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
geneA gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain their cells and pass genetic traits to offspring...
genealogyGenealogy 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
speciesIn biology, a species is:* a taxonomic rank or* a unit at that rank ....
. An explicit focus on a species'
biogeographyBiogeography is the study of the distribution of biodiversity over space and time. It aims to reveal where organisms live, and at what abundance....
/biogeographical past sets phylogeography apart from classical
population geneticsPopulation genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. As such, it attempts...
and
phylogeneticsIn biology, phylogenetics is the study of evolutionary relatedness among various 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 and
migrationHuman migration is movement by humans from one district to another, sometimes over long distances or in large groups....
.
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
geneA gene is the basic unit of heredity in a living organism. All living things depend on genes. Genes hold the information to build and maintain their cells and pass genetic traits to offspring...
genealogyGenealogy 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
speciesIn biology, a species is:* a taxonomic rank or* a unit at that rank ....
. An explicit focus on a species'
biogeographyBiogeography is the study of the distribution of biodiversity over space and time. It aims to reveal where organisms live, and at what abundance....
/biogeographical past sets phylogeography apart from classical
population geneticsPopulation genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary processes: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. As such, it attempts...
and
phylogeneticsIn biology, phylogenetics is the study of evolutionary relatedness among various 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 and
migrationHuman migration is movement by humans from one district to another, sometimes over long distances or in large groups....
. Recently developed approaches integrating
coalescent theoryIn genetics, coalescent theory is a retrospective model of population genetics. It employs a sample of individuals from a population to trace all alleles of a gene shared by all members of the 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.
Development
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 theoryPlate tectonics is a theory which 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,
geologyGeology is the science and study of the solid and liquid matter that constitutes the Earth. The field of geology encompasses the study of the composition, structure, physical properties, dynamics, and history of Earth materials, and the processes by which they are formed, moved, and changed...
and
paleoecologyPaleoecology uses data from fossils and subfossils to reconstruct the ecosystems of the past. It includes the study of fossil organisms and their bromalites and other trace fossils in terms of their life cycle, their living interactions, their natural environment, their manner of death and burial...
are all important fields that supply information that is integrated into phylogeographic analyses.
Phylogeography takes a population genetics and phylogenetic perspective on
biogeographyBiogeography is the study of the distribution of biodiversity over space and time. It aims to reveal where organisms live, and at what abundance....
. In the mid-1970s, population genetic analyses turned to mitochondrial markers. The advent of the
polymerase chain reactionIn molecular biology, the polymerase chain reaction is a technique to amplify a single or 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
DNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information...
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.
capillaryCapillaries are the smallest of a body's blood vessels and are part 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 sequencingThe term DNA sequencing refers to sequencing methods 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 theoryIn genetics, coalescent theory is a retrospective model of population genetics. It employs a sample of individuals from a population to trace all alleles of a gene shared by all members of the 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 TempletonAlan Templeton is an American geneticist and statistician from Washington University in St. Louis, known for his theories regarding the lack of genetic differences between humans of different races. According to Templeton's research, perceived differences in races are more related to cultural...
'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 as well as temperate regions that were 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 unitAn 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
crayfishCrayfish, crawfish, or crawdads — members of the superfamilies Astacoidea and Parastacoidea — are freshwater crustaceans resembling small lobsters, to which they are related...
in the
Appalachian MountainsThe Appalachian Mountains , often called the Appalachians, are a vast system of mountains in eastern North America. Definitions vary on the precise boundaries of 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
EuryceaEurycea is a genus of salamander, 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 CaliforniaBaja California is both the northernmost and westernmost state of Mexico. Before becoming a state in 1953, the area was known as the North Territory of Baja California. It has an area of , or 3.57% of the land mass of Mexico and comprises the northern half of the Baja California peninsula, 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
PleistoceneThe Pleistocene is the epoch from 2.588 million to 12 000 years BP covering the world's recent period of repeated glaciations. The name pleistocene is derived from the Greek and ....
or
PlioceneThe Pliocene epoch is the period in the geologic timescale that extends from 5.332 million to 2.588 million years before present....
.
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
speciationSpeciation 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
extinctionIn biology and ecology, extinction is the end of an organism or group of taxa. The moment of extinction is generally considered to be the death of the last individual of that species...
. 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.
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 replacementRecent African origin of modern humans is a model in mainstream paleoanthropology that attempts to describe the origin and early dispersal of anatomically modern humans, Homo sapiens sapiens...
model, which contends that the last expansion out of
AfricaAfrica 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. With a billion people in 61 territories, it accounts for about 14.8% of the...
around 100,000 years ago resulted in the modern humans displacing all previous
Homo spp. populations in
EurasiaEurasia is a large landmass covering about 52,990,000 km
2 or about 10.6% of the Earth's surface...
that were the result of an earlier wave of emigration out of Africa. The
multiregionalThe multiregional hypothesis is a model to account for the pattern of human evolution proposed by Milford H. Wolpoff in 1988. Multiregional origin holds that the evolution of humanity from the beginning of the Pleistocene 2.5 million years BP to the present day has been within a single, continuous...
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 EveMitochondrial Eve is the name given by researchers to the woman who is defined as the matrilineal most recent common ancestor for all currently living humans. Passed down from mother to offspring, derivatives of her mitochondrial DNA are now found in all living humans: all mtDNA in every living...
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 erectusHomo erectus is an extinct species of the genus Homo, which originated in Africa and spread as far as China and Java. Depending on the definition of the species, it is considered to be either a direct ancestor of modern humans, or a separate species which co-existed with the distinct Homo...
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
evolutionIn biology, evolution is change in the genetic material of a population of organisms from one generation to the next. Though changes produced in any one generation are normally small, differences accumulate with each generation and can, over time, cause substantial changes in the population, a...
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 feverDengue fever and dengue hemorrhagic fever are acute febrile diseases, found in the tropics, and caused by four closely related virus serotypes of the genus Flavivirus, family Flaviviridae. It is also known as breakbone fever...
,
rabiesRabies is a viral neuroinvasive disease that causes acute encephalitis in warm-blooded animals. It is zoonotic , most commonly by a bite from an infected animal but occasionally by other forms of contact...
,
influenzaInfluenza, commonly referred to as the flu, is an infectious disease caused by RNA viruses of the family Orthomyxoviridae , that affects birds and mammals. The name influenza is Italian and means "influence"...
and
HIVHuman immunodeficiency virus is a lentivirus that causes acquired immunodeficiency syndrome , a condition in humans in which the immune system begins to fail, leading to life-threatening opportunistic infections. Infection with HIV occurs by the transfer of blood, semen, vaginal fluid,...
. 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.