Dating gene duplications

Rates and Patterns of Gene Duplication and Loss in the Human Genome

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Large scale gene duplication is a major force driving the evolution of genetic functional innovation. Whole genome duplications are widely believed to have played an important role in the evolution of the maize, yeast, and vertebrate genomes. The use of evolutionary trees to analyze the history of gene duplication and estimate duplication times provides a powerful tool for studying this process. Many studies in the molecular evolution literature have used this approach on small data sets, using analyses performed by hand.

The dating gene duplications growth of genetic sequence data will soon allow similar studies on a genomic scale, but such studies will be limited unless the analysis can be automated. Even existing data sets admit alternative hypotheses that would be too tedious to consider without automation. In this paper, we describe a program called NOTUNG that facilitates large scale analysis, using both rooted and unrooted trees.

When tested on trees analyzed in the literature, NOTUNG consistently yielded results that agree with the assessments in the original publications. Thus, NOTUNG provides a basic building block for inferring duplication dates from gene trees automatically and can also be used as an exploratory analysis tool for evaluating alternative hypotheses. A Dating gene duplications for Dating Gene Duplications and Optimizing Gene Family Trees Kevin C. ChenDannie Dating gene duplicationsMartin Farach-Colton Journal of Computational Biology View PDF Cite Save Share.

Showing of 31 references. Newly identified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a T-box cluster duplication. I RuvinskyL M Silver Genomics Ancient large-scale genome duplications: Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. A L Hughes Molecular biology and evolution A Biologically Consistent Model for Comparing Molecular Phylogenies Boris Dating gene duplications. MirkinIlya B.

MuchnikTemple F. Smith Journal of Computational Biology From Gene Trees to Species Trees Bin MaMing LiLouxin Zhang SIAM J. New algorithms for the duplication-loss model Michael T. HallettJens Lagergren RECOMB ChenDannie DurandMartin Farach-Colton RECOMB Dating gene duplications Trees and Species Trees: The Gene-Duplication Problem in Fixed-Parameter Tractable Ulrike Stege WADS Increasing genomic complexity by gene duplication and the origin of vertebrates.

Increasing genomic complexity by gene duplication…. Cited By Sort by: Showing of extracted citations. Gamma paleohexaploidy in the stem lineage of core eudicots: Radiation and functional diversification of alpha keratins during early vertebrate evolution. Wim VandeberghFranky Bossuyt Molecular biology and evolution CarreteroYlenia Chiari Very low rate of gene conversion in the dating gene duplications genome. Claudio CasolaGavin C ConantMatthew W Hahn Molecular biology and evolution Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi Pierre-Yves DupontMurray P Cox G3 The Last Common Ancestor of Most Bilaterian Animals Possessed at Least Nine Opsins.

Molecular evolution and functional divergence dating gene duplications X-intrinsic protein genes in plants Jelli VenkateshJae-Woong YuDaniel GastonSe Won Park Molecular Genetics and Genomics See our FAQ for additional information. The Allen Institute for Artificial Intelligence Proudly built by AI2 with the help of our Collaborators using these Sources.

Chromosomal Deletion, Inversion, Duplication and Translocation

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