Biogeography

Biogeography is the science which deals with geographic patterns of species distribution and the processes that result in such patterns.
One broad pattern, for example, is that the large, native mammals in Australia are all marsupials, whereas almost all large mammals on other continents are placentals (Luria et al. 1981). This is despite the fact that many of the Australian marsupials share similar ecological roles and similarities in form to various placentals.
Darwin used biogeography as one of his principal proofs of the evolutionary theory of descent with modification, that organisms have descended from common ancestors, with each species arising in a single geographic location from another species that preceded it in time.
Biogeography essentially examines the geographic distribution of species and the various geological, evolutionary, climatic, and ecological conditions that influenced this distribution. The patterns of species distribution can usually be explained through a combination of historical factors such as speciation, extinction, continental drift, glaciation (and associated variations in sea level, river routes, and so on), and river capture, in combination with the area and isolation of landmasses (geographic constraints) and available energy supplies.

Contents

1 History
2 Classification
3 Divisions of Biogeography

3.1 Phylogeny

3.1.1 Gene transfer
3.1.2 Taxon sampling


3.2 Island biogeography

3.2.1 Theory of island biogeography
3.2.2 Island biogeography and conservation


3.3 Phylogeography

3.3.1 Development

3.3.1.1 Example


3.3.2 Phylogeography and conservation
3.3.3 Comparative phylogeography
3.3.4 Human phylogeography
3.3.5 Phylogeography of viruses




4 References
5 Credits


History
Prior to the publication of The Theory of Island Biogeography by Robert MacArthur and E.O. Wilson in 1967 (which expanded their 1963 paper on the same topic) the field of biogeography was seen as a primarily historical and descriptive one. MacArthur and Wilson changed this perception, and showed that the species richness of an area could be predicted in terms of such factors as habitat area, immigration rate, and extinction rate. This gave rise to an interest in island biogeography. The application of island biogeography theory to habitat fragments spurred the development of the fields of conservation biology and landscape ecology (at least among British and American academics; landscape ecology has a distinct genesis among European academics).
Classic biogeography has been given a boost through the development of molecular systematics—Phylogeography. This development allowed scientists to test theories about the origin and dispersal of populations (e.g., island endemics). For example, while classic biogeographers were able to speculate about the origins of species in the Hawaiian Islands, phylogeography allows them to test theories of relatedness between these populations and putative source populations in Asia and North America.

Classification
Biogeography is a synthetic science, related to geography, biology, soil science, geology, climatology, ecology, and evolution.
Some fundamental factors in biogeography are

evolution (change in genetic composition of a population)
extinction (disappearance of a species)
dispersal (movement of populations away from their point of origin, related to migration)
range and distribution
endemic areas
Divisions of Biogeography
Phylogeny
Phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e.g., species, populations). Also known as phylogenetic systematics, phylogenetics treats a species as a group of lineage-connected individuals over time. Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of, phylogenetic systematics, constitutes a means of classifying groups of organisms according to degree of evolutionary relatedness.
Phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually a set of species. A major task of systematics is to determine the ancestral relationships among known species (both living and extinct). The most commonly used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Distance-based methods construct trees based on overall similarity which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.

Gene transfer
Organisms can generally inherit genes in two ways: by speciation (vertical gene transfer), from parent to offspring, or by horizontal or lateral gene transfer, in which genes jump between unrelated organisms, a common phenomenon in prokaryotes.
Lateral gene transfer has complicated the determination of phylogenies of organisms since inconsistencies have been reported depending on the gene chosen.
Carl Woese came up with the three domain theory of life (Eubacteria, Archaea and Eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no lateral gene transfer. Therefore rRNA are commonly recommended as molecular clocks for reconstructing phylogenies.
This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits.

Taxon sampling
Due to the development of advanced sequencing techniques in molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to estimate phylogenies. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes. However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa, the more robust is the resulting phylogeny. This is partly due to the breaking up of long branches. It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible.
Using simulations, Zwickl and Hillis (2002) found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses.

Island biogeography
The study of island biogeography is a field within biogeography that attempts to establish and explain the factors that affect the species diversity of a particular community. In this context, the island can be any area of habitat surrounded by areas unsuitable for the species on the island; not just true islands surrounded by ocean, but also mountains surrounded by deserts, lakes surrounded by dry land, forest fragments surrounded by human-altered landscapes.

Theory of island biogeography
The theory of island biogeography, also known as the equilibrium theory of island biogeography (ETIB), holds that the number of species found on an island (the equilibrium number) is determined by two factors, the effect of distance from the mainland and the effect of island size. These would affect the rate of extinction on the islands and the level of immigration.
Islands closer to the mainland are more likely to receive immigrants from the mainland than those further away from the mainland. The equilibrium number of an island close to Africa is going to be larger than that of one found in the mid-Atlantic. This is the distance effect. The size effect reflects a long known relationship between island size and species diversity. On smaller islands that chance of extinction is greater than on larger ones. Thus larger islands can hold more species than smaller ones. The play between these two factors can be used to establish how many species an island can hold at equilibrium.
The theory of island biogeography was tested by Wilson and his student Daniel Simberloff in the mangroves off Florida. Small islands of mangroves were surveyed then fumigated with methyl bromide to clear their insect and arthropod communities. The islands were then monitored to study the immigration of species to the islands (the experimental equivalent of the creation of new islands). Within a year, the islands had been recolonised, and had reached equilibrium, with islands closer to the mainland having more species, as predicted.
Research conducted at the rainforest research station on Barro Colorado Island has yielded a large number of publications concerning the ecological changes following the formation of islands, such as the local extinction of large predators and the subsequent changes in prey populations.

Island biogeography and conservation
Within a few years of the publishing of the theory of island biogeography, its application to the field of conservation biology had been realized and was being vigorously debated in ecological circles. The realization that reserves and national parks formed islands inside human-altered landscapes (habitat fragmentation), and that these reserves could lose species as they 'relaxed towards equilibrium' (that is they would lose species as they achieved their new equilibrium number, known as ecosystem decay) caused a great deal of concern. This is particularly true when conserving larger species, which tend to have larger ranges.
A study by Newmark (1987) showed a strong correlation between the size of a protected National Park, in the United States, and the number of species of mammals. This led to the debate known as single large or several small (SLOSS), described by writer David Quammen (1997) as "ecology's own genteel version of trench warfare." This debate involved whether a single large reserve was preferable or a combination of several smaller reserves of equal area.
In the years after the publication of Wilson and Simberloff's papers on their work in mangrove swamps (Simberloff and Wilson 1969a, 1959b, 1970) ecologists had found more examples of the species area-relationship, and conservation planning was taking the view that the one large reserve could hold more species that several smaller reserves, and that larger reserves should be the norm in reserve design. This view was in particular championed by Jared Diamond. This led to concern by other ecologists, including Dan Simberloff himself. Simberloff, a proponent of the theory whose research with Wilson had provided support, reversed his views and considered the theory to be an unproven over-simplification that would damage conservation efforts. In particular, he expressed concern that applying the theory to nature reserves, involving the SLOSS perspective, would pose risks since it was unproven and lacked strong empirical support (Quammen 1997). Habitat diversity was as or more important than size in determining the number of species protected.
In species diversity, island biogeography most describes allopatric speciation. Allopatric speciation is where new gene pools arise in isolated gene pools. Island biogeography is also useful in considering sympatric speciation, the idea of different species arising from one ancestral species in the same area. Interbreeding between the two differently adapted species would prevent speciation, but in some species, sympatric speciation appears to have occurred.

Phylogeography
Phylogeography is the study of the processes controlling the geographic distributions of lineages by constructing the genealogies of populations and genes (Avise 2000). This term was introduced to describe geographically structured genetic signal within a single species. An explicit focus on a species' biogeographical past sets phylogeography apart from classical population genetics (Knowles et al. 2002). Phylogeographical inferences are usually made by studying the reconstructed genealogical histories of individual genes (gene trees) sampled from different populations (Knowles et al. 2002). Past events that can be inferred include population expansion, population bottlenecks, vicariance, and migration. One of the goals of phylogeographic analyses is to evaluate the relative role of history in shaping the genetic structure of populations relative to important ongoing processes. Approaches integrating genealogical and distributional information can address the relative roles of different historical forces in shaping current patterns (Cruzan and Templeton 2000).

Development
While the term phylogeography was first coined in 1987 (Avise et al. 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 (De Queiroz 2005). The resulting school of thought was vicariance biogeography, which explained the origin of new lineages through geological events like the drifting apart of continents or the formation of rivers. When a continuous population (or species) is divided by a new river or a new mountain range (i.e., a vicariance event), two populations (or species) are created. Paleogeography, geology and paleoecology are all important fields that supply information that is integrated into phylogeographic analyses.
Phylogeography takes a population genetic and phylogenetic perspective on biogeography. In the mid-1970s, population genetic analyses turned to mitochondrial markers (Avise 1998). The advent of the polymerase chain reaction (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 that allowed easier sequencing of DNA and computational methods that make better use of the data have helped improve phylogeographic inference. The development of coalescent theory has also played an important role (Avise 1998).
Early phylogeographic work was sometimes criticized for its narrative nature and lack of statistical rigor. Hypothesis testing was rarely done, and the explanation of genealogical patterns was essentially story telling. Recent approaches have taken a stronger statistical approach to phylogeography that was done initially. Statistical phylogeography has received an increasing amount of attention (e.g., Templeton 1995, 1998).

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 (Cruzan and Templeton 2000). This has occurred both in the tropics (Schneider et al. 1998, Da Silva and Patterson 1998), as well as temperate regions that were influenced by glaciers (Taberlet et al. 1998).

Phylogeography and conservation
Phylogeography can help in the prioritization of areas of high value for conservation. Phylogeographic analyses have also played an important role in defining evolutionary significant units (ESU), a unit of conservation below the species level that is often defined on unique geographic distribution and mitochondrial genetic patterns(Moritz 1994).
A somewhat surprising result of a phylogenetic analysis with high conservation value was the finding that the African elephant was in fact two divergent species, the forest elephant (Loxodonta cyclotis) and the savannah elephant (Loxodonta africana) (Roca et al. 2001). Another recent study on imperiled cave crayfish in the Appalachian Mountains of eastern North America (Buhay et al. 2005) demonstrates how phylogenetic analyses can aid in recognizing conservation priorities. Using phylogeographical approaches, the authors found that hidden within what was thought to be a single, widely distributed species, an ancient and previously undetected species was also present. Conservation decisions can now be made to ensure that both lineages received protection. Results like this are not an uncommon outcome from phylogeographic studies.
An analysis of salamanders of the genus Eurycea, also in the Appalachians, found that the current taxonomy of the group greatly underestimated species level diversity (Kozak et al. 2006). 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 accomplish a variety of objectives. For example, comparisons across multiple taxa can clarify the histories of biogeographical regions (Riginos 2005). For instance, phylogeographic analyses of terrestrial vertebrates on the Baja California peninsula (Riddle et al. 2000) and marine fish on both the Pacific and gulf sides of the peninsula (Riginos 2005) display genetic signatures that suggest a vicariance event effected multiple taxa during the Pleistocene or Pliocene.
Phylogeography also gives an important historical perspective on community composition. History is relevant to regional and local diversity in two ways (Schneider 1998). One, the size and makeup of the regional species pool results from the balance of speciation and extinction. Two, at a local level community composition is influenced by the interaction between local extinction of species’ populations and recolonization (Schneider 1998). 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 replacement model, which contends that the last expansion out of Africa around 100,000 years ago resulted in the modern humans displacing all previous Homo spp. populations in Eurasia that were the result of an earlier wave of emigration out of Africa. The multiregional scenario claims that individuals from the recent expansion out of Africa intermingled genetically with those human populations of more ancient African emigrations.
A phylogeographic study that uncovered a Mitochondrial Eve that lived in Africa 150,000 years ago provided early support for the Out-of-Africa model (Cann et al. 1987). While this study had its shortcomings, it received significant attention both within scientific circles and a wider audience. A more thorough phylogeographic analysis that used ten different genes instead of a single mitochondrial marker indicates that at least two major expansions out of Africa after the initial range extension of Homo erectus played an important role shaping the modern human gene pool and that recurrent genetic exchange is pervasive (Templeton 2002). These findings strongly demonstrated Africa’s central role in the evolution 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 (Holmes 2004). Phylogeography is a useful tool in understanding the origins and distributions of different viral strains. A phylogeographic approach has been taken for many diseases that threaten human health, including dengue fever, rabies, influenza and HIV (Holmes 2004). 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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