Molecular Ecology (2009) 18, 41374139

NEWS AND VIEWS

PERSPECTIVE 1997; Sullivan & Swofford 1997; Posada & Crandall 2001;
Posada & Buckley 2004; Sullivan & Joyce 2005; Posada
Expanding the toolbox for 2008). A hallmark of this statistical approach is that verbal
phylogeographic analysis hypotheses represented as mathematical models are evalu-
ated for fit to observed data (Burnham & Anderson 2002).
J E R A L D B . J O H N S O N and K E I T H A . This allows researchers to simultaneously evaluate multiple
CRANDALL hypotheses, shifting the focus away from accepting or
Department of Biology and Monte L. Bean Life Science rejecting a single null hypothesis, and towards comparing
Museum, Brigham Young University, Provo, UT 84602, USA the relative strength of support for competing explanations.
Received 14 July 2009; revision received 19 July 2009; accepted Successful application of model selection relies on carefully
23 July 2009 articulating an a priori set of hypotheses that can be repre-
sented as mathematical equations and that can be fit to
observed data, often using a maximum likelihood
approach in an information theoretic framework or using a
Phylogeography has emerged over the last two decades as
Bayesian framework. The key challenge is defining the can-
an exciting and informative field that spans the chasm
didate set of hypotheses and ensuring that the parameters
between population genetics and systematics. Population
and model construction accurately reflect the verbal con-
genetics has traditionally been interested in the processes
structs. Multi-model inference is an extension of model
of evolution, including estimates of associated parameters
selection wherein the relative importance of different
such as migration rates, genetic diversity, and measures of
parameters can be determined (e.g. base frequency differ-
selection; systematics has focused on historical patterns of
ences vs. transition transversion differences in models of
divergence and associated morphological, temporal, and
molecular evolution). Clearly, this statistical approach
ecological changes correlated with such patterns. Phyloge-
could have important application in the field of phylogeog-
ography attempts to merge these perspectives and capital-
raphy, where several historical scenarios might explain cur-
izes on gene divergence patterns and their fit to
rent patterns of spatial genetic variation within species
predictions derived from different models in population
with associated differences in historical and current param-
genetics. The seminal work of Avise et al. (1987) ushered
eter estimates (e.g. migration rates or genetic diversity).
in this approach to merging concepts from these two fields
The application of model selection by Carstens et al.
to study speciation and population divergence (Hickerson
(2009) illustrates the potential utility of this approach in
et al. 2009). Over the past two decades, an impressive set
phylogeography. In their study, these authors use multilo-
of analytical tools have been developed with advances in
cus data from a species of salamander from the Pacific
both population genetics and phylogenetics that have had
Northwest (Fig. 1) to rank 17 different models to explain
a significant impact in phylogeography (Pearse & Crandall
2004; Excoffier & Heckel 2006; Kuhner 2009). Yet phyloge-
ographers still face a fundamental question of whether
they are testing a priori hypotheses associated with the
species in question, estimating important population
genetic parameters of interest, developing post hoc hypothe-
ses of divergence, or attempting to distinguish among an
array of alternative models to explain the observed data
from the population(s) of interest (or some combination of
any or all of these). In this issue of Molecular Ecology, Car-
stens et al. (2009) advance the use of model selection and
multimodel inference as a means of exploring alternative
models of phylogeographic patterning and thereby add sig-
nificantly to the phylogeographers toolbox.
Model selection is currently enjoying increased use in
several biological disciplines (Johnson & Omland 2004);
many readers of this journal will be aware of its applica-
tion in molecular systematics (Huelsenbeck & Crandall
Fig. 1 Image of the salamander Plethodon idahoensis, a species
Correspondence: Jerald B. Johnson, Fax: 801-422-0090; distributed throughout the northern Rocky Mountains of North
E-mail: jerry.johnson@byu.edu America.

 2009 Blackwell Publishing Ltd

4138 N E W S A N D V I E W S : P E R S P E C T I V E
evolutionary processes impacting this species. Interestingly,
their two best-fitting models showed comparable support,
but differed dramatically from one another: one incorpo-
rates migration and the other does not (with implications
for determining divergence times). Consequently, the
authors used simulation to demonstrate that migration or
incomplete lineage sorting probably best explained their
results. Carstens and colleagues suggest that model selec-
tion is useful when historical data are not available to gen-
erate hypotheses. However, practitioners in other
disciplines argue against deploying model selection with-
out first justifying a biologically plausible set of competing
models. Failure to do so amplifies the risk of favoring
trivial hypotheses, especially when all possible (rather
than plausible) models are consideredan activity some
have referred to as a form of data dredging (Burnham &
Anderson 2002).
The use of model selection in phylogeography is prom-
ising and adds significantly to the phylogeographers tool-
box. Model selection provides a clean and efficient way to
evaluate multiple competing models. It also provides a
mechanism to estimate the values of parameters that com-
pose these models, in the case of Carstens and colleagues
these include divergence time, migration rates, and
genetic diversity. Curiously, in this study, the authors did
not find good discrimination between alternative models
that differed greatly in their associated migration rate
parameters. Models with poor fit to the data (those
rejected without the Bonferroni correction) had equal lev-
els of ancestral to current genetic diversity, whereas those
models with good fit to the data showed an increased
level of current genetic diversity compared to ancestral
diversity. However, the models examined here treat the
multi-locus data as if they have the same history (e.g.
providing a single genetic diversity estimate), yet we
know that mtDNA and nuclear genes can have very dif-
ferent histories (e.g. Shaw 2002) and averaging these his-
tories might not be advisable under such circumstances.
Thus, a limitation of the model selection approach as cur-
rently employed here is that the models remain narrowly
definedeach model included in the candidate set
assumes only two populations, no recombination, constant
migration, and constant population sizes (albeit a different
ancestral population size). Other phylogeographic meth-
ods allow for more flexibility, including divergence time
estimation and fluctuating population sizes (e.g. BEAST
Drummond et al. 2005) or partitioning of historical
impacting events across time and space (e.g. NCPA Tem-
pleton 2008). Hence, this study exposes a need for the
candidate set of models to reflect the full spectrum of
evolutionary processes that the phylogeographer might
want to consider.
The application of model selection in phylogeography
will inevitably stir discussion about the appropriateness of
different analytical approaches. The ongoing philosophical
debate about the appropriateness of post hoc inferences vs.
a priori null hypotheses might be supplanted by adopting
a model selection framework. For example, a strength of
post hoc inference is that these approaches generate testable
hypotheses that can be used to generate a candidate set of
competing models. A priori null hypotheses are valuable
in experimental settings, but are often of more limited use
in historical studies. For example, researchers often sup-
pose that rejecting a null hypothesis (usually one without
any biological meaning) lends credence to its alternative,
when in fact rejecting the null tells us nothing about the
relative support for the alternative. What we really want to
know is the degree of confidence that we can place in a
particular hypothesis, which is exactly the strength of the
model selection framework.
Carstens and colleagues deserve praise for moving
model selection further into mainstream phylogeography.
The challenge now is for researchers to build upon this
promising start. We still lack a cohesive framework for
model construction in phylogeography. Converting verbal
hypotheses of migration, changes in population size over
time, local extinction, recolonization, and all other poten-
tially important demographic processes into mathematical
models remains a formidable task. Equally important is the
implementation of these mathematical models into useful
software programs. However, once these challenges are
met we anticipate an important paradigm shift will occur
in phylogeographic analysis, resulting in more complete
understanding of the influence of past events on current
patterns of genetic diversity. Hence, although the applica-
tion of model selection by Carstens and colleagues is lim-
ited in scope, it offers a clear framework for moving
forward. This is an exciting advance that deserves
attention.
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