Phylogeography
KA Marske, Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen, Denmark
r 2016 Elsevier Inc. All rights reserved.
Glossary
Alpha-diversity Species richness, or the number of species
present at a location; a measure of biological diversity
(biodiversity).
Beta-diversity Species turnover between locations, or the
number of species present at one location which are not
present at the second; a measure of biological diversity
(biodiversity).
Coalescent The population genetic theory by which all
alleles present in an extant population trace their genealogy
back to a shared ancestor at some point in time.
Genetic drift The random change in frequency of alleles
within a population.
Glacial refugia A contraction in a species’ geographic
range during glacial conditions, often resulting in a genetic
Integrating Across Disciplines
Avise et al. (1987) originally envisioned phylogeography – the
study of the geographical context for genetic variation within
species – as a bridge between the processes acting on popu-
lations (e.g., genetic drift and selection) and supra-specific
evolutionary patterns (see Figure 1). Since its inception, phy-
logeography has rapidly grown in popularity, resulting in a
vast quantity of data from a myriad of taxa and environments,
a blossoming of methods to analyze those data, and con-
ceptual links with disciplines across evolution, ecology, and
earth and climate sciences, making phylogeography "one of
the most integrative disciplines in all of biology" (Hickerson
et al., 2010). Phylogeographic studies have facilitated a deeper
understanding of the prevalence of gene flow among spatially
structured populations (Knowles and Carstens, 2007); the
prevalence of cryptic diversification within species (Martin and
McKay, 2004); the complex roles of refugia, persistence, and
dispersal in shaping species’ geographic ranges after the last
glacial period (Moritz et al., 2009; Dasmahapatra et al., 2010);
and invaluable perspectives on genetic evolution (Singhal and
Moritz, 2012). Multi-taxon comparative phylogeography
studies have indicated the pervasiveness of idiosyncratic re-
sponses to past events among even co-distributed species with
apparently similar ecologies, providing important insights into
dispersal, adaptation, and other factors which mediate these
differences (Taberlet et al., 1998; Bell et al., 2012; Marske et al.,
2012). Like all popular disciplines, phylogeography has also
been the subject of pointed critique, particularly directed at the
initially descriptive way in which phylogenies were related to
historical events (Soltis et al., 2006). This criticism – while
largely warranted – sparked an explosion of analytical devel-
opment and synthesis with nongenetic methods which have
left phylogeography well placed to remain highly relevant to
our understanding of questions as varied as speciation and
Encyclopedia of Evolutionary Biology, Volume 3 doi:10.1016/B978-0-12-800049-6.00109-8
bottleneck; that part of the range in which
suitable environmental conditions allow a species to persist
until conditions improve.
Macroecology The discipline which investigates ecological
patterns and processes across multiple study systems or at
large spatial scales, to identify general rules governing the
distribution of biological diversity.
Macroevolution Evolutionary patterns and processes
detectable at the species level or above, or the study
thereof.
Microevolution Evolutionary patterns and processes
detectable within species, or the study thereof.
Phylogeography The discipline which investigates how
genetic diversity within species is related to geography and
geological events.
evolution to ecosystem stability and species responses to cli-
mate change.
History and Development
Avise et al. (1987) coined the term ‘intraspecific phylogeo-
graphy’ after observing that genetic discontinuities for multiple
North American fishes corresponded with long-term geographic
barriers, and described intraspecific phylogeographic structure
as a function of geographic isolation and species’ dispersal
ability. As well as launching the nascent discipline of phylo-
geography, their foundational paper elucidated two guiding
principles which formed the basis for subsequent study: First,
Avise et al. (1987) recognized that phylogeography represented
the theoretical evolutionary link necessary to infer species’ his-
tories across timescales, from population genetic patterns to
phylogenetic systematics, and proposed that these micro-
evolutionary processes reflected – and could predict – macro-
evolutionary phenomena. Second, phylogeography was
presented from the very beginning as a comparative endeavor,
namely, that “strong geographic barriers should mold the gen-
etic structure of independently evolving species in concordant
fashion” (Avise et al., 1987). A decade after its inception,
Bermingham and Moritz (1998) implicitly underscored these
two principles when they predicted that continued progress
within comparative phylogeography would allow ‘investigation
of the fundamental links between population processes and
regional patterns of diversity and biogeography.’
A third feature which has characterized many phylogeo-
graphic studies from the beginning is a focus on Pleistocene
processes and glacial refugia (reviewed by Hewitt, 1996;
Taberlet et al., 1998). Avise et al. (1987) never characterized
their phylogeographic patterns in terms of glaciation – they
described “long-term, extrinsic (i.e., zoographic) boundaries to
291
292 Phylogeography
Populations
Landscape genetics
Population genetics
Community ecology
Populations to species
Phylogeography
Dispersal Vicariance
Isolation Gene flow
Demography
Species and higher taxa
Phylogenetic systematics
Historical biogeography
Macroecology and macroevolution
Figure 1 Phylogeography was originally envisioned as the
conceptual bridge connecting processes acting on populations with
evolutionary patterns detectable among species or higher taxa (Avise
et al., 1987). Implicit within this conceptualization is a temporal and
spatial component, with population-level processes acting over shorter
periods and smaller spaces but scaling up to historical biogeographic
and macroecological patterns, which reflect deeper evolutionary
history acting at a broader spatial scale. Thus, the population-level
patterns detected using phylogeography are at the center of a
continuum of ecological and evolutionary processes (Marske et al.,
2013). Adapted from Avise, J.C., 2009. Phylogeography: Retrospect
and prospect. Journal of Biogeography 36, 3–15.
gene flow”; rather, this focus evolved as a natural result of the
temporal span encompassed by intraspecific variation in mito-
chondrial DNA (mtDNA), upon which phylogeography was
initially based (Avise et al., 1987; Bermingham and Moritz,
1998). In their comparative syntheses of the effects of Quater-
nary glaciation on genetic diversity within Europe, Hewitt
(1996, 2000) and Taberlet et al. (1998) emphasized both
the idiosyncratic histories of individual species, and similar
patterns of range expansion out of the peninsular refugia (the
“southern richness, northern purity” pattern; Hewitt, 2000)
with predictable suture zones where expanding lineages met.
Based on these patterns, Taberlet et al. (1998) hypothesized that
while phylogeographic congruence might occasionally occur
within restricted areas, it was highly unlikely across large spatial
scales, such as continents. Subsequent studies confirmed these
patterns: Sullivan et al. (2000), in one of the first studies which
explicitly tested a priori phylogeographic hypotheses, found
that phylogeographic histories of two rodent taxa in a geo-
logically complex region were neither entirely unique nor
identical, but somewhere in between. In a later synthetic an-
alysis of multiple North American taxa, Soltis et al. (2006)
warned of the risk of pseudocongruence, where similar spatial
patterns are driven by causal factors across different timescales.
They also suggested that pseudocongruence might stem, in part,
from the tendency among researchers to visually interpret and
categorize phylogeographic patterns across species (Soltis et al.,
2006; but see Pyron and Burbrink, 2010), echoing a growing
number of critics demanding a higher level of rigor in the
testing of phylogeographic scenarios (Edwards and Beerli, 2000;
Knowles and Maddison, 2002; Carstens et al., 2005; Kidd and
Ritchie, 2006).
One response to this criticism was the adoption of stat-
istical phylogeographic methods, such as ancestral state re-
construction, which directly estimates the geographic locations
of ancestral populations (Lemmon and Lemmon, 2008;
Lemey et al., 2009; Nylinder et al., 2014), or model selection
methods, which provide statistical support for explicit phylo-
geographic hypotheses (e.g., Carstens et al., 2005; Hickerson
et al., 2006; Chan et al., 2014; Pelletier and Carstens, 2014),
mostly using an approximate Bayesian computational frame-
work (Beaumont et al., 2002). A key motivating factor driving
the development of these methods and their implementation
within a coalescent framework (e.g., Rosenberg and Nordborg,
2002) was the realization that stochastic, as well as de-
terministic, processes had left their mark on species’ geneal-
ogies and hence, phylogeographic patterns (Edwards and
Beerli, 2000; Arbogast et al., 2002; Knowles and Maddison,
2002; Carstens et al., 2005). These stochastic processes can
result in discordant diversification among genetic loci, re-
sulting in gene trees which do not reflect the species tree
(Arbogast et al., 2002). Statistical phylogeography has thus
promoted both the widespread adoption and further devel-
opment of coalescent tools and the increasing prevalence of
multi-locus datasets within phylogeography (Knowles, 2009).
A second response to criticism was to explicitly or implicitly
associate genetic data with other information sources, such as
species distribution models (SDMs), to validate phylogeo-
graphic patterns (Kidd and Ritchie, 2006; Richards et al., 2007;
Kozak et al., 2008). SDMs, which predict species’ geographic
distributions by relating collection localities to environmental
data (Hugall et al., 2002; Richards et al., 2007), were first
combined with phylogeography to test whether glacial refugia
identified by genetic data coincided with areas of long-term
climatic stability (Hugall et al., 2002). SDMs are now hugely
popular within phylogeography as a means of providing in-
dependent support for phylogeographic scenarios (Waltari
et al., 2007; Alvarado-Serrano and Knowles, 2014). Further,
the two avenues of statistical phylogeography and independ-
ent verification with SDMs very quickly converged, with SDMs
generating explicit spatial hypotheses (Richards et al., 2007;
Carnaval et al., 2009), testing for potential environmental di-
vergence underlying genetic differentiation (McCormack et al.,
2010), or setting the baseline conditions for direct simulations
of species’ histories under different dispersal scenarios (Brown
and Knowles, 2012).
Current Status
Phylogeography provides a hypothetical framework with
which to test the processes underlying diversification,

providing invaluable insights into how biodiversity is gener-
ated and maintained. As such, the questions currently ad-
dressed by phylogeography cover the full spectrum of ecology
and evolution. A tremendous body of data across a variety of
taxa and systems, from relatively easily sampled regions such
as North America (Soltis et al., 2006) to the farthest reaches of
the globe, including Antarctica and the sub-Antarctic islands
(Fraser et al., 2012), suggest a myriad of responses to past
climate change and other geological events. Notably, the late
Quaternary history of many species was characterized by per-
sistence in relatively small, isolated refugia (e.g., Carnaval
et al., 2009; Moritz et al., 2009), many of which preserved
evidence of much deeper divergence than just the last glacial
period (Marske et al., 2011; Bell et al., 2012). Many studies
have also yielded a much deeper understanding of dispersal,
ranging from persistence in dynamic landscapes which func-
tion as temporally shifting habitat mosaics (Brown and
Knowles, 2012), to movement through intermittent or leaky
dispersal barriers (Burridge et al., 2008; Marske et al., 2009) to
how dispersal potential relates to life history traits (Dawson,
2014). In spite of these dramatic changes in environment and
species’ geographic ranges, phylogeographic studies have
largely discounted Late Pleistocene events as significant for
initiating speciation (Bermingham and Moritz, 1998), but
have illuminated other, older drivers of the speciation process,
in conjunction with a variety of phylogenetic methods (Kozak
et al., 2005, 2006).
Phylogeography has also yielded insights into the origin
and maintenance of regional to global biodiversity patterns,
such as the distribution and drivers of alpha- and beta-diver-
sity and the extent to which genetic diversity reflects these
species-level patterns. For example, Martin and McKay (2004)
proposed that if the global latitudinal diversity gradient results
from higher rates of species origination at lower latitudes,
genetic divergence among populations within species should
be greater at the lower latitude portion of species’ ranges. They
synthesized data for 60 vertebrates from regions across the
globe, and found that lower latitude populations do experi-
ence greater evolutionary independence, even when control-
ling for geographic distance and recent glacial activity (Martin
and McKay, 2004). Dexter et al. (2012) sampled community
composition and population genetic data for a genus of tro-
pical trees along a transect in Amazonian Peru, and found that
an ecological pattern of distance decay in compositional
similarity masked a zone of heightened turnover where species
expanding from separate refugia came into secondary contact,
signifying the necessity of accounting for both contemporary
and historical processes when examining the mechanisms
behind biodiversity patterns. Finally, Emerson et al. (2011)
have proposed using bulk genetic extraction techniques to
simultaneously infer comparative phylogeography, historical
biogeography, and phylogenetic beta-diversity among com-
munities of soil invertebrates, using DNA barcodes to directly
sample community composition for each soil sample rather
than trying to demarcate community boundaries a priori.
Numerous phylogeographic studies have also sought to
elucidate the processes shaping species’ contemporary geo-
graphical ranges. In particular, the central-marginal or abun-
dant center hypothesis states that species should achieve
highest abundance at the range core where conditions are most
Phylogeography 293
optimal, with populations growing smaller and more isolated
toward the range margins (Hengeveld and Haeck, 1982;
Brown, 1984; Brussard, 1984). Therefore, genetic diversity and
gene flow should be highest at the center of a species’ range,
with peripheral populations exhibiting less diversity but
higher differentiation from each other and from the core
(Eckert et al., 2008). In a synthetic study incorporating popu-
lation genetic data spanning the ranges of 115 taxa (animals
and plants), Eckert et al. (2008) detected this pattern, but
found that the difference in genetic diversity was relatively
small. Notably, relatively few of the studies they included in-
corporated a phylogeographic perspective or invoked historical
mechanisms, which Eckert et al. (2008) suggested might
underlie the relatively weak support for the central-marginal
hypothesis. Johansson et al. (2013) revisited the central-
marginal hypothesis in a phylogeographic study of five Euro-
pean damselfly species, and found no general adherence to the
patterns described above; rather, they found that genetic pat-
terns were better explained by historical and contemporary
ecological factors. Moritz et al. (2012) went a step further and
explored whether variation in environmental conditions across
the ranges of three skink species had resulted in different se-
lection regimes between central and marginal populations.
They found that the marginal populations were both physio-
logically differentiated from the core populations, and pos-
sessed thermal adaptations which might make them more
likely than the core populations to adapt to and persist under
contemporary climate change (Moritz et al., 2012).
Other studies have centered on the formation of range
margins, with a particular focus on where phylogeographic
breaks, or points of spatial turnover between phylogeographic
lineages, are shared across species. For example, Rissler and
Smith (2010) tested whether phylogeographic breaks clustered
together at contact zones between species as predicted by
Taberlet et al. (1998) and Hewitt (2000), using available data
for North American amphibians. They found significant clus-
tering of phylogeographic breaks and contact zones in regions
of known amphibian species richness, and highlighted these
areas as important natural laboratories for further investigating
the speciation process (Rissler and Smith, 2010). Moritz et al.
(2009) focused on the Australia Wet Tropics, a narrow habitat
corridor which forms a natural transect connecting regions of
long-term climatic stability, to test the roles of historical versus
contemporary climate conditions in driving diversification
among lineages. They found that the majority of phylogeo-
graphic breaks occurred within a suture zone between two
glacial refugia, but within this zone, individual phylogeo-
graphic breaks occurred in areas of relatively low con-
temporary environmental suitability (Moritz et al., 2009). In
contrast, Dasmahapatra et al. (2010) detected suture zones
which, while shared across multiple Amazonian butterflies,
failed to correspond to expectations based on several bio-
geographic hypotheses. They suggested that these zones might
instead reflect contemporary ecological conditions, with mul-
tiple phylogeographic breaks shifting independently and be-
coming stuck on a common ‘ecological hiatus’ (Dasmahapatra
et al., 2010).
Phylogeographic studies have also generated a wealth of
insight on modes of diversification and speciation. Allopatric
divergence is regarded as one of the most common modes of
294 Phylogeography
speciation (Coyne and Orr, 2004), and Pyron and Burbrink
(2010) explored how allopatry around hard physical barriers
versus environmental gradients has produced distinctly dif-
ferent phylogeographic patterns. They proposed that lineages
should show strong concordance in the location of the phy-
logeographic break in cases of ‘hard allopatry’ around hard
physical barriers, while break points might be more scattered
where ‘soft allopatry’ reflects historical climatic disjunctions or
environmental gradients. A synthetic study of genetic dis-
continuities around the Mississippi River Embayment and
Cochise Filter Barrier in North America confirmed these pre-
dictions, as well as clarifying the temporal distribution of
lineage breaks associated with each type of allopatry: under
soft allopatry, divergence coincided with the timing of climate
change, whereas under hard allopatry, divergence was
dependent upon rare dispersal events across the barrier, and
was therefore taxon specific rather than temporally clustered
(Pyron and Burbrink, 2010). Jordal et al. (2006) utilized
phylogeography to explore a putative case of sympatric spe-
ciation between two Canary Islands beetles. Rather than a
sympatric origin, however, they found that the taxa likely di-
verged on separate islands before coming into secondary
contact on La Palma, highlighting that contemporary sympatry
does not rule out previous opportunities for allopatric phases
of diversification (Jordal et al., 2006). The mechanisms driving
ecological speciation are more controversial than those for
allopatric speciation, with disagreement over whether di-
vergent natural selection leads to (Schluter, 2001) or follows
(Wiens, 2004) speciation. McCormack et al. (2010) investi-
gated whether allopatric lineages of Aphelocoma jays in the
process of speciation were more different than expected based
on a null model, and found little evidence for ecological di-
vergence except in lineages which exist in partial sympatry. In
contrast, Cooke et al. (2012) found that neutral and selected
genetic divergence in Amazonian fish was more strongly dri-
ven by water color than either river system or biogeographic
history. Further, they found that both selection and neutral
population structure were heightened at the environmental
interface between water types, providing strong evidence for
environmental, rather than allopatric, divergence (Cooke et al.,
2012). These studies, and those detailed above, represent but a
small sample of the diverse ecological and evolutionary in-
sights stemming from phylogeographic studies, and these data
still retain immense potential for broad-scale ecological and
evolutionary synthesis (Bermingham and Moritz, 1998;
Marske et al., 2013).
Challenges and Future Directions
Numerous analytical challenges remain within phylogeo-
graphy, such as the impact of parameter selection (e.g.,
Carstens et al., 2013), model specification (e.g., Pelletier and
Carstens, 2014), or underlying theoretical assumptions (e.g.,
Chikhi et al., 2010; Heller et al., 2013) on phylogeographic
inference. One persistent analytical challenge is a dearth of
methods which can directly deal with community-level data,
and with the notable exception of hierarchical approximate
Bayesian computation (Hickerson and Meyer, 2008), com-
parative phylogeography typically consists of inferring
individual species histories and comparing them post-hoc
(Andrew et al., 2013). One reason is the computational chal-
lenge of dealing with large comparative datasets (Andrew et al.,
2013), but the more critical aspect is conceptual: an increasing
number of studies indicate that co-distributed species often
exhibit consistent – but not concordant – phylogeographic
histories (Taberlet et al., 1998; Sullivan et al., 2000; Soltis et al.,
2006; Moritz et al., 2009; Bell et al., 2012; Marske et al., 2012).
This may be related to the methods with which species’ his-
tories are estimated: for example, detailed spatially explicit
simulations of range expansion (e.g., Brown and Knowles,
2012) or estimated dispersal routes leading out from multiple
refugia (e.g., Marske et al., 2012); repeated across multiple
taxa, may be more likely to highlight differences between
species’ histories, even where similarities exist. In contrast,
methods which rely upon summary statistics to test specific
hypotheses of population size changes (e.g., Chan et al., 2014)
can classify histories as similar or different, but lack the spatial
component which might tie together divergence events on
different timescales. These alternate views have implications
for interpretation of community assembly and stability over
time (i.e., Taberlet et al., 1998); for example, most species
likely have idiosyncratic histories, but the regional species pool
may have behaved in a more predictable way (Zink, 2002;
Marske et al., 2013). A more nuanced analytical approach is
needed to integrate these individual histories into a model of
community evolution.
The data challenge – what types of data are most appro-
priate and how best to procure them – remains one of the
longest-running conversations within the phylogeographic
community. Avise et al. (1987) first envisioned phylogeo-
graphy as the ‘mtDNA bridge’ between evolutionary discip-
lines, but relatively early on, Bermingham and Moritz (1998)
highlighted the rich potential for large-scale, multi-locus
comparative studies to tease apart evolution across timescales.
Adoption of coalescent methods quickly identified a weakness
inherent to many phylogeographic datasets, that mtDNA often
lacked sufficient resolution for robust parameter estimation
(Edwards and Beerli, 2000; Carstens and Knowles, 2007), but
gave rise to a variety of methods which integrate information
across multiple loci to estimate divergence history while ac-
counting for stochastic genetic processes (Knowles, 2009). In
that same vein, one of the greatest contemporary challenges in
phylogeography – and one of the areas with greatest promise –
is how to best make use of high-throughput sequencing
technologies. To date, the major hurdles have included de-
signing data capture in a way relevant for phylogeography,
developing the informatics pipeline to process the data, and
finding the right balance between spatial sampling and se-
quencing depth of individuals and populations (Carstens
et al., 2012; Lemmon and Lemmon, 2012; McCormack et al.,
2012; Andrew et al., 2013; O’Neill et al., 2013). Once these
challenges are addressed, the pitfalls and promises are the
same – how best to glean maximum evolutionary and eco-
logical insight from the data available.
This new era in phylogeography, in which data acquisition
is no longer a significant limiting factor on experimental
design, offers unprecedented opportunity for creating new
syntheses across disciplines and exploring creative new ques-
tions at the interface of ecology and evolution. Data-rich,

geographically comprehensive comparative studies within and
between regions and taxonomic groups, currently the purview
of macroecology and macroevolution, can tackle issues like
diversification and community assembly and significantly
contribute to our understanding of the organization of bio-
diversity. As new genomic sequencing methods erode the
distinction between model and non-model organisms, the
tantalizing possibility of associating neutral genetic diversifi-
cation with selection at the functionally important genes
underlying divergence draws closer to reality. Phylogeo-
graphy’s most important contribution to ecology and evo-
lution may be that it is integrative and flexible, and unraveling
the next set of interesting questions will likely require pairing
phylogeography with novel types of external data and meth-
ods from other disciplines. However, moving toward a more
complete and process-based understanding of evolution,
adaptation, community assembly, and the generation of bio-
diversity patterns such as richness gradients requires a multi-
faceted approach, of which phylogeography is an integral part.
See also: Biogeography, Evolutionary Theories in. Dispersal
Biogeography. Molecular Evolution, Models of. Population Structure
and Gene Flow. Quaternary Biogeography and Climate Change. Ring
Species
References
Alvarado-Serrano, D.F., Knowles, L.L., 2014. Ecological niche models in
phylogeographic studies: Applications, advances and precautions. Molecular
Ecology Resources 14, 233–248.
Andrew, R.L., Bernatchez, L., Bonin, A., et al., 2013. A road map for molecular
ecology. Molecular Ecology 22, 2605–2626.
Arbogast, B.S., Edwards, S.V., Wakely, J., Beerli, P., Slowinski, J.B., 2002.
Estimating divergence times from molecular data on phylogenetic and population
genetic timescales. Annual Review of Ecology and Systematics 33, 707–740.
Avise, J.C., Arnold, J., Ball, R.M., et al., 1987. Intraspecific phylogeography: The
mitochondrial DNA bridge between population genetics and systematics. Annual
Review of Ecology and Systematics 18, 489–522.
Beaumont, M.A., Zhang, W., Balding, D.J., 2002. Approximate Bayesian computation
in population genetics. Genetics 162, 2025–2035.
Bell, R.C., MacKenzie, J.B., Hickerson, M.J., et al., 2012. Comparative multi-locus
phylogeography confirms multiple vicariance events in co-distributed rainforest
frogs. Proceedings of the Royal Society B 279, 991–999.
Bermingham, E., Moritz, C., 1998. Comparative phylogeography: Concepts and
applications. Molecular Ecology 7, 367–369.
Brown, J.H., 1984. On the relationship between abundance and distribution of
species. American Naturalist 124, 255–279.
Brown, J.L., Knowles, L.L., 2012. Spatially explicit models of dynamic histories:
Examination of the genetic consequences of Pleistocene glaciation and recent
climate change on the American Pika. Molecular Ecology 21, 3757–3775.
Brussard, P.F., 1984. Geographic patterns and environmental gradients: The central-
marginal model in Drosophila revisited. Annual Review of Ecology and
Systematics 15, 25–64.
Burridge, C.P., Craw, D., Fletcher, D., Waters, J.M., 2008. Geological dates and
molecular rates: Fish DNA sheds light on time dependency. Molecular Biology
and Evolution 25, 624–633.
Carnaval, A.C., Hickerson, M.J., Haddad, C.F.B., Rodriguez, M.T., Moritz, C., 2009.
Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science
323, 785–789.
Carstens, B.C., Brunsfeld, S.J., Demboski, J.R., Good, J.M., Sullivan, J., 2005.
Investigating the evolutionary history of the Pacific Northwest mesic forest
ecosystem: Hypothesis testing within a comparative phylogeographic framework.
Evolution 59, 1639–1652.
Phylogeography 295
Carstens, B.C., Brennan, R.S., Chua, V., et al., 2013. Model selection as a tool for
phylogeographic inference: An example from the willow Salix melanopsis.
Molecular Ecology 22, 4014–4028.
Carstens, B.C., Knowles, L.L., 2007. Shifting distributions and speciation: Species
divergence during rapid climate change. Molecular Ecology 16, 619–627.
Carstens, B.C., Lemmon, A.R., Lemmon, E.M., 2012. The promises and pitfalls of
next-generation sequencing data in phylogeography. Systematic Biology 61,
713–715.
Chan, Y.L., Schanzenbach, E., Hickerson, M.J., 2014. Detecting concerted
demographic responses across community assemblages using hierarchical
approximate Bayesian computation. Molecular Biology and Evolution 31,
2501–2515.
Chikhi, L., Sousa, V.C., Luisi, P., Goossens, B., Beaumont, M.A., 2010. The
confounding effects of population structure, genetic diversity and the sampling
scheme on the detection and quantification of population size changes. Genetics
186, 983–995.
Cooke, G.M., Chao, N.L., Beheregaray, L.B., 2012. Divergent natural selection with
gene flow along major environmental gradients in Amazonia: Insights from
genome scans, population genetics and phylogeography of the characin fish
Triportheus albus. Molecular Ecology 21, 2410–2427.
Coyne, J.A., Orr, H.A., 2004. Speciation. Sunderland, MA: Sinauer Associates.
Dasmahapatra, K.K., Lamas, G., Simpson, F., Mallet, J., 2010. The anatomy of a
‘suture zone’ in Amazonian butterflies: A coalescent-based test for vicariant
geographic divergence and speciation. Molecular Ecology 19, 4283–4301.
Dawson, M.N., 2014. Natural experiments and meta-analyses in comparative
phylogeography. Journal of Biogeography 41, 52–65.
Dexter, K.G., Terborgh, J.W., Cunningham, C.W., 2012. Historical effects on beta
diversity and community assembly in Amazonian trees. Proceedings of the
National Academy of Sciences of the United States of America 109, 7787–7792.
Eckert, C.G., Samis, K.E., Lougheed, S.C., 2008. Genetic variation across species’
geographical ranges: The central-marginal hypothesis and beyond. Molecular
Ecology 17, 1170–1188.
Edwards, S.V., Beerli, P., 2000. Gene divergence, population divergence, and the
variance in coalescent time in phylogeographic studies. Evolution 54,
1839–1854.
Emerson, B.C., Cicconardi, F., Fanciulli, P.P., Shaw, P.J.A., 2011. Phylogeny,
phylogeography, phylobetadiversity and the molecular analysis of biological
communities. Philosophical Transactions of the Royal Society B 366,
2391–2402.
Fraser, C.I., Nikula, R., Ruzzante, D.E., Waters, J.M., 2012. Poleward bound:
Biological impacts of Southern Hemisphere glaciation. Trends in Ecology and
Evolution 27, 462–471.
Heller, R., Chikhi, L., Siegismund, H.R., 2013. The confounding effect of population
structure on bayesian skyline plot inferences of demographic history. PLoS ONE
8, e62992.
Hengeveld, R., Haeck, J., 1982. The distribution of abundance. 1 Measurements.
Journal of Biogeography 9, 303–316.
Hewitt, G.M., 1996. Some genetic consequences of ice ages, and their role in
divergence and speciation. Biological Journal of the Linnean Society 58,
247–276.
Hewitt, G.M., 2000. The genetic legacy of the Quaternary ice ages. Nature 405,
907–913.
Hickerson, M.J., Carstens, B.C., Cavender-Bares, J., et al., 2010. Phylogeography's
past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics
and Evolution 54, 291–301.
Hickerson, M.J., Dolman, G., Moritz, C., 2006. Comparative phylogeographic
summary statistics for testing simultaneous vicariance. Molecular Ecology 15,
209–223.
Hickerson, M.J., Meyer, C.P., 2008. Testing comparative phylogeographic models of
marine vicariance and dispersal using a hierarchical Bayesian approach. BMC.
Evolutionary Biology 8, 322.
Hugall, A., Moritz, C., Moussalli, A., Stanisic, J., 2002. Reconciling
paleodistribution models and comparative phylogeography in the wet tropics
rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875). Proceedings
of the National Academy of Sciences of the United States of America 99,
6112–6117.
Johansson, H., Stoks, R., Nilsson-Örtman, V., Ingvarsson, P.K., Johansson, F.,
2013. Large-scale patterns in genetic variation, gene flow and differentiation in
five species of European Coenagrionid damselfly provide mixed support for the
central-marginal hypothesis. Ecography 36, 744–755.
Jordal, B.H., Emerson, B.C., Hewitt, G.M., 2006. Apparent ‘sympatric’ speciation in
ecologically similar herbivorous beetles facilitated by multiple colonizations of an
island. Molecular Ecology 15, 2935–2947.
296 Phylogeography
Kidd, D.M., Ritchie, M.G., 2006. Phylogeographic information systems: Putting the
geography into phylogeography. Journal of Biogeography 33, 1851–1865.
Knowles, L.L., 2009. Statistical phylogeography. Annual Review of Ecology,
Evolution, and Systematics 40, 593–612.
Knowles, L.L., Carstens, B.C., 2007. Estimating a geographically explicit model of
population divergence. Evolution 61, 477–493.
Knowles, L.L., Maddison, W.P., 2002. Statistical phylogeography. Molecular Ecology
11, 2623–2635.
Kozak, K.H., Blaine, R.A., Larson, A., 2006. Gene lineages and eastern North
American palaeodrainage basins: Phylogeography ad speciation in salamanders
of the Eurycea bislineata complex. Molecular Ecology 15, 191–207.
Kozak, K.H., Graham, C.H., Wiens., J.J., 2008. Integrating GIS data into evolutionary
studies. Trends in Ecology and Evolution 23, 141–148.
Kozak, K.H., Larson, A., Bonett, R.M., Harmon, L.J., 2005. Phylogenetic analysis of
ecomorphological divergence, community structure, and diversification rates in
dusky salamanders (Plethodontidae: Desmognathus). Evolution 59, 2000–2006.
Lemey, P., Rambaut, A., Drummond, A.J., Suchard, M.A., 2009. Bayesian
phylogeography finds its roots. PLoS Computational Biology 5, e1000520.
Lemmon, A.R., Lemmon, E.M., 2008. A likelihood framework for estimating
phylogeographic history on a continuous landscape. Systematic Biology 57,
544–561.
Lemmon, A.R., Lemmon, E.M., 2012. High-throughput identification of informative
nuclear loci for shallow-scale phylogenetics and phylogeography. Systematic
Biology 61, 745–761.
Marske, K.A., Leschen, R.A.B., Barker, G.M., Buckley, T.R., 2009. Phylogeography
and ecological niche modeling implicate coastal refugia and trans-alpine
dispersal of a New Zealand fungus beetle. Molecular Ecology 18, 5126–5142.
Marske, K.A., Leschen, R.A.B., Buckley, T.R., 2011. Reconciling phylogeography and
ecological niche models for New Zealand beetles: Looking beyond glacial refugia.
Molecular Phylogenetics and Evolution 59, 89–102.
Marske, K.A., Leschen, R.A.B., Buckley, T.R., 2012. Concerted versus independent
evolution and the search for multiple refugia: Comparative phylogeography of
four forest beetles. Evolution 66, 1862–1877.
Marske, K.A., Rahbek, C., Nogués-Bravo, D., 2013. Phylogeography: Spanning the
ecology-evolution continuum. Ecography 36, 1169–1181.
Martin, P.R., McKay, J.K., 2004. Latitudinal variation in genetic divergence of
populations and the potential for future speciation. Evolution 58, 938–945.
McCormack, J.E., Maley, J.M., Hird, S.M., et al., 2012. Next-generation sequencing
reveals phylogeographic structure and a species tree for recent bird divergences.
Molecular Phylogenetics and Evolution 62, 397–406.
McCormack, J.E., Zellmer, A.J., Knowles, L.L., 2010. Does niche divergence
accompany allopatric divergence in Aphelocoma jays as predicted under ecological
speciation? Insights from tests with niche models. Evolution 64, 1231–1244.
Moritz, C., Hoskin, C.J., MacKenzie, J.B., et al., 2009. Identification and dynamics
of a cryptic suture zone in tropical rainforest. Proceedings of the Royal Society B
276, 1235–1244.
Moritz, C., Langham, G., Kearney, M., et al., 2012. Integrating phylogeography and
physiology reveals divergence of thermal traits between central and peripheral
lineages of tropical rainforest lizards. Philosophical Transactions of the Royal
Society B 367, 1680–1687.
Nylinder, S., Lemey, P., De Bruyn, M., et al., 2014. On the biogeography of
Centipeda: A species-tree diffusion approach. Systematic Biology 63, 178–191.
O’Neill, E.M., Schwartz, R., Bullock, C.T., et al., 2013. Parallel tagged amplicon
sequencing reveals major lineages and phylogenetic structure in the North
American tiger salamander (Ambystoma tigrinum) species complex. Molecular
Ecology 22, 111–129.
Pelletier, T.A., Carstens, B.C., 2014. Model choice for phylogeographic inference
using a large set of models. Molecular Ecology 23, 3028–3043.
Pyron, R.A., Burbrink, F.T., 2010. Hard and soft allopatry: Physically and
ecologically mediated modes of geographic speciation. Journal of Biogeography
37, 2005–2015.
Richards, C.L., Carstens, B.C., Lacey Knowles, L., 2007. Distribution modelling
and statistical phylogeography: An integrative framework for generating and
testing alternative biogeographical hypotheses. Journal of Biogeography 34,
1833–1845.
Rissler, L.J., Smith, W.H., 2010. Mapping amphibian contact zones and
phylogeographical break hotspots across the United States. Molecular Ecology
19, 5404–5416.
Rosenberg, N.A., Nordborg, M., 2002. Genealogical trees, coalescent theory and the
analysis of genetic polymorphisms. Nature Reviews Genetics 3, 380–390.
Schluter, D., 2001. Ecology and the origin of species. Trends in Ecology and
Evolution 16, 372–380.
Singhal, S., Moritz, C., 2012. Testing hypotheses for genealogical discordance in a
rainforest lizard. Molecular Ecology 21, 5059–5072.
Soltis, D.E., Morris, A.B., McLachlan, J.S., Manos, P.S., Soltis, P.S., 2006.
Comparative phylogeography of unglaciated eastern North America. Molecular
Ecology 15, 4261–4293.
Sullivan, J., Arellano, E., Rogers, D.S., 2000. Comparative phylogeography of
Mesoamerican highland rodents: Concerted versus independent response to past
climatic fluctuations. American Naturalist 155, 755–768.
Taberlet, P., Fumagalli, L., Wust-Saucy, A.-G., Cossons, J.-F., 1998. Comparative
phylogeography and postglacial colonization routes in Europe. Molecular Ecology
8, 1923–1934.
Waltari, E., Hijmans, R.J., Peterson, A.T., et al., 2007. Locating pleistocene refugia:
Comparing phylogeographic and ecological niche model predictions. PLoS ONE
2, e563.
Wiens, J.J., 2004. Speciation and ecology revisited: Phylogenetic niche conservatism
and the origin of species. Evolution 58, 193–197.
Zink, R.M., 2002. Methods in comparative phylogeography, and their applications to
studying evolution in the North American aridlands. Integrative and Comparative
Biology 42, 953–959.