This document discusses the importance of choosing the appropriate phylogenetic method when analyzing sequence data, as different methods can produce varying results. It analyzes several phylogenetic methods, including neighbor-joining with log-det distances, Bayesian mixture models, maximum likelihood models that recode codon positions or amino acids, and finds that phylogenetic method significantly impacts inferred tree topology. It concludes that analyses should not ignore heterogeneous base composition within groups, that methods should always be tested before making inferences, as even within families composition can vary, and not all phylogenetic methods are equal so the most appropriate one should be chosen.

1. The Importance of Method:
Lots of Phylogenetic
Signal, Lots of Problems
Liliana M. Dávalos, Paúl M. Velazco, Eliécer E. Gutiérrez

2. 0.8 units
knowlesi
vivax
falciparumreichenowi
gallinaceum
berghei
chabaudiyoelii
Base composition provides signal
Dávalos & Perkins 2008 Genomics

3. Agnarsson et al. 2011
PLoS Currents ToL

4. Original data
Some positions extremely saturated

6. • NJ log-det distances
• Bayesian mixture or cat
• ML model by site
• ML recode 3rd pos to RY
• ML recode RY to binary
• ML codon model
• ML protein model
Phylogenetic
methods
Dávalos, Cirranello et al. 2012 Biol Rev

8. Which method performs best?
monophyly ~ αclade + βphylogenetic method
phylogenetic method is observed across clades
(i.e., each clade has 8 observations of monophyly)
Which clade characteristics affect inference?
αclade ~ μall clades + βvariable+ εclade + ∑
variable is observed by clade (i.e., clade size,
base composition heterogeneity, saturation)
Yohe et al. 2015 Biol Lett

12. • Don’t ignore
heterogeneous base
composition
• Always test before
inferring
• Even within
families
• Not all methods
equal, choose
appropriately
Conclusions
Photo by B. Patterson

13. Thanks!