Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin

Molecular Phylogenetics and Evolution

Volumn 49, Issue 1, 2008, Pages 32-43

  Farias, Izeni Pires ^a   Hrbek, Tomas ^a,b  

^a FEDERAL UNIVERSITY OF AMAZONAS   (Brazil)

^b UNIVERSITY OF PUERTO RICO   (Puerto Rico)

Author keywords

Amazonian diversification; Discus fish; mtDNA control region; nuDNA RAG1; Phylogeography; Population genetics; Symphysodon spp.

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CICHLID; CLASSIFICATION; DNA SEQUENCE; GENE; GENETICS; HAPLOTYPE; MITOCHONDRIAL GENE; MITOCHONDRION; MOLECULAR EVOLUTION; PHENOTYPE; PHYLOGENY; POPULATION GENETICS; RIVER; SEQUENCE ALIGNMENT; SOUTH AMERICA; SPECIES DIFFERENCE; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; CICHLIDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENES, RAG-1; GENETIC SPECIATION; GENETICS, POPULATION; HAPLOTYPES; LIKELIHOOD FUNCTIONS; MITOCHONDRIA; MODELS, GENETIC; PHENOTYPE; PHYLOGENY; RIVERS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA; SPECIES SPECIFICITY;

CICHLIDAE; PISCES; SYMPHYSODON; SYMPHYSODON AEQUIFASCIATA; SYMPHYSODON DISCUS;

EID: 52049091241     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.05.033     Document Type: Article

References (96)

1. Aleixo A. Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves: Dendrocolaptidae). Biol. J. Linn. Soc. 89 (2006) 383-395
2. Allgayer, R., 2001. Les Discus. Les Guides de l'Aquarium, Paris, France.
3. Ayres J.M., and Clutton-Brock T.H. River boundaries and species range size in Amazonian primates. Am. Nat. 140 (1992) 531-537
4. Baum D.A., and Donoghue M.J. Choosing among alternative "phylogenetic" species concepts. Syst. Bot. 20 (1995) 560-573
5. Billuops K. Low-down on a rhythmic high. Nature 427 (2004) 686-687
6. Bleher H., Stölting K.N., Salzburger W., and Meyer A. Revision of the genus Symphysodon Heckel, 1840 (Teleostei: Perciformes: Cichlidae) based on molecular and morphological characters. Aqua 12 (2007) 133-174
7. Burgess W.E. Studies on the family Cichlidae: 10. New information on the species of the genus Symphysodon with the description of a new subspecies of S. discus Heckel. Trop. Fish Hobby. 29 (1981) 32-42
8. Bush M.B. Amazonian speciation: a necessarily complex model. J. Biogeogr. 21 (1994) 5-17
9. Castelloe J., and Templeton A.R. Root probabilities for intraspecific gene trees under neutral coalescent theory. Mol. Phylogenet. Evol. 3 (1994) 102-113
10. Chakraborty R., and Weiss K.M. Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium. Am. J. Hum. Genet. 86 (1991) 497-506
11. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1659
12. Cockerham C.C., and Weir B.S. Estimation of gene flow from F-statistics. Evolution 47 (1993) 855-863
13. Colinvaux P.A. Pleistocene biogeography and diversity in tropical forests of South America. In: Goldblatt P. (Ed). Biological Relationships Between Africa and South America (1993), Yale University Press, New Haven, CT 473-499
14. Cordani U.G., Sato K., Teixeira W., Tassinari C.C.G., and Basei M.A.S. Crustal evolution of the South American platform. In: Cordani U.G., Milani E.J., Thomaz-Filho A., and Campos D.d.A. (Eds). Tectonic Evolution of South America (2000), Academia Brasileira de Ciências, and Departamento Nacional da Produção Mineral (DNPM), Rio de Janeiro, RJ, Brazil 19-40
15. Costa J.B.S., Léa Bemerguy R., Hasui Y., and da Silva Borges M. Tectonics and paleogeography along the Amazon river. J. South Am. Earth Sci. 14 (2001) 335-347
16. Crandall K., and Templeton A.R. Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics 134 (1993) 959-969
17. Donaldson K.A., and Wilson Jr. R.R. Amphi-Panamic germinates of snook (Percoidei: Centropomidae) provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes. Mol. Phylogenet. Evol. 13 (1999) 208-213
18. Endler J.A. Geographic variation, speciation, and clines (1977), Princeton University Press, Princeton, NJ
19. Ewens W.J. The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3 (1972) 87-112
20. Excoffier L., Laval G., and Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. 1 (2005) 47-50
21. Farias I.P., Ortí G., and Meyer A. Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes. J. Exp. Zool. (Mol. Dev. Evol.) 288 (2000) 76-92
22. Farris J.S., Källersjö M., Kluge A.G., and Bult C. Testing significance of incongruence. Cladistics 10 (1994) 315-319
23. Fjeldså J. Geographical patterns for relict and young species of birds in Africa and South America and implications for conservation priorities. Biodivers. Conserv. 3 (1994) 207-226
24. Fu Y.-X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147 (1997) 915-925
25. Garrick R.C., Dyer R.J., Beheregaray L.B., and Sunnucks P. Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis. Mol. Ecol. 17 (2008) 1401-1403
26. Gelman A., and Rubin D.B. Inference from iterative simulation using multiple sequences. Stat. Sci. 7 (1992) 457-472
27. Goulding M., Barthem R.B., and Ferreira E.J.G. The Smithsonian Atlas of the Amazon (2003), Smithsonian Institution Press, Washington, DC
28. Gregory-Wodzicki K.M. Uplift history of the central and northern Andes: a review. Geol. Soc. Am. Bull. 112 (2000) 1091-1105
29. Gross, M.C., 2006. Comportamento cromossomico meiotico emitorico de acara-disco (Symphysodon aequifasciatus e Symphysodon discus, Cichlidae, Perciformes) da Amazonia Central. Genética, Conservação e Biologia Evolutiva. Instituto Nacional de Pesquisas da Amazônia (INPA) and Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil, p. 82.
30. Haffer J. Speciation in Amazonian forest birds. Science 165 (1969) 131-166
31. Haffer J. Alternative models of vertebrate speciation in Amazonia: an overview. Biodivers. Conserv. 6 (1997) 451-476
32. Hall T. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
33. Haq B.U., Hardenbol J., and Vail P.R. Chronology of fluctuating sea levels since the Triassic. Science 235 (1987) 1156-1167
34. Harpending H.C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66 (1994) 591-600
35. Hartl D.L., and Clark A.G. Principles of Population Genetics (2006), Sinauer Associates, Sunderland, MA
36. Hasegawa M., Kishino H., and Yano T.A. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22 (1985) 160-174
37. Hoorn C. Marine incursions and the influence of Andean tectonics on the Miocene depositional history of northwestern Amazonia: results of a palynostratigraphic study. Palaeogeogr. Palaeoclim. Palaeoecol. 105 (1993) 267-309
38. Hoorn C. Miocene deposits in the Amazonian foreland basin. Science 273 (1996) 122-123
39. Hoorn C., Guerrero J., Sarmiento G.A., and Lorente M.A. Andean tectonics as a cause for changing drainage patterns in Miocene northern South America. Geology 23 (1995) 237-240
40. Hrbek T., Seckinger J., and Meyer A. A phylogenetic and biogeographic perspective on the evolution of poeciliid fishes. Mol. Phylogenet. Evol. 43 (2007) 986-998
41. Hubert N., and Renno J.-F. Historical biogeography of South American freshwater fishes. J. Biogeogr. 33 (2006) 1414-1436
42. Huelsenbeck J.P., Ronquist F., Nielsen R., and Bollback J.P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294 (2001) 2310-2314
43. Jobb G., Haeseler A.v., and Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4 (2004) 1-9
44. Knowles L.L., and Maddison W.P. Statistical phylogeography. Mol. Ecol. 11 (2002) 2623-2635
45. Kokoscha M., and Greven H. Gibt es nur eine Art? Isoenzym-Elektrophorese bei Diskusfischen. D. Aqua. Terr. Z. Sonderheft Diskus 1 (1996) 20-21
46. Kullander S.O. Eine weitere Übersicht der Diskusfische, Gattung Symphysodon Heckel. D. Aqua. Terr. Z. Sonderheft Diskus 1 (1996) 10-16
47. Kullander, S.O., 2003. Family Cichlidae. In: Reis, R.E., Kullander, S.O., Ferraris, C.J. (Eds.), Check List of the Freshwater Fishes of South and Central America. EDIPUCRS, Porto Alegre, Brazil, pp. 605-654.
48. Liu Z., and Herbert T.D. High-latitude influence on the eastern equatorial Pacific climate in the early Pleistocene epoch. Nature 427 (2004) 720-723
49. Lundberg, J.G., Marshall, L.G., Guerrero, J., Horton, B., Malabarba, M.C.S.L., Wesselingh, F.P., 1998. The stage for Neotropical fish diversification: a history of tropical South American rivers. In: Malabarba, L.R., Reis, R.E., Vari, R.P., Lucena, Z.M.S., Lucena, C.A.S. (Eds.), Phylogeny and Classification of Neotropical Fishes. EDIPUCRS, Porto Alegre, Brazil, pp. 13-48.
50. Lyons E. Symphysodon discus Tarzoo. New blue discus electrify aquarium world. Trop. Mag. 4 (1959) 6-8 10
51. Mantel N. The detection of disease clustering and a generalized regression approach. Cancer Res. 27 (1967) 209-220
52. Marshall L.G., and Lundberg J.G. Technical comment: Miocene deposits in the Amazonian foreland basin. Science 273 (1996) 123-124
53. Mayr E. Systematics and the Origin of Species (1942), Columbia University Press, New York, NY
54. Mayr E. Populations, Species, and Evolution (1970), Belknap Press, Cambridge, MA
55. McKitrick M.C., and Zink R.M. Species concepts in ornithology. Condor 90 (1988) 1-14
56. Nei M. Molecular Evolutionary Genetics (1987), Columbia University Press, New York, NY
57. Nores M. An alternative hypothesis for the origin of Amazonian bird diversity. J. Biogeogr. 26 (1999) 475-485
58. Panchal M., and Beaumont M.A. The automation and evaluation of nested clade phylogeographic analysis. Evolution 61 (2007) 1466-1480
59. Pellegrin J. Contribution à l'étude anatomique, biologique et taxinomique des Poissons de la famille des Cichlidés. Mém. Soc. Zool. France 16 (1904) 41-399
60. Petit R.J. The coup de grâce for the nested clade phylogeographic analysis?. Mol. Ecol. 17 (2008) 516-518
61. Pillans B., Chappell J., and Naish T.R. A review of the Milankovitch climatic beat: template for Plio-Pleistocene sea-level changes and sequence stratigraphy. Sedimen. Geol. 122 (1998) 5-21
62. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
63. Posada D., and Crandall K.A. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol. Evol. 16 (2001) 37-45
64. Posada D., Crandall K.A., and Templeton A.R. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol. Ecol. 9 (2000) 487-488
65. Rand D.M. Neutrality tests of molecular markers and the connections between DNA polymorphism, demography, and conservation biology. Conserv. Biol. 10 (1996) 665-671
66. Rannala B., and Yang Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43 (1996) 304-311
67. Ready J.S., Ferreira E.J.G., and Kullander S.O. Discus fishes: mitochondrial DNA evidence for a phylogeographic barrier in the Amazonian genus Symphysodon (Teleostei: Cichidae). J. Fish Biol. 69 (2006) 200-211
68. Rogers A.R., and Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 99 (1992) 552-569
69. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
70. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Springs Harbor Laboratory Press, Cold Springs Harbor, NY
71. Sato A., Takezaki N., Tichy H., Figueroa F., Mayer W.E., and Klein J. Origin and speciation of haplochromine fishes in East African crater lakes investigated by the analysis of their mtDNA, Mhc genes, and SINEs. Mol. Biol. Evol. 20 (2003) 1448-1462
72. Schneider S., and Excoffier L. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics 152 (1999) 1079-1089
73. Schultz L.P. A review of the pompadour or discus fishes, genus Symphysodon of South America. Trop. Fish Hobby. 8 (1960) 5-17
74. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
75. Sioli H. The Amazon and its main affluents: hydrography, morphology of the river courses and river types. In: Sioli H. (Ed). The Amazon. Limnology and Landscape Ecology of a Mighty Tropical River and its Basin (1984), Springer-Verlag, New York, NY 127-165
76. Sivasundar A., Bermingham E., and Ortí G. Population structure and biogeography of migratory freshwater fishes (Prochilodus: Characiformes) in major South American rivers. Mol. Ecol. 10 (2001) 407-417
77. Suzuki Y., Glazko G.V., and Nei M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenies. Proc. Natl. Acad. Sci. USA 99 (2002) 16138-16143
78. Tajima F. Evolutionary relationships of DNA sequences in finite populations. Genetics 105 (1983) 437-460
79. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
80. Templeton A.R. Mechanisms of speciation-a population genetic approach. Annu. Rev. Ecol. Syst. 12 (1981) 23-48
81. Templeton A.R. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/control sampling designs: Alzheimer's disease and the apoprotein E locus. Genetics 140 (1995) 403-409
82. Templeton A.R. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol. Ecol. 7 (1998) 381-397
83. Templeton A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol. 13 (2004) 789-809
84. Templeton A.R. Using haplotype trees for phylogeographic and species inference in fish populations. Environ. Biol. Fishes 69 (2004) 7-20
85. Templeton A.R., Boerwinkle E., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 117 (1987) 343-351
86. Templeton A.R., Crandall K.A., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data: III. Cladogram estimation. Genetics 132 (1992) 619-633
87. Templeton A.R., and Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping: IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134 (1993) 659-669
88. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1996) 4673-4680
89. Vega, A.M.L., 2007. Reconstituição paleoambiental dos depósitos Miocenos na região centro-oriental da Bacia do Solimões, Amazonas. Geociencias. Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil, p. 92.
90. Wallace A.R. On the monkeys of the Amazon. Proc. Zool. Soc. Lond. 20 (1852) 107-110
91. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7 (1975) 256-276
92. Wesselingh F.P., Räsänen M.E., Irion G., Vonhof H.B., Kaandorp R.J.G., Renema W., Romero Pittman L., and Gingras M. Lake Pebas: a palaeoecological reconstruction of a Miocene, long-lived lake complex in western Amazonia. Cainozoic Res. 1 (2002) 35-81
93. Wesselingh F.P., and Salo J.A. A Miocene perspective on the evolution of the Amazonian biota. Script. Geol. 133 (2006) 439-458
94. Zar J.H. Biostatistical Analysis. fourth ed. (1999), Prentice Hall, Upper Saddle River, NJ
95. Zhang D.-X., and Hewitt G.M. Nuclear integrations: challenges for mitochondrial DNA markers. Trends Ecol. Evol. 11 (1996) 247-251
96. Zuanon J.A.S. História natural da ictiofauna de corredeiras do rio Xingú, na região de Altamira, Pará. Biology (1999), University of Campinas, Campinas, Brazil (p. 190)