Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2006 Oct;63(4):473-83.
doi: 10.1007/s00239-005-0216-y. Epub 2006 Oct 4.

Distance-based genome rearrangement phylogeny

Affiliations
Free article

Distance-based genome rearrangement phylogeny

Li-San Wang et al. J Mol Evol. 2006 Oct.
Free article

Abstract

Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, transpositions, and inverted transpositions, as well as through operations, such as duplications, losses, and transfers, that also affect the gene content of the genomes. Because these events are rare relative to nucleotide substitutions, gene order data offer the possibility of resolving ancient branches in the tree of life; the combination of gene order data with sequence data also has the potential to provide more robust phylogenetic reconstructions, since each can elucidate evolution at different time scales. Distance corrections greatly improve the accuracy of phylogeny reconstructions from DNA sequences, enabling distance-based methods to approach the accuracy of the more elaborate methods based on parsimony or likelihood at a fraction of the computational cost. This paper focuses on developing distance correction methods for phylogeny reconstruction from whole genomes. The main question we investigate is how to estimate evolutionary histories from whole genomes with equal gene content, and we present a technique, the empirically derived estimator (EDE), that we have developed for this purpose. We study the use of EDE on whole genomes with identical gene content, and we explore the accuracy of phylogenies inferred using EDE with the neighbor joining and minimum evolution methods under a wide range of model conditions. Our study shows that tree reconstruction under these two methods is much more accurate when based on EDE distances than when based on other distances previously suggested for whole genomes.

PubMed Disclaimer

References

    1. Science. 1992 Mar 27;255(5052):1697-9 - PubMed
    1. Mol Biol Evol. 1987 Jul;4(4):406-25 - PubMed
    1. Curr Opin Genet Dev. 1998 Dec;8(6):668-74 - PubMed
    1. Pac Symp Biocomput. 2002;:524-35 - PubMed
    1. Pac Symp Biocomput. 2002;:211-22 - PubMed

Publication types

LinkOut - more resources