Overview

This tutorial aims to guide you through our sequential (or stepwise) Bayesian inference pipeline using RevBayes (Höhna and Hsiang 2024). The exercises are based on a dataset of North American fireflies (genus Photinus) for which we have molecular sequence data for extant species (Catalan et al. 2022). Our goal is to estimate a time-calibrated phylogeny using a relaxed clock model. The two steps in our sequential Bayesian analysis are first to estimate the posterior distribution of phylogenies with branch lengths, and second to use these samples to infer a time-calibrated phylogeny.

In exercises 1 we’ll use the molecular sequence data to infer the relationships among living species. In exercise 2 we transform the branch lengths from units of substitution into units of time assuming a relaxed clock model.

The data

Create a directory on your computer for this tutorial. In this directory, create a subdirectory called data, and download the data files that you can find on the left of this page.

In the data folder, you should now have seven files. Each file is a fasta formatted alignment of a different protein coding gene. In the tutorial we are only going to use a single gene, COI, but as an exercise you should repeat the analysis with another gene and also with all genes concatenated together as a partitioned analysis.

Scripts

For more complex models and analyses, it’s useful to create separate Rev scripts that contain all the model parameters, moves, and functions for different model components (e.g., the substitution model and the clock model).

Create another subdirectory called scripts.

In this tutorial, you will work primarily in your text editor and create a set of modular files that can be easily managed and interchanged. Examples of all the commands used to perform each analysis are also provided at the top of this page under scripts but try to write the complete scripts yourself from the beginning to ensure you understand all the steps involved and the differences between setting up each analysis.

Exercises

Click on the first exercise to begin!

1. Estimating unrooted gene tree(s)
2. Rooting and time calibrating the gene tree(s)

1. Catalan A., Höhna S., Lower S.E., Duchen P. 2022. Inferring the demographic history of the North American firefly Photinus pyralis. Journal of Evolutionary Biology. 35:1488–1499.
2. Höhna S., Hsiang A.Y. 2024. Sequential Bayesian phylogenetic inference. Systematic Biology.:syae020.