In the Introduction to Phylogenetic Models of Discrete Biogeography tutorial, we went through the exercise of setting up the instantaneous rate matrix and cladogenetic transition probabilities for a simple DEC model. In this tutorial, we will complete a biogeographic analysis using an empirical dataset: the Hawaiian silverswords.

The following series of tutorials will estimate the ancestral ranges of
the silversword alliance (Tribe *Madiinae*), a young and
diverse clade of about 50 species and subspecies. Although silverswords
are endemic to Hawaii, they are nested within a larger clade alongside
tarweeds, which are native to western continental North America
(Baldwin et al. 1991). The size and age of the silversword clade, combined with
our knowledge of Hawaiian island formation, makes it an ideal system to
explore concepts in historical biogeography and phylogeny. For further
reading, consult Carlquist (1959) and Baldwin and Sanderson (1998).

For this tutorial we’ll focus entirely on the silversword alliance and the modern Hawaiian archipelago. To begin, we’ll use just four areas, K, O, M, and H, and include areas R and Z in later analyses (). The species ranges used in this exercise follow Gillespie and Baldwin (2009).

Range | Areas | Size | State |
---|---|---|---|

$\emptyset$ | 0000 | 0 | 0 |

K | 1000 | 1 | 1 |

O | 0100 | 1 | 2 |

M | 0010 | 1 | 3 |

H | 0001 | 1 | 4 |

KO | 1100 | 2 | 5 |

KM | 1010 | 2 | 6 |

OM | 0110 | 2 | 7 |

KH | 1001 | 2 | 8 |

OH | 0101 | 2 | 9 |

MH | 0011 | 2 | 10 |

KOM | 1110 | 3 | 11 |

KOH | 1101 | 3 | 12 |

KMH | 1011 | 3 | 13 |

OMH | 0111 | 3 | 14 |

KOMH | 1111 | 4 | 15 |

We have provided the following data files for this tutorial:

- silversword.tre: Dated phylogeny of the silversword alliance.
- silversword.n4.range.nex: A data matrix with the coded ranges for each species.

Once you have downloaded the zip file by clicking on the arrow above, Unzip that and navigate inside of that directory. This directory should be called

`revbayes_biogeo_biogeo_simple`

Once inside you should see two directories:

`data`

and`scripts`

Once you have all of the files, open RevBayes and ensure that your working directory is the top directory above the

`data`

folder (e.g.,`revbayes_biogeo_biogeo_simple`

).

First, create file management variables for input and output

```
range_fn = "data/n4/silversword.n4.range.nex"
tree_fn = "data/n4/silversword.tre"
out_fn = "output/simple"
```

then read in our character data as binary presence-absence characters

```
dat_range_01 = readDiscreteCharacterData(range_fn)
```

then encode the species ranges into natural numbers

```
dat_range_n = formatDiscreteCharacterData(dat_range_01, "DEC")
```

Record the number of areas (characters) from the discrete character data object

```
n_areas = dat_range_01.nchar()
```

You can view the taxon data to see how characters are coded both as human-readable presence-absence data

```
dat_range_01[1]
```

```
Argyroxiphium_grayanum_East_Maui:
0010
```

And as computer-readable natural numbers

```
dat_range_n[1]
```

```
Argyroxiphium_grayanum_East_Maui:
3
```

We’ll want to record the relationship between range states and range labels when producing an ancestral range estimate figure. First, store the vector of range state descriptions

```
state_desc = dat_range_n.getStateDescriptions()
```

then write it to file

```
state_desc_str = "state,range\n"
for (i in 1:state_desc.size()){
state_desc_str += (i-1) + "," + state_desc[i] + "\n"
}
write(state_desc_str, file=out_fn+".state_labels.txt")
```

For this tutorial we’ll assume we know the dated species phylogeny without error.

```
tree <- readTrees(tree_fn)[1]
```

Next, we’ll build the anagenetic rate matrix for the DEC model. In its
simplest form, the rate matrix requires a dispersal rate and an
extirpation rate. For this analysis, we’ll assume that all pairs of
areas share the same dispersal rate and all areas share the same
extirpation rate. To gain greater control to observe and manage prior
sensitivity, we’ll reparameterize the DEC rate matrix to report the
*relative* rates of dispersal versus extirpation events. In
order for anagenetic event rates to be measured on an absolute time
scale (*e.g.*, in millions of years), we will also introduce a
biogeographic rate parameter, similar to the molecular clock parameter
used in dating analyses.

First, create a parameter for the arrival rate of anagenetic range evolution events. We’ll apply an uninformative prior to the rate’s magnitude by first assigning it a log uniform prior.

```
rate_bg ~ dnLoguniform(1E-4,1E2)
rate_bg.setValue(1E-2)
```

Create a moves vector and create a proposal to update the rate parameter.

```
moves = VectorMoves()
moves.append( mvSlide(rate_bg, weight=4) )
```

This yields a uniform prior over orders of magnitude, ranging from $10^{-4}$ to $10^2$ events per million years.

Because the rate matrix will describe the relative anagenetic event rates, we can safely assume that dispersal occurs at the relative (fixed) rate of one.

```
dispersal_rate <- 1.0
```

then create the dispersal rate matrix

```
for (i in 1:n_areas) {
for (j in 1:n_areas) {
dr[i][j] <- dispersal_rate
}
}
```

Next, assign a prior distribution to the relative extirpation rate and
assign it a move. The prior distribution of extirpation rates is given
`log_sd`

and `log_mean`

values that give the
prior expected value of one – i.e. the mean rate of area gain and area
loss are equal under the prior.

```
log_sd <- 0.5
log_mean <- ln(1) - 0.5*log_sd^2
extirpation_rate ~ dnLognormal(mean=log_mean, sd=log_sd)
moves.append( mvScale(extirpation_rate, weight=2) )
```

then create a matrix of extirpation rates

```
for (i in 1:n_areas) {
for (j in 1:n_areas) {
er[i][j] <- 0.0
}
er[i][i] := extirpation_rate
}
```

Note that er is a diagonal matrix whose diagonal values are
determined (`:=`

) by the stochastic variable,
extirpation_rate. We can now create our relative rate
matrix, `Q_DEC`

, with the `fnDECRateMatrix`

function.

```
Q_DEC := fnDECRateMatrix(dispersalRates=dr, extirpationRates=er)
```

Note, `fnDECRateMatrix`

does not rescale its elements in any
way, so transition rates share the same time scale as the underlying
tree. This scaling is in contrast to the standard molecular substitution
processes that are available in RevBayes, such as `fnGTR`

,
whose rates are rescaled such that the process is expected to produce
one event per site per unit time.

Next, we need to create the cladogenetic probability matrix. Cladogenetic event probabilities are given by a transition probability matrix, not a rate matrix. First, we will provide the vector to indicate that we wish to consider only subset sympatry and allopatry events. Next, we will create a vector of prior weights on cladogenesis events that fixes all cladogenetic events to be equiprobable.

```
clado_event_types <- [ "s", "a" ]
clado_event_probs <- simplex(1, 1)
P_DEC := fnDECCladoProbs(eventProbs=clado_event_probs,
eventTypes=clado_event_types,
numCharacters=n_areas)
```

Finally, all our DEC model components are encapsulated in the
`dnPhyloCTMCClado`

distribution, which is similar to
`dnPhyloCTMC`

except specialized to integrate over
cladogenetic events. Although this dataset has four areas, it is
recognized single character with states valued from 1 to $2^4$, hence
`nSites=1`

.

```
m_bg ~ dnPhyloCTMCClado(tree=tree,
Q=Q_DEC,
cladoProbs=P_DEC,
branchRates=rate_bg,
nSites=1,
type="NaturalNumbers")
```

Finally, attach the observed ranges to the model. Be sure to use the
natural number valued range characters, `dat_range_n`

, and
not the presence-absence range characters, `dat_range_01`

.

```
m_bg.clamp(dat_range_n)
```

Add the monitors.

```
monitors = VectorMonitors()
monitors.append( mnScreen(rate_bg, extirpation_rate, printgen=100) )
monitors.append( mnModel(file=out_fn+".params.log", printgen=10) )
monitors.append( mnFile(tree, file=out_fn+".tre", printgen=10) )
monitors.append( mnJointConditionalAncestralState(tree=tree,
ctmc=m_bg,
filename=out_fn+".states.log",
type="NaturalNumbers",
printgen=10,
withTips=true,
withStartStates=true) )
monitors.append( mnStochasticCharacterMap(ctmc=m_bg,
filename=out_fn+".stoch.log",
printgen=100) )
```

The `mnJointConditionalAncestralState`

monitor samples
ancestral states from the phylogeny, tree, according to the
model of evolution, `m_bg`

, and stores it to the file named
“simple.states.log”. Each row in the states file lists the
joint sample of ancestral states conditioned on the tip values for the
entire tree (i.e. a *joint* ancestral state sample
*conditional* on the tip states). Each column corresponds
to the phylogenetic node index for that particular MCMC sample. The
index is used used to match the state samples with the tree samples,
which is especially important when the topology is a random variable
().

The remaining tasks should be familiar from previous tutorials, so we can proceed briskly. Prepare the model graph for analysis by creating a Model object.

```
mymodel = model(m_bg)
```

Create the MCMC object from the model, moves, and monitors variables, and run the MCMC analysis.

```
mymcmc = mcmc(mymodel, moves, monitors)
mymcmc.run(3000)
```

After opening a new RevBayes session, create helper variables for files we’ll work with.

```
out_str = "output/simple"
out_state_fn = out_str + ".states.log"
out_tree_fn = out_str + ".tre"
out_mcc_fn = out_str + ".mcc.tre"
```

Build a maximum clade credibility tree from the posterior tree distribution, discarding the first 25% of samples. (Note, this step is gratuitous when we assume a fixed phylogeny, but essential when we estimate the phylogeny in ).

```
tree_trace = readTreeTrace(file=out_tree_fn, treetype="clock")
tree_trace.setBurnin(0.25)
n_burn = tree_trace.getBurnin()
```

Compute and save the maximum clade credibility tree

```
mcc_tree = mccTree(tree_trace, file=out_mcc_fn)
```

Get the ancestral state trace from simple.states.log

```
state_trace = readAncestralStateTrace(file=out_state_fn)
```

Get the ancestral state tree trace from `simple.tre`

. It is
important to use `readAncestralTreeTrace`

and not
`readTreeTrace`

to properly annotate the tree with ancestral
states.

```
tree_trace = readAncestralStateTreeTrace(file=out_tree_fn, treetype="clock")
```

Finally, compute and save the ancestral state tree as
`simple.ase.tre`

.

```
anc_tree = ancestralStateTree(tree=mcc_tree,
ancestral_state_trace_vector=state_trace,
tree_trace=tree_trace,
include_start_states=true,
file=out_str+".ase.tre",
burnin=n_burn,
site=1)
```

We can review the output from ancestralStateTree in
`FigTree`

().

Ancestral state trees are annotated with the first three most probable ancestral states along with their posterior probabilities. When the tree is a random variable, as it is in later exercises, additional information about phylogenetic uncertainty is reported.

Finally, it is possible to generate a figure with ancestral states that is
suitable for publication using the `R`

package
RevGadgets ().
To create build this figure, open an `R`

session and load the plotting
script with the source function

```
source("scripts/plot_anc_state.simple.R")
```

Notice that the model prefers a widespread ancestral range for the clade
(KOH, KMH, or KM) approximately four million years ago when only Kauai existed.
Similar geologically unrealistic ranges are estimated for the
*Agyroxiphium* clade (H or MH) and the *D. sheriffiana* and *D. arborea* clade (OMH, OM, M) at times when Hawaii and Maui did not exist. The
remaining tutorials will focus on improvements to the simple DEC model
presented here.

Continue to the next tutorial: Advanced Phylogenetic Analysis of Historical Biogeography

- Baldwin B.G., Kyhos D.W., Dvorak J., Carr G.D. 1991. Chloroplast DNA evidence for a North American origin of the Hawaiian silversword alliance (Asteraceae). Proceedings of the National Academy of Sciences. 88:1840–1843. 10.1073/pnas.88.5.1840
- Baldwin B.G., Sanderson M.J. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proceedings of the National Academy of Sciences. 95:9402–9406. 10.1073/pnas.95.16.9402
- Carlquist S. 1959. Studies on Madinae: anatomy, cytology, and evolutionary relationships. Aliso. 4:171–236. 10.5642/aliso.19590402.02
- Gillespie G.R., Baldwin G.B. 2009. Island Biogeography of Remote Archipelagoes. The Theory of Island Biogeography Revisited.:358–387.