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Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
Williams, T.A.; Davín, A.A.; Szánthó, L.L.; Stamatakis, A.; Wahl, N.A.; Woodcroft, B.J.; Soo, R.M.; Eme, L.; Sheridan, P.; Gubry-Rangin, C.; Spang, A.; Hugenholtz, P.; Szöllosi, G.J. (2024). Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. ISME J. 18(1): wrae129. https://dx.doi.org/10.1093/ismejo/wrae129
In: The ISME Journal: Multidisciplinary Journal of Microbial Ecology. Nature Publishing Group: London. ISSN 1751-7362; e-ISSN 1751-7370, meer
Peer reviewed article  
Beschikbaar in  Auteurs 
Author keywords
    phylogenetics; gene tree–species tree reconciliation; microbial evolution; horizontal gene transfer
Auteurs  Top 
  • Williams, T.A.
  • Davín, A.A.
  • Szánthó, L.L.
  • Stamatakis, A.
  • Wahl, N.A.
  • Woodcroft, B.J.
  • Soo, R.M.
  • Eme, L.
  • Sheridan, P.
  • Gubry-Rangin, C.
  • Spang, A., meer
  • Hugenholtz, P.
  • Szöllosi, G.J.
Abstract
    In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host–microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature, and oxygen use offer enormous potential for understanding the rich tapestry of microbial life.
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