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Adiantum.png EEB 5349: Phylogenetics


To introduce you to the maximum likelihood software IQ-Tree, and to show you how to visualize and annotate trees with the R package ggtree.


Both IQ-Tree (2015) and ggtree (2017) are relative newcombers to their respective arenas, so let's road-test them. If that's not cutting-edge enough for you, we will be using them with the data from a 2018 study that was accepted on February 9th. It's not even officially published yet!

The Study

The study by Condamine et al. (2018) focuses on Apollo (Parnassius) butterflies which live high up in alpine regions of the Holarctic, and have long been a favorite genus for collectors due to their beauty and relatively high endemism (collectors like hard to find things). Also of note is the use of mating plugs by male Apollos to control paternity.

The authors were interested in testing test two hypotheses about how diversification and macroevolution proceed: the Red Queen and Court Jester Hypotheses. The Red Queen hypothesis, coined by Leigh Van Valen in 1973 posits that organisms must constantly adapt through evolutionary time in order to survive in a world of ever-evolving organisms (it's an allusion to Through the Looking-Glass by Lewis Carroll). An alternative hypothesis

previously published DNA data from Apollo (Parnassius), coupled with two fossil specimens to infer a complete (as in all 85 species in the genus are included) time-calibrated phylogeny for the genus. With time-calibrated phylogeny in hand, the authors harnessed historical data about climate and geology, coupled with inferred ancestral species ranges

Getting Started

Log into your account on the cluster (ssh

R and ggtree

Literature Cited

red queen hypothesis court-jester hypothesis