Phylogeography is the study of the historical processes that may be
responsible for the contemporary geographic distributions of
individuals. This is accomplished by considering the geographic
distribution of individuals in light of genetics, particularly
This term was introduced to describe geographically structured genetic
signals within and among species. An explicit focus on a species'
biogeography/biogeographical past sets phylogeography apart from
classical population genetics and phylogenetics.
Past events that can be inferred include population expansion,
population bottlenecks, vicariance and migration. Recently developed
approaches integrating coalescent theory or the genealogical history
of alleles and distributional information can more accurately address
the relative roles of these different historical forces in shaping
Phylogeography and conservation
3 Comparative phylogeography
4 Human phylogeography
Phylogeography of viruses
Phylogeography of languages
7 See also
The term phylogeography was first used by
John Avise in his 1987 work
Intraspecific Phylogeography: The Mitochondrial
DNA Bridge Between
Genetics and Systematics. Historical biogeography
addresses how historical geological, climatic and ecological
conditions influenced the current distribution of species. As part of
historical biogeography, researchers had been evaluating the
geographical and evolutionary relationships of organisms years before.
Two developments during the 1960s and 1970s were particularly
important in laying the groundwork for modern phylogeography; the
first was the spread of cladistic thought, and the second was the
development of plate tectonics theory.
The resulting school of thought was vicariance biogeography, which
explained the origin of new lineages through geological events like
the drifting apart of continents or the formation of rivers. When a
continuous population (or species) is divided by a new river or a new
mountain range (i.e., a vicariance event), two populations (or
species) are created. Paleogeography, geology and paleoecology are all
important fields that supply information that is integrated into
Phylogeography takes a population genetics and phylogenetic
perspective on biogeography. In the mid-1970s, population genetic
analyses turned to mitochondrial markers. The advent of the
polymerase chain reaction (PCR), the process where millions of copies
DNA segment can be replicated, was crucial in the development of
Thanks to this breakthrough, the information contained in
DNA sequences was much more accessible. Advances in both
laboratory methods (e.g. capillary
DNA sequencing technology) that
allowed easier sequencing
DNA and computational methods that make
better use of the data (e.g. employing coalescent theory) have helped
improve phylogeographic inference.
Early phylogeographic work has recently been criticized for its
narrative nature and lack of statistical rigor (i.e. it did not
statistically test alternative hypotheses). The only real method was
Alan Templeton's Nested
Clade Analysis, which made use of an inference
key to determine the validity of a given process in explaining the
concordance between geographic distance and genetic relatedness.
Recent approaches have taken a stronger statistical approach to
phylogeography than was done initially.
Climate change, such as the glaciation cycles of the past 2.4 million
years, has periodically restricted some species into disjunct refugia.
These restricted ranges may result in population bottlenecks that
reduce genetic variation. Once a reversal in climate change allows for
rapid migration out of refugial areas, these species spread rapidly
into newly available habitat. A number of empirical studies find
genetic signatures of both animal and plant species that support this
scenario of refugia and postglacial expansion. This has occurred
both in the tropics (where the main effect of glaciation is increasing
aridity, i.e. the expansion of savanna and retraction of tropical
rainforest) as well as temperate regions that were directly
influenced by glaciers.
Phylogeography and conservation
Phylogeography can help in the prioritization of areas of high value
for conservation. Phylogeographic analyses have also played an
important role in defining evolutionary significant units (ESU), a
unit of conservation below the species level that is often defined on
unique geographic distribution and mitochondrial genetic patterns.
A recent study on imperiled cave crayfish in the Appalachian Mountains
of eastern North America demonstrates how phylogenetic analyses
along with geographic distribution can aid in recognizing conservation
priorities. Using phylogeographical approaches, the authors found that
hidden within what was thought to be a single, widely distributed
species, an ancient and previously undetected species was also
present. Conservation decisions can now be made to ensure that both
lineages received protection. Results like this are not an uncommon
outcome from phylogeographic studies.
An analysis of salamanders of the genus Eurycea, also in the
Appalachians, found that the current taxonomy of the group greatly
underestimated species level diversity. The authors of this study
also found that patterns of phylogeographic diversity were more
associated with historical (rather than modern) drainage connections,
indicating that major shifts in the drainage patterns of the region
played an important role in the generation of diversity of these
salamanders. A thorough understanding of phylogeographic structure
will thus allow informed choices in prioritizing areas for
These figures map out the phylogeographic history of poison frogs in
The field of comparative phylogeography seeks to explain the
mechanisms responsible for the phylogenetic relationships and
distribution of different species. For example, comparisons across
multiple taxa can clarify the histories of biogeographical
regions. For example, phylogeographic analyses of terrestrial
vertebrates on the
Baja California peninsula and marine fish on
both the Pacific and gulf sides of the peninsula display genetic
signatures that suggest a vicariance event affected multiple taxa
Pleistocene or Pliocene.
Phylogeography also gives an important historical perspective on
community composition. History is relevant to regional and local
diversity in two ways. One, the size and makeup of the regional
species pool results from the balance of speciation and extinction.
Two, at a local level community composition is influenced by the
interaction between local extinction of species’ populations and
recolonization. A comparative phylogenetic approach in the
Australian Wet Tropics indicates that regional patterns of species
distribution and diversity are largely determined by local extinctions
and subsequent recolonizations corresponding to climatic cycles.
Phylogeography integrates biogeography and genetics to study in
greater detail the lineal history of a species in context of the
geoclimatic history of the planet. An example study of poison frogs
living in the South American neotropics (illustrated to the left) is
used to demonstrate how phylogeographers combine genetics and
paleogeography to piece together the ecological history of organisms
in their environments. Several major geoclimatic events have greatly
influenced the biogeographic distribution of organisms in this area,
including the isolation and reconnection of South America, the uplift
of the Andes, an extensive Amazonian floodbasin system during the
Miocene, the formation of
Orinoco and Amazon drainages, and dry−wet
climate cycles throughout the
Using this contextual paleogeographic information (paleogeographic
time series is shown in panels A-D) the authors of this study
proposed a null-hypothesis that assumes no spatial structure and two
alternative hypothesis involving dispersal and other biogeographic
constraints (hypothesis are shown in panels E-G, listed as SMO, SM1,
and SM2). The phylogeographers visited the ranges of each frog species
to obtain tissue samples for genetic analysis; researchers can also
obtain tissue samples from museum collections.
The evolutionary history and relations among different poison frog
species is reconstructed using phylogenetic trees derived from
molecular data. The molecular trees are mapped in relation to
paleogeographic history of the region for a complete phylogeographic
study. The tree shown in the center of the figure has its branch
lengths calibrated to a molecular clock, with the geological time bar
shown at the bottom. The same phylogenetic tree is duplicated four
more times to show where each lineage is distributed and is found
(illustrated in the inset maps below, including Amazon basin, Andes,
Guiana-Venezuela, Central America-Chocó).
The combination of techniques used in this study exemplifies more
generally how phylogeographic studies proceed and test for patterns of
common influence. Paleogeographic data establishes geological time
records for historical events that explain the branching patterns in
the molecular trees. This study rejected the null model and found that
the origin for all extant Amazonian poison frog species primarily stem
from fourteen lineages that dispersed into their respective areas
after the Miocene floodbasin receded. Regionally based
phylogeographic studies of this type are repeated for different
species as a means of independent testing. Phylogeographers find
broadly concordant and repeated patterns among species in most regions
of the planet that is due to a common influence of paleoclimatic
Recent single-origin hypothesis
Recent single-origin hypothesis and Multiregional
Phylogeography has also proven to be useful in understanding the
origin and dispersal patterns of our own species, Homo sapiens. Based
primarily on observations of skeletal remains of ancient human remains
and estimations of their age, anthropologists proposed two competing
hypotheses about human origins.
The first hypothesis is referred to as the Out-of-
replacement model, which contends that the last expansion out of
Africa around 100,000 years ago resulted in the modern humans
displacing all previous Homo spp. populations in
Eurasia that were the
result of an earlier wave of emigration out of Africa. The
multiregional scenario claims that individuals from the recent
expansion out of
Africa intermingled genetically with those human
populations of more ancient African emigrations. A phylogeographic
study that uncovered a
Mitochondrial Eve that lived in
years ago provided early support for the Out-of-
While this study had its shortcomings, it received significant
attention both within scientific circles and a wider audience. A more
thorough phylogeographic analysis that used ten different genes
instead of a single mitochondrial marker indicates that at least two
major expansions out of
Africa after the initial range extension of
Homo erectus played an important role shaping the modern human gene
pool and that recurrent genetic exchange is pervasive. These
findings strongly demonstrated Africa's central role in the evolution
of modern humans, but also indicated that the multiregional model had
some validity. These studies have largely been supplanted by
population genomic studies that use orders of magnitude more data.
In light of these recent data from the 1000 genomes project,
genomic-scale SNP databases sampling thousands of individuals globally
and samples taken from two non-
Homo sapiens hominins (Neanderthals and
Denisovans), the picture of human evolutionary has become more
resolved and complex involving possible Neanderthal and Denisovan
admixture, admixture with archaic African hominins, and Eurasian
expansion into the Australasian region that predates the standard out
of African expansion.
Phylogeography of viruses
Viruses are informative in understanding the dynamics of evolutionary
change due to their rapid mutation rate and fast generation time.
Phylogeography is a useful tool in understanding the origins and
distributions of different viral strains. A phylogeographic approach
has been taken for many diseases that threaten human health, including
dengue fever, rabies, influenza and HIV. Similarly, a
phylogeographic approach will likely play a key role in understanding
the vectors and spread of avian influenza (HPAI H5N1), demonstrating
the relevance of phylogeography to the general public.
Phylogeography of languages
Phylogeographic analysis of ancient and modern languages has been used
to test whether
Indo-European languages originated in
Anatolia or in
the steppes of Central Asia. Language evolution was modeled in
terms of the gain and loss of cognate words in each language over
time, to produce a cladogram of related languages. Combining those
data with known geographic ranges of each language produced strong
support for an Anatolian origin approximately 8000–9500 years ago.
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Topics in phylogenetics
Long branch attraction
Clade vs Grade
Phylogenetic comparative methods
Phylogenetic niche conservatism
List of evolutionary biology topics