Not a simple case - A first comprehensive phylogenetic hypothesis for the Midas cichlid complex in Nicaragua (Teleostei: Cichlidae: Amphilophus)

Molecular Phylogenetics and Evolution

Volumn 56, Issue 3, 2010, Pages 1011-1024

  Geiger, Matthias F ^a   McCrary, Jeffrey K ^b   Schliewen, Ulrich K ^a  

^a ZOOLOGISCHE STAATSSAMMLUNG MÜNCHEN   (Germany)

^b Laguna de Apoyo Nature Reserve   (Nicaragua)

Author keywords

AFLP; Amphilophus citrinellus; Apoyo; Crater lake; Midas cichlid; Xilo

Indexed keywords

MITOCHONDRIAL DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CICHLID; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOTYPE; HISTOLOGY; MOLECULAR EVOLUTION; NICARAGUA; PHYLOGENY; SPECIES DIFFERENTIATION;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; BAYES THEOREM; CICHLIDS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC SPECIATION; GENOTYPE; MODELS, GENETIC; NICARAGUA; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

AMPHILOPHUS; AMPHILOPHUS CITRINELLUS; CICHLIDAE; TELEOSTEI;

EID: 77954427992     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2010.05.015     Document Type: Article

References (72)

1. Albertson R.C., Markert J.A., Danley P.D., Kocher T.D. Phylogeny of a rapidly evolving clade: the cichlid fishes of Lake Malawi, East Africa. Proc. Natl. Acad. Sci. USA 1999, 96:5107-5110.
2. Bandelt H.J., Forster P., Sykes B.C., Richards M.B. Mitochondrial portraits of human populations using median networks. Genetics 1995, 141:743-753.
3. Bandelt H.J., Forster P., Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
4. Barlow G.W. Competition between color morphs of the polychromatic Midas cichlid Cichlasoma citrinellum. Science 1973, 179:806-807.
5. Barlow G.W. The Midas cichlid in Nicaragua. Investigations of the Ichthyofauna of Nicaraguan Lakes 1976, 333-358. University of Nebraska Press, Lincoln, NB. T.B. Thorsen (Ed.).
6. Barlow G.W., Munsey J.W. The red devil-Midas-arrow cichlid species complex in Nicaragua. Investigations of the Ichthyofauna of Nicaraguan Lakes 1976, 359-369. University of Nebraska Press, Lincoln, NB. T.B. Thorsen (Ed.).
7. Barlow G.W., Rogers W. Female Midas cichlid's choice of mate in relation to parents' and own color. Biol. Behav. 1978, 3:137-145.
8. Barluenga M., Meyer A. The Midas cichlid complex: incipient sympatric speciation in Nicaraguan cichlid fishes?. Mol. Ecol. 2004, 13:2061-2076.
9. Barluenga M., Stölting K.N., Salzburger W., Muschik M., Meyer A. Sympatric speciation in Nicaraguan crater lake cichlid fish. Nature 2006, 439:719-723.
10. Barluenga M., Stölting K.N., Salzburger W., Muschik M., Meyer A. Evidence for sympatric speciation? (reply). Brief communication arising. Nature 2006, 444:E13.
11. Bryant D., Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004, 21:255-265.
12. Bunje P.M.E., Barluenga M., Meyer A. Sampling genetic diversity in the sympatrically speciating Nicaraguan Midas cichlids species complex over a 16 years time series. BMC Evol. Biol. 2007, 7:25.
13. Buntjer, J.B., 1997-2001. Phylogenetic Computer Tools v. 1.3 Wageningen University, The Netherlands.
14. Bussing W.A. Geographic distribution of the San Juan Ichthyofauna of Central America with remarks on its origin and ecology. Investigations of the Ichthyofauna of Nicaraguan Lakes 1976, 157-175. University of Nebraska Press, Lincoln, NB. T.B. Thorsen (Ed.).
15. Concheiro Pérez G.A., Říčan O., Ortí G., Bermingham E., Doadrio I., Zardoya R. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 2007, 43:91-110.
16. Cowan H., Prentice C., Pantosti D., de Martini P., Strauch W. Late Holocene Earthquakes on the Aeropuerto Fault, Managua. Nicaragua. Bull. Seismol. Soc. Am. 2002, 92:1694-1707.
17. Elmer K.R., Lehtonen T.K., Meyer A. Color assortative mating contributes to sympatric divergence of Neotropical cichlid fishes. Evolution 2009, 63:2750-2757.
18. Elmer K.R., Fan S., Gunter H.M., Jones J.C., Boekhoff S., Kuraku S., Meyer A. Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes. Mol. Ecol. 2010, 19(Suppl. 1):197-211.
19. Elmer K.R., Kusche H., Lehtonen T.K., Meyer A. Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes. Phil. Trans. R. Soc. B 2010, 365:1763-1782.
20. Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol. Ecol. 2005, 14:2611-2620.
21. Falush D., Stephens M., Pritchard J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164:1567-1587.
22. Falush D., Stephens M., Pritchard J.K. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes 2007, 7:574-578.
23. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author 2004, Department of Genome Sciences, University of Washington, Seattle.
24. Freundt A., Kutterolf S., Schmincke H.-U., Hansteen T., Wehrman H., Pérez W., Strauch W., Navarro M. Volcanic hazards in Nicaragua: Past, present, and future. Volcanic hazards in Central America 2006, 141-165. Geol. Soc. Am. Spec. Publ. W.I. Rose, G.J.S. Bluth, M.J. Carr, J. Ewert, L.C. Patino, J.W. Vallance (Eds.).
25. Günther A. On some new species of Central-American fishes. Proc. Zool. Soc. 1864, 1:23-27.
26. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. 1999, 41:95-98.
27. Herder F., Pfaender J., Schliewen U.K. Adaptive sympatric speciation of polychromatic " roundfin" sailfin silverside fish in Lake Matano (Sulawesi). Evolution 2008, 62:2178-2195.
28. Huson D. Splitstree - a program for analyzing and visualizing evolutionary data. Bioinformatics 1998, 14:68-73.
29. Jaccard P. Nouvelles recherches sur la distribution florale. Bull. Soc. Vaud. Sci. Nat. 1908, 44:223-270.
30. Klingenberg C.P., Barluenga M., Meyer A. Body shape variation in cichlid fishes of the Amphilophus citrinellus species complex. Biol. J. Linn. Soc. 2003, 80:397-408.
31. Kocher T.D., Thomas W.K., Meyer A., Edward S.V., Päabo S., Villablanca F.X., Wilson A.C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. PNAS 1989, 86:6196-6200.
32. Kocher T.D. Adaptive evolution and explosive speciation: the cichlid fish model. Nat. Rev. Genet. 2004, 5:288-298.
33. Krüger D., Gargas A. New measures of topological stability in phylogenetic trees - taking taxon composition into account. Bioinformation 2006, 1:327-330.
34. Kutterolf S., Freundt A., Pérez W., Wehrmann H., Schmincke H.U. Late Pleistocene to Holocene temporal succession and magnitudes of highly explosive volcanic eruptions in west-central Nicaragua. J. Volcanol. Geotherm. Res. 2007, 163:55-82.
35. Kutterolf, S., Freundt, A., Peréz, W., 2008. Pacific offshore record of plinian arc volcanism in Central America: 2. Tephra volumes and erupted masses. Geochem. Geophys. Geosyst. 9, doi:10.1029/2007GC001791.
36. Lehtonen, T.K., McCrary, J.K., Meyer, A., 2010. Territorial aggression can be sensitive to the status of heterospecific intruders. Behavioural Processes. doi:10.1016/j.beproc.2010.02.021.
37. Link W., Dixkens C., Singh M., Schwall M., Melchinger A.E. Genetic diversity in European and Mediterranean faba bean germ plasm revealed by RAPD markers. Theor. Appl. Genet. 1995, 90:27-32.
38. McKaye K.R. Competition for breeding sites between the cichlid fishes of Lake Jiloa, Nicaragua. Ecology 1977, 58:291-302.
39. McKaye K.R. Seasonality in habitat selection by the gold color morph of Cichlasoma citrinellum and its relevance to sympatric speciation in the family Cichlidae. EnvIRON. Biol. Fishes 1980, 5:75-78.
40. McKaye K.R., Stauffer J.R., van den Berghe E.P., Vivas R., Lopez Perez L.J., McCrary J.K., Waid R., Konings A., Lee W.-J., Kocher T.D. Behavioral, morphological and genetic evidence of divergence of the Midas cichlid species complex in two Nicaraguan crater lakes. Cuadernos de Investigación de la UCA 2002, 12:19-47.
41. Meek S.E. Synopsis of the fishes of the great lakes of Nicaragua. Field Columbo Mus. Pub. 121 Zool. Ser 1907, 7:97-132.
42. Meyer A., Morrissey J.M., Schartl M. Recurrent origin of a sexually selected trait in Xiphophorus fishes inferred from a molecular phylogeny. Nature 1994, 368:39-542.
43. Nei M., Li W.-H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 1979, 76:5269-5273.
44. Parsons K.J., Robinson B.W., Hrbek T. Getting into shape: an empirical comparison of traditional truss-based morphometric methods with a newer geometric method applied to New World cichlids. Environ. Biol. Fishes 2003, 67:417-431.
45. Pritchard J.K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
46. Posada, D., 2004. Collapse ver. 1.2. A tool for collapsing sequences to haplotypes. [Online] Available from: http://darwin.uvigo.es.
47. Říčan O., Zardoya R., Doadrio I. Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology. Mol. Phylogenet. Evol. 2008, 49:941-957.
48. Rohlf F.J., Marcus L.F. A revolution in morphometrics. Trends Ecol. Evol. 1993, 8:129-132.
49. Rohlf, F.J., 2006a. TpsUtil, file utility program, version 1.38. Department of Ecology and Evolution, State University of New York at Stony Brook.
50. Rohlf, F.J., 2006b. TpsDig, digitize landmarks and outlines, version 2.10. Department of Ecology and Evolution, State University of New York at Stony Brook.
51. Schliewen U., Rassmann K., Markmann M., Markert J., Kocher T., Tautz D. Genetic and ecological divergence of a monophyletic cichlid species pair under fully sympatric conditions in Lake Ejagham. Cameroon. Mol. Ecol. 2001, 10:1471-1488.
52. Schliewen U., Klee B. Reticulate sympatric speciation in Cameroonian crater lake cichlids. Front. Zool. 2004, 1:1-12.
53. Schliewen U.K., Kocher T.D., McKaye K.R., Seehausen O., Tautz D. Evidence for sympatric speciation? Brief Communication Arising. Nature 2006, 444:E12-E13.
54. Schwarzer J., Misof B., Tautz D., Schliewen U.K. The root of the East African cichlid radiations. BMC Evol. Biol. 2009, 9:186.
55. Sheets, H.D., 2003. IMP - Integrated Morphometrics Package. Department of Physics, Canisius College, Buffalo, New York.
56. Schlüter P.M., Harris S.A. Analysis of multilocus fingerprinting datasets containing missing data. Mol. Ecol. Notes 2006, 6:569-572.
57. Seehausen O. Hybridization and adaptive radiation. Trends Ecol. Evol. 2004, 19:198-207.
58. Seehausen O. African cichlid fish: a model system in adaptive radiation research. Proc. R. Soc. Lond., B, Biol. Sci. 2006, 273:1987-1998.
59. Siddall M.E. Another monophyly index: revisiting the jackknife. Cladistics 1995, 11:33-56.
60. Smith S.A., Dunn C.W. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 2008, 24:715-716.
61. Stauffer J.R., McKaye K.R. Description of Three New Species of Cichlid Fishes (Teleostei: Cichlidae) from Lake Xiloá, Nicaragua. Cuadernos de Investigación de la U.C.A. 2002, 12:1-18.
62. Stauffer J.R., McCrary J.K., Black K.E. Three new species of cichlid fishes (Teleostei: Cichlidae) from Lake Apoyo. Nicaragua. Proc. Biol. Soc. Wash. 2008, 121:117-129.
63. Stiassny M.L.J., Schliewen U.K., Dominey W.J. A new species flock of cichlid fishes from Lake Bermin, Cameroon with a description of eight new species of Tilapia (Labroidei: Cichlidae). Ichthyol. Explor. Freshw. 1992, 3:311-346.
64. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The ClustalX windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 24:4876-4882.
65. Trewavas E., Green J., Corbet S.A. Ecological studies on crater lakes in West Cameroon. Fishes of Barombi Mbo. J. Zool. (Lond.) 1972, 167:41-95.
66. Van de Peer Y., De Wachter R. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 1994, 10:569-570.
67. Villa J. Some speculations about 'The Great Nicaraguan Lake'. Investigations of the ichthyofauna of Nicaraguan Lakes 1976, 191-196. University of Nebraska Press, Lincoln, NB. T.B. Thorsen (Ed.).
68. Villa J. Systematic status of the cichlid fishes Cichlasoma dorsatum, C. granadense and C. nigritum Meek. Investigations of the Ichthyofauna of Nicaraguan lakes 1976, 375-383. University of Nebraska Press, Lincoln, NB. T.B. Thorsen (Ed.).
69. Weir B.S., Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 1984, 38:1358-1370.
70. Vos P., Hogers R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M., Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23:4407-4414.
71. Wilson A.B., Noack-Kunnmann K., Meyer A. Incipient speciation in sympatric Nicaraguan crater lake cichlid fishes: sexual selection versus ecological diversification. Proc. R. Soc. Lond. 2000, 267:2133-2141.
72. Zelditch M., Swiderski D.L., Sheets D.H., Fink W.L. Geometric Morphometrics for Biologists 2004, Elsevier Academic Press, San Diego.