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 Augustinian friar wor ...

, particularly

population genetics Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and pop ...

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

species In biology, a species is the basic unit of classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of the appropriate s ...

. An explicit focus on a species'

biogeography Biogeography is the study of the distribution of species and ecosystems in geographic space and through geological time. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, ...

/biogeographical past sets phylogeography apart from classical

and

phylogenetics In biology, phylogenetics (; from Greek language, Greek wikt:φυλή, φυλή/wikt:φῦλον, φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary his ...

. Past events that can be inferred include population expansion,

population bottlenecks A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as specicide, widespread violen ...

vicariance Allopatric speciation () – also referred to as geographic speciation, vicariant speciation, or its earlier name the dumbbell model – is a mode of speciation that occurs when biological populations become geographically isolated from ...

, 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 or the genealogical history of

alleles An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chro ...

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

Development

The term phylogeography was first used by

John Avise John Charles Avise (born 1948) is an American evolutionary geneticist, conservationist, ecologist and natural historian. He is a Distinguished Professor of Ecology & Evolution, University of California, Irvine, and was previously a Distinguished Pr ...

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 (; ) 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 typically shared derived char ...

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 Palaeogeography (or paleogeography) is the study of historical geography, generally physical landscapes. Palaeogeography can also include the study of human or cultural environments. When the focus is specifically on landforms, the term pale ...

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

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 genetic Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and popu ...

s and

phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

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 rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) t ...

(PCR), the process where millions of copies of a DNA 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 (μm) in diameter. Capillaries are composed of only the tunica intima, consisting of a thin wall of simple squamous endothelial cells. They are the smallest blood vessels in the body: ...

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, guanine, cytosine, and thymine. Th ...

technology) that allowed easier sequencing of DNA and computational methods that make better use of the data (e.g. employing coalescent theory) 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: ''Statistik'', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industria ...

rigor ( i.e. it did not statistically test alternative hypotheses). The only real method was

Alan Templeton Alan R. Templeton is an American geneticist and statistician at Washington University in St. Louis, where he is the Charles Rebstock emeritus professor of biology. From 2010 to 2019, he held positions in the Institute of Evolution and the Depart ...

'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

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 arid when it severely lacks available water, to the extent of hindering or preventing the growth and development of plant and animal life. Regions with arid climates tend to lack vegetation and are called xeric or desertic. Most ar ...

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

tropical rainforest Tropical rainforests are rainforests that occur in areas of tropical rainforest climate in which there is no dry season – all months have an average precipitation of at least 60 mm – and may also be referred to as ''lowland equatori ...

) 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 An evolutionarily significant unit (ESU) 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, ge ...

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 are freshwater crustaceans belonging to the clade Astacidea, which also contains lobsters. In some locations, they are also known as crawfish, craydids, crawdaddies, crawdads, freshwater lobsters, mountain lobsters, rock lobsters, mu ...

in the

Appalachian Mountains The Appalachian Mountains, often called the Appalachians, (french: Appalaches), are a system of mountains in eastern to northeastern North America. The Appalachians first formed roughly 480 million years ago during the Ordovician Period. They ...

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 ten ...

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.

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 (; 'Lower California'), officially the Free and Sovereign State of Baja California ( es, Estado Libre y Soberano de Baja California), is a state in Mexico. It is the northernmost and westernmost of the 32 federal entities of Mex ...

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 ( , often referred to as the ''Ice age'') is the geological Epoch (geology), epoch that lasted from about 2,580,000 to 11,700 years ago, spanning the Earth's most recent period of repeated glaciations. Before a change was fina ...

Pliocene The Pliocene ( ; also Pleiocene) is the epoch in the geologic time scale that extends from 5.333 million to 2.58 One, the size and makeup of the regional

species pool The ecological and biogeographical concept of the species pool describes all species available that could potentially colonize and inhabit a focal habitat area. The concept lays emphasis on the fact that "local communities aren't closed systems, and ...

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 a kind of organism or of a group of kinds (taxon), usually 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 ...

. 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 tropics, tropical Ecoregion#Terrestrial, terrestrial ecoregions of the Americas and the entire South American temperat ...

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

and

paleogeography Palaeogeography (or paleogeography) is the study of historical geography, generally physical landscapes. Palaeogeography can also include the study of human or cultural environments. When the focus is specifically on landforms, the term pale ...

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

Pliocene The Pliocene ( ; also Pleiocene) is the epoch in the geologic time scale that extends from 5.333 million to 2.58Pleistocene The Pleistocene ( , often referred to as the ''Ice age'') is the geological Epoch (geology), epoch that lasted from about 2,580,000 to 11,700 years ago, spanning the Earth's most recent period of repeated glaciations. Before a change was fina ...

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 (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological spec ...

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 nucleoti ...

, 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.

Human phylogeography

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

Homo sapiens Humans (''Homo sapiens'') are the most abundant and widespread species of primate, characterized by bipedalism and exceptional cognitive skills due to a large and complex brain. This has enabled the development of advanced tools, culture, ...

''. 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 in both cases. At about 30.3 million km2 (11.7 million square miles) including adjacent islands, it covers 6% of Earth's total surface area ...

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

Eurasia Eurasia (, ) is the largest continental area on Earth, comprising all of Europe and Asia. Primarily in the Northern and Eastern Hemispheres, it spans from the British Isles and the Iberian Peninsula in the west to the Japanese archipelago a ...

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 (also ''mt-Eve, mt-MRCA'') is the matrilineal most recent common ancestor (MRCA) of all living humans. In other words, she is defined as the most recent woman from whom all living humans descend in an ...

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'' (; meaning "upright man") is an extinct species of archaic human from the Pleistocene, with its earliest occurrence about 2 million years ago. Several human species, such as '' H. heidelbergensis'' and '' H. antecessor' ...

'' 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 change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...

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 Dengue fever is a mosquito-borne tropical disease caused by the dengue virus. Symptoms typically begin three to fourteen days after infection. These may include a high fever, headache, vomiting, muscle and joint pains, and a characterist ...

rabies Rabies is a viral disease that causes encephalitis in humans and other mammals. Early symptoms can include fever and tingling at the site of exposure. These symptoms are followed by one or more of the following symptoms: nausea, vomiting, vi ...

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 symptoms ...

and

HIV The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immune ...

. Similarly, a phylogeographic approach will likely play a key role in understanding the vectors and spread of

avian influenza Avian influenza, known informally as avian flu or bird flu, is a variety of influenza caused by viruses adapted to birds.

( 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 The Indo-European languages are a language family native to the overwhelming majority of Europe, the Iranian plateau, and the northern Indian subcontinent. Some European languages of this family, English, French, Portuguese, Russian, Dutc ...

originated in

Anatolia Anatolia, tr, Anadolu Yarımadası), and the Anatolian plateau, also known as Asia Minor, is a large peninsula in Western Asia and the westernmost protrusion of the Asian continent. It constitutes the major part of modern-day Turkey. The re ...

or in the

steppe In physical geography, a steppe () is an ecoregion characterized by grassland plains without trees apart from those near rivers and lakes. Steppe biomes may include: * the montane grasslands and shrublands biome * the temperate grasslands, ...

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 ''clados'' "branch" and ''gramma'' "character") is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to d ...

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

{{Biogeography Human evolution Biogeography Evolutionary biology