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 the patterns associated with a gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...

Genealogy is the study of families and the tracing of their lineages and history. Genealogists use oral traditions, historical records, genetic analysis, and other records to obtain information about a family and to demonstrate kinship and pedigrees of its members...


This term was introduced to describe geographically structured genetic signals within and among species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...

. An explicit focus on a species' biogeography
Biogeography is the study of the distribution of species , organisms, and ecosystems in space and through geological time. Organisms and biological communities vary in a highly regular fashion along geographic gradients of latitude, elevation, isolation and habitat area...

/biogeographical past sets phylogeography apart from classical population genetics
Population genetics
Population genetics is the study of allele frequency distribution and change under the influence of the four main evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes into account the factors of recombination, population subdivision and population...

 and phylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...


Past events that can be inferred include population expansion, population bottlenecks, vicariance
Vicariance is a process by which the geographical range of an individual taxon, or a whole biota, is split into discontinuous parts by the formation of a physical barrier to gene flow or dispersal. Vicariance of whole biotas occurs following large-scale geophysical events such as the uplift of a...

 and migration
Human migration
Human migration is physical movement by humans from one area to another, sometimes over long distances or in large groups. Historically this movement was nomadic, often causing significant conflict with the indigenous population and their displacement or cultural assimilation. Only a few nomadic...

. Recently developed approaches integrating coalescent theory
Coalescent theory
In genetics, coalescent theory is a retrospective model of population genetics. It attempts to trace all alleles of a gene shared by all members of a population to a single ancestral copy, known as the most recent common ancestor...

 or the genealogical history of alleles and distributional information can more accurately address the relative roles of these different historical forces in shaping current patterns.


While the term phylogeography was first coined in 1987, it has existed as a field of study for much longer. 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
Plate tectonics
Plate tectonics is a scientific theory that describes the large scale motions of Earth's lithosphere...


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
Geology is the science comprising the study of solid Earth, the rocks of which it is composed, and the processes by which it evolves. Geology gives insight into the history of the Earth, as it provides the primary evidence for plate tectonics, the evolutionary history of life, and past climates...

 and paleoecology
Paleoecology uses data from fossils and subfossils to reconstruct the ecosystems of the past. It involves the study of fossil organisms and their associated remains, including their life cycle, living interactions, natural environment, and manner of death and burial to reconstruct the...

 are all important fields that supply information that is integrated into phylogeographic analyses.

Phylogeography takes a population genetics and phylogenetic perspective on biogeography
Biogeography is the study of the distribution of species , organisms, and ecosystems in space and through geological time. Organisms and biological communities vary in a highly regular fashion along geographic gradients of latitude, elevation, isolation and habitat area...

. In the mid-1970s, population genetic analyses turned to mitochondrial markers. The advent of the polymerase chain reaction
Polymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....

 (PCR), the process where millions of copies of a DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 segment can be replicated, was crucial in the development of phylogeography.

Thanks to this breakthrough, the information contained in mitochondrial DNA sequences was much more accessible. Advances in both laboratory methods (e.g. capillary
Capillaries are the smallest of a body's blood vessels and are parts of the microcirculation. They are only 1 cell thick. These microvessels, measuring 5-10 μm in diameter, connect arterioles and venules, and enable the exchange of water, oxygen, carbon dioxide, and many other nutrient and waste...

 DNA sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....

 technology) that allowed easier sequencing DNA and computational methods that make better use of the data (e.g. employing coalescent theory
Coalescent theory
In genetics, coalescent theory is a retrospective model of population genetics. It attempts to trace all alleles of a gene shared by all members of a population to a single ancestral copy, known as the most recent common ancestor...

) 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
Alan Templeton
Alan R. Templeton is an American geneticist and statistician from Washington University in St. Louis, where he holds the Charles Rebstock professorship in biology. He is known for his work demonstrating the lack of genetic differences between humans of different races...

'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 arid
A region is said to be arid when it is characterized by a severe lack of available water, to the extent of hindering or even preventing the growth and development of plant and animal life...

ity, i.e. the expansion of savanna and retraction of tropical rainforest
Tropical rainforest
A tropical rainforest is an ecosystem type that occurs roughly within the latitudes 28 degrees north or south of the equator . This ecosystem experiences high average temperatures and a significant amount of rainfall...

) 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 unit
Evolutionary Significant Unit
An Evolutionarily Significant Unit is a population of organisms that is considered distinct for purposes of conservation. Delineating ESUs is important when considering conservation action.This term can apply to any species, subspecies, geographic race, or population...

s (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
Crayfish, crawfish, or crawdads – members of the superfamilies Astacoidea and Parastacoidea – are freshwater crustaceans resembling small lobsters, to which they are related...

 in the Appalachian Mountains
Appalachian Mountains
The Appalachian Mountains #Whether the stressed vowel is or ,#Whether the "ch" is pronounced as a fricative or an affricate , and#Whether the final vowel is the monophthong or the diphthong .), often called the Appalachians, are a system of mountains in eastern North America. The Appalachians...

 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
Eurycea is a genus of salamanders, native to North America. These salamanders are commonly referred to as brook salamanders.- Taxonomy :...

, 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 conservation.

Comparative phylogeography

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
Baja California
Baja California officially Estado Libre y Soberano de Baja California is one of the 31 states which, with the Federal District, comprise the 32 Federal Entities of Mexico. It is both the northernmost and westernmost state of Mexico. Before becoming a state in 1953, the area was known as the North...

 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 during the Pleistocene
The Pleistocene is the epoch from 2,588,000 to 11,700 years BP that spans the world's recent period of repeated glaciations. The name pleistocene is derived from the Greek and ....

 or Pliocene
The Pliocene Epoch is the period in the geologic timescale that extends from 5.332 million to 2.588 million years before present. It is the second and youngest epoch of the Neogene Period in the Cenozoic Era. The Pliocene follows the Miocene Epoch and is followed by the Pleistocene Epoch...


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
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...

 and extinction
In biology and ecology, extinction is the end of an organism or of a group of organisms , normally a species. The moment of extinction is generally considered to be the death of the last individual of the species, although the capacity to breed and recover may have been lost before this point...

. 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
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....

 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
Great American Interchange
The Great American Interchange was an important paleozoogeographic event in which land and freshwater fauna migrated from North America via Central America to South America and vice versa, as the volcanic Isthmus of Panama rose up from the sea floor and bridged the formerly separated continents...

, the uplift of the Andes, an extensive Amazonian
Amazon Rainforest
The Amazon Rainforest , also known in English as Amazonia or the Amazon Jungle, is a moist broadleaf forest that covers most of the Amazon Basin of South America...

 floodbasin system during the Miocene, the formation of Orinoco
The Orinoco is one of the longest rivers in South America at . Its drainage basin, sometimes called the Orinoquia, covers , with 76.3% of it in Venezuela and the remainder in Colombia...

 and Amazon drainages, and dry−wet climate cycles throughout the Pliocene
The Pliocene Epoch is the period in the geologic timescale that extends from 5.332 million to 2.588 million years before present. It is the second and youngest epoch of the Neogene Period in the Cenozoic Era. The Pliocene follows the Miocene Epoch and is followed by the Pleistocene Epoch...

 to Pleistocene
The Pleistocene is the epoch from 2,588,000 to 11,700 years BP that spans the world's recent period of repeated glaciations. The name pleistocene is derived from the Greek and ....

 epochs. 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 tree
Phylogenetic tree
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics...

s 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
Molecular clock
The molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...

, 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, Giuana-Venuzuala, 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 history.

Human phylogeography

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-Africa with replacement model, which contends that the last expansion out of Africa
Africa is the world's second largest and second most populous continent, after Asia. At about 30.2 million km² including adjacent islands, it covers 6% of the Earth's total surface area and 20.4% of the total land area...

 around 100,000 years ago resulted in the modern humans displacing all previous Homo spp. populations in Eurasia
Eurasia is a continent or supercontinent comprising the traditional continents of Europe and Asia ; covering about 52,990,000 km2 or about 10.6% of the Earth's surface located primarily in the eastern and northern hemispheres...

 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
Mitochondrial Eve
In the field of human genetics, Mitochondrial Eve refers to the matrilineal "MRCA" . In other words, she was the woman from whom all living humans today descend, on their mother's side, and through the mothers of those mothers and so on, back until all lines converge on one person...

that lived in Africa 150,000 years ago provided early support for the Out-of-Africa model.

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
Homo erectus
Homo erectus is an extinct species of hominid that lived from the end of the Pliocene epoch to the later Pleistocene, about . The species originated in Africa and spread as far as India, China and Java. There is still disagreement on the subject of the classification, ancestry, and progeny of H...

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
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...

 of modern humans, but also indicated that the multiregional model had some validity.

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
Dengue fever
Dengue fever , also known as breakbone fever, is an infectious tropical disease caused by the dengue virus. Symptoms include fever, headache, muscle and joint pains, and a characteristic skin rash that is similar to measles...

, rabies
Rabies is a viral disease that causes acute encephalitis in warm-blooded animals. It is zoonotic , most commonly by a bite from an infected animal. For a human, rabies is almost invariably fatal if post-exposure prophylaxis is not administered prior to the onset of severe symptoms...

, influenza
Influenza, commonly referred to as the flu, is an infectious disease caused by RNA viruses of the family Orthomyxoviridae , that affects birds and mammals...

 and HIV
Human immunodeficiency virus is a lentivirus that causes acquired immunodeficiency syndrome , a condition in humans in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive...

. 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.
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