Phylogeography is the study of the historical processes that may be responsible for the past to present geographic distributions of genealogical lineages. This is accomplished by considering the geographic distribution of individuals in light of

genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian ...

, particularly

population genetics Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...

. This term was introduced to describe geographically structured genetic signals within and among

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

. An explicit focus on a species'

biogeography Biogeography is the study of the species distribution, distribution of species and ecosystems in geography, geographic space and through evolutionary history of life, geological time. Organisms and biological community (ecology), communities o ...

/biogeographical past sets phylogeography apart from classical

and

phylogenetics In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

. Past events that can be inferred include population expansion, population bottlenecks, vicariance, dispersal, and

migration Migration, migratory, or migrate may refer to: Human migration * Human migration, physical movement by humans from one region to another ** International migration, when peoples cross state boundaries and stay in the host state for some minimum le ...

. Recently developed approaches integrating

coalescent theory Coalescent theory is a Scientific modelling, model of how alleles sampled from a population may have originated from a most recent common ancestor, common ancestor. In the simplest case, coalescent theory assumes no genetic recombination, recombina ...

or the genealogical history of

alleles An allele is a variant of the sequence of nucleotides at a particular location, or locus, on a DNA molecule. Alleles can differ at a single position through single nucleotide polymorphisms (SNP), but they can also have insertions and deletions ...

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

Historical development

The term phylogeography was first used by John Avise in his 1987 work ''Intraspecific Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics and Systematics''. Historical biogeography is a synthetic discipline that addresses how historical, geological, climatic and ecological conditions influenced the past and 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 Cladistics ( ; from Ancient Greek 'branch') is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is ...

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 Geology (). is a branch of natural science concerned with the Earth and other astronomical objects, the rocks of which they are composed, and the processes by which they change over time. Modern geology significantly overlaps all other Earth ...

and

paleoecology Paleoecology (also spelled palaeoecology) is the study of interactions between organisms and/or interactions between organisms and their environments across geologic timescales. As a discipline, paleoecology interacts with, depends on and informs ...

are all important fields that supply information that is integrated into phylogeographic analyses. Phylogeography takes a population genetics and

phylogenetic In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

perspective on

. In the mid-1970s, population genetic analyses turned to mitochondrial markers. The advent of the

polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed st ...

(PCR), the process where millions of copies of a

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

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 A capillary is a small blood vessel, from 5 to 10 micrometres in diameter, and is part of the microcirculation system. Capillaries are microvessels and the smallest blood vessels in the body. They are composed of only the tunica intima (the inn ...

DNA sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, thymine, cytosine, and guanine. The ...

technology) that allowed easier sequencing of DNA and computational methods that make better use of the data (e.g. employing

) have helped improve phylogeographic inference. By 2000, Avise generated a seminal review of the topic in book form, in which he defined phylogeography as the study of the "principles and processes governing the geographic distributions of genealogical lineages... within and among closely related species." Early phylogeographic work has recently been criticized for its narrative nature and lack of

statistical Statistics (from German language, German: ', "description of a State (polity), state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a s ...

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. Example 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 Aridity is the condition of geographical regions which make up approximately 43% of total global available land area, characterized by low annual precipitation, increased temperatures, and limited water availability.Perez-Aguilar, L. Y., Plata ...

ity, i.e. the expansion of savanna and retraction of

tropical rainforest Tropical rainforests are dense and warm rainforests with high rainfall typically found between 10° north and south of the Equator. They are a subset of the tropical forest biome that occurs roughly within the 28° latitudes (in the torrid zo ...

) as well as temperate regions that were directly influenced by glaciers.

In 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 Crayfish are freshwater crustaceans belonging to the infraorder Astacidea, which also contains lobsters. Taxonomically, they are members of the superfamilies Astacoidea and Parastacoidea. They breathe through feather-like gills. Some spe ...

in the

Appalachian Mountains The Appalachian Mountains, often called the Appalachians, are a mountain range in eastern to northeastern North America. The term "Appalachian" refers to several different regions associated with the mountain range, and its surrounding terrain ...

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 Salamanders are a group of amphibians typically characterized by their lizard-like appearance, with slender bodies, blunt snouts, short limbs projecting at right angles to the body, and the presence of a tail in both larvae and adults. All t ...

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 conservation.

Comparing phylogenetic relationships

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, officially the Free and Sovereign State of Baja California, is a state in Mexico. It is the northwesternmost of the 32 federal entities of Mexico. Before becoming a state in 1952, the area was known as the North Territory of B ...

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 ( ; referred to colloquially as the ''ice age, Ice Age'') is the geological epoch (geology), epoch that lasted from to 11,700 years ago, spanning the Earth's most recent period of repeated glaciations. Before a change was fin ...

Pliocene The Pliocene ( ; also Pleiocene) is the epoch (geology), epoch in the geologic time scale that extends from 5.33 to 2.58 One, the size and makeup of the regional species pool results from the balance of

speciation Speciation is the evolutionary process by which populations evolve to become distinct species. The biologist Orator F. Cook coined the term in 1906 for cladogenesis, the splitting of lineages, as opposed to anagenesis, phyletic evolution within ...

and

extinction Extinction is the termination of an organism by the death of its Endling, last member. A taxon may become Functional extinction, functionally extinct before the death of its last member if it loses the capacity to Reproduction, reproduce and ...

. 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 The Neotropical realm is one of the eight biogeographic realms constituting Earth's land surface. Physically, it includes the tropical terrestrial ecoregions of the Americas and the entire South American temperate zone. Definition In biogeog ...

(illustrated to the left) is used to demonstrate how phylogeographers combine

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 The Orinoco () is one of the longest rivers in South America at . Its drainage basin, sometimes known as the Orinoquia, covers approximately 1 million km2, with 65% of it in Venezuela and 35% in Colombia. It is the List of rivers by discharge, f ...

and Amazon drainages, and dry−wet climate cycles throughout the

Pliocene The Pliocene ( ; also Pleiocene) is the epoch (geology), epoch in the geologic time scale that extends from 5.33 to 2.58Pleistocene The Pleistocene ( ; referred to colloquially as the ''ice age, Ice Age'') is the geological epoch (geology), epoch that lasted from to 11,700 years ago, spanning the Earth's most recent period of repeated glaciations. Before a change was fin ...

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 A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

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 The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleot ...

, 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 history.

In humans

Phylogeography has also proven to be useful in understanding the origin and dispersal patterns of our own species, ''

Homo sapiens Humans (''Homo sapiens'') or modern humans are the most common and widespread species of primate, and the last surviving species of the genus ''Homo''. They are Hominidae, great apes characterized by their Prehistory of nakedness and clothing ...

''. 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 30.3 million km2 (11.7 million square miles) including adjacent islands, it covers 20% of Earth's land area and 6% of its total surfac ...

around 100,000 years ago resulted in the modern humans displacing all previous ''Homo'' spp. populations in

Eurasia Eurasia ( , ) is a continental area on Earth, comprising all of Europe and Asia. According to some geographers, Physical geography, physiographically, Eurasia is a single supercontinent. The concept of Europe and Asia as distinct continents d ...

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 In human genetics, the Mitochondrial Eve (more technically known as the Mitochondrial-Most Recent Common Ancestor, shortened to mt-Eve or mt-MRCA) is the matrilineal most recent common ancestor (MRCA) of all living humans. In other words, she ...

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'' ( ) is an extinction, extinct species of Homo, archaic human from the Pleistocene, spanning nearly 2 million years. It is the first human species to evolve a humanlike body plan and human gait, gait, to early expansions 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 the change in the heritable Phenotypic trait, characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, re ...

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.

In 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 is a mosquito-borne disease caused by dengue virus, prevalent in tropical and subtropical areas. Asymptomatic infections are uncommon, mild cases happen frequently; if symptoms appear, they typically begin 3 to 14 days after i ...

rabies Rabies is a viral disease that causes encephalitis in humans and other mammals. It was historically referred to as hydrophobia ("fear of water") because its victims panic when offered liquids to drink. Early symptoms can include fever and abn ...

influenza Influenza, commonly known as the flu, is an infectious disease caused by influenza viruses. Symptoms range from mild to severe and often include fever, runny nose, sore throat, muscle pain, headache, coughing, and fatigue. These sympto ...

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.

Of languages

Phylogeographic analysis of ancient and modern languages has been used to test whether

Indo-European languages The Indo-European languages are a language family native to the northern Indian subcontinent, most of Europe, and the Iranian plateau with additional native branches found in regions such as Sri Lanka, the Maldives, parts of Central Asia (e. ...

originated in

Anatolia Anatolia (), also known as Asia Minor, is a peninsula in West Asia that makes up the majority of the land area of Turkey. It is the westernmost protrusion of Asia and is geographically bounded by the Mediterranean Sea to the south, the Aegean ...

or in the

steppe In physical geography, a steppe () is an ecoregion characterized by grassland plains without closed forests except near rivers and lakes. Steppe biomes may include: * the montane grasslands and shrublands biome * the tropical and subtropica ...

s 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 A cladogram (from Greek language, Greek ''clados'' "branch" and ''gramma'' "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an Phylogenetic tree, evolutionary tree because it does not s ...

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.

References

{{Authority control Human evolution Biogeography Evolutionary biology