Molecular Biology and Evolution 18:2057-2066 (2001)
© 2001 Society for Molecular Biology and Evolution
Phylogenetic Relationships and Ancient Incomplete Lineage Sorting Among Cichlid Fishes in Lake Tanganyika as Revealed by Analysis of the Insertion of Retroposons
Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan;
Division of Molecular Marine Biology, Ocean Research Institute, University of Tokyo, Tokyo, Japan
Lake Tanganyika harbors numerous endemic species of extremely diverse cichlid fish that have been classified into 12 major taxonomic groups known as tribes. Analysis of short interspersed element (SINE) insertion data has been acknowledged to be a powerful tool for the elucidation of phylogenetic relationships, and we applied this method in an attempt to clarify such relationships among these cichlids. We studied insertion patterns of 38 SINEs in total, 24 of which supported the monophyly of three clades. The other 14 loci revealed extensive incongruence in terms of the patterns of SINE insertions. These incongruencies most likely stem from a period of adaptive radiation. One possible explanation for this phenomenon is the extensive incomplete lineage sorting of alleles for the presence or absence of a SINE during successive speciation events which took place about 5–10 MYA. The present study is the first to report the successful application of the SINE method in demonstrating the existence of such possible "ancient" incomplete lineage sorting. We discuss the possibility that it might potentially be very difficult to resolve the species phylogeny of a group that radiated explosively, even by resolving the genealogies of more than 10 nuclear loci, as a consequence of incomplete lineage sorting during speciation.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. E. Horvath, D. W. Weisrock, S. L. Embry, I. Fiorentino, J. P. Balhoff, P. Kappeler, G. A. Wray, H. F. Willard, and A. D. Yoder Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs Genome Res., March 1, 2008; 18(3): 489 - 499. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A. Ray, H. J. T. Pagan, M. L. Thompson, and R. D. Stevens Bats with hATs: Evidence for Recent DNA Transposon Activity in Genus Myotis Mol. Biol. Evol., March 1, 2007; 24(3): 632 - 639. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Nikaido, H. Hamilton, H. Makino, T. Sasaki, K. Takahashi, M. Goto, N. Kanda, L. A. Pastene, and N. Okada Baleen Whale Phylogeny and a Past Extensive Radiation Event Revealed by SINE Insertion Analysis Mol. Biol. Evol., May 1, 2006; 23(5): 866 - 873. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Bashir, C. Ye, A. L. Price, and V. Bafna Orthologous repeats and mammalian phylogenetic inference Genome Res., July 1, 2005; 15(7): 998 - 1006. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Sugawara, Y. Terai, H. Imai, G. F. Turner, S. Koblmuller, C. Sturmbauer, Y. Shichida, and N. Okada Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi PNAS, April 12, 2005; 102(15): 5448 - 5453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Pecon-Slattery, A. J. Pearks Wilkerson, W. J. Murphy, and S. J. O'Brien Phylogenetic Assessment of Introns and SINEs Within the Y Chromosome Using the Cat Family Felidae As a Species Tree Mol. Biol. Evol., December 1, 2004; 21(12): 2299 - 2309. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Roos, J. Schmitz, and H. Zischler Primate jumping genes elucidate strepsirrhine phylogeny PNAS, July 20, 2004; 101(29): 10650 - 10654. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Sasaki, K. Takahashi, M. Nikaido, S. Miura, Y. Yasukawa, and N. Okada First Application of the SINE (Short Interspersed Repetitive Element) Method to Infer Phylogenetic Relationships in Reptiles: An Example from the Turtle Superfamily Testudinoidea Mol. Biol. Evol., April 1, 2004; 21(4): 705 - 715. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Terai, N. Morikawa, K. Kawakami, and N. Okada The complexity of alternative splicing of hagoromo mRNAs is increased in an explosively speciated lineage in East African cichlids PNAS, October 28, 2003; 100(22): 12798 - 12803. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Terai, K. Takahashi, M. Nishida, T. Sato, and N. Okada Using SINEs to Probe Ancient Explosive Speciation: "Hidden" Radiation of African Cichlids? Mol. Biol. Evol., June 1, 2003; 20(6): 924 - 930. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Sugawara, Y. Terai, and N. Okada Natural Selection of the Rhodopsin Gene During the Adaptive Radiation of East African Great Lakes Cichlid Fishes Mol. Biol. Evol., October 1, 2002; 19(10): 1807 - 1811. [Full Text] [PDF]
|
|
|
|
|
|
Y. Terai, N. Morikawa, and N. Okada 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., September 1, 2002; 19(9): 1628 - 1632. [Full Text] [PDF]
|
|
|
|
|
|
K. Takahashi and N. Okada Mosaic Structure and Retropositional Dynamics During Evolution of Subfamilies of Short Interspersed Elements in African Cichlids Mol. Biol. Evol., August 1, 2002; 19(8): 1303 - 1312. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Terai, N. Morikawa, K. Kawakami, and N. Okada Accelerated Evolution of the Surface Amino Acids in the WD-Repeat Domain Encoded by the hagoromo Gene in an Explosively Speciated Lineage of East African Cichlid Fishes Mol. Biol. Evol., April 1, 2002; 19(4): 574 - 578. [Full Text] [PDF]
|
|