Divergence Dating Tutorial with BEAST 2.2.

x
Alexei Drummond, Andrew Rambaut, Remco Bouckaert, and Walter Xie
January 29, 2015

1 Introduction
This tutorial introduces the BEAST software for Bayesian evolutionary anal-
ysis through a simple tutorial. The tutorial involves co-estimation of a gene
phylogeny and associated divergence times in the presence of calibration in-
formation from fossil evidence.
You will need the following software at your disposal:

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

notator and other utility programs. This tutorial is written for BEAST
v2.2.x, which has support for multiple partitions. It is available for
download from http://www.beast2.org/.

• Tracer - this program is used to explore the output of BEAST (and

other Bayesian MCMC programs). It graphically and quantitively sum-
marizes the distributions of continuous parameters and provides diag-
nostic information. At the time of writing, the current version is v1.6.
It is available for download from
http://tree.bio.ed.ac.uk/software/.

• 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 v1.4.2. It is available for download from
http://tree.bio.ed.ac.uk/software/.

This tutorial will guide you through the analysis of an alignment of se-
quences sampled from twelve primate species (see Figure 1). The goal is to

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 Figure 1: Part of the alignment for primates.

estimate the phylogeny, the rate of evolution on each lineage and the ages of
the uncalibrated ancestral divergences.
The first step will be to convert a NEXUS file with a DATA or CHARAC-
TERS block into a BEAST XML input file. This is done using the program
BEAUti (which stands for Bayesian Evolutionary Analysis Utility). This is
a user-friendly program for setting the evolutionary model and options for
the MCMC analysis. The second step is to actually run BEAST using the
input file generated by BEAUTi, which contains the data, model and anal-
ysis settings. The final step is to explore the output of BEAST in order to
diagnose problems and to summarize the results.

2 BEAUti
The program BEAUti is a user-friendly program for setting the model param-
eters for BEAST. Run BEAUti by double clicking on its icon. Once running,
BEAUti will look similar irrespective of which computer system it is running
on. For this tutorial, the Mac OS X version is used in the figures but the
Linux and Windows versions will have the same layout and functionality.

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Figure 2: Add Partition window (Only appear if related packages are in-
stalled).

Figure 3: Warning message window (Only appear if there is any coding

overlaps in the partitions).

2.1 Loading the NEXUS file

To load a NEXUS format alignment, simply select the Import Alignment...
option from the File menu, or drag the file into the middle of Partitions
panel.
The example file called primate-mtDNA.nex is available from the examples/nexus/
directory for Mac and Linux and examples/nexus/for Windows inside the
directory where BEAST was installed. This file contains an alignment of
sequences of 12 species of primates.
An Add Partition window (Figure 2) would pop up if the related package
is installed. If you are using “pure” BEAST 2, you can go to the next
paragraph. Otherwise, select Add Alignment and click OK to continue.
If there is any coding overlaps in the partitions, the warning message
window (Figure 3) will appear. Read and click OK to continue.
Once loaded, five character partitions are displayed in the main panel
(Figure 4). The alignment is divided into a protein coding part and a non-
coding part,and the coding part is divided in codon positions 1, 2 and 3.

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Figure 4: A screenshot of the data tab in BEAUti. This and all following
screenshots were taken on an Apple computer running Mac OS X and will
look slightly different on other operating systems.

You must remove the ‘coding’ partition before continuing to the

next step as it refers to the same nucleotides as partitions ‘1stpos’,
‘2ndpos’ and ‘3rdpos’. To remove the ‘coding’ partition select the row and
click the ‘-’ button at the bottom of the table. You can view the alignment
by double clicking the partition.

Link/Unlink partition models

Since the sequences are linked (i.e. they are all from the mitochondrial
genome which is not believed to undergo recombination in birds and mam-
mals) they share the same ancestry, so the partitions should share the same
time-tree in the model. For the sake of simplicity, we will also assume the
partitions share the same evolutionary rate for each branch, and hence the
same “clock model”. We will restrict our modelling of rate heterogeneity to
among-site heterogeneity within each partition, and also allow the partitions
to have different mean rates of evolution.
So, at this point we will need to link the clock model and tree. In the

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Figure 5: A screenshot of the Partitions tab in BEAUti after linking and
renaming the clock model and tree.

Partitions panel, select all four partitions in the table (or none, by default
all partitions are affected) and click the Link Trees button and then the
Link Clock Models button (see Figure 5). Then click on the first drop-
down menu in the Clock Model column and rename the shared clock model
to ‘clock’. Likewise rename the shared tree to ‘tree’. This will make following
options and generated log files more easy to read.

2.2 Setting the substitution model

The next step is to set up the substitution model. Then, select the Site
Models tab at the top of the main window (we skip the Tip Dates tab since
all taxa are from contemporary samples). This will reveal the evolutionary
model settings for BEAST. The options available depend on whether the data
are nucleotides, or amino acids, binary data, or general data. The settings
that will appear after loading the primate nucleotide alignment will be the
default values for nucleotide data so we need to make some changes.
Most of the models should be familiar to you. First, set the Gamma
Category Count to 4 and then tick the ‘estimate’ box for the Shape pa-

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 Figure 6: A screenshot of the site model tab in BEAUti.

rameter. This will allow rate variation between sites in each partition to
be modelled. Note that 4 to 6 categories works sufficiently well for most
data sets, while having more categories takes more time to compute for little
added benefit. We leave the Proportion Invariant entry set to zero.
Then select HKY from the Subst Model drop-down menu. Ideally, a
substitution model should be selected that fit the data best for each partition,
but here for the sake of simplicity we use HKY for all partitions. Further,
select Empirical from the Frequencies drop-down menu. This will fix
the frequencies to the proportions observed in the data (for each partition
individually, once we unlink the site models). This approach means that we
can get a good fit to the data without explicitly estimating these parameters.
We do it here simply to make the log files a bit shorter and more readable in
later parts of the exercise.
Finally check the ‘estimate’ box for the Substitution rate parameter
and select the Fix mean mutation rate check box. This will allow the
individual partitions to have their relative rates estimated for unlinked the
site models (Figure 6).
At last, hold ‘shift’ key to select all site models on the left side, and click
OK to clone the setting from noncoding into 1stpos, 2ndpos and 3rdpos

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 Figure 7: clone configuration from one site model to others.

(Figure 7). Go through each site model, as you can see, their configurations
are same now.

2.3 Setting the clock model

The next step is to select the Clock Models tab at the top of the main
window. This is where we select the molecular clock model. For this exercise
we are going to leave the selection at the default value of a strict molecular
clock, because this data is very clock-like, and does not need rate variation
among branches to be included in the model.
To test for clock-likeness, you can (i) run the analysis with a relaxed
clock model and check how much variation among rates are implied by the
data (see coefficient of variation for more on this), or (ii) perform a model
comparison between a strict and relaxed clock using path sampling, or (iii)
use a random local clock model [2] which explicitly considers whether each
branch in the tree needs its own branch rate.

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 Figure 8: A screenshot of the Priors tab in BEAUti.

2.4 Priors
The Priors tab allows priors to be specified for each parameter in the model.
The model selections made in the site model and clock model tabs, result in
the inclusion of various parameters in the model, and these are shown in the
priors tab (see Figure 8).
Here we also specify that we wish to use the Calibrated Yule model [4] as
the tree prior. The Yule model is a simple model of speciation that is gen-
erally more appropriate when considering sequences from different species.
Select the Calibrated Yule Model from the Tree prior dropdown menu.

2.4.1 Defining the calibration node

We now need to specify a prior distribution on the calibrated node, based
on our fossil knowledge. This is known as calibrating our tree. To define an
extra prior, press the small + button below list of priors. If it is not visible
in your view, please scroll down the panel to the bottom to find + button.

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 Figure 9: Taxon set editor in BEAUti.

You will see a dialog that allows you to define a subset of the taxa in the
phylogenetic tree. Once you have created a taxa set you will be able to add
calibration information for its most recent common ancestor (MRCA) later
on.
Name the taxa set by filling in the taxon set label entry. Call it human-chimp,
since it will contain the taxa for Homo sapiens and Pan. In the list below
you will see the available taxa. Select each of the two taxa in turn and press
the >> arrow button. (Figure 9). Click OK and the newly defined taxa set
will be added in to the prior list. As this is a calibrated node to be used
in conjunction with the Calibrated Yule prior, monophyly must be enforced,
so select the checkbox marked Monophyletic. This will constrain the tree
topology so that the human-chimp grouping is kept monophyletic during the
course of the MCMC analysis.
To encode the calibration information we need to specify a distribution
for the MRCA of human-chimp. Select the Log-normal distribution from
the drop down menu to the right of the newly added human-chimp.prior.
Click on the black triangle and a graph of the probability density function
will appear, along with parameters for the log normal distribution. We are
going to set M = 1.78 and S = 0.085 which will specify a distribution centred
at about 6 million years with a standard deviation of about 0.5 million years.
This will give a central 95% probability range covering 5-7 Mya. This roughly
corresponds to the current consensus estimate of the date of the most recent
common ancestor of humans and chimpanzees (Figure 10).
We should convince ourselves that the priors shown in the priors panel
really reflect the prior information we have about the parameters of the

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Figure 10: A screenshot of the calibration prior options in the Priors panel
in BEAUti.

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 Figure 11: Gamma prior.

model. Finally we will also specify some diffuse “uninformative” but proper
priors on the overall molecular clock rate (clockRate) and the speciation
rate (birthRateY) of the Yule tree prior. For each of them, select Gamma
from the drop-down menu and using the arrow button, expand the view to
reveal the parameters of the Gamma prior. For both the clock rate and the
Yule birth rate set the Alpha (shape) parameter to 0.001 and the Beta (scale)
parameter to 1000 (Figure 11).
By default each of the gamma shape parameters has an exponential prior
distribution with a mean of 1. This implies (see Figure 3.7) we expect some
rate variation. By default the kappa parameters for the HKY model have
a log normal(1,1.25) prior distribution, which broadly agrees with empiri-
cal evidence [6] on the range of realistic values for transition/transversion
bias. These default priors are kept since they are suitable for this particular
analysis.

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2.5 Setting the MCMC options
The next tab, MCMC, provides more general settings to control the length
of the MCMC run and the file names.
Firstly we have the Chain Length. This is the number of steps the
MCMC will make in the chain before finishing. How long this should be de-
pends on the size of the data set, the complexity of the model and the quality
of answer required. The default value of 10,000,000 is entirely arbitrary and
should be adjusted according to the size of your data set. For this data set
let’s set the chain length to 6,000,000 as this will run reasonably quickly
on most modern computers (a few minutes).
The Store Every field determines how often the state is stored to file.
Storing the state periodically is useful for situations where the computing
environment is not very reliable and a BEAST run can be interrupted. Hav-
ing a stored copy of the recent state allows you to resume the chain instead
of restarting from the beginning, so you do not need to get through burn-in
again. The Pre Burnin field specifies the number of samples that are not
logged at the very beginning of the analysis. We leave the Store Every and
Pre Burnin fields set to their default values. Below these are the details of
the log files. Each one can be expanded by clicking the black triangle.
The next options specify how often the parameter values in the Markov
chain should be displayed on the screen and recorded in the log file. The
screen output is simply for monitoring the programs progress so can be set
to any value (although if set too small, the sheer quantity of information
being displayed on the screen will actually slow the program down). For
the log file, the value should be set relative to the total length of the chain.
Sampling too often will result in very large files with little extra benefit
in terms of the accuracy of the analysis. Sample too infrequently and the
log file will not record sufficient information about the distributions of the
parameters. You probably want to aim to store no more than 10,000 samples
so this should be set to no less than chain length / 10,000.
For this exercise we will set the trace log and the tree log frequency
to 1,000 and the screen log to 10,000. Also specify Primates.log as the
file name of the trace log file and Primates.trees as the file name of the
tree log file. Make sure that the file name filed of the screen log is left empty,
or the screen log will not be written to the screen.

• If you are using the Windows operating system then we suggest you add

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 the suffix .txt to both of these (so, Primates.log.txt and Primates.trees.txt)
so that Windows recognizes these as text files.

2.6 Generating the BEAST XML file

We are now ready to create the BEAST XML file. To do this, select the
Save option from the File menu. Check the default priors, and save the
file with an appropriate name (we usually end the filename with .xml, i.e.,
Primates.xml). We are now ready to run the file through BEAST.

3 Running BEAST
Now run BEAST and when it asks for an input file, provide your newly cre-
ated XML file as input. BEAST will then run until it has finished reporting
information to the screen. The actual results files are save to the disk in the
same location as your input file. The output to the screen will look something
like this:

BEAST v2.2.0, 2002-2014

Bayesian Evolutionary Analysis Sampling Trees
Designed and developed by
Remco Bouckaert, Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard

Department of Computer Science

University of Auckland
[email protected]
[email protected]

Institute of Evolutionary Biology

University of Edinburgh
[email protected]

David Geffen School of Medicine

University of California, Los Angeles
[email protected]

Downloads, Help & Resources:

http://beast2.org/

Source code distributed under the GNU Lesser General Public License:
http://github.com/CompEvol/beast2

BEAST developers:
Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled,
Sebastian Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li,
Gerton Lunter, Sidney Markowitz, Vladimir Minin, Michael Defoin Platel,
Oliver Pybus, Chieh-Hsi Wu, Walter Xie

Thanks to:
Roald Forsberg, Beth Shapiro and Korbinian Strimmer

Random number seed: 777

12 taxa
898 sites
413 patterns

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Figure 12: A screenshot of BEAST.

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TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4
TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4
TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4
TreeLikelihood uses beast.evolution.likelihood.BeerLikelihoodCore4
===============================================================================
Citations for this model:

Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA,
Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian
evolutionary analysis. PLoS Computational Biology 10(4): e1003537

Heled J, Drummond AJ (2012) Calibrated Tree Priors for Relaxed Phylogenetics

and Divergence Time Estimation. Systematic Biology 61(1):138-149.

Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a

molecular clock of mitochondrial DNA. Journal of Molecular Evolution
22:160-174.

===============================================================================
Writing file /Primates.log
Writing file /Primates.trees
Sample posterior ESS(posterior) likelihood prior
0 -7924.3599 N -7688.4922 -235.8676 --
10000 -5529.0700 2.0 -5459.1993 -69.8706 --
20000 -5516.8159 3.0 -5442.3372 -74.4786 --
30000 -5516.4959 4.0 -5439.0839 -77.4119 --
40000 -5521.1160 5.0 -5445.6047 -75.5113 --
50000 -5520.7350 6.0 -5444.6198 -76.1151 --
60000 -5512.9427 7.0 -5439.2561 -73.6866 2m39s/Msamples
70000 -5513.8357 8.0 -5437.9432 -75.8924 2m39s/Msamples
...
5990000 -5516.6832 474.6 -5442.5945 -74.0886 2m40s/Msamples
6000000 -5512.3802 472.2 -5440.8928 -71.4874 2m40s/Msamples

Operator Tuning #accept #reject total prob.acc

ScaleOperator(treeScaler.t:tree) 0.703 39935 174155 214090 0.187
ScaleOperator(treeRootScaler.t:tree) 0.644 37329 177166 214495 0.174
Uniform(UniformOperator.t:tree) 479419 1668915 2148334 0.223
SubtreeSlide(SubtreeSlide.t:tree) 9.922 272787 801404 1074191 0.254
Exchange(narrow.t:tree) 744 1074261 1075005 0.001
Exchange(wide.t:tree) 9 214594 214603 0.000
WilsonBalding(WilsonBalding.t:tree) 4 214548 214552 0.000
ScaleOperator(KappaScaler.s:noncoding) 0.352 1739 5375 7114 0.244
DeltaExchangeOperator(FixMeanMutationRatesOperator) 0.425 17277 126203 143480 0.120
ScaleOperator(gammaShapeScaler.s:noncoding) 0.375 1729 5428 7157 0.242
ScaleOperator(CalibratedYuleBirthRateScaler.t:tree) 0.245 58005 156128 214133 0.271
ScaleOperator(StrictClockRateScaler.c:clock) 0.706 50080 164952 215032 0.233
UpDownOperator(strictClockUpDownOperator.c:clock) 0.589 50809 163882 214691 0.237
ScaleOperator(KappaScaler.s:1stpos) 0.44 1816 5388 7204 0.252
ScaleOperator(gammaShapeScaler.s:1stpos) 0.42 1927 5129 7056 0.273
ScaleOperator(KappaScaler.s:2ndpos) 0.332 1964 5301 7265 0.270
ScaleOperator(gammaShapeScaler.s:2ndpos) 0.303 2033 5177 7210 0.282
ScaleOperator(KappaScaler.s:3rdpos) 0.505 1424 5860 7284 0.195
ScaleOperator(gammaShapeScaler.s:3rdpos) 0.267 1569 5536 7105 0.221

Total calculation time: 964.067 seconds

Note that there is some useful information at the start concerning the
alignments and which tree likelihoods are used. Also, all citations relevant
for the analysis are mentioned at the start of the run, which can easily be
copied to manuscripts reporting about the analysis. Then follows reporting
of the chain, which gives some real time feedback on progress of the chain.
At the end, an operator analysis is printed, which lists all operators used
in the analysis together with how often the operator was tried, accepted,
and rejected (see columns #total, #accept and #reject respectively). The
acceptance rate is the proportion of times an operator is accepted when it
is selected for doing a proposal. In general, an acceptance rate that is high,

15
say over 0.5 indicates the proposals are conservative and do not explore
the parameter space efficiently. On the other hand a low acceptance rate
indicates that proposals are too aggressive and almost always result in a
state that is rejected because of its low posterior. Both too high and too low
acceptance rates result in low ESS values. An acceptance rate of 0.234 is the
target (based on very limited evidence provided by [3]) for many (but not
all) operators implemented in BEAST.
Some operators have a tuning parameter, for example the scale factor of
a scale parameter. If the final acceptance rate is not near the target, BEAST
will suggest a new value for the tuning parameter, which is printed in the
operator analysis. In this case, all acceptance rates are good for the operators
that have tuning parameters. Operators without tuning parameters include
the wide exchange and Wilson-Balding operators for this analysis. Both
these operators attempt to change the topology of the tree with large steps,
but since the data supports a single topology overwhelmingly, these radical
proposals are almost always rejected.

4 Analyzing the results

Run the program called Tracer to analyze the output of BEAST. When the
main window has opened, choose Import Trace File... from the File menu
and select the file that BEAST has created called Primates.log (Figure 13).
Remember that MCMC is a stochastic algorithm so the actual numbers
will not be exactly the same as those depicted in the figure.
On the left hand side is a list of the different quantities that BEAST
has logged to file. There are traces for the posterior (this is the natural
logarithm of the product of the tree likelihood and the prior density), and
the continuous parameters. Selecting a trace on the left brings up analyses
for this trace on the right hand side depending on tab that is selected. When
first opened, the ‘posterior’ trace is selected and various statistics of this
trace are shown under the Estimates tab. In the top right of the window is
a table of calculated statistics for the selected trace.
Select the clockRate parameter in the lefthand list to look at the average
rate of evolution (averaged over the whole tree and all sites). Tracer will plot
a (marginal posterior) histogram for the selected statistic and also give you
summary statistics such as the mean and median. The 95% HPD stands for
highest posterior density interval and represents the most compact interval

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 Figure 13: A screenshot of Tracer v1.6.

on the selected parameter that contains 95% of the posterior probability. It

can be loosely thought of as a Bayesian analog to a confidence interval. The
TreeHeight parameter gives the marginal posterior distribution of the age
of the root of the entire tree.
Select the TreeHeight parameter and then Ctrl-click mrcatime(human-chimp)
(Command-click on Mac OS X). This will show a display of the age of the root
and the calibration MRCA we specified earlier in BEAUti. You can verify
that the divergence that we used to calibrate the tree (mrcatime(human-chimp))
has a posterior distribution that matches the prior distribution we specified
(Figure 14).

5 Marginal posterior estimates

To show the relative rates for the four partitions, select the mutationRate
parameter for each of the four partitions, and select the marginal density tab
in Tracer. Figure 15 shows the marginal densities for the relative substitu-
tion rates. The plot shows that codon positions 1 and 2 have substantially

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Figure 14: A screenshot of the 95% HPD intervals of the root height and the
user-specified (human-chimp) MRCA in Tracer.

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Figure 15: A screenshot of the marginal posterior densities of the relative
substitution rates of the four partitions (relative to the site-weighted mean
rate).

different rates (0.456 versus 0.183) and both are far slower than codon po-
sition 3 with a relative rate of 2.941. The noncoding partition has a rate
intermediate between codon positions 1 and 2 (0.346). Taken together this
result suggests strong purifying selection in both the coding and noncoding
regions of the alignment.

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 0.4

0.3
Density

0.2

0.1

0.0

0 10 20 30 40

Transition/transversion bias (κ)

Figure 16: The marginal prior and posterior densities for the shape (α)
parameters. The prior is in gray. The posterior density estimate for each
partition is also shown: noncoding (orange) and first (red), second (green)
and third (blue) codon positions.

3
Density

0 1 2 3 4 5
20
Gamma shape (α)

Figure 17: The marginal prior and posterior densities for the transi-
tion/tranversion bias (κ) parameters. The prior is in gray. The posterior
density estimate for each partition is also shown: noncoding (orange) and
Questions

What is the estimated rate of molecular evolution for this gene tree (include
the 95% HPD interval)?
What sources of error does this estimate include?
How old is the root of the tree (give the mean and the 95% HPD range)?

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 Figure 18: A screenshot of TreeAnnotator.

6 Obtaining an estimate of the phylogenetic

tree
BEAST also produces a posterior sample of phylogenetic time-trees along
with its sample of parameter estimates. These need to be summarized using
the program TreeAnnotator. This will take the set of trees and find the
best supported one. It will then annotate this representative summary tree
with the mean ages of all the nodes and the corresponding 95% HPD ranges.
It will also calculate the posterior clade probability for each node. Run the
TreeAnnotator program and set it up as depicted in Figure 18.
The burnin is the number of trees to remove from the start of the sample.
Unlike Tracer which specifies the number of steps as a burnin, in TreeAn-
notator you need to specify the actual number of trees. For this run, you
specified a chain length of 6,000,000 steps sampling every 1,000 steps. Thus
the trees file will contain 6,000 trees and so to specify a 10% burnin in the
top text field.

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 The Posterior probability limit option specifies a limit such that if
a node is found at less than this frequency in the sample of trees (i.e., has
a posterior probability less than this limit), it will not be annotated. The
default of 0.5 means that only nodes seen in the majority of trees will be
annotated. Set this to zero to annotate all nodes.
The Target tree type specifies the tree topology that will be annotated.
You can either choose a specific tree from a file or ask TreeAnnotator to find
a tree in your sample. The default option, Maximum clade credibility
tree, finds the tree with the highest product of the posterior probability of
all its nodes.
For node heights, the default is Common Ancestor Heights, which cal-
culates the height of a node as the mean of the MRCA time of all pairs of
nodes in the clade. For trees with large uncertainty in the topology and thus
many clades with low support, some other methods can result in trees with
negative branch lengths. In this analysis, the support for all clades in the
summary tree is very high, so this is no issue here. Choose Mean heights
for node heights. This sets the heights (ages) of each node in the tree to the
mean height across the entire sample of trees for that clade.
For the input file, select the trees file that BEAST created and select a
file for the output (here we called it Primates.MCC.tree). Now press Run
and wait for the program to finish.

7 Visualizing the tree estimate

Finally, we can visualize the tree in another program called FigTree. Run
this program, and open the Primates.MCC.tree file by using the Open com-
mand in the File menu. The tree should appear. You can now try selecting
some of the options in the control panel on the left. First of all, expend
Trees option in the panel, and check Order nodes and choose Ordering by
decreasing. Try selecting Node Bars to get node age error bars. Also turn
on Branch Labels and select posterior to get it to display the posterior
probability for each node. If you use a non strict clock model then under
Appearance you can also tell FigTree to colour the branches by the rate.
You should end up with something similar to Figure 19.
An alternative view of the tree can be made with DensiTree, which is part
of Beast 2. The advantage of DensiTree is that it is able to visualize both
uncertainty in node heights and uncertainty in topology. For this particular

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Figure 19: A screenshot of FigTree and DensiTree.
24
dataset, the dominant topology is present in more than 99% of the samples.
So, we conclude that this analysis results in a very high consensus on topology
(Figure 19).

25
Questions
1. Does the rate of evolution differ substantially amongst different lineages
in the tree?

2. DensiTree has a clade bar (Menu Window/View clade toolbar) to show

information on clades.
What is the support for the clade [Homo sapiens, Pan, Gorilla, Hylo-
bates]?

3. You can browse through the topologies in DensiTree using the Browse
menu. The most popular topology has a support of over 99%.
What is the support for the second most popular topology?

4. Under the help menu, DensiTree shows some information.

How many topologies are in the tree set?

26
8 Comparing your results to the prior
It is a good idea to rerun the analysis while sampling from the prior to make
sure that interactions between priors are not affecting your prior information.
The interaction between priors can be problematic especially when using
calibrations since it means putting multiple priors on the tree.
Using BEAUti, set up the same analysis but under the MCMC options,
select the Sample from prior only option. This will allow you to visualize
the full prior distribution in the absence of your sequence data. Summarize
the trees from the full prior distribution and compare the summary to the
posterior summary tree.
Divergence time estimation using “node dating” of the type described
in this chapter has been applied to answer a variety of different questions
in ecology and evolution. For example, node dating with fossils was used in
determining the species diversity of cycads [5], analysing the rate of evolution
in flowering plants [7], and investigating the origins of hot and cold desert
cyanobacteria [1].

References
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termine global biogeography of hot and cold desert cyanobacteria, Nature
communications 2 (2011), 163.
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