Lineages Through Time Plot

These functions provide tools for plotting the numbers of lineages through time from phylogenetic trees.

hplot, aplot
ltt.plot(phy, xlab = "Time", ylab = "N",
         backward = TRUE, tol = 1e-6, ...)
ltt.lines(phy, backward = TRUE, tol = 1e-6, ...)
mltt.plot(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE,
          xlab = "Time", ylab = "N", log = "", backward = TRUE,
          tol = 1e-6)
ltt.coplot(phy, backward = TRUE, ...)
ltt.plot.coords(phy, backward = TRUE, tol = 1e-6)

ltt.plot does a simple lineages through time (LTT) plot. Additional arguments (...) may be used to change, for instance, the limits on the axes (with xlim and/or ylim) or other graphical settings (col for the color, lwd for the line thickness, lty for the line type may be useful; see par for an exhaustive listing of graphical parameters). The $y$-axis can be log-transformed by adding the following option: log = "y".

The option tol is used as follows: first the most distant tip from the root is found, then all tips whose distance to the root is not different from the previous one than tol are considered to be contemporaneous with it.

If the tree is not ultrametric, the plot is done assuming the tips, except the most distant from the root, represent extinction events. If a root edge is present, it is taken into account.

ltt.lines adds a LTT curve to an existing plot. Additional arguments (...) may be used to change the settings of the added line.

mltt.plot does a multiple LTT plot taking as arguments one or several trees. These trees may be given as objects of class "phylo" (single trees) and/or "multiPhylo" (multiple trees). Any number of objects may be given. This function is mainly for exploratory analyses with the advantages that the axes are set properly to view all lines, and the legend is plotted by default. The plot will certainly make sense if all trees have their most-distant-from-the-root tips contemporaneous (i.e., trees with only extinct lineages will not be represented properly). For more flexible settings of line drawings, it may be better to combine ltt.plot() with successive calls of ltt.lines() (see examples).

ltt.coplot is meant to show how to set a tree and a LTT plots on the same scales. All extra arguments modify only the appearance of the tree. The code can be easily edited and tailored.


ltt.plot.coords returns a two-column matrix with the time points and the number of lineages, respectively. The $i$th value of the second column is the number of lineages for the interval defined by the $(i - 1)$th and the $i$th values of the first column. These are then plotted with the option type = "S" by the other functions.


Harvey, P. H., May, R. M. and Nee, S. (1994) Phylogenies without fossils. Evolution, 48, 523--529.

Nee, S., Holmes, E. C., Rambaut, A. and Harvey, P. H. (1995) Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London. Series B. Biological Sciences, 349, 25--31.

See Also

kronoviz, skyline, branching.times, birthdeath, bd.ext, yule.cov, bd.time; plot for the basic plotting function in R

opar <- par(mfrow = c(2, 1))
title("Lineages Through Time Plot of the Bird Families")
ltt.plot(bird.families, log = "y")
title(main = "Lineages Through Time Plot of the Bird Families",
      sub = "(with logarithmic transformation of the y-axis)")

### to plot the tree and the LTT plot together
layout(matrix(1:4, 2, 2))
plot(bird.families, show.tip.label = FALSE)
ltt.plot(bird.families, main = "Bird families")
plot(bird.orders, show.tip.label = FALSE)
ltt.plot(bird.orders, main = "Bird orders")

### better with ltt.coplot():
ltt.coplot(bird.families, show.tip.label = FALSE, x.lim = 27.5)
chiroptera <- compute.brlen(chiroptera)
ltt.coplot(chiroptera, show.tip.label = FALSE, type = "c")

### with extinct lineages and a root edge:
omar <- par("mar")
tr <- rlineage(0.2, 0.15)
tr$root.edge <- 5
ltt.coplot(tr, show.tip.label = FALSE, x.lim = 55)
## compare with:
## ltt.coplot(drop.fossil(tr), show.tip.label = FALSE)
par(mar = omar)

mltt.plot(bird.families, bird.orders)
### Generates 10 random trees with 23 tips:
TR <- replicate(10, rcoal(23), FALSE)
### Give names to each tree:
names(TR) <- paste("random tree", 1:10)
### And specify the class of the list so that mltt.plot()
### does not trash it!
class(TR) <- "multiPhylo"
mltt.plot(TR, bird.orders)
### And now for something (not so) completely different:
ltt.plot(bird.orders, lwd = 2)
for (i in 1:10) ltt.lines(TR[[i]], lty = 2)
legend(-20, 10, lwd = c(2, 1), lty = c(1, 2), bty = "n",
       legend = c("Bird orders", "Random (coalescent) trees"))
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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