Modeling gene family evolution and reconciling phylogenetic discord.

作者: Gergely J. Szöllősi , Vincent Daubin

DOI: 10.1007/978-1-61779-585-5_2

关键词: GenomicsGene duplicationGenomeBiologyPhylogenetic treePhylogeneticsGene familyThree-domain systemEvolutionary biologyGene

摘要: Large-scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences across the three domains life. Here, we discuss approaches increasing complexity aimed at extracting information on pattern and process family evolution such datasets. In particular, consider models invoke processes birth (duplication transfer) death (loss) to explain families. First, review birth-and-death size their implications in light universal features distribution observed different species Subsequently, proceed recent developments capable more completely considering through probabilistic reconciliation phylogenetic histories individual genes with history genomes which they have resided. To illustrate methods results presented, use data HOGENOM database, demonstrating sizes eukaryota, archaea, bacteria exhibits remarkably similar shapes. We show these distributions best described by evolution, where for rate is larger than but new continually supplied a origination. Finally, take into consideration additional phylogenies, find that, prokaryotes, majority events result transfer.

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