421-444.
65. Cortes-Ortiz L, Bermingham E, Rico C, Rodriguez-Luna E, Sampaio I, Ruiz-Garcia M (2003) Molecular systematics and biogeography bf the Neotropical monkey genus, Alouatta. Molecular Phylogenetics and Evolution 26: 64-81.
66. Grau ET, Pereira SL, Silveira LF, Hofling E, Wajntal A (2005) Molecular. phylogenetics and biogeography of Neotropical piping guans (Aves: Galliformes): Pipile Bonaparte, 1856 is synonym of Aburria Reichenbach, 1853. Molecular Phylogenetics and Evolution 35: 637-645.
67. Salazar-Bravo J, Dragoo, JW, Tirmin PS, Yates TL (2001) Phylogeny and evolution of the neotropical rodent genus Calomys: Inferences from mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution 20: 173-184.
68. Evans BJ, Kalley DB, Tinsley RC, Melnick DJ, Cannatella DC (2004) A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. Molecular Phylogenetics and Evolution 33: 197-213.
69. Faivovich J, Haddad CFB, Garcia PGA, Frost DR, Campbell JA, Wheeler WC (2005) Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision. Bulletin of the American Museum of Natural History 294: 240.
70. Wollenberg KC, Veith M, Noonan BP, Lötters S (2006) Polymorphism versus species richness - Systematics of large Dendrobates from the eastern Guiana shield (Amphibia: Dendrobatidae). Copeia. pp 623-629.
71. Martin PR, McKay JK (2004) Latitudinal variation in genetic divergence of populations and the potential for future speciation. Evolution 58: 938-945.
72. Chek AA, Austin JD, Lougheed SC (2003) Why is there a tropical-temperate disparity in the genetic diversity and taxonomy of species? Evolutionary Ecology Research 5: 69-70.
73. T.Hackett SJ, Rosenberg KV (1990) Comparison of phenotypic and genetic differentiation in South American Antwrens (Formicariidae). The Auk 107: 473-489.
74. Moritz C, Cicero C (2004) DNA barcoding: Promise and pitfalls. PLoS Biology 2(10): e354:
75. Fromhage L, Vences M, Veith M (2003) Testing alternative vicariance scenarios in Western Mediterranean discoglossid frogs. Molecular Phylogenetics and Evolution 31: 308-322.
76. Lymberakis P, Poulakakis N, Manthalou G, Tsigenopoulos CS, Magoulas A, Mylonas M (2007) Mitochondrial phylogeography of Rana (Pelophylax) populations in the Eastern Mediterranean region. Molecular Phylogenetics and Evolution 44: 115-125.
77. Veith M, Kosuch J, Vences M (2003) Climatic oscillations triggered post-Messinian speciation of Western Palearctic brown frogs (Amphibia, Ranidae). Molecular Phylogenetics and Evolution 26: 310-327.
78. Sites JW, Marshall JC (2004) Operational criteria for delimiting species. Annual Review of Ecology Evolution and Systematics 35: 199-227.
79. Boistel R, de Massary C, Angulo A (2006) Description of A new species of the genus Adenomera (Amphibia, Anura, Leptodactylidae) from French Guiana. Acta Herpetologica 1: 1-14.
80. Lescure J, Marty C (2000) Atlas des amphibiens de Guyane. Muséum national d'Histoire naturelle. Patrimoines Naturels 45: 388.
81. Gemmell NJ, Akiyama S (1996) An efficient method for the extraction of DNA from vertebrate tissues. Trends in Genetics 12: 338-339.
82. Salducci M-D, Marty C, Fouquet A, Gilles A (2005) Phylogenetic relationships and biodiversity in hylids (Anura : Hylidae) fi7om French Guiana. Comptes Rendus Biologies 328: 1009-1024.
83. 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 Research 25: 4876-4882.
84. Van de Peer Y, Caers A, de Rijk P, de Wachter R (1998) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Research 26: 179-182.
85. Smith MA, Poyarkov NA, Hebert, PDN (2007) CO1 DNA barcoding amphibians: take the chance, meet the challenge. Molecular Ecology Notes (In Press).
86. Swofford DL (1997) Test version 4.0.0d64 of PAUP. Sinauer.
87. Efron B (1979) 1977 Rietz Lecture-bootstrap methods-another look at the jackknife. Annals of Statistics 7: 1-26.
88. Felsenstein J (1985) Confidence limits on phylogenies-an approach using the bootstrap. Evolution 39: 783-791.
89. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
90. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818.
91. Akaike H (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19: 716-723.
92. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17: 1244-1245.
93. Draper NR, Smith H (1990) Applied Regression Analysis. Wiley. 736 p.