The Importance of Method: Lots of Phylogenetic

Signal, Lots of ProblemsLiliana M. Dávalos, Paúl M. Velazco, Eliécer E. Gutiérrez

0.8 unitsknowlesi

vivax

falciparumreichenowi

gallinaceumbergheichabaudiyoelii

Base composition provides signalDávalos & Perkins 2008 Genomics

Agnarsson et al. 2011PLoS Currents ToL

Original dataSome positions extremely saturated

• 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

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

• Don’t ignore heterogeneous base composition• Always test before

inferring• Even within

families• Not all methods

equal, choose appropriately

Conclusions

Photo by B. Patterson

Thanks!