Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data

BMC Bioinformatics. 2005 May 27:6:127. doi: 10.1186/1471-2105-6-127.

Abstract

Background: As genomes evolve after speciation, gene content, coding sequence, gene expression, and splicing all diverge with time from ancestors with close relatives. A minimum evolution general method for continuous character analysis in a phylogenetic perspective is presented that allows for reconstruction of ancestral character states and for measuring along branch evolution.

Results: A software package for reconstruction of continuous character traits, like relative gene expression levels or alternative splice site usage data is presented and is available for download at http://www.rossnes.org/phyrex. This program was applied to a primate gene expression dataset to detect transcription factor binding sites that have undergone substitution, potentially having driven lineage-specific differences in gene expression.

Conclusion: Systematic analysis of lineage-specific evolution is becoming the cornerstone of comparative genomics. New methods, like phyrex, extend the capabilities of comparative genomics by tracing the evolution of additional biomolecular processes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Animals
  • Biological Evolution
  • Brain / metabolism
  • Cell Lineage
  • Computational Biology / methods*
  • Evolution, Molecular
  • Gene Expression
  • Gene Expression Regulation*
  • Genome
  • Genomics
  • Humans
  • Liver / metabolism
  • Models, Genetic
  • Molecular Sequence Data
  • Pan troglodytes / genetics
  • Phylogeny
  • Pongo pygmaeus / genetics
  • RNA, Messenger / metabolism*
  • Sequence Analysis, Protein
  • Software

Substances

  • RNA, Messenger