BEAST计算分化时间

Relaxed Phylogenetics and Dating with Confidence

Alexei J Drummond and Andrew Rambaut

April 1, 2010

Introduction

This practical will introduce the BEAST software for Bayesian evolutionary analysis,

with a focus on estimating phylogenies and divergence times when you have calibration

information from fossil evidence or other prior knowledge.

You will need the following software at your disposal:

• BEAST - this package contains the BEAST program, BEAUti, TreeAnnotator

time of writing, the current version is v1.5.. It is available for download from

http://beast.bio.ed.ac.uk/.

• FigTree - this is an application for displaying and printing molecular phylogenies,

in particular those obtained using BEAST. At the time of writing, the current

version is v1.3.1. It is available for download from http://tree.bio.ed.ac.uk/.

Rates and dates

This tutorial will guide you through the analysis of an alignment of sequences sampled

from twelve primate species. The goal is to estimate the phylogeny as well as the rate

of evolution on each lineage based on dates of divergence of their host species.

The first step will be to convert a NEXUS file with a DATA or CHARACTERS

The final step is to explore the output of BEAST in order to diagnose problems and to

summarize the results.

BEAUti

The program BEAUti is a user-friendly program for setting the model parameters for

BEAST. Run BEAUti by double clicking on its icon.

Loading the NEXUS file

To load a NEXUS format alignment, simply select the Import Alignment... option

from the File menu:

Select the file called primates.nex. This file contains an alignment of sequences of

Once loaded, the two character partitions are displayed in the main panel:

Select the Taxon Sets tab at the top of the main window. You will see the panel that

allows you to create sets of taxa. Once you have created a taxa set you will be able

to add calibration information for its most recent common ancestor (MRCA) later on.

Press the small “plus” button at the bottom left of the panel. This will create a new

taxon set.

Rename it by double-clicking on the entry that appears (it will initially be called

untitled1). Call it ingroup (it will contain all taxa except the lemur, which will

only Homo sapiens and Pan taxa. The screen should look like this:

Finally, create a taxon group that contains everything under the hominoid/cercopithecoid

split (i.e. everything except Lemur, Saimiri and Tarsius). Call this taxon set something

like HomiCerco.

Setting the substitution model

The next thing to do is to click on the Site Models tab at the top of the main

window. This will reveal the evolutionary model settings for BEAST. Exactly which

options appear depend on whether the data are nucleotides, or amino acids, or binary

data, or general data. The settings that will appear after loading the Primates data set

will be the default values so we need to make some changes.