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Genetics. Feb 2001; 157(2): 777–784.
PMCID: PMC1461532

SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates.

Abstract

Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

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Selected References

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  • Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci U S A. 1981 Jan;78(1):454–458. [PMC free article] [PubMed]
  • Leeflang EP, Liu WM, Hashimoto C, Choudary PV, Schmid CW. Phylogenetic evidence for multiple Alu source genes. J Mol Evol. 1992 Jul;35(1):7–16. [PubMed]
  • Miyamoto MM. Molecular systematics: Perfect SINEs of evolutionary history? Curr Biol. 1999 Nov 4;9(21):R816–R819. [PubMed]
  • Murata S, Takasaki N, Saitoh M, Okada N. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):6995–6999. [PMC free article] [PubMed]
  • Andrews TD, Jermiin LS, Easteal S. Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins? J Mol Evol. 1998 Sep;47(3):249–257. [PubMed]
  • Nikaido M, Rooney AP, Okada N. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10261–10266. [PMC free article] [PubMed]
  • Okada N. SINEs. Curr Opin Genet Dev. 1991 Dec;1(4):498–504. [PubMed]
  • Purvis A. A composite estimate of primate phylogeny. Philos Trans R Soc Lond B Biol Sci. 1995 Jun 29;348(1326):405–421. [PubMed]
  • Quentin Y. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol. 1988;27(3):194–202. [PubMed]
  • Ryan SC, Dugaiczyk A. Newly arisen DNA repeats in primate phylogeny. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9360–9364. [PMC free article] [PubMed]
  • Feng Q, Moran JV, Kazazian HH, Jr, Boeke JD. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell. 1996 Nov 29;87(5):905–916. [PubMed]
  • Schmid CW. Alu: structure, origin, evolution, significance and function of one-tenth of human DNA. Prog Nucleic Acid Res Mol Biol. 1996;53:283–319. [PubMed]
  • Goodman M, Porter CA, Czelusniak J, Page SL, Schneider H, Shoshani J, Gunnell G, Groves CP. Toward a phylogenetic classification of Primates based on DNA evidence complemented by fossil evidence. Mol Phylogenet Evol. 1998 Jun;9(3):585–598. [PubMed]
  • Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. Bioessays. 2000 Feb;22(2):148–160. [PubMed]
  • Hamdi H, Nishio H, Zielinski R, Dugaiczyk A. Origin and phylogenetic distribution of Alu DNA repeats: irreversible events in the evolution of primates. J Mol Biol. 1999 Jun 18;289(4):861–871. [PubMed]
  • Shoshani J, Groves CP, Simons EL, Gunnell GF. Primate phylogeny: morphological vs. molecular results. Mol Phylogenet Evol. 1996 Feb;5(1):102–154. [PubMed]
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997 Dec 15;25(24):4876–4882. [PMC free article] [PubMed]
  • Jurka J, Klonowski P. Integration of retroposable elements in mammals: selection of target sites. J Mol Evol. 1996 Dec;43(6):685–689. [PubMed]
  • Zietkiewicz E, Richer C, Sinnett D, Labuda D. Monophyletic origin of Alu elements in primates. J Mol Evol. 1998 Aug;47(2):172–182. [PubMed]
  • Jurka J, Klonowski P, Trifonov EN. Mammalian retroposons integrate at kinkable DNA sites. J Biomol Struct Dyn. 1998 Feb;15(4):717–721. [PubMed]
  • Zietkiewicz E, Richer C, Labuda D. Phylogenetic affinities of tarsier in the context of primate Alu repeats. Mol Phylogenet Evol. 1999 Feb;11(1):77–83. [PubMed]
  • Kapitonov V, Jurka J. The age of Alu subfamilies. J Mol Evol. 1996 Jan;42(1):59–65. [PubMed]

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