Assessment of phylogenomic and orthology approaches for phylogenetic inference.

Full Abstract

MOTIVATION:
Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination:
pairwise orthology, cluster orthology and tree-based orthology.

RESULTS:
Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content.

CONCLUSIONS:
Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years.

SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online.

Learn Faster Today Improve your study skills

Author information

Author/s: Dutilh, B E (BE); van Noort, V (V); van der Heijden, R T J M (RT); Boekhout, T (T); Snel, B (B); Huynen, M A (MA);

Affiliation: Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. dutilh(-atsign-)cmbi.ru.nl

Journal and publication information

Publication Type: Comparative Study; Evaluation Studies; Journal Article

Journal: Bioinformatics (Oxford, England) (Bioinformatics), published in England. (Language: eng)

Reference: 2007-Apr; vol 23 (issue 7) : pp 815-24

Dates: Created 2007/04/25; Completed 2007/05/15; Revised 2008/11/21;

PMID: 17237036, status: MEDLINE (last retrieval date: 12/26/2008)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

External Links for this article (including full text providers, if available):

Click Electronic Full-text Provider Links to see options for finding the electronic full text links to this article. Note there may be a subscription or fee required for access to the full text. See our FAQ for information on finding FREE full text articles.

This article may also be located in paper journal collections available in many libraries. Use the Journal and Publication Information above to find the full article.

MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Genome, Fungal - genetics
Molecular Sequence Data
Phylogeny
Sequence Alignment - methods
Sequence Analysis, DNA - methods

These are the highest related articles currently in the database:

See 100+ related articles.