Exploring the relationship between sequence similarity and accurate phylogenetic trees.

Exploring the relationship between sequence similarity and accurate phylogenetic trees. Research Abstract Details 

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Exploring the relationship between sequence similarity and accurate phylogenetic trees. Abstract Text:

Brandi L Cantarel,Hilary G Morrison,William Pearson,

We have characterized the relationship between accurate phylogenetic reconstruction and sequence similarity, testing whether high levels of sequence similarity can consistently produce accurate evolutionary trees. We generated protein families with known phylogenies using a modified version of the PAML/EVOLVER program that produces insertions and deletions as well as substitutions. Protein families were evolved over a range of 100-400 point accepted mutations; at these distances 63% of the families shared significant sequence similarity. Protein families were evolved using balanced and unbalanced trees, with ancient or recent radiations. In families sharing statistically significant similarity, about 60% of multiple sequence alignments were 95% identical to true alignments. To compare recovered topologies with true topologies, we used a score that reflects the fraction of clades that were correctly clustered. As expected, the accuracy of the phylogenies was greatest in the least divergent families. About 88% of phylogenies clustered over 80% of clades in families that shared significant sequence similarity, using Bayesian, parsimony, distance, and maximum likelihood methods. However, for protein families with short ancient branches (ancient radiation), only 30% of the most divergent (but statistically significant) families produced accurate phylogenies, and only about 70% of the second most highly conserved families, with median expectation values better than 10(-60), produced accurate trees. These values represent upper bounds on expected tree accuracy for sequences with a simple divergence history; proteins from 700 Giardia families, with a similar range of sequence similarities but considerably more gaps, produced much less accurate trees. For our simulated insertions and deletions, correct multiple sequence alignments did not perform much better than those produced by T-COFFEE, and including sequences with expressed sequence tag-like sequencing errors did not significantly decrease phylogenetic accuracy. In general, although less-divergent sequence families produce more accurate trees, the likelihood of estimating an accurate tree is most dependent on whether radiation in the family was ancient or recent. Accuracy can be improved by combining genes from the same organism when creating species trees or by selecting protein families with the best bootstrap values in comprehensive studies.

Exploring the relationship between sequence similarity and accurate phylogenetic trees. Publishing Authors By Initials

BL Cantarel,HG Morrison,W Pearson,

For similar genetic phenomena: variation (genetics) research abstracts see: genetic phenomena: variation (genetics) research

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Exploring the relationship between sequence similarity and accurate phylogenetic trees. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Molecular biology and evolution

VOLUME: 23

Page Numbers: 2090-100

Journal Abbreviation: Mol. Biol. Evol.

ISSN: 0737-4038

DAY: 4

MONTH: 08

YEAR: 2006

Exploring the relationship between sequence similarity and accurate phylogenetic trees. Information

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LANGUAGE: eng

NlmUniqueID: 8501455

Exploring the relationship between sequence similarity and accurate phylogenetic trees. Keywords Mesh Terms:

KEYWORDS: Variation (Genetics)

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Grant and Affiliation Information for Exploring the relationship between sequence similarity and accurate phylogenetic trees.

AFFILIATION: Department of Biochemistry and Molecular Genetics, University of Virginia, VA, USA.

Country: United States

AGENCY: United States NIAID

GRANT: AI1058054

ACRONYM: AI

MEDLINETA: Mol Biol Evol

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