Reconstructing the Phylogeny of Mobile Elements

The study of mobile element evolution yields valuable insights into the mechanism and history of genome rearrangement, and can help answer questions about our evolutionary history. However, because the mammalian genome contains millions of copies of mobile elements exhibiting a complex evolutionary history, traditional phylogenetic methods are ill-suited to reconstructing their history. New phylogenetic reconstruction algorithms which exploit the unique properties of mobile elements and handle large numbers of repeats are therefore necessary to better understand both mobile elements' evolution and our own. We describe a randomized algorithm for phylogenetic reconstruction that scales easily to a million or more elements. We apply our algorithm to human and chimpanzee Alu and L1 elements, and to SINE elements from 61 species, finding 32 new L1, 111 new SINE, and over 1000 new Alu subfamilies. Our results suggest that the history of mobile elements is significantly more complex than we currently understand.

[1]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[2]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[3]  D. Labuda,et al.  Monophyletic Origin of Alu Elements in Primates , 1998, Journal of Molecular Evolution.

[4]  Marina Meila,et al.  An Experimental Comparison of Several Clustering and Initialization Methods , 1998, UAI.

[5]  D. Labuda,et al.  Evolutionary inventions and continuity of CORE-SINEs in mammals. , 2000, Journal of molecular biology.

[6]  J. Jurka.  Repbase update: a database and an electronic journal of repetitive elements. , 2000, Trends in genetics : TIG.

[7]  Tal Pupko,et al.  A structural EM algorithm for phylogenetic inference , 2001, J. Comput. Biol..

[8]  M. Batzer,et al.  Alu repeats and human genomic diversity , 2002, Nature Reviews Genetics.

[9]  Nancy F. Hansen,et al.  Comparative analyses of multi-species sequences from targeted genomic regions , 2003, Nature.

[10]  Jerilyn A. Walker,et al.  Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. , 2003, Genome research.

[11]  E. Eichler,et al.  An Alu transposition model for the origin and expansion of human segmental duplications. , 2003, American journal of human genetics.

[12]  M. Batzer,et al.  Alu elements and hominid phylogenetics , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[13]  David Maxwell Chickering,et al.  Efficient Approximations for the Marginal Likelihood of Bayesian Networks with Hidden Variables , 1997, Machine Learning.

[14]  M. Batzer,et al.  Retrotransposition of Alu elements: how many sources? , 2004, Trends in genetics : TIG.

[15]  W. Miller,et al.  Mobile Genetic Elements , 2004 .

[16]  J. Jurka.  Evolutionary impact of human Alu repetitive elements. , 2004, Current opinion in genetics & development.

[17]  P. Pevzner,et al.  Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. , 2004, Genome research.

[18]  Zaher Dawy,et al.  An approximation to the distribution of finite sample size mutual information estimates , 2005, IEEE International Conference on Communications, 2005. ICC 2005. 2005.

[19]  M. Batzer,et al.  From the margins of the genome: mobile elements shape primate evolution , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[20]  M. Batzer,et al.  Under the genomic radar: the stealth model of Alu amplification. , 2005, Genome research.

[21]  E. Ostertag,et al.  Genetics: LINEs in mind , 2005, Nature.

[22]  B. Mishra,et al.  Quantifying the mechanisms for segmental duplications in mammalian genomes by statistical analysis and modeling. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Chun Jimmie Ye,et al.  Orthologous Repeats and Mammalian Phylogenetic Inference , 2005 .