Phylogeny Reconstruction


Phylogenies provide the necessary comparative framework to study biological problems from an evolutionary perspective. Molecular phylogenies reconstructed with probabilistic methods (i.e. maximum likelihood and Bayesian inference) are the most popular because they enable statistical inference from a potentially large number of characters (sequences). The main steps to infer phylogenies from sets of homologous sequences using probabilistic methods include sequence masking, multiple sequence alignment, trimming and phylogenetic inference under the concatenation or coalescent approaches. Commonly used software is listed. Given the increasing use of genomic data, I comment on the specifics of phylogenomics and emphasise the importance of data quality and systematic error assessment. Understanding the properties and assumptions, strengths and limitations of available phylogenetic methods is essential for adequately selecting inference methods and for correctly interpreting their results.

Key Concepts

  • Phylogenies are hypotheses of the evolutionary history of organisms (or their sequences).
  • Phylogenetic trees are essential for comparative studies in ecology and evolution.
  • Probabilistic phylogenetic methods provide a statistical framework for estimating historical patterns, inferring parameters of evolutionary processes and testing of hypotheses.
  • Coalescent methods that account for gene tree discordance are an alternative to data concatenation.
  • Phylogenomics provides an increased resolving power but might require especial attention to data quality and systematic error.
  • Mixture models can increase data fit and reduce some systematic errors.

Keywords: Bayesian; coalescence; evolution; maximum likelihood; molecular evolution; molecular phylogenetics; phylogenetic tree; systematics

Figure 1. Flowchart of the main steps for phylogeny reconstruction.


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Further Reading

Bleidorn C (2017) Phylogenomics: an Introduction, p 222. Springer.

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Scornavacca C, Delsuc F, Galtier N (eds.) (2020) Phylogenetics in the Genomic Era, 568 pp. Authors open access book, hal‐02535070.

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Irisarri, Iker(Oct 2020) Phylogeny Reconstruction. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0029211]