The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

Walker Pett, Marcin Adamski, Maya Adamska, Francis Warren, Michael Eitel, Davide Pisani, Gert Wörheide

Research output: Contribution to journalArticle (Academic Journal)peer-review

19 Citations (Scopus)
95 Downloads (Pure)


Resolving animal (Metazoa) relationships is crucial to our understanding of, for example, the origin of their key traits such as muscles, guts and nerves. However, a broadly accepted metazoan consensus phylogeny has yet to emerge. In part this is because the genomes of deeply-diverging and fast-evolving lineages may undergo significant gene turnover, reducing the number of orthologs shared with related phyla. This can limit the usefulness of traditional phylogenetic methods that rely on alignments of orthologous sequences. Phylogenetic analysis of gene content has the potential to circumvent this orthology requirement, with binary presence/absence of homologous gene families representing a source of phylogenetically informative characters. Applying binary substitution models to the gene content of 26 complete animal genomes, we demonstrate that patterns of gene conservation differ markedly depending on whether gene families are defined by orthology or homology, i.e., whether paralogs are excluded or included. We conclude that the placement of deeply-diverging lineages, like ctenophores, may exceed the limit of resolution afforded by methods based on comparisons of orthologous protein supermatrices, and novel approaches are required to fully capture the evolutionary signal from genes within genomes.
Original languageEnglish
Pages (from-to)643-649
Number of pages7
JournalMolecular Biology and Evolution
Issue number4
Early online date28 Jan 2019
Publication statusPublished - Apr 2019


  • phylogenomicsy
  • gene content
  • animal phylogeny
  • homology
  • ortholog

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