Diverse Considerations for Successful Phylogenetic Tree Reconstruction: Impacts from Model Misspecification, Recombination, Homoplasy, and Pattern Recognition

• Published in: Pattern Recognition in Computational Molecular Biology pp. 439 - 456
• Main Authors: Mallo, Diego, Sánchez‐Cobos, Agustín, Arenas, Miguel
• Format: Book Chapter
• Language: English
• Published: Hoboken, NJ, USA John Wiley & Sons, Inc 19.11.2015
• Subjects: diverse evolutionary processes; genetic recombination; homoplasy; pattern recognition; phylogenetic tree reconstruction; substitution model misspecification
• ISBN: 9781118893685; 1118893689
• DOI: 10.1002/9781119078845.ch23

This chapter describes the influences of diverse evolutionary phenomena on phylogenetic tree reconstruction and provides strategies to consider such phenomena. Three main approaches are currently applied to reconstruct phylogenetic trees, namely, distance‐based methods (Neighbor‐Joining (NJ)), maximum likelihood (ML) methods, and Bayesian methods. It is clear that nucleotide, codon, or amino acid substitution models of evolution are fundamental in phylogenetic inferences because the substitution model may affect the estimates of topology, substitution rates, bootstrap values, posterior probabilities, or the molecular clock. Recombination can seriously bias phylogenetic tree reconstruction. Phylogenetic tree reconstruction methods assume a common ancestor and, as a consequence, homoplasy can lead to phylogenetic uncertainty. It is therefore fundamental to search for homology in the data before building a phylogenetic tree, for example, by using computer tools such as BLAST. This consideration is related with the use of pattern recognition techniques to reconstruct phylogenetic histories through cluster analysis.