Continental monophyly of cichlid fishes and the phylogenetic position of Heterochromis multidens

Molecular Phylogenetics and Evolution

Volumn 73, Issue 1, 2014, Pages 53-59

  Keck, Benjamin P ^a   Hulsey, C Darrin ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

Author keywords

Continental Drift; East African Rift Lakes; Gondwana; Tilapia

Indexed keywords

AFRICA; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CICHLID; CLASSIFICATION; CONTINENTAL DRIFT; DNA SEQUENCE; EAST AFRICAN RIFT LAKES; FEMALE; GENE LOCUS; GENETICS; GONDWANA; PHYLOGENY; TILAPIA; TROPIC CLIMATE;

CONTINENTAL DRIFT; EAST AFRICAN RIFT LAKES; GONDWANA; TILAPIA;

AFRICA; ANIMALS; CICHLIDS; FEMALE; GENETIC LOCI; MODELS, BIOLOGICAL; PHYLOGENY; SEQUENCE ANALYSIS, DNA; TROPICAL CLIMATE;

EID: 84893716761     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2014.01.011     Document Type: Article

References (70)

1. Ane C., Larget B., Baum D.A., Smith S.D., Rokas A. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 2007, 24:412-426.
2. Arbour J.H., Lopez-Fernandez H. Ecological variation in South American geophagine cichlids arose during an early burst of adaptive morphological and functional evolution. Proc. R. Soc. B-Biol. Sci. 2013, 280:20130849.
3. Azuma Y., Kumazawa Y., Miya M., Mabuchi K., Nishida M. Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. BMC Evol. Biol. 2008, 8:215.
4. Carstens B.C., Pelletier T.A., Reid N.M., Satler J.D. How to fail at species delimitation. Mol. Ecol. 2013, 22:4369-4383.
5. Chakrabarty P. Cichlid biogeography: comment and review. Fish Fish. 2004, 5:97-119.
6. Chakrabarty P. Systematics and historical biogeography of Greater Antillean Cichlidae. Mol. Phylogenet. Evol. 2006, 39:619-627.
7. Degnan J.H., Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2006, 2:762-768.
8. Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
9. Edgar R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
10. Edwards S.V., Liu L., Pearl D.K. High-resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 2007, 104:5936-5941.
11. Efron B., Halloran E., Holmes S. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 1996, 93:13429-13434.
12. Farias I.P., Orti G., Meyer A. Total evidence: molecules, morphology, and the phylogenetics of cichlid fishes. J. Exp. Zool. 2000, 288:76-92.
13. Farias I.P., Orti G., Sampaio I., Schneider H., Meyer A. Mitochondrial DNA phylogeny of the family Cichlidae: monophyly and fast molecular evolution of the neotropical assemblage. J. Mol. Evol. 1999, 48:703-711.
14. Farias I.P., Orti G., Sampaio I., Schneider H., Meyer A. The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes. J. Mol. Evol. 2001, 53:89-103.
15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39:783-791.
16. Flicek P., Amode M.R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., Coates G., Fairley S., Fitzgerald S., Gil L., Gordon L., Hendrix M., Hourlier T., Johnson N., Kahari A.K., Keefe D., Keenan S., Kinsella R., Komorowska M., Koscielny G., Kulesha E., Larsson P., Longden I., McLaren W., Muffato M., Overduin B., Pignatelli M., Pritchard B., Riat H.S., Ritchie G.R.S., Ruffier M., Schuster M., Sobral D., Tang Y.A., Taylor K., Trevanion S., Vandrovcova J., White S., Wilson M., Wilder S.P., Aken B.L., Birney E., Cunningham F., Dunham I., Durbin R., Fernandez-Suarez X.M., Harrow J., Herrero J., Hubbard T.J.P., Parker A., Proctor G., Spudich G., Vogel J., Yates A., Zadissa A., Searle S.M.J. Ensembl 2012. Nucleic Acids Res. 2012, 40:D84-D90.
17. Friedman M., Keck B.P., Dornburg A., Eyton R., Martin C., Hulsey C.D., Wainwright P.C., Near T.J. Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting. Proc. R. Soc. B-Biol. Sci. 2013, 280:20131733.
18. Genner M.J., Seehausen O., Lunt D.H., Joyce D.A., Shaw P.W., Carvalho G.R., Turner G.F. Age of cichlids: new dates for ancient lake fish radiations. Mol. Biol. Evol. 2007, 24:1269-1282.
19. Goldman N., Anderson J.P., Rodrigo A.G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 2000, 49:652-670.
20. Gonzalez-Voyer A., Kolm N. Rates of phenotypic evolution of ecological characters and sexual traits during the Tanganyikan cichlid adaptive radiation. J. Evol. Biol. 2011, 24:2378-2388.
21. Hasegawa M., Kishino H. Confidence limits on the maximum-likelihood estimate of the homonid tree from mitochondrial-DNA sequences. Evolution 1989, 43:672-677.
22. Hasegawa M., Kishino H. Accuracies of the simple methods for estimating the bootstrap prabability of a maximum-likelihood tree. Mol. Biol. Evol. 1994, 11:142-145.
23. Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 2010, 27:570-580.
24. Hoerner M.E. Testing for differences in rates of speciation, extinction, and morphological evolution in four tribes of cichlids endemic to lake Tanganyika, east Africa. Evolution 2011, 65:3398-3412.
25. Hulsey C.D., Keck B.P., Hollingsworth P.R. Species tree estimation and the historical biogeography of heroine cichlids. Mol. Phylogenet. Evol. 2011, 58:124-131.
26. Hulsey C.D., Mims M.C., Parnell N.F., Streelman J.T. Comparative rates of lower jaw diversification in cichlid adaptive radiations. J. Evol. Biol. 2010, 23:1456-1467.
27. Kasahara M., Naruse K., Sasaki S., Nakatani Y., Qu W., Ahsan B., Yamada T., Nagayasu Y., Doi K., Kasai Y., Jindo T., Kobayashi D., Shimada A., Toyoda A., Kuroki Y., Fujiyama A., Sasaki T., Shimizu A., Asakawa S., Shimizu N., Hashimoto S.I., Yang J., Lee Y., Mastsushima K., Sugano S., Sakaizumi M., Narita T., Ohishi K., Haga S., Ohta F. The medaka draft genome and insights into vertebrate genome evolution. Nature 2007, 447:714-719.
28. Kishino H., Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 1989, 29:170-179.
29. Kishino H., Miyata T., Hasegawa M. Maximum-likelihood inference of protein phylogeny and the origin of chloroplats. J. Mol. Evol. 1990, 31:151-160.
30. Klett V., Meyer A. What, if anything, is a Tilapia? - Mitochondrial ND2 phylogeny of Tilapiines and the evolution of parental care systems in the African cichlid fishes. Mol. Biol. Evol. 2002, 19:865-883.
31. Kubatko L.S., Carstens B.C., Knowles L.L. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973.
32. Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
33. Kullander S.O. A phylogeny and classification of the South American Cichlidae (Teleostei: Perciformes). Phylogeny and Classification of Neotropical Fishes 1998, 461-498. EDIPUCRS, Porto Alegre, Brasil. L.R. Malabarba, R.E. Reis, R.P. Vari, Z.M. Lucena, C.A.S. Lucena (Eds.).
34. Larget B.R., Kotha S.K., Dewey C.N., Ane C. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 2010, 26:2910-2911.
35. Li C.H., Orti G., Zhang G., Lu G.Q. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol. Biol. 2007, 7:44.
36. Li C.H., Orti G., Zhao J.L. The phylogenetic placement of sinipercid fishes ("Perciformes") revealed by 11 nuclear loci. Mol. Phylogenet. Evol. 2010, 56:1096-1104.
37. Li C.H., Riethoven J.J.M., Ma L.B. Exon-primed intron-crossing (EPIC) markers for non-model teleost fishes. BMC Evol. Biol. 2010, 10.
38. Lippitsch E. Scale and squamation character polarity and phyletic assessment in the family Cichlidae. J. Fish Biol. 1995, 47:91-106.
39. Lopez J.A., Chen W.J., Orti G. Esociform phylogeny. Copeia 2004, 2004:449-464.
40. Lopez-Fernandez H., Arbour J.H., Winemiller K.O., Honeycutt R.L. Testing for ancient adaptive radiations in neotropical cichlid fishes. Evolution 2013, 67:1321-1337.
41. Lopez-Fernandez H., Honeycutt R.L., Winemiller K.O. Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei). Mol. Phylogenet. Evol. 2005, 34:227-244.
42. Lopez-Fernandez H., Winemiller K.O., Honeycutt R.L. Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae). Mol. Phylogenet. Evol. 2010, 55:1070-1086.
43. Maddison W.P. Gene trees in species trees. Syst. Biol. 1997, 46:523-536.
44. Maddison W.P., Knowles L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55:21-30.
45. Martin A.P., Bermingham E. Systematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences. Mol. Phylogenet. Evol. 1998, 9:192-203.
46. McMahan C.D., Chakrabarty P., Sparks J.S., Smith W.L., Davis M.P. Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae). PLoS ONE 2013, 8:e71162.
47. McVay J.D., Carstens B. Testing monophyly without well-supported gene trees: evidence from multi-locus nuclear data conflicts with existing taxonomy in the snake tribe Thamnophiini. Mol. Phylogenet. Evol. 2013, 68:425-431.
48. McVay J.D., Carstens B.C. Phylogenetic model choice: justifying a species tree or concatenation analysis. Phylogenet. Evolut. Biol. 2013, 1:114.
49. Near T.J., Keck B.P. Free from mitochondrial DNA: nuclear genes and the inference of species trees among closely related darter lineages (Teleostei: Percidae: Etheostomatinae). Mol. Phylogenet. Evol. 2013, 66:868-876.
50. Niemiller M.L., McCandless J.R., Reynolds R.G., Caddle J., Near T.J., Tillquist C.R., Pearson W.D., Fitzpatrick B.M. Effects of climatic and geological processes during the Pleistocene on the evolutionray history of the Northern Cavefish, Amblyopsis spelaea (Teleostei: Amblyopsidae). Evolution 2013, 67:1011-1025.
51. Oliver M.K. Heterochromis multidens: the most plesiomorphic African cichlid fish?. Am. Zool. 1979, 19. 892-892.
52. Oliver M.K. Systematics of African Cichlid Fishes: Determination of the Most Primitive Taxon, and Studies on the Haplochromines of Lake Malawi. Ecology and Evolutionary Biology 1984, Yale University, New Haven.
53. Patel S., Kimball R.T., Braun E.L. Error in phylogenetic estimation for bushes in the Tree of Life. Phylogenet. Evolut. Biol. 2013, 1:110.
54. Posada D. JModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
55. Pyron R.A., Burbrink F.T., Wiens J.J. A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes. BMC Evol. Biol. 2013, 13:93.
56. Rambaut, A., Drummond, A.J., 2003. Tracer v1.4, MCMC Trace Analysis Package.
57. Reynolds R.G., Niemiller M.L., Hedges S.B., Dornburg A., Puente-Rolon A.R., Revell L.J. Molecular phylogeny and historical biogeography of West Indian boid snakes (Chilabothrus). Mol. Phylogenet. Evol. 2013, 68:461-470.
58. Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Hohna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61:539-542.
59. Sanders K.L., Rasmussen A.R., Mumpuni, Elmberg J., De Silva A., Guinea M.L., Lee M.S.Y. Recent rapid speciation and ecomorph divergence in Indo-Australian sea snakes. Mol. Ecol. 2013, 22:2742-2759.
60. Schwarzer J., Misof B., Ifuta S.N., Schliewen U.K. Time and origin of cichlid colonization of the lower Congo rapids. PLoS ONE 2011, 6:e22380.
61. Schwarzer J., Misof B., Tautz D., Schliewen U.K. The root of the East African cichlid radiations. BMC Evol. Biol. 2009, 9:186.
62. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 2002, 51:492-508.
63. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 1999, 16:1114-1116.
64. Shimodaira H., Hasegawa M. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 2001, 17:1246-1247.
65. Smith W.L., Chakrabarty P., Sparks J.S. Phylogeny, taxonomy, and evolution of Neotropical cichlids (Teleostei: Cichlidae: Cichlinae). Cladistics 2008, 24:625-641.
66. Stiassny M.L.J. Phylogenetic intrarelationships of the family Cichlidae: an overview. Cichlid Fishes: Behaviour, Ecology, and Evolution 1991, 1-35. Chapman & Hall, London. M.H.A. Keenleyside (Ed.).
67. Sturmbauer C., Salzburger W., Duftner N., Schelly R., Koblmuller S. Evolutionary history of the Lake Tanganyika cichlid tribe Lamprologini (Teleostei: Perciformes) derived from mitochondrial and nuclear DNA data. Mol. Phylogenet. Evol. 2010, 57:266-284.
68. Terai Y., Morikawa N., Okada N. The evolution of the pro-domain of bone morphogenetic protein 4 (Bmp4) in an explosively speciated lineage of East African cichlid fishes. Mol. Biol. Evol. 2002, 19:1628-1632.
69. Yang Z.H. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 1997, 13:555-556.
70. Yang Z.H. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24:1586-1591.