|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 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). On the other hand, The Court Jester Hypothesis, coined by Anthony Barnosky in 1999, posits that it is interactions between species and the non-living world around it that are the main drivers of diversification and macroevolution.
previously published DNA data from Apollo (Parnassius), coupled with two fossil specimens to infer a time-calibrated and complete (as in all 85 living species in the genus are included) With time-calibrated phylogeny in hand, the authors harnessed historical climatic and geological data, coupled with inferred ancestral species ranges to try to tease apart who rules the Parnassius Court: The Red Queen or the Jester?
Log into your account on the cluster (ssh firstname.lastname@example.org)
R and ggtree
red queen hypothesis court-jester hypothesis