Practice

Introduction

There are two widely used approaches to getting a time-stamped phylogeny or 'time tree'

'Clockify' a maximum likelihood tree
- Rate smoothing
- Least squares dating
Fit a model that explicitly considers a strict or molecular clock

Rate smoothing with `chronos`

Rate smoothing involves constraining a tree to have clock-like branch lengths, but allowing the evolutionary rate to vary in a possibly complex manner
Given a fixed, rooted phylogeny, and a set of temporal constraints on sampling time, the function chronos will return a time tree
- We will use a slightly modified version of the code

Rooting the tree

chronos needs a rooted tree
We can estimate the root of the tree by maximising the association between the root-to-tip distance and the sampling times
The function rtt in the library ape allows one to do this

Least squares dating

Least squares dating, implemented in a program LSD also takes a fixed tree, and also estimates the root
We can use R to generate the data files and run lsd

Bayesian approaches

We can also fit phylogenies with time constraints using the popular Bayesian phylogenetic programs BEAST (version 1 or 2) and MrBayes
R can help to generate the input files for these programs