Branch-Specific Diversification Rate Estimation

How to estimate branch-specific shifts in diversification rates

Sebastian Höhna and Michael R. May

Last modified on September 12, 2019

Outline: Estimating Branch-Specific Speciation & Extinction Rates


This tutorial describes how to specify a branch-specific branching-process models in RevBayes; a birth-death process where diversification rates vary among branches, similar to Rabosky (2014). The probabilistic graphical model is given for each component of this tutorial. The goal is to obtain estimate of branch-specific diversification rates using Markov chain Monte Carlo (MCMC).

The Birth-Death-Shift Process


An example of a tree with a single event of diversification rate change, from $(\lambda_1, \mu_1)$ to $(\lambda_2, \mu_2)$. a) A tree showing the complete cladogenetic process, including extinct lineages. b) The reconstructed process for the tree shown in a.

shows an example in which speciation and extinction rates change among lineages. The speciation and extinction rates at the root of the tree of are $(\lambda_1, \mu_1)$. There was one event of change to the speciation and extinction rates on the tree from $(\lambda_1, \mu_1)$ to $(\lambda_2, \mu_2)$. From a casual inspection of the tree, it appears that the single change in speciation and/or extinction rate in the tree of affected the diversity. Note that the clade above the event of speciation/extinction rate change has fewer living species, and more extinct species, than the clade that maintained the ancestral speciation and extinction rates. This is exactly the type of situation we attempt to uncover.

Here we will describe the birth-death-shift process. The parameters in this model are:

The process is described as follows. In a small interval of time, $\Delta t$, a lineage speciates with probability $\lambda \Delta t$, goes extinct with probability $\mu \Delta t$, or changes its rate with probability $\eta \Delta t$. When a speciation event occurs, both daughter lineages inherit the speciation and extinction rates of the parent lineage. When an event of rate change occurs, new speciation and extinction rates are drawn from the probability distributions, $f_{\lambda}(\cdot)$ and $f_{\mu}(\cdot)$. The affected lineage then continues, but with the modified speciation and extinction rates. When an extinction event occurs, the lineage is terminated at the event time.

Samples of an MCMC analysis under a Birth-Death-Shift model. The colors represent different classes of rates for the speciation and extinction rates ($\lambda$ and $\mu$, respectively. Note that the speciation and extinction rates at the root of the tree differ for the different MCMC samples: $(\lambda’,\mu’)$, $(\lambda’’,\mu’’)$, and $(\lambda’’’,\mu’’’)$.

Estimating Branch-Specific Diversification Rates


In this analysis we are interested in estimating the branch-specific diversification rates. We show how to implement and use the model developed by Höhna et al. (2019) We are going to use the dnCBDP distribution which uses a finite number of rate-categories instead of drawing rates from a continuous distribution directly.

Here we adopt an approach using (few) discrete rate categories. This allows us to numerically integrate over all possible rate categories using a system of differential equations originally described by Maddison et al. (2007) (see also FitzJohn et al. (2009) and FitzJohn (2010)). The numerical procedure breaks time into very small time intervals and sums over all possible events occurring in that interval (see ).

Possible scenarios that could occur over the interval $\Delta t$ along a lineage that is observed at time $t$. To compute the probability under the birth-death-shift process, we traverse the tree from the tips to the root in small time steps, $\Delta t$. For each step into the past, from time $t$ to time ($t+\Delta t$), we compute the change in probability of the observed lineage by enumerating all of the possible scenarios that could occur over the interval $\Delta t$: (i) nothing happens, (ii) a speciation event occurs, where the right descendant survives and the left descendant goes extinct before the present, or (iii) a speciation event occurs, where the left descendant survives but the right goes extinct before the present, or (iv) a diversification-rate shift from category $i$ to $j$ occurs. Color key: segment(s) of the tree within the interval $\Delta t$ are colored blue for state $i$ and/or green for state $j$ to reflect the conditioning of the corresponding scenarios, segment(s) of the tree between $t$ and the present are colored gray because we have integrated over the $k$ discrete rate categories (no specific assignment of rate categories), and segments of the tree between $t+\Delta t$ and the root are colored gray because we will integrated over the $k$ discrete rate categories.

You don’t need to worry about any of the technical details. It is important for you to realize that this model assumes that new rates at a rate-shift event are drawn from a given (discrete) set of rates (see ).

Read the tree


Begin by reading in the observed tree.

observed_phylogeny <- readTrees("data/primates_tree.nex")[1]

From this tree, we can get some helpful variables:

taxa <- observed_phylogeny.taxa()
root <- observed_phylogeny.rootAge()
tree_length <- observed_phylogeny.treeLength()

Additionally, we initialize a variable for our vector of moves and monitors.

moves    = VectorMoves()
monitors = VectorMonitors()

Finally, we create a helper variable that specifies the number of discrete rate categories, another helper variable for the total number of species and our constant for specifying the standard deviation of the lognormal distribution.

NUM_RATE_CATEGORIES = 6
NUM_TOTAL_SPECIES = 367
H = 0.587405

Using these variables we can easily change our script, for example, to use more or fewer categories and test the impact.

Specifying the model


Priors on rates


Approximation of the continuous base distributions for the diversification-rate parameters using discrete rate categories. From left to right, we show a discretization of a lognormal distribution with k={2,4,6,8,10,20} bins. Our approach for computing the probability of the data under the lineage-specific birth-death-shift model specifies k quantiles of the continuous base distributions for the speciation and extinction rates. We compute probabilities by marginalizing (averaging) over the k discrete rate categories, where the diversification rate for a given category is the median of the corresponding quantile (colored dots). This approach provides an efficient alternative to computing the continuous integral, and will provide a reliable approximation of the continuous integral when the number of categories k is sufficiently large to resemble the underlying continuous distribution.

Instead of using a continuous probability distribution we will use a discrete approximation of the distribution, as done for modeling rate variation across sites (Yang 1994) and for modeling relaxed molecular clocks (Drummond et al. 2006). That means, we assume that the speciation rates are drawn from one of the $N$ quantiles of the lognormal distribution. For this we will use the function fnDiscretizeDistribution which takes in a distribution as its first argument and the number of quantiles as the second argument. The return value is a vector of quantiles. We use it as a deterministic variable and every time the parameters of the base distribution (i.e., the lognormal distribution in our case) change the quantiles will update automatically as well. Thus we only need to specify parameters for our base distribution, the lognormal distribution. We choose a log-uniform distribution as the prior distribution for the mean parameter of the lognormal distribution.

speciation_mean ~ dnLoguniform( 1E-6, 1E2)
moves.append( mvScale(speciation_mean, lambda=1, tune=true, weight=2.0) )

Next, we choose an exponential prior distribution with mean of $H$ for the variation in speciation rates.

speciation_sd ~ dnExponential( 1.0 / H )
moves.append( mvScale(speciation_sd, lambda=1, tune=true, weight=2.0) )

Now, we can compute the speciation rate categories. We will use a lognormal distribution discretized into NUM_RATE_CATEGORIES quantiles and the parameters that we should created.

speciation := fnDiscretizeDistribution( dnLognormal(ln(speciation_mean), speciation_sd), NUM_RATE_CATEGORIES )

Similarly, we define the prior on the extinction rate in the same way as we did for the speciation rate.

extinction_mean ~ dnLoguniform( 1E-6, 1E2)
extinction_mean.setValue( speciation_mean / 2.0 )
moves.append( mvScale(extinction_mean, lambda=1, tune=true, weight=2.0) )

However, we assume that extinction rate is the same for all categories. Therefore, we simply replicate using the rep function the extinction rate NUM_RATE_CATEGORIES times.

extinction := rep( extinction_mean, NUM_RATE_CATEGORIES )

Next, we need a rate parameter for the rate-shifts events. We do not have much prior information about this rate but we can provide some realistic ranges. For example, we can specify a uniform distribution that the goes from 0 to 100 expected events. Remember that this is only possible if the tree is known and not estimated simultaneously because only if the tree is known, then we also know the tree length. As usual for rate parameter, we apply a scaling move to the event_rate variable.

event_rate ~ dnUniform(0.0, 100.0/tree_length)
moves.append( mvScale(event_rate, lambda=1, tune=true, weight=2.0) )

Additionally, we need a parameter for probability that the process starts at the root in any of the diversification-rate categories. We use a uniform/equal prior distribution on the diversification-rate categories.

rate_cat_probs <- simplex( rep(1, NUM_RATE_CATEGORIES) )

Shifts in the Extinction Rate

We might want to allow the extinction rate to change as well. As with the speciation rate, we discretize the lognormal distribution into a finite number of rate categories.

extinction_categories := fnDiscretizeDistribution( dnLognormal(ln(extinction_mean), H), NUM_RATE_CATEGORIES )

Now, we must create a vector that contains each combination of speciation- and extinction-rates. This allows the rate of speciation to change without changing the rate of extinction and vice versa. The resulting vector should be $N^2$ elements long. We call these the `paired’ rate categories.

k = 1
for(i in 1:NUM_RATE_CATEGORIES) {
    for(j in 1:NUM_RATE_CATEGORIES) {
        speciation[k]   := speciation_categories[i]
        extinction[k++] := extinction_categories[j]
    }
}

Now we also need to specify a root prior for $N^2$ elements.

rate_cat_probs <- simplex( rep(1, NUM_RATE_CATEGORIES * NUM_RATE_CATEGORIES) )

Note however, that this type of analysis will take significantly longer to run!

Incomplete Taxon Sampling


We know that we have sampled 233 out of 367 living primate species. To account for this we can set the sampling parameter as a constant node with a value of 233 / 367.

rho <- observed_phylogeny.ntips() / NUM_TOTAL_SPECIES

Root age


The birth-death process requires a parameter for the root age. In this exercise we use a fix tree and thus we know the age of the tree. Hence, we can get the value for the root from the (Magnuson-Ford and Otto 2012) tree. This is done using our global variable root defined above and nothing else has to be done here.

The time tree


Now we have all of the parameters we need to specify the full branch-specific birth-death model. We initialize the stochastic node representing the time tree.

timetree ~ dnCDBDP( rootAge           = root,
                    speciationRates   = speciation,
                    extinctionRates   = extinction,
                    Q                 = fnJC(NUM_RATE_CATEGORIES),
                    delta             = event_rate,
                    pi                = rate_cat_probs,
                    rho               = rho,
                    condition         = "time" )

And then we attach data to it.

timetree.clamp(observed_phylogeny)

Finally, we create a workspace object of our whole model using the model() function.

mymodel = model(speciation)

The model() function traversed all of the connections and found all of the nodes we specified.

Running an MCMC analysis


Specifying Monitors


For our MCMC analysis, we need to set up a vector of monitors to record the states of our Markov chain. First, we will initialize the model monitor using the mnModel function. This creates a new monitor variable that will output the states for all model parameters when passed into a MCMC function.

monitors.append( mnModel(filename="output/primates_BDS.log",printgen=1, separator = TAB) )

For summary and plotting purposes, we need to obtain the branch-specific diversification rate estimate along the tree. We will use a stochastic rate mapping algorithm Freyman and Höhna (2019). Thus, we create an mnStochasticBranchRate. The stochastic branch-rate monitor draws stochastic character maps and writes the simulated branch rates into a file. We will need this file later to estimate and visualize the posterior distribution of the rates at the branches.

monitors.append( mnStochasticBranchRate(cdbdp=timetree, printgen=1, filename="output/primates_BDS_rates.log") )

Finally, create a screen monitor that will report the states of specified variables to the screen with mnScreen:

monitors.append( mnScreen(printgen=10, event_rate, speciation_mean, extinction_mean) )

Initializing and Running the MCMC Simulation


With a fully specified model, a set of monitors, and a set of moves, we can now set up the MCMC algorithm that will sample parameter values in proportion to their posterior probability. The mcmc() function will create our MCMC object:

mymcmc = mcmc(mymodel, monitors, moves, nruns=2, combine="mixed")

Now, run the MCMC:

mymcmc.run(generations=2500,tuning=200)

⇨ The Rev file for performing this analysis: mcmc_BDS.Rev

When the analysis is complete, you will have the monitored files in your output directory. You can then visualize the branch-specific rates by plotting them using our R package RevGadgets.

Just start R in the main directory for this analysis and then type the following commands:

library(RevGadgets)

my_tree_file = "data/primates_tree.nex"
my_branch_rates_file = "output/primates_BDS_rates.log"
tree_plot = plot_branch_rates_tree( tree_file=my_tree_file,
                                    branch_rates_file=my_branch_rates_file)

ggsave("BDS.pdf", width=15, height=15, units="cm")

Estimated branch-specific speciation rates. Here we show the results of our example analysis. You’ll see that there is a speciation rate increase for the New World Monkeys.

Exercise 1


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