Installation

The data in these examples are taken from an MCMCtree divergence time analysis. Morris et al 2018. From the MCMCtreeR package, users can directly call (using the data function) the object MCMCtree.output that contains a phylogeny output from MCMCtree MCMCtree.phy and a full posterior output from the analysis MCMCtree.posterior.

if (!any(rownames(installed.packages()) == "MCMCtreeR")) install.packages("MCMCtreeR")
library(MCMCtreeR, quietly = TRUE, warn.conflicts = FALSE)
data(MCMCtree.output)
attach(MCMCtree.output)
names(MCMCtree.output)

## [1] "MCMCtree.phy"       "MCMCtree.posterior"

phy <- readMCMCtree(MCMCtree.phy, from.file = FALSE)

Plot geological and absolute ages on plot

For all plot types, MCMC.tree.plot includes options to incorporate absolute and geological timescales on the tree figure. For example, in Figure 1 the geologic times Eon and Period are displayed at the bottom of the tree, with absolute ages in millions of years before present at the top. The plotting of absolute timescales is controlled by setting the add.time.scale option to TRUE (the default). The absolute ages that are included reflect the designations marked by the geologic time periods scale res argument. So here absolute ages are shown for each Period at the top of the plot. As grey.bars is TRUE shading is also used to delimit each geologic Period.

MCMC.tree.plot(phy, cex.tips = 0.2, time.correction = 100, scale.res = c("Eon", 
    "Period"), plot.type = "phylogram", cex.age = 0.6, cex.labels = 0.6, 
    relative.height = 0.08, col.tree = "grey40", label.offset = 4, 
    node.method = "none", no.margin = TRUE)

Figure 1 Phylogeny with posterior distributions of age on nodes and timescale

In Figure 2, the same plot is shown with scale res set to show all geological age options (Eon, Period, Epoch, Age), which looks too busy for this tree as it spans > 900 million years, but may be better for other trees that span smaller time frames.

MCMC.tree.plot(phy, cex.tips = 0.2, time.correction = 100, scale.res = c("Eon", 
    "Period", "Epoch", "Age"), plot.type = "phylogram", cex.age = 0.4, 
    cex.labels = 0.5, relative.height = 0.08, col.tree = "grey40", 
    label.offset = 4, node.method = "none", no.margin = TRUE)

Figure 2 Phylogeny with posterior distributions of age on nodes and timescale showing all units

Plot node uncertainty

Timescaled phylogenies can be plotted as the default ‘phylogram’ type. On these phylogenies uncertainty can be plotted as node bars, similar to those used in FigTree. Note the argument time.correction is used to rescale the MCMCtree ages to absolute time by multiplying all ages by 100. In Figure 3, uncertainty is presented using bars to highight the upper and lower Highest Posterior Density of each age.

MCMC.tree.plot(phy, analysis.type = "MCMCtree", cex.tips = 0.2, 
    time.correction = 100, plot.type = "phylogram", lwd.bar = 2, 
    scale.res = c("Eon", "Period"), node.method = "bar", col.age = "navy", 
    no.margin = TRUE, label.offset = 4)

Figure 3 Phylogeny with age uncertainty displayed as bars on nodes.

In this example (Figure 4), the age range of uncertainty for bars are spread across the vertical height of each node using the option node.length.

MCMC.tree.plot(phy, analysis.type = "MCMCtree", cex.tips = 0.2, 
    time.correction = 100, plot.type = "phylogram", lwd.bar = 2, 
    scale.res = c("Eon", "Period"), node.method = "node.length", 
    col.age = "#008b0040", no.margin = TRUE, label.offset = 4)

Figure 4 Phylogeny with age uncertainty displayed spanning the vertical height of the node.

Finally, bars can be displayed across the entire vertical range of the plot. This is useful if one node age is of particular interest, such as in Figure 4 in which the age uncertainty (HPD interval) for node 110 (embryophytes) is highlighted alone.

MCMC.tree.plot(phy, analysis.type = "MCMCtree", cex.tips = 0.2, 
    time.correction = 100, plot.type = "phylogram", lwd.bar = 2, 
    scale.res = c("Eon", "Period"), node.method = "full.length", 
    all.nodes = 110, col.age = "#ff000040", no.margin = TRUE, 
    label.offset = 4)

Figure 5 Phylogeny with age uncertainty of one node spanning the height of the phylogeny.

# directory.mb <- '/User/MrBayes/output.nex.con.tre'
# MCMC.tree.plot(analysis.type='mrbayes',
# directory.files=directory.mb, cex.tips=0.33,
# plot.type='phylogram', lwd.bar=2, add.time.scale=FALSE,
# node.method='bar', col.age='navy')

# directory.rb <- '/User/RevBayes/output.nex.con.tre'
# MCMC.tree.plot(analysis.type='revbayes',
# directory.files=directory.rb, cex.tips=0.33,
# plot.type='phylogram', lwd.bar=2, add.time.scale=FALSE,
# node.method='bar', col.age='navy')

Cladogram

Cladogram trees can be plot for output from MCMCtree analysis. In Figure 6, the ‘MCMCtree’ node uncertainty is summarised using phylogenetic cladogram plot in which with HPD age uncertainty spans the entire branch length.

MCMC.tree.plot(phy, analysis.type = "MCMCtree", cex.tips = 0.2, 
    time.correction = 100, plot.type = "cladogram", lwd.bar = 2, 
    scale.res = c("Eon", "Period"), node.method = "node.length", 
    col.age = "#008b0080", no.margin = TRUE, cex.labels = 0.5)

Figure 6 Cladogram plot

Plot full distribution on nodes

If the full posterior is supplied as well as the tree, the plot.type argument can be set to distributions to display the full distribution of age estimates for each node of the plot. In Figure 7, the full sample of ages is displayed for every node on the phylogeny.

MCMC.tree.plot(phy, MCMC.chain = MCMCtree.posterior, cex.tips = 0.2, 
    time.correction = 100, plot.type = "distributions", cex.age = 0.4, 
    cex.labels = 0.5, relative.height = 0.08, col.tree = "grey40", 
    scale.res = c("Eon", "Period"), no.margin = TRUE, label.offset = 4, 
    density.col = "#00000050", density.border.col = "#00000080")

Figure 7 Phylogeny with posterior distributions of age on nodes.

The colour of the node distributions is set using density.col and density.border.col. Some nodes can be given different colours. In Figure 8, the root node here is coloured red and all other nodes are blue.

node.colours <- rep("#ff008050", Nnode(phy$apePhy))
node.colours.border <- rep("#ff008090", Nnode(phy$apePhy))
node.colours[1] <- "#00008050"
node.colours.border[1] <- "#00008090"
MCMC.tree.plot(phy, MCMC.chain = MCMCtree.posterior, cex.tips = 0.2, 
    time.correction = 100, scale.res = c("Eon", "Period"), plot.type = "distributions", 
    cex.age = 0.4, cex.labels = 0.5, relative.height = 0.08, 
    col.tree = "grey40", col.age = "black", density.col = node.colours, 
    density.border.col = node.colours.border, grey.bars = TRUE, 
    no.margin = TRUE)

Figure 8 Phylogeny with posterior distributions of age on nodes, with the root a different colour.

Plot tree and timescale from any software

Using the ‘user’ option in the argument analysis.type it is possible to plot trees, timescales, and age uncertainty, with files output from any software.

The function only needs to be provided with a time-scaled phylogeny, and the full posterior age estimates for each node. This user input information is provided as a list to the argument node.ages.

For this example, we are using the MCMCtree output, but the process should be applicable to any divergence time software output. The MCMC.tree.plot function requires that the object node.ages is organised so the each element contains the full age posterior for each node, and this element is allocated a name that match the labels APE tree$edge object. The first element in the list supplied to node.ages is the root node.

Here the ‘user’ approach is set-up step-by-step. First we store the tree in APE format as a new object, and also create a new object for the phy$edge object which summarises the tree structure in the APE matrix format. Finally the MCMC chain is stored as a new object. For the purposes of these examples, we use a subset of the phylogeny the descends from node 177.

data(MCMCtree.output)
attach(MCMCtree.output)

## The following objects are masked from MCMCtree.output (pos = 3):
## 
##     MCMCtree.phy, MCMCtree.posterior

## The following objects are masked from MCMCtree.output (pos = 4):
## 
##     MCMCtree.phy, MCMCtree.posterior

phy <- readMCMCtree(MCMCtree.phy, from.file = FALSE)
phy <- phy$apePhy
# Here a smaller tree is shown as an example.
phy.small <- extract.clade(phy, 177)
plot(phy.small, no.margin = TRUE, cex = 0.6)
# view nodelabels on the tree
nodelabels(cex = 1)

Figure 9 Phylogeny showing the node and tip labels.

This tree plot in Figure 9 shows the timescaled phylogeny. On this plot the blue squares correspond to internal node labels. The input needs a list with each element containing the ages from the appropriate node (Figure 9).

Here the list is constructing and each element name is assigned with the corresponding node value, and these are filled with random ages from a normal distribution. In a real example this would be subsituted with real data.

node.numbers <- c(9, 10, 11, 12, 13, 14, 15)
# create a list to store each posterior sample for every node
node.posteriors <- vector(mode = "list", length = Nnode(phy.small))
names(node.posteriors) <- node.numbers
for (i in 1:Nnode(phy.small)) node.posteriors[[i]] <- rnorm(1000, 
    mean = branching.times(phy.small)[i], sd = 0.1)
## substitute the random numbers with the appropriate
## posterior distribution for that node e.g., your.age.values
## <- read.csv('posterior.ages.from.an.analysis') for(i in
## 1:Nnode(phy.small)) node.posteriors[[i]] <- your.age.values

These data can now be displayed using the MCMC.tree.plot function (Figure 10) in which the node.posteriors are provided to the function as a list using the node.ages argument.

MCMC.tree.plot(phy = phy.small, node.ages = node.posteriors, 
    analysis.type = "user", cex.tips = 0.7, time.correction = 100, 
    scale.res = c("Eon", "Period"), plot.type = "distributions", 
    cex.age = 0.7, cex.labels = 0.5, relative.height = 0.08, 
    col.tree = "grey40", no.margin = TRUE)

Figure 10 Phylogeny showing the node and tip labels.

This is a second example in which we use real data from an MCMCtree analysus. Again, the names of the list elements storing the posterior age arguments need match the nodelabels from the APE tree. As above, a good way to investigate this is to plot trees and then using the nodelabels() function to visualise how the nodelabels are found on the tree.

In the MCMCtree output file, node ages are stored in the second column onwards. So we extract these data and then remove the ‘t_n’ label from each column header so we are left with just the node numbers. And then we sort the node numbers from MCMCtree analysis so that they match the node labels in the APE format.

# Not run. Plot tree with node labels to help work out how
# labels correspond to tree from software output.  plot(ape)
# nodelabels() extract the MCMC chain and the phylogeny edge
# object
MCMC.chain <- MCMCtree.posterior
phy.edge <- phy$edge
# extract ages with node age posteriors from column 2
MCMC.node.ages <- MCMC.chain[, 2:Ntip(phy)]
# extract the names from these data so they are numeric node
# labels that match the APE tree format
all.nodes <- as.numeric(gsub("t_n", "", colnames(MCMC.node.ages)))
# create a vector of names for each list element as internal
# nodes from APE tree, using phy$edge object.
node.ages.names <- c(Ntip(phy) + 1, phy.edge[which(phy.edge[, 
    2] > Ntip(phy)), 2])
# find where each posterior node age appears in APE edge
# object.
match.nodes <- match(all.nodes, as.numeric(node.ages.names))
# create a list extracting the information from the MCMC
# chain in APE node order.
node.ages <- lapply(match.nodes, function(uu) MCMC.node.ages[, 
    uu])
# name each element in list.
names(node.ages) <- node.ages.names

The node.ages object is input to MCMC.tree.plot with the argument analysis.type set to ‘user’ to plot the timescaled tree and full distributions on each node (Figure 11).

MCMC.tree.plot(phy = phy, node.ages = node.ages, analysis.type = "user", 
    cex.tips = 0.2, time.correction = 100, scale.res = c("Eon", 
        "Period"), plot.type = "distributions", cex.age = 0.4, 
    cex.labels = 0.5, relative.height = 0.08, col.tree = "grey40", 
    no.margin = TRUE)

Figure 11 Phylogeny plotted with user-formatted data.

References

• Morris JL, Puttick MN, Clark JW, Edwards, Kenrick PD, Pressel S, Wellman CH, Yang Z, Schneider H, and Donoghue PCJ. 2018. The timescale of early land plant evolution. Proceedings of the National Academy of Sciences USA. (https://doi.org/10.1073/pnas.1719588115)