Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA

Abstract

Over 200 described endemic species make up the adaptive radiation of cichlids in Lake Tanga-nyika. This species assemblage has been viewed as both an evolutionary reservoir of old cichlid lineages and an evolutionary hotspot from which the modern cichlid lineages arose, seeding the adaptive radiations in Lakes Victoria and Malawi. Here we report on a phylogenetic analysis of Lake Tanganyika cichlids combining the previously determined sequences of the mitochondrial ND2 gene (1047 bp) with newly derived sequences of the nuclear RAG1 gene (∼700 bp of intron 2 and ∼1100 bp of exon 3). The nuclear data—in agreement with mitochondrial DNA—suggest that Lake Tanganyika harbors several ancient lineages that did not undergo rampant speciation (e.g., Bathybatini, Trematocarini). We find strong support for the monophyly of the most species-rich Tanganyikan group, the Lamprologini, and we propose a new taxonomic group that we term the C-lineage. The Haplochromini and Tropheini both have an 11-bp deletion in the intron of RAG1, strongly supporting the monophyly of this clade and its derived position. Mapping the phylogenetically informative positions revealed that, for certain branches, there are six times fewer apomorphies in RAG1. However, the consistency index of these positions is higher compared to the mitochondrial ND2 gene. Nuclear data therefore provide, on a per–base pair basis, less but more reliable phylogenetic information. Even if in our case RAG1 has not provided as much phylogenetic information as we expected, we suggest that this marker might be useful in the resolution of the phylogeny of older groups.

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References

  1. Abila R, Barluenga M, Engelken J, Meyer A, Salzburger W (2004) Population-structure and genetic diversity in a haplochromine cichlid of a satellite lake of Lake Victoria. Mol Ecol 13(9):2589–2602

    Article  PubMed  Google Scholar 

  2. Albertson RC, Markert JA, Danley PD, Kocher TD (1999) Phylogeny of a rapidly evolving clade: The cichlid fish of Lake Malawi, East Africa. Proc Natl Acad Sci USA 96:5107–5110

    Article  PubMed  Google Scholar 

  3. Allender CJ, Seehausen O, Knight ME, Turner GF, Maclean N (2003) Divergent selection during speciation of Lake Malawi cichlid fish inferred from parallel radiations in nuptial coloration. Proc Natl Acad Sci USA 100:14074–14079

    Article  PubMed  Google Scholar 

  4. Anderson S, deBruijn MHL, Coulson AR, Eperon IC, Sanger F, Young I (1982) Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol 156:683–717

    Article  PubMed  Google Scholar 

  5. Avise JC (1984) Molecular markers, natural history and evolution. Chapmann & Hall, New York

    Google Scholar 

  6. Bininda-Edmonds ORP, Sanderson MJ (2001) Assessment of the accuracy of matrix representation with parsimony analysis supertree reconstruction. Syst Biol 50:565–579

    Article  PubMed  Google Scholar 

  7. Brinkmann H, Venkatesh B, Brenner S, Meyer A (2004a) Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates. Proc Natl Acad of Sci 101:4900–4905

    Article  Google Scholar 

  8. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18:225–239

    Article  PubMed  Google Scholar 

  9. Brower AVZ, DeSalle R, Vogler A (1996) Gene trees, species tree, and systematics. Annu Rev Ecol Syst 27:423–450

    Article  Google Scholar 

  10. Brufford MW, Hanotte O, Brookfield JFY, Burke T (1998) Multilocus and single-locus DNA fingerprinting. In: Hoelzel A (ed) Molecular genetic analysis of populations: a practical approach. Oxford University Press, Oxford, pp 287–336

    Google Scholar 

  11. Cohen A, Lezzar K, Tiercelin J, Soreghan M (1997) New paleontologic and lake level reconstructions of Lake Tanganyika: implication for tectonic, climatic and biological evolution in a rift lake. Basin Res 7:107–132

    Article  Google Scholar 

  12. Cohen A, Soreghan M, Scholz C (1993) Estimating the age of formation of lakes: An example from Lake Tanganyika, East African Rift system. Geology 21:511–514

    Article  Google Scholar 

  13. Cummings MP, Otto SP, Wakeley J (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol 12:814–822

    PubMed  Google Scholar 

  14. De Vos L, Seegers L (1998) Seven new Orthochromis species (Teleostei: Cichlidae) from the Malagarazi, Luiche und Rugufu basins (Lake Tanganyika drainage), with notes on their reproductive biology. Ichthyol Explor Freshwaters 9:371–420

    Google Scholar 

  15. Farias IP, Orti G, Meyer A (2000) Total evidences: molecules, morphology, and the phylogenetics of cichlids fish. Mol Dev Evol 288:76–92

    Article  Google Scholar 

  16. Felsenstein J (2004) Inferring phylogenies. Sinauer Associate, Sunderland, MA

    Google Scholar 

  17. Flynn JJ, Nedbal MA (1998) Phylogeny of the Carnivora (Mammalia): Congruence vs. incompatibility among multiple data sets. Mol Phylogenet Evol 9:414–426

    Article  PubMed  Google Scholar 

  18. Fryer G, Iles TD (1972) The cichlid fish of the Great Lakes of Africa. T.H.F., Neptune City, NJ

    Google Scholar 

  19. Greenwood PH (1973) A revision of Haplochromis and related species (pisces, Cichlidae) from Lake George, Uganda. Bull Br Mus Nat Hist (Zool) 25:141–242

    Google Scholar 

  20. Greenwood PH (1980) Towards a phyletic classification of the “genus” Haplochromis (Pisces, Cichlidae) and related taxa. Part II. The species from Lakes Victoria, Nabugabo, Edward, Georg and Kivu. Bull Br Mus Nat Hist (Zool) 39:1–101

    Google Scholar 

  21. Greenwood PH (1981) The haplochromine fish of the East African lakes. Cornell University Press, Ithaca, NY

    Google Scholar 

  22. Hasegawa M, Kishino H, Yano T (1985) Dating of the human–ape splitting by a molecular clock of mitchondrial DNA. J Mol Evol 22:160–174

    Article  PubMed  Google Scholar 

  23. Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference of phylogeny. Bioinformatics 17:754–755

    Article  PubMed  Google Scholar 

  24. Klett V, Meyer A (2002) What, if anything, is a Tilapia?—Mitochondrial ND2 phylogeny of Tilapiines and the evolution of parental care systems in the african cichlid fish. Mol Biol Evol 19:865–883

    PubMed  Google Scholar 

  25. Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32

    Google Scholar 

  26. Koblmüller S, Salzburger W, Stumbauer C (2004) Evolutionary relationships in the sand-dwelling cichlid lineage of Lake Tanganyika suggest multiple colonization of rocky habitats and convergent origin of biparental mouthbrooding. J Mol Evol 58:79–96

    Article  PubMed  Google Scholar 

  27. Kocher TD, (2004) Adaptive evolution and explosive speciation: the cichlid fish model. Nat Rev Genet 5:288–298

    Article  PubMed  Google Scholar 

  28. Kocher TD, Conroy JA, McKaye KR, Stauffer JR (1993) Similar morphologies of cichlid fish in Lakes Tanganyika and Malawi are due to convergence. Mol Phyl Evol 4:420–432

    Article  Google Scholar 

  29. Kocher TD, Conroy JA, McKaye KR, Stauffer JR, Lockwood SF (1995) Evolution of NADH Dehydrogense Subunit 2 in East African cichlid fish. Mol Phylogenet Evol 4:420–432

    Article  PubMed  Google Scholar 

  30. Kocher TD, Fernald R, Hofmann H, Meyer A, Okada N, Penman D, Seehausen O (2004) Genome sequence of a cichlid fish: the Nile tilapia (Oreochromis niloticus). Proposal submitted to the JGI Community Sequencing Program by the Cichlid Genome Consortium. Available at: http://www.hcgs.unh.edu/cichlid/

  31. Koepfli K-P, Wayne RK (2003) Type I STS markers are more informative than cytochrome b in phylogenetic reconstruction of the Mustilidae (Mammalia:Carnivora). Syst Biol 52:571–593

    Article  PubMed  Google Scholar 

  32. Kornfield I, Smith PF (2000) African cichlid fish: model systems for evolutionary biology. Annu Rev Ecol Syst 31:163–196

    Article  Google Scholar 

  33. Li W-H (1997) Molecular evolution. Sinauer Associates, Sunderland, MA

    Google Scholar 

  34. Lippitsch E (1995) Scale and squamation character polarity and phyletic assessment in the family Cichlidae. J Fish Biol 47:91–106

    Article  Google Scholar 

  35. Lippitsch E (1998) Phylogenetic study of cichlid fish in Lake Tanganyika: a lepidological approach. J Fish Biol 53:752–766

    Article  Google Scholar 

  36. Mayer WE, H. T, Klein J (1998) Phylogeny of African cichlid fish as revealed by molecular markers. Heredity 80:702–714

    PubMed  Google Scholar 

  37. Meyer A (1993a) Phylogenetic relationships and evolutionary processes in East African cichid fish TREE 8:279–284

    Google Scholar 

  38. Meyer A (1993b) Evolution of mitochondrial DNA in fish. In: Hochachka PW, Mommsen TP (eds) Molecular biology frontiers, biochemistry and molecular biology of fish. Elsevier Science, Amsterdam, pp 1–38

    Google Scholar 

  39. Moran P, Kornfield I (1995) Were population bottlenecks associated with radiation of the mbuna species flock (Teleostei: Cichlidae) of Lake Malawi? Mol Biol Evol 12:1085–1093

    Google Scholar 

  40. Nagl S, Tichy H, Mayer WE, Takahata N, Klein. J (1998) Persistence of neutral polymorphisms in Lake Victoria cichlid fish. Proc Natl Acad Sci USA 95:14238–14243

    Article  PubMed  Google Scholar 

  41. Nishida M (1991) Lake Tanganyika as an evolutionary reservoir of old lineages of East African fish: inferring form allozymes data. Experientia 47:974–979

    Article  Google Scholar 

  42. Nishida M (1997) Phylogenetic relationships and evolution of Lake Tanganyika cichlids: a molecular perspective. In: Kawanabe H, Hori M, Nagoshi M (eds) Fish communities in Lake Tanganyika. Kyoto University Press, Kyoto, pp 1–24

    Google Scholar 

  43. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Syst Biol 53:47–67

    Article  PubMed  Google Scholar 

  44. Poll M (1956) Resultats scientifique. Exploration hydrobiologique belge au lac Tanganyika (1946–1947). Poissons Cichlidae. Institut Royal des Sciences Naturelles de Belgique, Brussels

  45. Poll M (1986) Classification des Cichlidae du lac Tanganyika—Tribus, genres et especes. Académie royale de Belgique, Memoires de la Classe des Sciences, coll. in 8°, 2 ème série, T. XVL, fascicule Z

  46. Posada D, Crandall KA (1998) ModelTest: Testing the model of DNA substitution. Bioinformatics 14:817–818

    Article  PubMed  Google Scholar 

  47. Rodriguez F, Oliver JF, Marin A, Medina JR (1990) The general stochastic model of nucleotide substitutions. J Theor Biol 142:485–501

    PubMed  Google Scholar 

  48. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  Google Scholar 

  49. Rüber L, Meyer A, Sturmbauer C, Verheyen E (2001) Population structure in two sympatric species of Lake Tanganyika cichlid tribe Eretmodini: evidence for introgression. Mol Ecol 10:1207–1225

    Article  PubMed  Google Scholar 

  50. Rüber L, Britz R, Tan HH, Ng PKL, Zardoya R (2004) Evolution of mouthbrooding and life-history correlates in the fighting fish genus Betta. Evolution 58:799–813

    PubMed  Google Scholar 

  51. Russo CA, Takezaki N, Nei M (1996) Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny. Mol Biol Evol 13:525–536

    PubMed  Google Scholar 

  52. Salzburger W, Meyer A (2004) The species flocks of East African cichlid fish: recent advances in molecular phylogenetics and population genetics. Naturwissenschaften 91:277–290

    Article  PubMed  Google Scholar 

  53. Salzburger W, Meyer A, Baric S, Verheyen E, Stumbauer C (2002a) Phylogeny of the Lake Tanganyika Cichlid species flock and its relationship to the central and East African Haplochromine cichlid fish faunas. Syst Biol 51:113–135

    Article  Google Scholar 

  54. Salzburger W, Baric S, Sturmbauer C (2002b) Speciation via introgressive hybridization in East African cichlids? Mol Ecol 11:619

    Article  Google Scholar 

  55. Salzburger W, Mack T, Verheyen E, Meyer A (2005) Out of Tanganyika: Genesis, explosive speciation, key innovations and phylogeography of the haplochromine cichlid fish. BMC Evol Biol 5:17

    Article  PubMed  Google Scholar 

  56. Santini S, Boore JL, Meyer A (2003) Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genet Res 13:1111–1122

    Google Scholar 

  57. Schelly RC, Stiassny MLJ (2004) Revision of the congo river Lamprologus Schilthuis, 1891 (Teleostei: Cichlidae), with descriptions of two new species. Am Mus Nov 3451:1–40

    Article  Google Scholar 

  58. Schelly R, Salzburger W, Koblmüller S, Duftner N, Sturmbauer C (2005) Phylogenetic relationships of the lamprologine cichlid genus Lepidiolamprologus (Teleostei: Perciformes) based on mitochondrial and nuclear sequences, suggesting introgressive hybridization. MPE (in press)

  59. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504

    Article  PubMed  Google Scholar 

  60. Seehausen O, (2004) Hybridization and adaptive radiation. TREE 19:198–207

    Google Scholar 

  61. Seehausen O, Koetsier E, Schneider MV, Chapman LJ, Chapman CA, Knight ME, Turner GF, van Alphen JJM, Bills R (2003) Nuclear markers reveal unexpected genetic variation and a Congolese/Nilotic origin of the Lake Victoria cichlid species flock. Proc Roy Soc Lond 270:129–137

    Article  Google Scholar 

  62. Shaw PW, Turner GF, Idid MR, Robinson RL, Carvalho GR (2000) Genetic population structure indicates sympatric speciation of Lake Malawi pelagic cichlids. Proc Roy Soc Lond B 267:2273–2280

    Article  Google Scholar 

  63. Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114–1116

    Google Scholar 

  64. Snoeks J, Rüber L, Verheyen E (1994) The Tanganyika problem: comments on the taxonomy and distribution patterns of its cichlid fauna. Adv Limnol 44:355–372

    Google Scholar 

  65. Stiassny MLJ, (1990) Tylochromis, relationships and the phylogenetic status of the African Cichlidae. Am Mus Novit 1993:1–14

    Google Scholar 

  66. Stiassny MLJ, Meyer A (1999) Cichlids of the African rift lakes. Sci Am February:44–49

    Google Scholar 

  67. Strimmer K, von Haeseler A (1996) Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969

    Google Scholar 

  68. Strimmer K, von Haeseler A (1997) Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA 94:6815–6819

    Article  PubMed  Google Scholar 

  69. Sturmbauer C, Meyer A (1992) Genetic divergence, speciation and morphological stasis in a lineage of African cichlid fish. Nature 358:578–581

    Article  PubMed  Google Scholar 

  70. Sturmbauer C, Meyer A (1993) Mitochondrial phylogeny of the endemic mouthbrooding lineages of cichlid fish of Lake Tanganyika, East Africa. Mol Biol Evol 10:751–768

    PubMed  Google Scholar 

  71. Sturmbauer CE, Verheyen E, Meyer A (1994) Mitochondrial phylogeny of the Lamprologini, the major substrate spawning lineage of cichlid fish from Lake Tanganyika in Eastern Africa. Mol Biol Evol 10:751–768

    Google Scholar 

  72. Sturmbauer C, Hainz U, Baric S, Verheyen E, Salzburger W (2003) Evolution of the tribe Tropheini form Lake Tanganyika: synchronized explosive speciation producing multiple evolutionary parallelism. Hydrobiologia 500:51–64

    Article  Google Scholar 

  73. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0. Sinnauer Associates, Sunderland, MA

    Google Scholar 

  74. Swofford DL, Sullivan J (2003) Phylogeny inference based on parsimony and other methods: Practice. In: Salemi M, Vandamme A-M (eds) The phylogenetic handbook, a practical approach to DNA and protein phylogeny. Cambridge University Press, Cambridge, pp 182–206

    Google Scholar 

  75. Takahashi K, Terai Y, Nishida M, Okada N (1998) A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fish in Lake Tanganyika. Mol Biol Evol 15:391–407

    PubMed  Google Scholar 

  76. Takahashi K, Terai Y, Nishida M, Okada N (2001) Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fish in Lake Tanganyika as revealed by analysis of the insertion of retrotransposons. Mol Biol Evol 18:2057–2066

    PubMed  Google Scholar 

  77. Takahashi T (2003) Systematics of Tanganyikan cichlid fish (Teleostei: Perciformes). Ichtyological Res 50:367–382

    Article  Google Scholar 

  78. Terai Y, Takezaki N, Mayer WE, Tichy H, Takahata N, Klein J, Okada N (2004) Phylogenetic relationships among east african Haplochromine fish as revealed by short interspersed elements (SINEs). J Mol Evol 58:64–78

    Article  PubMed  Google Scholar 

  79. Turner GF, Seehausen O, Knight ME, Allender CJ, Robinson RL (2001) How many species of cichlid fish are there in African lakes? Mol Ecol 10:793–806

    Article  PubMed  Google Scholar 

  80. Van der Meijden A, Vences M, Meyer A (2004) Novel Phylogenetic relationships of the enigmatic brevicipitine and scaphiophrynine toads as revealed by sequences from the nuclear RAG1 gene. Proc Roy Soc B (Suppl) 271:S378–S381

    Google Scholar 

  81. Venkatesh B, Ning Y, Brenner S (1999) Late changes in spliceosomal introns define clades in vertebrate evolution. Proc Natl Acad Sci USA 96:10267–71

    Article  PubMed  Google Scholar 

  82. Verheyen E, Salzburger W, Snoeks J, Meyer A (2003) Origin of the superflock of cichlid fish from Lake Victoria East Africa. Science 300:325–329

    Article  PubMed  Google Scholar 

  83. Wiens JJ (2003) Missing data, incomplete taxa, and phylogenetic accuracy. Syst Biol 52:528–538

    PubMed  Google Scholar 

  84. Zardoya R, Meyer A (1996) Phylogenetic performance of mitochondrial protein–coding genes in resolving relationships among vertebrates. Mol Biol Evol 13:933–942

    PubMed  Google Scholar 

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Acknowledgments

We thank S. Koblmüller, J. Snoeks, C. Sturmbauer, E. Verheyen, and L. De Vos for provision and identification of some of the specimens and R. Gueta, I. Eistetter, T. Mack, and the other members of the Meyer lab for technical assistance. We are grateful to M. Cummings and L. Rüber and the second anonymous reviewer for discussions and valuable comments on the manuscript. This study was supported by the Landesstiftung Baden-Württemberg, the Center for Junior Research Fellows (University Konstanz), and the EU (Marie Curie fellowship) to W.S. and grants from the Deutsche Forschungsgemeinschaft to A.M.

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Correspondence to Axel Meyer.

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Clabaut, C., Salzburger, W. & Meyer, A. Comparative Phylogenetic Analyses of the Adaptive Radiation of Lake Tanganyika Cichlid Fish: Nuclear Sequences Are Less Homoplasious But Also Less Informative Than Mitochondrial DNA. J Mol Evol 61, 666–681 (2005). https://doi.org/10.1007/s00239-004-0217-2

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Keywords

  • Adaptive radiation
  • Cichlid species flocks
  • Explosive speciation
  • Nuclear DNA phylogeny
  • NADH Dehydrogenase Subunit II
  • RAG1
  • C-lineage