Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.

Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies.
Syst. Biol. 58(6):595–611, 2009
c The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved.
For Permissions, please email: [email protected]
DOI:10.1093/sysbio/syp067
Advance Access publication on October 15, 2009
Estimating Trait-Dependent Speciation and Extinction Rates from Incompletely Resolved
Phylogenies
R ICHARD G. F ITZ J OHN1,2,∗ , WAYNE P. M ADDISON 1,2,3 ,
1 Department
AND
S ARAH P. O TTO1,2
of Zoology, 2 Biodiversity Research Centre and 3 Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada;
∗ Correspondence to be sent to: Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada;
E-mail: [email protected]
Abstract.—Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification
among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential
diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny.
We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without
complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches
can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant
species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using
simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected
with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our
unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our
methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved
phylogenies. [Bayesian inference; birth–death process; BISSE ; extinction; phylogenetics; sampling; speciation.]
Just as differences in traits may affect the relative
survival and reproductive success of individuals, traits
may affect the relative rate at which lineages go extinct or speciate (Stanley 1975; Coyne and Orr 2004;
Ricklefs 2007). Sister-clade comparisons (Barraclough
et al. 1998) have been widely used to detect traits that
are correlated with differential diversification. Using
this method, traits that have been found to have a significant impact on diversification rates include diet in
insects (Mitter et al. 1988; Farrell 1998), latitude in birds
and butterflies (Cardillo 1999), mating system in birds
(Mitra et al. 1996), and sex allocation in flowering plants
(Heilbuth 2000). These analyses have often been framed
as tests of whether a character is a “key innovation;”
that is, has a particular character state lead to elevated
rates of diversification? More recently, a variety of statistical approaches that directly estimate speciation rates
have been developed that incorporate phylogenetic tree
topology and the pattern of branching times (e.g., Pagel
1997; Paradis 2005; Ree 2005; Maddison et al. 2007).
These approaches allow for greater statistical power
than sister-clade comparisons because they incorporate
more information about the patterns of diversification.
Among these is the binary-state speciation and extinction ( BISSE) method (Maddison et al. 2007), a whole-tree
likelihood method that can be used to detect the effect of
a trait on diversification, where the trait can be classified
into 2 states.
The BISSE method as formulated by Maddison et al.
(2007) assumes that the phylogenetic tree is complete
and fully resolved; that is, the tree must include every
extant species. It also assumes that all character state
information is known. These assumptions currently restrict its applicability, as few published phylogenies are
both complete to the species level and large enough to
detect differential diversification. Without appropriate
correction, BISSE will not produce valid likelihoods for
incompletely resolved trees. Incomplete phylogenetic
coverage decreases the apparent number of events over
a phylogeny; there are fewer inferred speciation and
character change events. Because of this, the BISSE likelihood surface shifts to favor lower rates of diversification
and character change. Furthermore, inferred phylogenies that include only a fraction of extant species tend to
have longer terminal branches (Fig. 1b), and as a result,
the estimated extinction rates approach 0 because there
is a smaller increase in the number of lineages in time
near the present (Nee et al. 1994).
Similar limitations have been overcome in likelihood
approaches that estimate speciation and extinction
rates when these rates do not depend on a character
(character-independent diversification). The characterindependent likelihood method of Nee et al. (1994) includes corrections that assume that the species present
in a phylogeny represent a random sample of extant
species from a clade by incorporating the sampling process into the likelihood calculations. Recently, Bokma
(2008) developed a Bayesian approach for estimating
character-independent diversification rates that treats
the branching times for missing taxa as additional
parameters to be estimated. In these studies, because
speciation and extinction rates do not depend on a
species’ character state, only the branching times are
required. However, if speciation and extinction rates
depend on a character’s state, then branching times are
insufficient because the topology of the tree will depend
on how the character evolves.
Here, we extend BISSE to allow estimation of
character-dependent speciation and extinction rates
from incompletely resolved phylogenies. We develop
likelihood calculations that compensate for incomplete
phylogenetic knowledge in 2 cases: 1) where the species
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FIGURE 1. Different ways that phylogenetic information may be incomplete. Tree (a) is complete; every extant species is included and the
tree is fully resolved. Black and white boxes above the tips refer to different character states. Tree (b) is a “skeletal tree”; species are included
randomly from the full tree in (a). Sampled taxa are indicated by solid lines, and missing taxa are indicated by dashed lines. In general, nothing
is known about the placement of these taxa. Tree (c) is a “terminally unresolved tree”; in this case, the species not explicitly included as tips
in the phylogeny are all known to belong to terminal unresolved clades. This tree is therefore “complete” in that it includes all extant taxa but
is incompletely resolved. This tree has the same branching structure as (b). Tree (d) contains a paraphyletic unresolved group and cannot be
directly handled by either of the methods presented here. The relationships among species n − q are not resolved, and this group is known to
be paraphyletic (see panel a). To convert this tree into a terminally unresolved tree, the known relationships within the r − t clade would have
to be discarded to create an unresolved clade spanning species n − t.
in a phylogeny represent a random sample of all extant
species within a group (Fig. 1b) and 2) where species
not directly represented as tips in the phylogeny can
be assigned to terminal unresolved clades (Fig. 1c). We
also develop methods to allow for incomplete character
state knowledge for both complete and incompletely
resolved trees. We describe how these likelihoods can
be used in Bayesian inference and apply our methods to simulated data sets. Finally, we demonstrate
our method by applying it to the correlation between
diversification and sexual dimorphism in shorebirds
(Charadriiformes).
BISSE FOR C OMPLETE P HYLOGENIES
Because our aim is to generalize the BISSE model of
Maddison et al. (2007), we start with a brief description
of this method. BISSE computes the probability of a phylogenetic tree and the observed distribution of character
states among extant species, given a model of character evolution, speciation, and extinction. The character
states must be binary; we denote the possible character
states as 0 or 1 (e.g., herbivorous or nonherbivorous insects). The likelihood calculation tracks 2 variables for
each character state i along branches in a phylogeny:
DNi (t)—the probability that a lineage in state i at time
t would evolve into the extant clade N as observed and
Ei (t)—the probability that a lineage in state i at time t
would go completely extinct by the present, leaving no
extant members. (For compactness, we will often refer to
the clade whose most recent common ancestor is node
N as “clade N.”) Time is measured backward with the
present at t = 0 and t > 0 representing some time in the
past. The changes in these quantities over time are described by a set of ordinary differential equations
dDNi
= − (λi + μi + qij )DNi (t) + qij DNj (t)
dt
+ 2λi Ei (t)DNi (t),
(1a)
dEi
= μi − (λi + μi + qij )Ei (t) + qij Ej (t) + λi Ei (t)2 , (1b)
dt
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597
FIGURE 2. BISSE with (a) and without (b) full phylogenetic knowledge. In panel (a), the values at the base of the nodes leading to the first tips
(DNi (t1 ) and DMi (t1 )) are calculated backward in time using Equations (1) and then combined with Equation (2) to become the initial condition
DN0 i (t1 ) for calculating DN0 i (t2 ). In panel (b), the four species on the left are unresolved but can be assigned to a tip that branches at time t1 .
DNi (t) would be calculated forward in time using our new method, and DMi (t) with BISSE, with these values combined as above.
where λi is the speciation rate in state i, μi is the extinction rate in state i, and qij is the rate of transition from
state i to j forward in time (Maddison et al. 2007). These
equations are solved numerically along each branch
backward in time to compute DNi (t) (Fig. 2).
On each branch, the character state at the tip provides
the initial conditions for Equations (1). DNi (0) = 1 if the
tip N is in state i and 0 otherwise because the lineage
must be in its observed state. Similarly, E0 (0) = E1 (0) = 0
as a lineage cannot go extinct in zero time. At a node
joining the lineages leading to clades N and M, the probability of generating both daughter clades given that the
node is in state i is
DN0 i (t) = DNi (t)DMi (t)λi ,
(2)
where N0 represents the union of clades N and M (see
Fig. 2). The likelihood calculation proceeds backward
in time down the tree from the tips until it reaches the
root. At the root, R, we have the two probabilities, DR0
and DR1 , corresponding to the possible character states
at the root. The overall likelihood, DR , must sum over
the probabilities that the root was in each state (see
Appendix 1).
L IKELIHOOD C ALCULATIONS FOR I NCOMPLETELY
R ESOLVED P HYLOGENIES
Incompleteness in phylogenetic information can come
in many forms. A species may be entirely unplaced
phylogenetically or placed into a clade but not into
a precise relationship within the clade. Its character
state may be known or unknown. We will derive methods for two situations: “skeletal trees,” where we have
a fully resolved tree for a random sample of species
whose states are fully known, and “terminally unresolved trees,” where trees include all extant species
and are fully resolved except for terminal clades that
are completely unresolved phylogenetically and whose
character states are known to varying degrees. Skeletal
trees (Fig. 1b) could arise when a biologist samples
species simultaneously for their presence in a phylogenetic analysis and having data for the character
of interest. For these trees, we assume that nothing is
known about the phylogenetic placement of the missing taxa. Terminally unresolved trees arise frequently
when the species included in a molecular phylogeny are
exemplars and where information on the nonincluded
(unplaced) species is available (e.g., from previous systematic studies). If the unplaced species can be assigned
to terminal clades containing the exemplar species, then
our method can be used (Fig. 1c). Here, we assume that
every species can be assigned to an unresolved clade.
Note that terminally unresolved trees are phylogenetically complete, in that they include all extant taxa, but
are incompletely resolved, in that not all phylogenetic
relationships are known. A broader class of incomplete phylogenies do not match either of these cases,
and the methods we describe below cannot be used
directly. This includes paraphyletic unresolved groups
(Fig. 1d).
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Skeletal Trees: Unplaced Missing Taxa
First, we consider skeletal trees, where a given phylogenetic tree represents a random sample of all extant
species in a taxonomic group. To account for incomplete phylogenies, we model a “sampling” event at the
present that corresponds to a biologist obtaining data
for the species. This event occurs during an infinitesimally small time period during which a species in state
i has a probability fi of being sampled for inclusion in a
phylogeny. The fi values should be determined from estimates of the numbers of species having each character
state that are unsampled versus sampled. If the character states of unsampled species are unknown, then the
fi values could be set equal for all states and reflect the
proportion of all extant species that have been sampled.
With this sampling event, Ei (t) can be interpreted as the
probability of a lineage not being present in the phylogeny, either by going extinct or not being sampled.
The initial condition Ei (0) is therefore (1 − fi ). Similarly,
rather than representing the probability that a lineage in
state i at time t would evolve into the full extant clade
N at the present, DNi (t) includes the probability that the
tip taxa present in the phylogeny are sampled. The initial conditions become DNi (0) = fi if the sampled tip is in
state i and 0 otherwise. After these modifications to the
initial conditions, the calculations continue as described
in Maddison et al. (2007). This is similar to the method
used by Nee et al. (1994) to correct likelihood calculations for inferring character-independent speciation and
extinction rates from incomplete phylogenies. Indeed,
in Appendix 2, we show that when the speciation and
extinction rates are independent of character state, the
calculations are equivalent.
This approach assumes that the taxon sampling process is independent of the position in the phylogeny.
However, it need not be independent of the character
state as the fi can differ between states 0 and 1. However, this approach also assumes that taxon sampling
is even across the phylogeny, which in many cases
it is not.
Terminally Unresolved Trees
Terminally unresolved trees contain all species, but
their relationships are not fully resolved, with some
species grouped into unresolved clades (Fig. 1c). We
can envision this situation as comparable to the skeletal
trees, but with the unplaced species not entirely unknown: we know to which terminal clades they belong
and we may know their character states. This extra information about placement and character states can be
used to improve inference.
We will use the word “tip” to refer to a terminal unit
in the tree, which may represent either a single extant
species or a terminal unresolved clade. Thus, the number of tips in the tree will be less than the number of
species implied if there are unresolved terminal clades.
We assume that the sampling of species is complete;
that is, every extant species is either present directly
as a tip or can be assigned to a tip that represents an
unresolved clade. We do not assume knowledge of
the timing of the last common ancestor for a terminal
unresolved clade, instead we assume that diversification happens at any point after splitting from its sister
clade (Fig. 2). We also do not assume any particular
topology for the unresolved clades, rather we sum over
all possible phylogenetic histories, according to their
probability. We initially assume complete knowledge of
character states, but we relax this assumption in the next
section.
If we can compute the probability of a terminal clade,
DNi (t), then we can combine this with the probability
of their sister lineages using Equation (2) and continue
with BISSE down the rest of the tree (Fig. 2b). In contrast
to the backward-time approach employed by BISSE,
we use a forward-time method to calculate DNi (t) for
an unresolved clade. Because it has no phylogenetic
structure, we cannot distinguish among the different
possible evolutionary histories of an unresolved clade.
Consequently, we model clade evolution as a Markov
process, tracking only the probability of different clade
compositions over time. The possible clade compositions can be distinguished by the number of species in
each state; let (n0 , n1 ) represent a clade with n0 species
in state 0 and n1 species in state 1. Even though the
number of possible clade types is infinite, we truncate
state space to a finite number of species. This process is
similar to two birth–death processes (Nee 2006), one for
each character state, but includes transitions between
the processes. We term this a “birth–death-transition
process.”
If ~x(t) is a column vector representing probabilities of
different clade types at time t and Q is a transition rate
matrix describing the rates of changes between clade
types, then the probability of generating any possible
clade is given by
~x(t0 ) = exp((t1 − t0 )Q) ∙ ~x(t1 ),
t 1 > t0 ,
(3)
where t1 represents an earlier point in time to t0 and
“exp” represents the matrix exponential (Sidje 1998).
The values of ~x(t0 ) that correspond to the observed data
can then be used as the probability of the clade evolving
as observed, DNi (t1 ), for subsequent BISSE calculations.
For example, for a clade that begins in state 0 at time
t1 and ends in clade type (3, 1) at the present (t0 , as in
Fig. 2b), we find ~x(t0 ) from Equation (3) and pick out
the probability of generating a (3, 1) clade from this
vector, which is used as DN0 (t1 ). The probability of generating a clade with no species, (0, 0), is the probability
that the clade would have gone extinct, E0 (t1 ). This
process is then repeated assuming that the lineage leading to the clade was initially in state 1, giving DN1 (t1 )
and E1 (t1 ).
Before describing the transition rate matrix Q, we
must first specify the structure of the state space
~x(t). Let the first element represent the probability of
having zero species, the next two elements represent the
two single-species clades with one species in state 0 or 1
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FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
species in state 1 (respectively) and so on. That is,
probabilities are assigned to the positions of ~x(t) in the
order:
0 species
1 species
z }| { z
}|
{
(0, 0), (1, 0), (0, 1),
2 species
z
}|
{
(2, 0), (1, 1), (0, 2), . . . ,
(k, 0), (k − 1, 1), (k − 2, 2), . . . , (1, k − 1), (0, k), . . . ,
|
{z
}
k species
(4)
so that a clade with k species is represented by the k + 1
elements in positions k(k + 1)/2 + 1 to (k + 1)(k + 2)/2.
To keep the state space finite, the final element of ~x(t)
is an absorbing state, representing the probability that
a clade has at least nmax species. By doing this, we assume that once a clade reaches nmax species, it is so large
that there is a negligible probability of generating the observed number of species by time t0 . In practice, nmax can
be chosen to be large enough so that it does not significantly affect calculations (e.g., by monitoring the change
in relevant values in ~x(t0 ) as nmax is increased). At the
base of the clade, t1 , there must have been a single ancestral lineage in either state 0 or 1. The state of the system
at this time must have been a vector of zeros except for
a 1 in either the second position (corresponding to (1, 0)
to calculate DN0 (t)) or the third position (corresponding
to (0, 1) to calculate DN1 (t)).
To calculate Q, we assume that each time step is small
enough that only a single event may happen; a lineage
currently in state (n0 , n1 ) may have one species:
• speciate, moving from state (n0 , n1 ) to (n0 + 1, n1 ) or
(n0 , n1 + 1) at rate n0 λ0 or n1 λ1 , respectively,
• go extinct, moving to (n0 − 1, n1 ) or (n0 , n1 − 1) at rate
n0 μ0 or n1 μ1 ,
• change character state, moving to state (n0 − 1, n1 + 1)
or (n0 + 1, n1 − 1) at rate n0 q01 or n1 q10 .
Using these rules, the transition rate matrix has a block
structure, involving the blocks Sk , Ek , and Ck . The block
Sk is a (k + 2) × (k + 1) matrix describing speciation from
k to k + 1 species:

kλ0

 0


 0




Sk =  0








0
0
(k − 1)λ0
0
λ1
(k − 2)λ0
0
2λ1

..
.
..
.
λ0
(k − 1)λ1
0









.



0 


0 

kλ1
Ek is a k × (k + 1) matrix describing extinction from k to
k − 1 species:


kμ0
μ1
0


 0 (k − 1)μ0

2μ1






..


.
0
(k − 2)μ0
Ek =  0
.






..

. (1 − k)μ1 0 


μ0
kμ1
Ck is a (k + 1) × (k + 1) square matrix describing character state changes, leaving the number of species constant
at k:


∙
q10
0


kq01

∙
2q10






..
 0 (k − 1)q

.
∙
01




Ck = 
,
..


 0
0
(k − 2)q01 . (k − 1)q10 0 






.
..

∙
kq10 


q01
∙
where the dotted elements along the diagonal of Ck are
chosen so that the columns of Q sum to zero. Denoting
matrices of zeros with 0, the transition rate matrix Q is


C0 E1 0



 0 C 1 E2







 0 S C ...
1
2




(5)
Q=
.
..


. Enmax −1 0
0
0 S2






..


.
C
0
nmax −1


Snmax −1
0
The final speciation block Snmax −1 , describing speciation
into the absorbing state is an nt element row vector:
((nmax − 1)λ0 , (nmax − 2)λ0 + λ1 , . . . , (nmax − 1)λ1 ).
As a special case, this approach can be used to calculate likelihoods for terminally unresolved trees where
speciation and extinction do not depend on a character’s
state, as described in Appendix 2.
Incomplete Character State Knowledge
Regardless of the level of phylogenetic completeness
and resolution, character state information may be unknown for some species. Here, we describe corrections
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to the BISSE likelihood for missing character state information for fully resolved phylogenies, skeletal trees, and
terminally unresolved trees.
For fully resolved phylogenies, if no information on a
character for a tip is available, then the “data” become
the presence of the tip only. On the single branch leading to this tip, we can then interpret DNi (t) as the probability of giving rise to a single species, regardless of its
character state. The initial conditions must therefore be
DNi (0) = 1 for both states because with no time for extinction, there is a 100% probability that the branch will
lead to the observed data. Using this logic, for skeletal
trees, the initial conditions are DNi (t) = fi .
For terminally unresolved trees, character state information may not be known for all members of an unresolved clade. In this case, we can calculate the joint
probability that a clade evolved to a particular composition and that it was sampled as observed. Say that the
unresolved clade of interest truly has x0 species in state 0
and x1 species in state 1 but that we know the state information only for a sample of these species so that si
species are known to be in state i. If the probability of
a species’ state being known is independent of its state,
then we can assume that the sN = s0 + s1 known species
represent samples without replacement from a pool of
xN = x0 + x1 species and compute the sampling proba-
bility using the hypergeometric distribution. Of the xsNN
ways
of sampling sN species from this pool, there are
xi
si ways of sampling si species in state i. The sampling
probability is therefore given by:
x0
x1
s0
s1
.
Pr(s0 , s1 |x0 , x1 ) =
(6)
xN
sN
Although we do not know the true number of species in
each state, we can use Equation (3) to compute the probability that the clade composition is (x0 , x1 ) and then use
Equation (6) to give the probability of knowing that si
species are in state i. To do this, we multiply the probability of generating the clade by the probability of sampling the clade as observed and sum over all possible
clade compositions:
j
xN − j
xX
N −s1
s1
s0
Pr(j, xN − j)
.
(7)
DNi (t) =
xN
j=s0
sN
Here, Pr(x0 , x1 ) is the probability of a clade with x0
species in state 0 and x1 species in state 1, calculated
from Equation (3). This calculation assumes that we
know that there are xN species in the clade, but this calculation can be generalized if xN itself is not known exactly but can be described by a probability distribution.
Where we have full state information (i.e., s0 + s1 = xN ),
Equation (7) reduces to Pr(s0 , s1 ).
B AYESIAN I NFERENCE
The above equations can be used to calculate the
likelihood from an incomplete phylogeny, that is, the
probability of the data given a model of speciation, extinction, and character evolution. This method can then
be used to estimate rates using maximum likelihood
and to compare models using likelihood ratio tests.
Here, we will discuss their application to Bayesian inference so that measures of parameter uncertainty can
be simultaneously obtained. For a general introduction
to Bayesian inference in phylogenetics, see Huelsenbeck
et al. (2002). We will focus on the posterior probability distribution of the model parameters; that is, the
probability of the parameters given the data.
To compute the posterior probability, we need to specify the prior probability distribution for the parameters.
We use an exponential prior for the six parameters (see
Churchill 2000). This choice reflects the philosophical
preference for explanations requiring fewer events, all
else being equal (Occam’s razor). For example, if few
species are present in state 0, then there is no information about the extinction rate for species in state 0 (μ0 ).
An exponential prior would then generate a posterior
distribution with the same mean as the prior. Other common priors include a uniform prior and a uniform prior
on the log of each parameter (e.g., on ln(μ0 )). These are
both “improper priors” because they do not integrate
to a finite value over the possible range of the parameters (0, ∞). Because of this, in the case where little
signal is present in the data, the posterior will not integrate to a finite value and cannot easily be interpreted
(Gelman et al. 1995). Because it is itself proper, the exponential prior always produces a proper posterior probability distribution, and it has the additional benefit that
its influence on the posterior distribution can be easily
detected by comparing the mean of prior and posterior
distributions. The prior probability density associated
with the parameter θj is set to:
Pr(θj ) = cj e−cj θj ,
(8)
where θj is the value of the jth parameter and cj is a rate
parameter. The posterior probability of the model given
the data is proportional to
DR (tR )
Y
cj e−cj θj ,
(9)
j
where the product is taken over the six model parameters. An exploration of the alternative priors indicated
that the priors generally had negligible influence except
where there were very few extant species in a given
character state.
To choose values for cj , we use a preliminary measure of the rate of diversification from the tree. Ignoring
state changes and asymmetries in speciation or extinction rates, the expected number of species in a tree of
length tR is n = e(λ−μ)tR , where λ and μ are the characterindependent speciation and extinction rates (Nee et al.
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FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
1994). Rearranging, the diversification rate (λ − μ) that
would produce n species at time tR is ln(n)/tR . We chose
the prior rates so that the mean of the exponential distribution was twice this value (i.e., cj = tR /2 ln(n)). The
same prior was used for all model parameters.
N UMERICAL M ETHODS AND A PPLICATION
To test our method, we followed the same approach
as Maddison et al. (2007) by simulating trees and character states using known rates and then attempting to
infer those rates from the tree. We simulated trees containing 500 species with rates λ0 = λ1 = 0.1, μ0 = μ1 =
0.03, and q01 = q10 = 0.01 (equal rate trees) or with
λ1 = 0.2 (unequal rate trees). These are the same rates as
Maddison et al. (2007) for comparison, and the trees
were simulated using their method.
We generated random incomplete phylogenies from
these complete simulated phylogenies. To perform
random taxonomic sampling to create skeletal trees
(Fig. 1b), we sampled a proportion of all tips independently of tip state. The per-state fraction of species in
each state that were present in the final sample was
calculated and used to specify f0 and f1 when calculating likelihoods. To simulate terminally unresolved
trees, a similar sampling routine can be used. Insofar
as terminally unresolved trees can arise when character
data are available for all species but detailed phylogenetic placement is available for only a sample of
species, we can simulate this by choosing which species
were sampled for detailed phylogenetic placement. The
remaining unsampled species would be assigned to
terminally unresolved clades represented by a single
species that was sampled, the exemplar of the clade.
However, this sampling requires some additional care
because every extant species must be either present in
the phylogeny or assigned to an unresolved clade (cf.
Fig. 1c,d). Simply sampling species can leave orphaned
species that fall below resolved clades and so cannot be
placed into fully unresolved clades. For example, suppose that species j and k were chosen to have resolved
placement from the phylogeny in Fig. 1a, but species
i left unresolved. The species i cannot be placed into
an unresolved clade represented by a single sampled
exemplar species and is thus “orphaned.” As a way of
guaranteeing that there were no orphans in the final
tree, we included a fraction of the orphan species in
the sample and reassessed which species remained orphans, repeating until no orphan species were present.
Note that this sampling approach does not generate a
random sample of species, as assumed in our skeletal
tree approach. For the results reported in this paper,
we assumed that the character states of all species were
known.
Implementation
We implemented the above methods were in the
R package “diversitree” (available from http://www.
601
zoology.ubc.ca/prog/diversitree). The diversitree package will also be accessible through an upcoming version
of Mesquite (Maddison WP and Maddison DR 2008).
The matrix exponentiations were calculated numerically using the DMEXPV routine in Expokit (Sidje 1998).
Because the transition rate matrix Q is very sparse, it
is practical to use this approach for unresolved clades
containing up to several hundred species. The posterior probability distribution cannot be sampled from
directly, so we use Markov chain Monte Carlo (MCMC)
to approximate the distribution using slice sampling
for the parameter updates (MacKay 2003; Neal 2003).
For each tree, we ran 3 independent MCMC chains
for 10,000 steps from random starting locations, discarding the first 2500 steps of each chain. Although
these chains are short compared with those used in tree
inference, the sampler here is exploring a reasonably
smooth continuous probability surface, rather than tree
space, with disjoint regions of high probability separated by areas of low probability (data not shown). Consequently, convergence of the MCMC chains was very
rapid.
R ESULTS
We briefly present the results of Bayesian inference
using BISSE with complete phylogenetic knowledge,
then discuss how the statistical power is affected by
incomplete phylogenetic knowledge.
Bayesian Inference with BISSE
Where speciation rates were equal for each character
state (λ0 = λ1 ; equal rate trees), the mean inferred speciation rates were close to the true values used to simulate
the trees, and the posterior probability density was
tightly distributed around this true value (Fig. 3, solid
curves). Where speciation rates were unequal (λ0 < λ1 ),
species in state 0 were relatively rare (approximately
10% of extant species). Consequently, the rates for transitions in state 0 (λ0 , μ0 , and q01 ) were less precisely
estimated than for state 1, although still largely centered
around their true values (Fig. 3, dashed curves). This
pattern is consistent with that in Maddison et al. (2007),
who found that the maximum likelihood estimates for
the rare character state were more widely distributed
than the estimates for the more common character state
(their fig. 4).
Some of the model parameter estimates were correlated; in particular, the speciation and extinction rates
for a particular character state were positively and linearly correlated (data not shown), indicating that a
range of speciation/extinction rate combinations had
similar posterior probabilities. The diversification rate
is the difference between the speciation and the extinction rates (ri = λi − μi ; Nee et al. 1994). The uncertainty
around the diversification rate estimate was similar
to the uncertainty around the speciation rates, even
where extinction rates were poorly estimated (Fig. 4).
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FIGURE 3. Posterior probability densities for the 6 BISSE parameters on a fully resolved phylogeny. Two trees were generated, each containing
500 species and with either all rates equal (λ0 = λ1 , μ0 = μ1 , q01 = q10 ; solid curves) or with unequal speciation rates (λ0 < λ1 ; dashed curves).
The histograms display posterior probabilities over the last 7500 points from 3 independent MCMC chains, discarding the first 2500 points of
each chain. The vertical lines indicate the true parameter values used in simulating the trees. The y-axes differ between plots but are scaled so
the area under each curve integrates to 1. The horizontal bars indicate the 95% credibility intervals for the equal rate (upper bar) and unequal
rate (lower bar) tree.
The difference between the diversification rates for
the two character states (relative diversification rate;
rrel = r1 − r0 ) gives a summary of the strength of differential diversification. The relative diversification rate
for equal rate trees was well estimated, centered around
the true value and with a narrow credibility interval. For
unequal rate trees, the posterior probability distribution
was flatter but still centered around the true value. For
FIGURE 4. Posterior probability distribution for the diversification rates (a) in state 0 (r0 ) and (b) in state 1 (r1 ) and (c) the relative diversification rate (rrel = r1 − r0 ) for an equal rate tree (λ0 = λ1 , solid curves) and an unequal rate tree (λ0 < λ1 , dashed curves). The 95% credibility
intervals are indicated by the horizontal bars, and the vertical lines indicate the true parameter values used in simulating the trees. Parameters
are as indicated in text.
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FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
the example shown in Fig. 4, the posterior probability of
rrel ≤ 0 for the unequal rate tree was 0.004, so we would
correctly conclude that character state 1 increased diversification rate in this case.
Effect of Decreasing Phylogenetic Knowledge
As fewer species were included in a phylogeny or as
more species fell within unresolved clades, parameters
were less accurately and precisely estimated (Fig. 5).
Accuracy and precision were essentially unaffected for
nearly completely resolved phylogenies (75–100% complete) and for most parameters precision did not deteriorate substantially until trees contained fewer than
≈ 50% of the total possible tips. For all parameters, the
mean parameter estimate increased when phylogenetic
603
resolution became very low. This reflects the skew in
the posterior probability distribution (Fig. 3), which
increased with reduced phylogenetic resolution as the
prior distribution increasingly dominates the posterior
distribution. In addition, the prior means were higher
than any of the simulated rates (approximately 0.35
for unequal rate trees and 0.16 for equal rate trees).
Because medians are less sensitive to skew, the median
parameter estimates were less affected by decreasing
phylogenetic information than the mean, but they still
tended to increase at very low phylogenetic resolution (not shown). The decrease in accuracy and precision was most pronounced for the rate parameters for
the rare state on unequal rate trees (λ0 , μ0 , and q01 ).
Decreasing phylogenetic resolution increased the uncertainty of the parameter estimates, with the widths
of the credibility intervals growing as the proportion of
FIGURE 5. Uncertainty around BISSE parameter estimates as a function of phylogenetic knowledge. Points represent the mean for the estimate of each parameters, and the curves above and below indicate the mean 95% credibility interval, averaged over 30 different phylogenies.
Dashed curves/open circles represent skeletal trees and solid curves/filled circles represent terminally unresolved trees. The horizontal dotted
line indicates the true rate from the simulations. For skeletal trees, the proportion of tips reflects phylogenetic completeness, whereas for terminally unresolved trees, it represents the level of phylogenetic resolution. Trees were evolved with unequal speciation rates ( λ1 > λ0 , first two
columns) or equal speciation rates (final column) and contained 500 species before sampling. Credibility intervals were calculated over the last
7500 points of three independent MCMC chains per tree, discarding the first 2500 points.
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SYSTEMATIC BIOLOGY
tips sampled decreased (Fig. 5). On unequal rate trees
at very low phylogenetic resolution, the posterior probability distribution for q01 became very similar to the
prior distribution.
The decrease in accuracy and precision with decreasing phylogenetic knowledge was more pronounced for
skeletal trees than for terminally unresolved trees. This
is because of the additional information that the unresolved clades contain in addition to the branching
structure (i.e., the number of species and their states).
In general, for a given number of tips present in a phylogeny (i.e., sampled species in skeletal trees, resolved
species plus unresolved clades in terminally unresolved
trees), terminally unresolved trees had lower bias in
the mean parameter estimates and narrower credibility intervals than did skeletal trees. However, for
well-estimated parameters (e.g., λ1 and μ1 on the unequal rate tree; Fig. 5b,e), the difference in uncertainty
between these methods was small. The difference in
precision was particularly pronounced for the character
transition rates, which were typically well estimated on
terminally unresolved trees, even with low phylogenetic
resolution (Fig. 5g–i).
Rates of net diversification were well estimated as
phylogenetic resolution decreased, despite increasing uncertainty in extinction rates (Fig. 6). For equal
rate trees, the net diversification rate for each trait
(ri = λi − μi ) and the relative diversification rate rrel
were fairly insensitive to phylogenetic resolution, with
no bias in the mean parameter estimates and little increase in the width of the credibility intervals, especially
for terminally unresolved trees (Fig. 6a,c,e). Where speciation rates differed (unequal rate trees), the estimated
diversification rates were sensitive to decreasing phylogenetic resolution, but less so than for the individual
parameters. Particularly for terminally unresolved trees,
the net diversification rate was well estimated even with
low phylogenetic resolution. With the parameters used
here, differential diversification was detectable on unequal rate trees at the 5% significance level until fewer
than 30% of taxa were explicitly included in terminally
unresolved trees and until 50% of taxa were included
using skeletal trees (Fig. 6f).
A PPLICATION TO S HOREBIRD D ATA
Sexual dimorphism in body size or other traits in
birds is thought be driven by sexual selection (Darwin
1871). Larger males might be favored by females or fare
better in intrasexual conflict over mates, whereas small
males (reversed sexual dimorphism) might be favored
when sexual displays are acrobatic (Figuerola 1999).
Sexual differences in any trait may indicate different
optima for the two sexes, and therefore, intersexual
conflict, which may increase speciation rates (Parker
and Partridge 1998; Gavrilets 2000; Jablonski 2008).
Comparative evidence linking sexual dimorphism with
speciation is mixed. Several studies have found that
sexual dimorphism in plumage or other display traits
might promote increased diversification (Barraclough
VOL. 58
et al. 1995; Parker and Partridge 1998; Owens et al.
1999), whereas other studies failed to find correlations
between measures of sexual selection and diversification rates (e.g., Gage et al. 2002; Morrow and Pitcher
2003; Morrow et al. 2003).
Here, we use a recent supertree of shorebirds
(Charadriiformes) to investigate the correlation between speciation rate and sexual dimorphism. Thomas
et al. (2004) constructed a complete supertree of all 350
shorebird species. Although complete, this tree lacks
resolution among many of the terminal clades, with
large polytomies including up to 50 species. For each
polytomy, we collapsed all species descended from any
lineage within the polytomy into a terminal unresolved
clade (Fig. 7). The resulting tree had 134 tips (with the
215 unresolved species included in 14 unresoved terminal clades). Many of the branch lengths in this tree
are not strictly proportional to time, which reduces the
information about extinction rates available in the tree.
We used a database of bird traits with separate
measurements for males and females of body mass,
wing length, tarsus length, bill length, and tail length
(Lislevand et al. 2007). For each trait, we computed a
standardized measure of dimorphism as (xm − xf )/ˉx,
where xm and xf are the trait values in the males and
females, respectively, and xˉ is the mean of the male and
female values. We regarded species as dimorphic if the
absolute value of this dimorphism measure was greater
than some threshold value for at least one of the five
traits. This data set did not include state information for
77 species (22%). These were treated using the methods
described in the Incomplete Character State Knowledge
section.
Although the general form of the marginal posterior
distributions was well characterized after 10,000 steps
of the MCMC algorithm, it was difficult to characterize
some of the peaks in the multimodal posterior distributions. To improve resolution, we ran eight independent
MCMC chains for 100,000 iterations. The precise credibility intervals changed slightly, but not our general
conclusions.
The relationship between sexual dimorphism and
speciation and diversification rates depended on the
threshold difference in body size used. For low to
medium thresholds of sexual dimorphism (≤15%), the
maximum likelihood and mean posterior probability
speciation and diversification rates were higher for sexually dimorphic lineages than monomorphic lineages
(Fig. 8). In contrast, for very high thresholds (20%), the
diversification rate for dimorphic species was lower
than that of monomorphic species. The difference was
supported by high posterior probability values only
for the 15% threshold. The maximum likelihood extinction rate and the mode of the posterior probability
distribution was generally zero for both character states
across all threshold values examined. We found that
character transition rates from sexual dimorphism to
monomorphism were higher than the reverse across
most thresholds used (Fig. 8), with this difference being
most pronounced at 15% (significant at the 5% level for
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FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
605
FIGURE 6. Uncertainty around diversification rate estimates as a function of phylogenetic knowledge. Panels a and b show the net diversification rate in state 0 (λ0 − μ0 ), panels c and d show the net diversification rate in state 1 (λ1 − μ1 ), and panels e and f show the relative
diversification rate, rrel . See Fig. 5 for details.
the 10% and 15% thresholds). It is perhaps not surprising that the choice of threshold has such an effect, as the
dimorphic state becomes rare as the threshold is raised,
and the rarer a state the more likely its diversification
rate would be biased downward.
As with previous studies, our results suggest that
evidence for a correlation between sexual dimorphism
and diversification rates is mixed at best (Barraclough
et al. 1995; Parker and Partridge 1998; Owens et al. 1999;
Gage et al. 2002; Morrow and Pitcher 2003; Morrow et al.
2003). However, rather than dividing groups arbitrarily
into clades that have just one character state (e.g.,
Barraclough et al. 1995), our approach allowed us to
make use of all of the available phylogenetic and character state information.
D ISCUSSION
In this paper, we have developed two methods for estimating the effect of a trait on speciation and extinction rates from incomplete and incompletely resolved
phylogenies. Testing these methods with simulations, it
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F IGURE 7. (Continued)
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FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
was possible to estimate diversification rates from even
poorly sampled phylogenies (Fig. 6). Where trees were
simulated with equal speciation rates, there was little increase in uncertainty in the estimates of differential diversification with decreasing phylogenetic information,
even when as few as 20% of species were phylogenetically placed. This is surprising because terminally unresolved trees lack much of the fine branching structure
present at the tips of a completely resolved phylogeny
(Fig. 1). However, the power to detect differences in individual parameters depended more strongly on phylogenetic structure.
Because the terminally unresolved clade method uses
the branching structure available to the skeletal method
(for a given number of tips in a tree), differences between these two methods are due to the additional
information about the placement of the missing taxa
in the terminal unresolved clades. In cases where a
given species sample can be reasonably assumed to be
a random draw from all extant species, the skeletal tree
method provides a simple way of estimating speciation
and extinction. In particular, the phylogenetic relationships and character states of nonsampled species do
not need to be incorporated. Where phylogenies are
almost complete, the loss of power using this method
is fairly low. For poorly sampled phylogenies (fewer
than 25% species included in our 500 species phylogenies), the uncertainty around parameters became very
large to the point where inference was not possible
(Figs. 5–6).
The terminal unresolved clade approach can avoid
most of this loss of power, provided all species not
included in the phylogeny can be grouped into terminally unresolved clades. The effect of including the
terminally unresolved clades was strongest for the character transition rates (q01 and q10 , Fig. 5), and it allowed
detection of differential diversification on poorly sampled trees (Fig. 6). However, the terminally unresolved
tree method can only be used where every species can
be assigned to a terminal unresolved clade. Deeper
phylogenetic uncertainties such as unresolved paraphyletic groups have not yet been incorporated, and
some known phylogenetic information may need to be
discarded to use the current methods by including only
terminal unresolved clades (see Fig. 1d). This method
is also substantially more computationally demanding than the skeletal tree approach and is limited at
present to unresolved clades that contain fewer than
approximately 200 species. With 200 species, there are
more than 20,000 possible clade compositions (numbers of species in each state), and even with modern
matrix exponentiation techniques, the calculations become both very slow and prone to numerical underflow
(Sidje 1998).
607
Missing data and incompleteness are generally unavoidable in comparative macroevolutionary analyses.
Frequently, phylogenetic trees will contain species that
are less related than expected by chance to maximize
coverage over the true phylogeny (e.g., Moyle et al.
2009). In these cases, the terminally unresolved tree
method will be appropriate. If a phylogeny is almost
complete, missing only a few taxa, but for which the
placement is uncertain (e.g., the cases considered by
Bokma 2008), the skeletal tree method should be satisfactory (Fig. 5). It may not always be possible to know
with complete certainty where taxa that are not included in a tree should be placed within a terminally
unresolved tree. In this case, one could run an analysis
over possible placements of missing taxa, integrating
over this uncertainty (Lutzoni et al. 2001). It is probably not possible to know in general for cases such as
Fig. 1d whether collapsing known structure into an terminal unresolved clade or treating the tree as a skeleton
tree will suffer the least reduction in power, as these
approaches both lose data. A final caution about the
pattern of missing taxa: outgroups are generally poorly
sampled relative to the ingroup and should be removed
from the tree prior to calculation of likelihoods with
BISSE . Poorly sampled outgroups would certainly violate assumptions of random taxon sampling.
Maddison et al. (2007) tested whether simpler models
may fit the data better by comparing models where rates
were character dependent to simpler models where
rates were character independent (e.g., a model where
/ λ1 to a model where λ0 = λ1 ) using likelihood
λ0 =
ratio tests. Model selection between the full model and
reduced models could also be done in a Bayesian framework using reversible jump Markov chain Monte Carlo
(RJMCMC; Green 1995). RJMCMC alters the Markov
chain to propose different models at some steps, for
example, changing from the full six parameter model
to one of the three simpler five parameter models. The
posterior probability distribution of different models
can then be directly compared. An RJMCMC approach
would provide a natural way of removing parameters
from the analysis where there is little to no phylogenetic
signal (e.g., q01 in the poorly resolved unequal rate tree,
Fig. 5g). This approach has been used successfully elsewhere in phylogenetic inference (e.g., Pagel and Meade
2006).
Using either of the sampling methods explored here,
BISSE likelihoods may be computed for partially complete phylogenies. Future work is needed to handle
much larger unresolved clades (> 200 species) and to
handle orphan taxa, whose phylogenetic position is
deep in the tree and uncertain. Such extensions are
needed to analyze “higher level” phylogenies that are
complete at a taxonomic level above species but contain
FIGURE 7. Phylogenetic tree of the 350 species of shorebirds (Charadriiformes) and measures of sexual dimorphism are based on Thomas
et al. (2004). Gray triangles indicate unresolved clades, with the height of the triangle being proportional to the square root of the number of
species. Character states at the 15% threshold level are indicated at the tips; gray = sexually dimorphic, black = sexually monomorphic, and
white = no data. For clarity, only family or subfamily names are shown.
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FIGURE 8. Marginal posterior probability distributions for the sexual dimorphism-dependent diversification rates (a–d) and character transition rates (e–h) inferred from a supertree of shorebirds (Thomas et al. 2004). Panels in different rows use a different threshold level of sexual
dimporphism to classify species as monomorphic and dimorphic. Solid curves show the distribution for sexually monomorphic species and
dashed curves for dimorphic species. The horizontal bar and point indicate the 95% credibility interval and maximum likelihood estimate.
large numbers of species in their unresolved clades (e.g.,
Davies et al. 2004; Hackett et al. 2008).
Research (R.G.F.) and Discovery Grants from the Natural
Sciences and Engineering Research Council of Canada
(W.P.M. and S.P.O.).
F UNDING
A CKNOWLEDGEMENT
We thank Rick Ree, who initially suggested that we
expand BISSE to account for trees containing
exemplars.
This work was supported by a University Graduate
Fellowship from the University of British Columbia and
the Capability Fund from Manaaki Whenua Landcare
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FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
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Received 30 October 2008; reviews returned 3 March 2009;
accepted 3 September 2009
Associate Editor: Olaf Bininda-Emonds
A PPENDIX 1
Root-State Calculations
At the root, R, we have the two probabilities, DR0 and
DR1 , corresponding to the possible character states at
the root. The overall likelihood must sum over the probabilities that the root was in each state. In Schluter et al.
(1997), the Ds at the root were weighted evenly, which
assumes that the lineage arose out of a group with 50%
of taxa in each state, therefore potentially being out of
equilibrium with the inferred model of evolution. The
model parameters provide some knowledge, however.
For example, if transitions away from character state 0
are much more frequent than the reverse (q01 > q10 ) and
if speciation/extinction rates do not depend strongly
on the character state, then we would expect that the
system is more likely to be in state 1 than in state 0 at
any point in time, including at the root. In Maddison
et al. (2007), the information provided by the model was
used to weight the Ds at the root by the equilibrium
frequencies for the character states given by the model
(following Maddison WP and Maddison DR 2006). This
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VOL. 58
SYSTEMATIC BIOLOGY
implicitly assumes that a sufficient amount of time has
passed prior to the root, so that the root state can be
assumed to be a random draw from an equilibrium distribution. However, this assumption does not account
for cases where the traits are novel or have yet to reach
equilibrium.
Here, we treat the root state as a nuisance parameter (Gelman et al. 1995) and use an alternative root
assignment that weights each root state according to
its probability of giving rise to the extant data, given
the model parameters and the tree. This probability is
given by the likelihood given that the root is in state
i divided by the sum of the likelihoods over both root
states, DRi /(DR0 + DR1 ). The overall likelihood is then as
follows:
DR = DR0
DR0
DR1
+ DR1
.
DR0 + DR1
DR0 + DR1
(10)
As a test case, consider a tree that consists of a single branch with an infinitesimally short branch length
where the single extant taxon is in state 0. Assuming
that none of the transition parameters is very large, then
DR0 is nearly one and DR1 is nearly zero. Assigning the
root state according to the probability of the root leading to the data, as we do in Equation (10), we infer that
there is nearly a 100% probability that the root was in
state 0 and the overall probability of the data given the
model is nearly 1. Assigning the root state uniformly,
we would be assuming that there is a 50% probability
that the root state was 1, even though we know this to
be impossible (more precisely, it has an infinitesimally
small probability of being true given the infinitesimally
short branch and the fact that the single extant taxon
is in state 0). Similarly, assigning the root state according to the equilibrium distribution would give some
nonzero probability to the root being in state 1, unless
q01 = 0.
Furthermore, if there is directional change in the character, assigning the root to the equilibrium distribution
incorrectly forces the character to take on the value that
it will have in the long-term future, not what it is likely
to have been in the past. For example, if all organisms
started in state 0 and are evolving into state 1 (q01 q10 ,
with all else equal), the equilibrium distribution method
will incorrectly assign the root to state 1, even if most extant species are still in state 0. By contrast, assigning the
root states according to their relative likelihoods of explaining the data will assign a high probability on the
root having been in state 0 when most species are in
state 0. Equation (10) has the further advantage that the
only quantities needed for its calculation are DR0 and
DR1 , which are already known once BISSE has traversed
the tree. Goldberg and Igić (2008) have recently explored
the effect of root state on BISSE calculations and found
that they can have a strong effect on conclusions, especially where character change is unidirectional. Our
approach (Equation (10)) can approximate the ancestral
root state and result in reasonable character change rate
estimates for the situations described above. In practice,
sensitivity to the root state is easily detected by comparing DR0 and DR1 .
A PPENDIX 2
Character-Independent Model
When the speciation and extinction rates do not depend on a character, our likelihood calculations reduce
to existing models of character-independent evolution.
Analytical solutions for these models are known, removing the need to use numerical approaches to calculating the likelihoods.
Skeletal trees.—With character-independent speciation
rates, the skeletal tree likelihoods reduce to the method
of Nee et al. (1994). The character-independent analogues of Equation (1) are as follows:
dDN
= − (λ + μ)DN (t) + 2λE(t)DN (t),
dt
dE
= μ − (μ + λ)E(t) + λE(t)2
dt
(11a)
(11b)
(Maddison et al. 2007), where λ and μ are the characterindependent speciation and extinction rates. If a fraction, f , of all species are sampled in the phylogeny, then
the initial conditions are E(0) = 1 − f and D(0) = f . It
is possible to derive an analytical solution to Equations
(11) describing changes along a single branch. Using the
initial condition E(0) = 1 − f , the solution to Equation
(11b) for the extinction rate is as follows:
E(t)=1 −
E(t)=
f (λ − μ)
f λ − e(λ−μ)t (μ − λ(1 − f ))
1 − f + f λt
1 − f λt
if λ = μ.
if λ =
/ μ,
(12a)
(12b)
Substituting Equation (12) into Equation (11a) and
solving for DN (t) gives
DN (t) = e−(λ−μ)(t−tN )
(f λ − e−(λ−μ)tN (μ − λ(1 − f )))2
(f λ − e−(λ−μ)t (μ − λ(1 − f )))2
× DN (tN ) if λ =
/ μ,
DN (t) =
(1 + f λtN )2
DN (tN )
(1 + f λt)2
(13a)
if λ = μ,
(13b)
where tN represents the time depth (since the present)
of node N. Equations (12) and (13) reduce to Equations
(9) and (10) in Maddison et al. (2007) if sampling is complete (f = 1).
These equations can be used as in Maddison et al.
(2007) to compute the likelihood for the entire
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611
FITZJOHN ET AL.—TRAIT-DEPENDENT SPECIATION AND EXTINCTION
phylogeny:
DR (tR ) =
" 2n
Y
and us (t) is
us (t) = 1 −
e−(λ−μ)(tk,b −tk,t )
k=1
×
f λ − e−(λ−μ)tk,t (μ − λ(1 − f ))
f λ − e−(λ−μ)tk,b (μ − λ(1 − f ))
" 2n
#
Y (1 + f λtk,t )2
DR (tR ) =
λn
(1 + f λtk,b )2
2 #
λn
if λ =
/ μ,
(14a)
if λ = μ
(14b)
k=1
where tk,b and tk,t are the times at the base and tip of the
kth branch, respectively, and the product is taken over
all 2n branches for a tree containing n nodes.
Equation (14) is consistent with the results from Nee
et al. (1994) for the character-independent case. Nee
et al. (1994) does not explicitly give equations for the
probability of a sampled phylogeny, given a speciation
rate, extinction rate, and sampling probability, so we
state them here. Using the notation of Nee et al. (1994),
the probability of the data is as follows:
L = (N − 1) ! f
N−2 N−2
λ
× (1 − us (x2 ))
N
Y
Ps (ti , T)
i=3
2
N
Y
i=3
(1 − us (xi )),
!
where N is the number of tips in the phylogeny, xi is the
time between the present and the node that splits the
phylogeny into i branches (so that x2 is the distance to
the root), Ps (ti , T) is the probability that a lineage originating at time ti leaves at least one descendant at the
present, time T (given by Nee et al. 1994, equation (34)),
1−a
,
−a+1−f
(16)
where a = μ/λ and r = λ−μ. Equation (16) can be derived
from equations (29) and (33) in Nee et al. (1994). After
some algebra, equation (14a) can be shown to be equal
to equation (15), after conditioning on the existence of
a root node and two surviving lineages (see Maddison
et al. 2007 for similar calculations with f = 1).
Terminally unresolved trees.—To calculate the likelihood
for terminally unresolved trees, we must first calculate
the probability of unresolved clades given the speciation and extinction rates. We could rederive Q and ~x,
ignoring character state changes, which now do not affect diversification, and use Equation (3) to compute the
probability of the clade. However, without transitions,
this can be viewed as a birth–death process for which an
analytical solution is available. The probability of k lineages arising and surviving to the present from a single
ancestor over a period of time t is given by Nee et al.
(1994):
P(k, t) =
(15)
f
erxi
P(k, t) =
λ−μ
(1 − u(t))u(t)k−1 ,
λ − μe−(λ−μ)t
(tλ)i−1
,
(1 + tλ)i+1
k > 0, λ = μ,
k > 0, λ =
/ μ,
(17a)
(17b)
where u(t) is us (t) from Equation (16) with f = 1. If an
unresolved clade has n species and originated at time
tN , then P(n, tN ) can be used for DN (tN ) in Equation
(9) of Maddison et al. (2007). This approach has been
used by Rabosky et al. (2007) to estimate speciation
and extinction rates from a terminally unresolved lizard
phylogeny.
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