Biogeography Study PDF

**BIOGEOGRAPHY** **UNIT-I: INTRODUCTION TO BIOGEOGRAPHY** **1.1 Biogeography-Concept, definition, nature and scope** **1.2. Historical development and branches of Biogeography** **1.3. Approaches in Biogeography** **1.4. Importance of Biogeographic studies** **1.1 Biogeography-Concept, definit...

**BIOGEOGRAPHY** **UNIT-I: INTRODUCTION TO BIOGEOGRAPHY** **1.1 Biogeography-Concept, definition, nature and scope** **1.2. Historical development and branches of Biogeography** **1.3. Approaches in Biogeography** **1.4. Importance of Biogeographic studies** **1.1 Biogeography-Concept, definition, nature and scope** **1.1.1 Concept of Biogeography:** Biogeography is the geography of organic life, the study of the spatial distribution of animate nature, including both plants and animals and the processes that produce variations in the patterns of distribution. This branch of geography is concerned with the multitudinous forms of plant and animal life which inhabit the densely populated zone over the earth's surface, as well as the complex biological activities which are controlled by natural environment. Biogeography forms an important link between the disciplines of geography and ecology, the ecosystem providing the fundamental integrating concept for the scientific study of many aspects of the man-environment complex. Geography itself has been variously defined as the study of areal distributions, spatial patterns, locational analysis, man-earth relationships and the environmental relationships of man. Biogeography, in a similar way, encompasses all these aspects of study in relation to the living beings with an emphasis on the man's relations. Thus this branch of geography studies all biotic things consisting of the earth's environment in respect to man. Its study, therefore, involves the evaluation of distribution areas of biota which necessitates the deciphering of information available from propagation areas concerning the ecological potential, genetic viability, phylogeny of biotic communities as well as the spatially and temporally varying behaviour of environmental factors. The basic material for biogeographic investigations consists of the organisms, plant and animal communities which exhibit wide extensions over the globe with varying degrees of concentrations. So more accurately, it is the study of the biosphere which envelops the surface of the earth and consists of all living organisms living on land, aquatic and aerial areas. The environmental factors and the human activities which affect the distribution of living-being form the main substratum of biogeography. **1.1.2 Definition** 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, isolation and habitat area. Phytogeography is the branch of biogeography that studies the distribution of plants. Zoogeography is the branch that studies distribution of animals. Mycogeography is the branch that studies distribution of fungi, such as mushrooms. Knowledge of spatial variation in the numbers and types of organisms is as vital to us today as it was to our early human ancestors, as we adapt to heterogeneous but geographically predictable environments. Biogeography is an integrative field of inquiry that unites concepts and information from ecology, evolutionary biology, taxonomy, geology, physical geography, palaeontology, and climatology. Modern biogeographic research combines information and ideas from many fields, from the physiological and ecological constraints on organismal dispersal to geological and climatological phenomena operating at global spatial scales and evolutionary time frames. The short-term interactions within a habitat and species of organisms describe the ecological application of biogeography. Historical biogeography describes the long-term, evolutionary periods of time for broader classifications of organisms. Early scientists, beginning with Carl Linnaeus, contributed to the development of biogeography as a science. The scientific theory of biogeography grows out of the work of Alexander von Humboldt (1769--1859), Francisco Jose de Caldas (1768-1816), Hewett Cottrell Watson (1804--1881), Alphonse de Candolle (1806--1893), Alfred Russel Wallace (1823--1913), Philip Lutley Sclater (1829--1913) and other biologists and explorers. **1.1.3 Nature** Biosphere, the organic world, is that part of the earth which contains living organisms, comprising the biologically inhabited soil, air and water. It is a relatively shallow zone in comparison the lithosphere and the atmosphere, as most of the organisms need specific climatic conditions to grow and survive. In the oceans also life is mainly confined to a depth of few hundred metres as far as the solar radiations can penetrate. But for all its limited extent, biosphere is a densely populated zone teeming with; a myriad form of life which exhibit bewildering varieties and complexities. The most readily visible part of the biosphere consists of larger plants and animals but they constitute a very small percentage of the whole. It is now known that about half a million species of plants and an equal number of species of animals inhabit the globe. Besides the larger animals and plants, small microscopic organisms called micro-flora and micro-fauna inhabit the soil, water and air. A microscopic examination of the humus-rich top soil reveals that in one gram of soil there may be as many as 100,000 algae, 16 million fungi and perhaps several billion bacteria. Any study of biosphere involves the study of the habits and habitats of all plants and animals against the backdrop of environment. All living creatures show inter-dependence on each other rind a complexity of inter-relations, as they do not exist in isolation. In this complexity of inter-relationship the key position is occupied by green plants which have the unique ability to use solar energy to manufacture food from simple substances like carbon, hydrogen, nitrogen, oxygen etc. The food thus manufactured and the solar energy stored is essential not for them alone but also for the multitudes of various animals through which it is circulated. Animals are therefore, directly or indirectly dependent on plants. In some cases such activities are mutually beneficial, in others antagonistic. For example, many plants rely on animals for pollination or seed dispersal, while plants frequently provide food, shelter and protection to animals. Biosphere is not just a collection of living organisms, rather it is a place where its animate and inanimate objects interplay and display a spectrum of life-forms and environment. The animate parts of biosphere are wholly dependent on the inanimate environment of land, soil, air and water within which they exist. Living organisms have their total dependence on this environment for water, light, oxygen, carbon dioxide and other mineral nutrients, all of which are necessary for the very existence of life. Conversely, the inorganic environment is profoundly affected by the existence of the organisms which inhabit it. There is thus a continual exchange of energy and mineral nutrients within the organic and inorganic parts of the biosphere. Biosphere includes man as well, who through his various activities has changed the various life-forms and the landscape. Domestication of animals and plants and the resulting activities of ranching, pastoralism, livestock-rearing, agriculture, deforestation etc. have changed the original landscape of this planet to a large extent. Human is the main agent who has destroyed and altered the nature's equilibrium at every location and compelled the plants and animals to adopt various modifications in their form and physiology. Still the main stem of biogeography lies in the study of plants and animals as the study of major world soil- climate-vegetation units, vegetation history, energy and chemical nutrient flows, ecosystems and distribution patterns of plants and animals. The biosphere consists of all animate objects including man, and the various activities of man in relation to the biosphere form the core of biogeographical studies. **1.1.4 SCOPE OF BIOGEOGRAPHY**: However, the primary subject matter of biogeography comprises the analysis and interpretation of different aspects of living organisms including plants and animals of the biospheric ecosystem. Thus, on the basis on plant and animal, biogeography is divided into three basic branches and these three also divided in sub-discipline. They are given below: 1. **Plant Biogeography or Phytogeography** 2. **Zoogeography or Animal Geography** 3. **Pedology or Soil Geography** **Plant Biogeography or Phytogeography :** The study of plants communities as social groups in terms of their evolution, spatial and temporal changes, dispersal and distribution patterns, processes and causes of their spatial variations and ecological changes through time, their interactions with the environment of their habitats and responses coming there from etc., is called phytogeography (plant geography). **Zoogeography or Animal Geography :** The study of animal communities of both land and marine habitats and environment in terms of speciation and evolution, dispersal, extinction and distribution patterns of animals, interactions of animals with environment, responses of animal communities to. Human activities etc. is called animal or zoogeography. Zoogeography also studies the abilities of animals to adapt to varying environmental conditions of their habitats which vary both spatially-and temporally. **Pedology or Soil Geography :** Soil geography or pedology also the subject matter of biogeography. It is the study of soils in their natural environment. It is one of two main branches of soil science, the other being edaphology. Pedology deals with pedogenesis, soil morphology, and soil classification, while edaphology studies the way soils influence plants, fungi, and other living things. Today, the subject matter of biogeography is also broken on the basis of approaches to the study of plants and animals communities into three main fields of study: - **Historical Biogeography,** - **Ecological Biogeography, and** - **Conservation Biogeography.** **Historical Biography :** Historical biogeography is called pale biogeography and studies the past distributions of species. It looks at their evolutionary history and things like past climate change to determine why a certain species may have developed in a particular area. The branch of historical biogeography is called pale biogeography because it often includes pale geographic ideas---most notably plate tectonics. **Ecological Biogeography :** Ecological biogeography looks at the current factors responsible for the distribution of plants and animals, and the most common fields of research within ecological biogeography are climatic equability, primary productivity, and habitat heterogeneity. **Conservation Biogeography :** Scientists in the field of conservation biogeography study ways in which humans can help restore the natural order of plant and animal life in a region. In recent years, scientists and nature enthusiasts alike have further expanded the field of biogeography to include conservation biogeography---the protection or restoration of nature and its flora and fauna, whose devastation is often caused by human interference in the natural cycle. - **Biogeography is also divided on the basis of habitats into 3 categories as follows :** **Mainland or Terrestrial Biogeography:** Mainland or terrestrial biogeography is concerned with the study of flora and fauna of the continents and parts thereof adopting both historical (evolutionary) and ecological approaches. **Marine Biogeography :** Marine biogeography is the study of marine organisms of plankton, nekton and benthos communities in different marine bio zones. **Island Biogeography :** Island biogeography is quite different from terrestrial and marine biogeography because each island has different history of its origin and different patterns of evolution of its flora and fauna. **1.1 SUMMARY** Biogeography is the scientific study of the distribution of living organisms on Earth and the processes that have shaped their geographic patterns over time. It is a multidisciplinary field that integrates concepts and methods from biology, geography, geology, ecology, and evolutionary biology to understand why species are found where they are and how they have come to be distributed across different regions. Here\'s a more detailed breakdown of the concept, definition, nature, and scope of biogeography: 1. Concept: Biogeography explores the spatial distribution of organisms, including plants, animals, fungi, and microorganisms, across various scales, from local habitats to global ecosystems. It seeks to answer questions about why certain species are found in specific geographic areas, how they have migrated or dispersed over time, and what environmental and historical factors have influenced these patterns. 2. Definition: Biogeography can be defined as the scientific study of the distribution and abundance of life forms (organisms) in relation to the environment, both past and present. This field investigates the spatial and temporal variations in species diversity, composition, and richness, as well as the ecological and historical factors responsible for these variations. 3. Nature: Biogeography is a diverse and dynamic field that encompasses various sub-disciplines and approaches, including: - Historical biogeography: Focuses on the study of past distribution patterns, including understanding how continental drift, climatic changes, and evolutionary processes have shaped the distribution of species. - Ecological biogeography: Examines the present-day distribution of species in relation to contemporary environmental factors, such as climate, habitat, and human activities. - Island biogeography: Concentrates on the study of species richness and composition on islands, providing insights into factors like isolation, area, and immigration. - Phylogeography: Combines genetic and geographic data to study the historical processes that have shaped the genetic diversity and distribution of populations and species. 4. Scope: The scope of biogeography is broad and includes the following key aspects: - Spatial distribution: Understanding the patterns of species distribution on Earth, including the identification of biogeographic regions and boundaries. - Historical biogeography: Investigating the evolutionary history of species and how past geological and climatic events have influenced their distribution. - Ecological biogeography: Analyzing the ecological factors that determine the current distribution of species, including climate, habitat, and interactions with other organisms. - Conservation biogeography: Applying biogeographic principles to guide conservation efforts, such as identifying areas of high biodiversity and conservation priorities. - Applied biogeography: Utilizing biogeographic knowledge in fields like agriculture, forestry, epidemiology, and wildlife management to make informed decisions about resource management and disease control. In summary, biogeography is a multidisciplinary science that seeks to unravel the complex relationships between living organisms and their environment, both past and present, to gain insights into the patterns and processes of life on Earth. It has practical applications in conservation, resource management, and understanding the impacts of environmental change. Top of Form **1.2. Historical development and branches of Biogeography** Biogeography is the discipline of biology that studies the present and past distribution patterns of biological diversity and their underlying environmental and historical causes. For most of its history, biogeography has been divided into proponents of vicariance explanations, who defend that distribution patterns can mainly be explained by geological, tectonic-isolating events; and dispersalists, who argue that current distribution patterns are largely the result of recent migration events. This paper provides an overview of the evolution of the discipline from methods focused on finding general patterns of distribution (cladistic biogeography), to those that integrate biogeographic processes (event-based biogeography), to modern probabilistic approaches (parametric biogeography). The latter allows incorporating into biogeographic inference estimates of the divergence time between lineages (usually based on DNA sequences) and external sources of evidence, such as information on past climate and geography, the organism fossil record, or its ecological tolerance. This has revolutionized the discipline, allowing it to escape the dispersal versus vicariance dilemma and to address a wider range of evolutionary questions, including the role of ecological and historical factors in the construction of biomes or the existence of contrasting patterns of range evolution in animals and plants. The five basic historical biogeographic methods are: 1. **dispersalism,** 2. **phylogenetic biogeography,** 3. **panbiogeography,** 4. **cladistic biogeography, and** 5. **Parsimony analysis of endemicity**. 1. **Vicariance vs. Dispersal: The Case of the Ratite Birds** Biogeography is a very old discipline, dating back to the time when the first naturalist explorers, such as Alexander von Humboldt (1805), were intrigued by the fact that regions with similar climates like the Mediterranean Basin and Chile in South America exhibited faunas with similar physiognomies (life forms) but in which the inhabiting species were very different. Conversely, regions such as Africa and South America separated by large geographic barriers like the Atlantic Ocean show faunas of similar composition (Cox and Moore 2010). One of the best examples of this type of disjunct geographic distribution is that of ratites, a primitive group of birds (Palaeognatha) that includes the ostriches, cassowaries, emus, rheas and kiwis. This clade is distributed in all major southern continents (Fig. 1a), but how did these flightless birds come to be confined to a distribution scattered across different continents, now separated by thousands of miles of ocean? Fig 1 Biogeographic history of the ratite birds (ostriches, emus, reas, etc.). a. Current geographic distribution of extant and extinct ratite genera; areas in *yellow* (Antarctica, Europe) harbor fossil remains but no extant species. b. Two alternative hypotheses to explain this disjunct distribution: recent, ocean-crossing dispersal events (*left*) or ancient, tectonic-isolating vicariance events (*right*). c. A cladistic biogeographic analysis comprising three steps: (*left*) DNA-based phylogeny representing the relationships among ratite genera and their relatives: tinamous (adapted from Pereira and Baker (#ref-CR51)); (*center*) a taxon-area cladogram is constructed by replacing the taxon names in the phylogeny with the areas where they occur; (*right*) a cladistic biogeographic method (Brooks Parsimony analysis, Brooks (#ref-CR3)) is used to derive an "area cladogram" showing the relationships among the areas in Fig. [1a](#Fig1) based on their shared endemic taxa. This area cladogram presumably represents the history of biotic connections between the areas of endemism for the ratite genera: tinamous (*Tinamu*, *Eudromia*), extinct moas (*Dinornis*, *Anomalopteryx*, *Emeus*), reas (*Rhea*, *Pterocmemia*), ostriches (*Struthio*), kiwis (*Apteryx*), cassowaries (*Casuarius*), and emus (*Dromaius*). Adapted from Sanmartín ((#ref-CR67)). Paleomaps 0 million years (*left*) and 100 million years (*right*) adapted from ODSN Two alternative biogeographic processes have been proposed (Fig. [1b](#Fig1)): *dispersal*---the ancestor of the group was originally distributed in one of the areas, the "center of origin," from which it dispersed to the other areas by crossing a geographic barrier (e.g., the Southern Hemisphere ocean basins, Fig. [1b](#Fig1) left); *vicariance*---the group ancestor was distributed in a widespread area, then covering all its present distribution, which became fragmented by successive geographic barriers; this geographic division was followed by allopatric speciation, so that each member now survives in an isolated continent. The best example is the breakup of the ancient supercontinent of Gondwana during the Mesozoic-Cenozoic, which has often been argued to explain austral disjunct distribution patterns such as that of ratites (Fig. [1b](#Fig1) right). In the dispersal explanation, the barrier predates the geographic disjunction, whereas in the vicariant explanation, the appearance of the barrier causes the geographic division, so it must be of the same age as the resulting allopatric speciation event. Naturally, these processes are not mutually exclusive: for example, the formation of the Panama isthmus between North and South America at the end of the Tertiary (3.5 million years ago) was simultaneously a vicariant event---by isolating marine organisms between the Atlantic and Pacific Oceans---and a dispersal event, since it established a new migration route between North and South America for terrestrial mammals, the "Great American Biotic Interchange" (Simpson (#ref-CR76)). But for many decades, these two explanations were viewed as competing hypotheses in historical biogeography, with proponents of one or another engaged in a polarized and sometimes heated debate (review in Cox and Moore (#ref-CR8) and Lomolino et al. (#ref-CR37)). The current tendency is to accept both dispersal and vicariance explanations as equally likely hypotheses and use other information sources (e.g., the fossil record, information on past climates and geography, or the ecological tolerance of the group) to discriminate between them (Stigall and Lieberman (#ref-CR80); Ronquist and Sanmartín (#ref-CR64)). In this review, I use the example of ratites to show how incorporating new sources of evidence into biogeographic reconstructions has allowed researchers to address a wider range of evolutionary questions than the simple search for congruent distribution patterns. - **Dispersalism & Center of Origin** For centuries, dispersal was the dominant explanation supported by a static concept of Earth and life. Darwin\'s theory of evolution ((#ref-CR15)) changed this immutable view of species by identifying the mechanism, natural selection, by which organisms evolve into new species. But Darwin and his contemporaries, like Wallace ((#ref-CR81)), still believed on the idea of geological stability, according to which the position and size of continents had not changed over time. New species evolved in a limited area, a "center of origin," from which they dispersed to other regions over the same pattern of world geography that we see today (Cox and Moore (#ref-CR8); Lomolino et al. (#ref-CR37)). This view was challenged by "extensionists" such as Joseph Dalton Hooker (1844), who argued that long-distance dispersal across persistent barriers was unlikely, and instead continents must have been connected in the past by tracts of dry land and now-submerged landbridges over which organisms dispersed. Darwin and Wallace\'s idea of dispersal from a center of origin continued to be dominant through the first half of the twentieth century, represented by the "New York school of zoographers," of which Matthew ((#ref-CR40)), Darlington ((#ref-CR14)), and Simpson ((#ref-CR75)) were the most important proponents. The introduction of the theory of plate tectonics in geology, and especially the arrival of cladistics (see below), led to a new approach, *Phylogenetic Biogeography* (Brundin (#ref-CR5); Hennig (#ref-CR25)) that departed from the narrative dispersal scenarios of the past. Although it was still based on the idea of "dispersal" and "centers of origin," it was also the first approach to use information about the evolutionary relationships of organisms (in the form of a tree or cladogram) as the basis to infer their biogeographic history. For example, it assumed that in every speciation event, the species that retained the ancestral ("plesiomorphic") characteristics stayed closer to the original area, while the most derived ("apomorphic") species was the one that dispersed (Crisci et al. (#ref-CR10); Cox and Moore (#ref-CR8)). Brundin ((#ref-CR5)) was also pioneer in using geological information to interpret biogeographic histories (Lomolino et al. (#ref-CR37)). Two criticisms have been raised against the dispersalist approach to biogeography, especially by cladistic biogeographers (see below): a. **Lack of scientific basis**: Since any distribution pattern can be explained by invoking a sufficient number of dispersal events, dispersal-based hypotheses cannot be refuted scientifically within a rigorous hypothetic-deductive framework. Also, if we accept dispersal as a possible explanation for disjunct patterns, vicariance explanations would never be inferred (Platnick and Nelson (#ref-CR53); Morrone and Crisci (#ref-CR43)). b. **Lack of predictive power:** Dispersal-based hypotheses are lineage-specific, idiosyncratic scenarios that can only explain the biogeographic history of individual lineages (e.g., Brundin (#ref-CR5)) but cannot provide a general theory to explain how organisms with different ecologies and dispersal abilities came to occupy the same biogeographic regions and to exhibit similar distribution patterns (Croizat et al. (#ref-CR13); Nelson and Platnick (#ref-CR45); Humphries and Parenti (#ref-CR28)). As we will see below, this is not necessarily true, and dispersal can sometimes generate congruent distribution patterns similar to those expected from vicariance. 2. **Vicariance and Cladistic Biogeography** **In the second half of the twentieth century, two scientific revolutions contributed to the appearance of a new paradigm in historical biogeography. The first revolution was the surge of cladistics (Hennig 1966), a new method to reconstruct evolutionary relationships among organisms based on shared, derived biological characteristics ("synapomorphies"). When competing hypotheses of evolutionary relationships exist, those that imply the minimum number of changes or ad hoc assumptions are preferred---the principle of "parsimony" or "Occam\'s razor" (Cox and Moore 2010; Lomolino et al. 2006). The second revolution was the development in the 1960s of the "theory of plate tectonics." The Earth\'s outer layer, the lithosphere, is divided into rigid rocky plates comprised of continental and oceanic crust that move over the surface of the Earth by sliding on the plastic upper layer mantle, the athenosphere. The idea that species could passively ride on the continents as they split and dispersed across the surface of the Earth led to the concept of "vicariance," summarized on the Italian botanist Leon Croizat\'s (1958) famous sentence: "Life and Earth evolve together," meaning that geological barriers evolve together with biotas (Cox and Moore 2010).** **Cladistic vicariance biogeography (Rosen 1978; Platnick and Nelson 1978; Nelson and Platnick 1981; Wiley 1988) was born from the fusion of cladistics and Croizat\'s concept of vicariance (Fig. 1c). In the vicariant model, an ancestral area is divided by the appearance of successive geographic barriers. Since each geographic division would have been followed by allopatric speciation, one can reconstruct the sequence of vicariance events from the sequence of cladogenetic (speciation) events in the phylogeny of the lineages endemic to the area (Fig. 1c, left). A cladistic biogeographic analysis starts with the construction of an "area cladogram," in which the name of taxa in the phylogeny is replaced with the areas where they occur (Fig. 1c, center). If every taxon is endemic to one area and every area harbors one taxon, the construction of area cladograms is trivial. But often, area cladograms include widespread taxa (taxa present in more than one area), such as the ratite genus Casuarius in Australia and New Guinea, or redundant distributions (several taxa occurring in the same area), such as the kiwis and moas in New Zealand (Fig. 1c, center). This introduces ambiguity in the inference of the area cladogram because these areas may occupy different positions in the area cladogram depending on which relationships are allowed between the areas occupied by the non-endemic taxa. Cladistic biogeographers use different methods that differ in the way they treat these ambiguous data to derive a "resolved" area cladogram in which each area is represented only once (Fig 1c, right). These include Component Analysis (Nelson and Platnick 1981; Page 1990), Brooks Parsimony Analysis (BPA, Brooks 1990; Wiley 1988), Tree Reconciliation (Page 1994), and Paralogy-free subtrees (Nelson and Ladiges 1996) and more recently, Phylogenetic Analysis for Comparing Trees (PACT, Wojciki and Brooks 2005) and Three-area-cladistics (Ebach et al. 2003); see Crisci et al. 2003 and Morrone 2009 for a more detailed explanation on these methods. An area cladogram is a hierarchical, branching pattern of relationships that groups areas based on their shared endemic taxa and which presumably reflects the history of biotic connections between the areas of endemism for the group of organisms analyzed. For example, "sister" areas that form a clade in the area cladogram, such as Australia and New Guinea, would have shared a more recent biotic connection in the past for ratite birds; that is, the barrier between these two areas was formed more recently than other barriers with the remaining areas. Furthermore, by comparing area cladograms of several groups of organisms that inhabit the same region, one might find general biogeographic patterns---a "general area cladogram"---that presumably reflect the relationships among the areas of endemism based on their shared biotas (Nelson and Platnick 1981; Wiley 1988). For example, Crisci et al. (1991) compared the area cladograms of numerous animal and plant lineages from South America and found two different biogeographic regions: northern "tropical" South America was related biogeographically to North America, whereas southern "temperate" South American showed closer biotic links to Australia.** **In comparison with the narrative dispersal scenarios that had earlier dominated the field, cladistic biogeography represented a huge leap forward because it provided for the first time an analytical framework with which to reconstruct the biogeographic history of lineages and biotas. Taxa that shared similar phylogenetic and distribution patterns were assumed to have shared a common biogeographic history; i.e., they were part of the same ancestral biota that became divided by geologic or climatic vicariant isolating events. Thus, unlike dispersalist hypotheses, vicariance hypotheses could be tested by searching for congruence in phylogenetic and distribution patterns among different organisms (Humphries and Parenti 1999; Parenti 2007). Cladistic biogeography also helped to move the discipline from a taxon-based approach centered on reconstructing the evolutionary history in space and time of individual lineages (e.g., Brundin 1966) toward a comparative "area biogeography" approach that aims to understand global distribution patterns through the comparison of area cladograms (Crisci et al. 1991; Humphries and Parenti 1999).** **Nevertheless, as with dispersalism before, cladistic biogeography became in time a too "reductionist" explanation because it denied dispersal of any major role in generating global biodiversity patterns. Dispersal was considered a rare and random phenomenon that affected individual lineages but did not produce congruent distribution patterns (Humphries and Parenti 1999). Similarly, dispersal histories---because they were idiosyncratic and lineage-specific events---could not be addressed within a hypothetic-deductive framework like cladistic biogeography. This view of dispersal as a unique event instead of a pattern-generating process is challenged by the case of oceanic islands of volcanic origin, such as the Hawaiian Archipelago, which could only have been colonized by over-water dispersal. Funk and Wagner (1995) found that patterns of island colonization in these islands were highly congruent across multiple lineages, proceeding from one island to the next along the island chain. Similarly, Sanmartín et al. (2008) inferred highly concordant, non-random colonization patterns across numerous organisms endemic to the Atlantic Canary Islands.** **So far, we have been discussing about the traditional form of dispersal that involves individual species moving over a geographic barrier (Humphries and Parenti 1986), also termed "jump" or "random" dispersal (Ronquist 1998). But there is another type of dispersal, "dispersion" or "range expansion," in which an individual species expands its geographic** **range in response to the disappearance of a previous geographic (dispersal) barrier. This type of dispersal has been termed "geodispersal" (Lieberman and Eldredge 1996) or "predicted dispersal" (Ronquist 1998) when it involves congruent, temporally correlated range expansion in independent clades. Unlike jump dispersal, it is not lineage-specific but usually connected to geological or global climatic events that cause several different lineages to expand their ranges congruently. Therefore, as expected from vicariance, geodispersal events can give rise to biogeographic patterns that are congruent across groups with different ecologies and dispersal abilities (Lieberman 2000, 2003). One example is the closing of an ocean barrier previously separating two continents, such as the Turgai Strait between Europe and Asia 30 million years ago, which led to episodes of range expansion occurring simultaneously in multiple animal clades (Sanmartín et al. 2001).** **Unlike jump dispersal, cladistic biogeographers accept dispersion as a necessary process to explain how ancestors obtained their widespread distribution prior to the first vicariance event (Humphries and Parenti 1999). In addition, new cladistic methods such as PACT and modified Brooks Parsimony analysis (Lieberman and Eldredge 1996; Lieberman 2000), from the so-called "Phylogenetic Biogeography II" school (Lomolino et al. 2006), recognize geodispersal as a process that results in congruent distribution patterns across multiple lineages like vicariance, and which therefore might be inferred through a general area cladogram approach. But the distinction between jump dispersal and geodispersal (or land dispersal) is not always clear. The breaking or forming of land connections in plate tectonics is a gradual process, so there may be a temporal transition from land dispersal to jump dispersal with other types of dispersal falling in between. For example, the land connection over Antarctica that allowed marsupials to migrate from South America to Australia before the Antarctic continent became glaciated went through several phases (Woodburne and Case 1996; Sanmartín 2002): land dispersal was possible through the South Tasman Rise until the Early Paleocene (64 million years), followed by "stepping-stone" island dispersal across the shallow marine seaway separating Australia and Antarctica until the Early Eocene (52 million years); eventually, fully marine conditions were established with the opening of the South Tasman Sea 35 million years ago, after which only jump dispersal was possible (Sanmartín 2002). Finally, land dispersal not only requires a geological connection, e.g., a land bridge, but that the environmental conditions along the bridge are within the ecological limits of the dispersing organisms (Wiens and Donoghue 2004). A "filter corridor" involves land dispersal with a more selective connection restricted to organisms exhibiting the right ecological tolerance. For example, migration across Beringia during the Quaternary glaciations was restricted to cold adapted, tundra organisms (Sanmartín et al. 2001).** **A second criticism against cladistic biogeography is that it ignores processes in the biogeographic inference: the area cladogram is inferred without any reference to the underlying biogeographic events. Cladistic methods have been termed "pattern-based" (Ronquist 2003; Sanmartín 2007) because they are allegedly process-free. They focus on finding patterns of relationships among areas of endemism, which are later interpreted in terms of events, and this sequence---first discovering a pattern, then inferring its cause---is the foundation of the cladistic biogeographic approach (Ebach et al. 2003; Parenti 2007). Cladistic biogeographic methods interpret congruence between distributional patterns as the result of vicariance, whereas any case of incongruence between the general area cladogram and the individual patterns is explained by additional processes, such as jump dispersal, speciation, or extinction (Brooks 1990; Humphries and Parenti 1999). One problem with this approach is that usually several different processes can explain the same biogeographic pattern (see below), so it is difficult to compare alternative biogeographic scenarios using cladistic methods (Sanmartín 2007).** **Phylogenetic biogeographic methods such as PACT and modified BPA depart from this standard approach in that in addition to searching for a general area cladogram, the "backbone" of the tree, which is interpreted as resulting from vicariance or geodispersal events, they attempt to infer other processes that are lineage-specific. These unique events that affect single lineages can include extinction, postspeciation range expansion, jump dispersal, or failure to speciate in response to a vicariant event (Wojciki and Brooks 2005; Lieberman 2000, 2003; Stigall and Lieberman 2005). Still, these methods share the goal with standard cladistic approaches of producing "area cladograms," hierarchical patterns of biotic relationships between areas of endemism that are interpreted in terms of processes (e.g., Maguire and Stigall 2008), but which are inferred without explicit reference to an underlying statistical process model (see below).** **Finally, as seen above, geodispersal events caused by continental collision can create patterns of area relationships in which areas and their biotas become connected instead of splitting as in the vicariance model. Most regions actually conform to a "reticulate" pattern with alternative cycles of area collision (geodispersal) and area splitting (vicariance), as barriers form and close over time. For example, during the Mesozoic era, the Northern Hemisphere continents were joined into a paleocontinental configuration, Asiamerica--Euramerica, that was very different from the current one in which we find the separate continents of North America and Eurasia (Fig. 2; Sanmartín et al. 2001). This complex reticulate scenario cannot be represented by a single area cladogram because the hierarchical relationships between areas change over time (Fig. 2). Phylogenetic biogeographic methods such as modified BPA (Lieberman 2000) address this problem by inferring two different area cladograms, one reflecting the vicariance (geographic division) events and the other the geodispersal (area collision) events. If the vicariance and geodispersal cladograms exhibit congruent topologies, it is assumed that cyclical events had produced the observed biogeographic pattern (Maguire and Stigall 2009).** **Fig 2** Reticulate biogeographic history: **a** Geological history of the Northern Hemisphere, showing how northern landmasses joined and split repeatedly over time as barriers (epicontinental seas) and connections (landbridges) arose and fell. **b** Scheme representing the difficulties to represent such a history into a single pattern of relationships between areas of endemism or "area cladogram." In the Mesozoic, the northern landmasses were joined into the paleocontinents of Euramerica (EN--WP) and Asiamerica (WN--EP), whereas the present continental configuration between North America (EN--WN) and Eurasia (WP--EP) was attained during Cenozoic times. During some time periods, the four landmasses were isolated. Abbreviations: *EN* and *WN*: Eastern and Western North America divided by the Rocky Mountains; *EP* and *WP*: Asia and Europe separated by the Ural Mountains. Adapted from Sanmartín et al. ((#ref-CR71)) and Sanmartín ((#ref-CR66)) 3. **Event-Based Biogeography: Integrating Processes and Patterns** **Event-based methods were born as a response to the limitations of cladistic biogeography as explained above (Page 1995; Ronquist 1997, 1998, 2003). These methods use a deterministic cost-model approach in which each event or biogeographic process (e.g., dispersal, vicariance) is assigned a given cost according to its likelihood of occurrence. Figure 3 shows an event-based reconstruction of the biogeographic history of ratites. Besides dispersal and vicariance, the biogeographic cost model includes two additional processes (Fig. 3a): extinction, the disappearance of a lineage from part of its ancestral distribution, and duplication ("within-area speciation"), which is sometimes equated to sympatric speciation or to allopatric speciation in response to a temporary dispersal barrier affecting a single organism lineage (Ronquist 2003). By fitting the organism phylogeny to an area cladogram reflecting the relationships between the areas of endemism (Fig. 3b), we can obtain the biogeographic reconstruction (Fig. 3c) with the minimum cost in terms of the events that need to be postulated to explain the observed distribution pattern (Ronquist 2003; Sanmartín 2007).** **Fig 3** Event-based reconstruction of the biogeographic history of ratites. Given a cost-based biogeographic model in which each biogeographic event is assigned a cost (**a**), and a geological area cladogram specifying the relationships between the areas of endemism, i.e., the breakup sequence of the southern continents from Gondwana (**b**), it is possible to infer how much the biogeographic history of ratites may be explained by geological vicariance and how much by additional processes, such as dispersal, extinction, and duplication (see text for an explanation). **d** The significance of the inferred reconstruction can be tested by comparing the frequency of events in the original phylogeny against a distribution of frequencies obtained by randomizing the distributions in the original phylogeny 100 times. Abbreviations as in Fig. (#Fig1). Adapted from Ronquist and Sanmartín ((#ref-CR64)) **Notice that an event-based reconstruction not only specifies the set of events (dispersal, extinction, duplication, and vicariance) that have led to this pattern of biogeographic distributions, but also their relative timing (Fig. 3c). It suggests that the ancestor of ratites and tinamous (Tinamu, Eudromia) was present in the landmasses that once formed part of East Gondwana before they broke apart (New Zealand, South America, Australia-New Guinea), and that the divergence of moas (Dinornis, Anomalopteryx, Emeus) and rheas (Rhea, Pterocnemia) was the result of vicariance, geologically isolating events (the breakup of connections between New Zealand and South America and East Antarctica); by contrast, the occurrence of ostriches (Struthio) in Africa and kiwis (Apteryx) in New Zealand was the result of dispersal events that took place after these landmasses broke away from Antarctica (Fig. 3c). In the ratite example, the area cladogram represents the geological sequence of Gondwana breakup (Fig. 3b), and the reconstruction in Fig. 3c indicates how much the biogeographic history of ratites can be explained by this sequence of vicariant isolating events. In other cases, the area cladogram can be inferred by searching for the pattern of area relationships that best explains the phylogeny and terminal lineage distributions or, in other words, the pattern of area relationships that produces the biogeographic reconstruction with the minimum cost in terms of the inferred biogeographic events.** **The main difference between this event-based reconstruction and the cladistic biogeographic approach in Fig. 2 is that processes are not inferred "a posteriori" from the area cladogram, but instead the inference of processes is directly tied to the inference of biogeographic patterns through the cost-matrix model. A different biogeographic model with different costs might result in a different pattern of area relationships and a different set of biogeographic events. This explicit connection between the process-based model and the expected patterns makes it possible to compare alternative biogeographic hypotheses or scenarios within a statistical inference framework (Sanmartín 2007). For example, one can compare the observed frequency of biogeographic events with a null distribution obtained from randomizing the distributions in the original phylogeny to test whether the observed patterns are phylogenetically conserved (Fig. 3d).** **An obvious difficulty of the event-based approach is how to decide the cost of the biogeographic events. The most common method is to use a parsimony-based optimality criterion and choose costs that maximize the chances to recover "phylogenetically conserved" distribution patterns, that is, distribution patterns that do not change from ancestor to descendants and are conserved along the phylogeny. This is equivalent to the most parsimonious ("minimum change") explanation for the observed biogeographic pattern. Given that vicariance is a process that produces congruent ("conserved") distribution patterns across lineages, one option is to maximize the number of vicariance events by assigning this process a negative cost or benefit (Page 1995). Another option is to penalize those biogeographic events that break up the geographic association between ancestor and descendants (Ronquist 2003; Sanmartín et al. 2007). Under this criterion, dispersal and extinction must have a higher cost than vicariance and duplication because they both generate distribution patterns that are not phylogenetically conserved. For example, through dispersal the descendants may come to occupy a different range than the ancestor, such as in the case of kiwis (Apteryx in Fig. 3c), which are endemic to New Zealand but whose ancestor is inferred to have been present in Australia-New Guinea. Similarly, through extinction, one of the two descendants gets extinct in part of the ancestral range, breaking the geographic association between ancestor and descendants, such as the extinction of the ancestor of ratites in New Zealand after an initial "duplication" event in East Gondwana (Fig. 3c).** **One of the most popular event-based methods is dispersal--vicariance analysis (DIVA, Ronquist 1996, 1997). DIVA uses a cost-matrix approach in which extinction and dispersal events are assigned a higher cost in relation to vicariance and duplication. But unlike all other methods, it is not based on finding an area cladogram but on mapping area distributions onto the phylogeny and inferring the ancestral areas at cladogenetic events by minimizing the number of dispersal and extinction events. Because vicariance events are not ordered into a strictly bifurcating, splitting pattern like an area cladogram, DIVA is especially powerful for inferring reticulate biogeographic scenarios, such as the Northern Hemisphere (Fig. 2), in which areas join and split in different combinations over time with the arising and falling of barriers (Sanmartín et al. 2001; Donoghue and Smith 2004).** **Although initially developed for inferring the history of single lineages ("taxon biogeography"), DIVA and other event-based methods can be used to infer general biogeographic patterns by summarizing frequencies of dispersal and vicariance events across multiple groups distributed in the same set of areas. This has provided some novel insights on the relative role of dispersal and vicariance in shaping general biogeographic patterns. For example, event-based meta-analyses of the Northern Hemisphere (Sanmartín et al. 2001; Donoghue and Smith 2004) and Southern Hemisphere (Sanmartín and Ronquist 2004) biotas suggest that animals and plants showed fundamentally different biogeographic patterns, with animal distributions more likely to reflect ancient vicariance events and plant distributions more often shaped by recent dispersal events. This has been explained by the fact that plants are better colonizers due to the higher ability of plant seeds to disperse, whereas animals exhibit higher resilience or the ability to cope with the changing environments; this might have important implications for the construction of biomes (Donoghue and Smith 2004; Sanmartín 2007). Event-based meta-analyses also contributed to the recognition in biogeography of the concept of "concerted dispersal," by which jump dispersal (i.e., dispersal crossing a barrier as opposed to geodispersal), if channeled by abiotic factors such as prevailing winds or ocean currents, can generate congruent, non-random distribution patterns across multiple co-distributed lineages similar to those expected from vicariance (Sanmartín and Ronquist 2004). For example, many New Zealand plant species have their sister group in Australia, even though New Zealand separated from Australia ca. 80 million years ago. Paleobotanical evidence (Pole 2001) and event-based reconstructions (Sanmartín et al. 2007) suggest that these New Zealand plants dispersed from Australia by long-distance dispersal after the two continents broke apart, probably driven by the eastward-moving West Wind Drift.** **Proponents of cladistic biogeography often criticize event-based methods because they "over-simplify" the data by imposing a particular model, i.e., the cost-matrix approach (Ebach et al. 2003; Brooks 2005). Others argue that biogeographic inference must focus on finding patterns, not looking for ad hoc explanatory processes (Parenti 2007). But as seen above, the explicit connection between processes and the expected patterns make it easier for event-based methods to evaluate alternative biogeographic hypotheses (Crisp et al. 2011). A more serious criticism against these methods lies in the inference of processes that are not tied to speciation, such as extinction. Unlike cost constraints in relation to geology are introduced (Ronquist 1996; Sanmartín 2007; Nylander et al. 2008; Kodandaramaiah 2010). Also, complete extinction events, in which a lineage disappears from the entire ancestral range, or full dispersal events, in which one lineage leaves the ancestral range to colonize a different area without speciating, cannot be inferred with event-based methods because these events do not leave a trace in the phylogeny. For a dispersal or extinction event to be inferred, it must be tied to a speciation event, that is, dispersal and extinction must leave at least one descendant in the original area to be traceable from the phylogeny. In fact, this problem affects all biogeographic methods that are parsimony-based, including cladistic biogeography (see below). Lieberman (2002) showed that extinction events may erase the signal of vicariance and create artificially incongruent distribution patterns when no fossil information is included in a cladistic biogeographic analysis.** 4. **Parsimony in Biogeography** **Perhaps the most serious limitation of event-based and cladistic biogeographic methods is their reliance on the principle of parsimony for biogeographic inference (reviewed in Sanmartín 2010). Parsimony is a "minimization" criterion - i.e., the "most parsimonious" explanation is the one that implies the minimum number of changes in the geographic range that are needed to explain the current lineage distributions. Therefore, parsimony-based reconstructions tend to underestimate the frequency of events such as dispersal and extinction that break the geographic association between ancestor and descendants.** **Time is also a difficult dimension to incorporate within the parsimony framework. The branches in an area cladogram or an event-based reconstruction reflect the relative order of branching (vicariant) or fusing (geodispersal) events (Lieberman 2003; Sanmartín et al. 2007) but not the degree of divergence between lineages or the time since cladogenesis. This stands in contrast with the vicariance paradigm that has a clear temporal component: it predicts that clades showing disjunct distributions must be older than the geographic barrier that fragmented their geographic range. Thus, comparing the age of the barrier with the time of cladogenesis should allow discriminating between dispersal and vicariance explanations. The perils of ignoring time in biogeography are demonstrated by the phenomenon of "pseudocongruence": when two groups show similar biogeographic patterns but with a different temporal origin, and are therefore unlikely to have been caused by the same biogeographic events (Upchurch and Hunn 2002; Donoghue and Moore 2003). Parsimony-based methods cannot truly discriminate between pseudocongruence and true "shared biogeographic history," which implies both topological and temporal congruence between biogeographic patterns (Donoghue and Moore 2003). This is a serious flaw of these methods because, as we saw above, biogeographic barriers are often cyclical and the same barrier might have arisen at different points in time (Lieberman 2000; Sanmartín et al. 2001).** **Despite these drawbacks, parsimony-based methods, such as event-based or phylogenetic cladistic approaches are still a valuable option when time-calibrated branch lengths are not easily available. For example, they are often used in paleontological research (Lieberman 2000; Stigall and Lieberman 2006; Maguire and Stigall 2008; Prieto-Marquez 2010). Moreover, time can be incorporated indirectly in DIVA by separating events into time bins (Sanmartín et al. 2001), or in phylogenetic paleobiogeography (Maguire and Stigall 2008), by using a "temporally calibrated cladogram" in which time is given by the stratigraphic age and position of the fossil lineage in the phylogeny.** 5. **Parametric Biogeography: Integrating Processes, Patterns, and Time** **The role of time in biogeography became more relevant with the introduction of the concept of the "molecular clock." The vast majority of DNA-changes (mutations) are neutral from the point of view of fitness, and therefore tend to accumulate over time. If calibrated with independent information such as the fossil record, the molecular divergence between two organisms can be used to infer their time of divergence (Cox and Moore 2010). Many recent molecular studies have used this correlation to discriminate between dispersal and vicariance explanations and to show that dispersal had a larger role in generating distribution patterns than traditionally assumed (Renner 2004; Sanmartín and Ronquist 2004; Cook and Crisp 2005; de Queiroz 2005). This molecular approach to biogeography has been criticized by some biogeographers (Heads 2005) because of the inherent errors associated with the molecular clock: violated assumptions of rate constancy, incompleteness of the fossil record, use of molecular clocks from distantly related taxa, difficulties to assign the fossil to a particular clade in the phylogeny (e.g., "stem" or "crown" node), etc. Many of these criticisms have become less relevant, however, with recent developments in phylogenetic dating methods that permit relaxing the molecular clock assumption, i.e., allowing rate heterogeneity across lineages (e.g., Drummond and Rambaut 2007), or incorporating the uncertainty in the fossil calibration through the use of probabilistic approaches (Ho 2007).** **In recent years, new parametric statistical approaches have been developed in biogeography to incorporate the time dimension into the inference and as a response to what was perceived as the major weakness of the parsimony approach (Ree and Sanmartín 2009; Sanmartín 2010). These methods are termed "model based" or "parametric" because they are based on statistical models of range evolution, whose parameters ("variables") are biogeographic processes such as dispersal, range expansion, or extinction. Range evolution---i.e., the change in geographic range from ancestor to descendants---is modeled as a stochastic process that changes along the branches of the phylogenetic tree according to a probabilistic "Markov-chain" model. At the heart of a Markov-chain model, there is a "matrix of transition probabilities" (Fig. 4a) that determines the instantaneous rate of change from one state to another. In biogeographic models, the states of the Markov process are the set of discrete geographic areas that form the distribution range of the group (A, B, and AB; Fig. 4a), and the parameters of the model are biogeographic processes that change the geographic range of the species, such as range contraction (extinction, EA) or range expansion (DAB, Fig. 4a). By letting the model evolve along the branches of the phylogeny, which here represent the time since cladogenesis (Fig. 4b), we can estimate the rates (probability) of occurrence of the biogeographic processes (DAB, DBA, EA, EB) and infer the most probable ancestral ranges at every cladogenetic event (Fig. 4c; Sanmartín 2010).** **Fig 4** Parametric, time-based reconstruction of the biogeographic history of ratites. **a** Range evolution is modeled as a stochastic process ("Markov chain") that evolves along the branches of a phylogeny from ancestor to descendants as a function of time. The Markov process is governed by a matrix of transition probabilities (**a**) that determines the rate of change between geographic states (here the geographic ranges A, B, and AB), and whose parameters are biogeographic processes such as range expansion (*D*~AB~) and area-related extinction (*E*~A~). Given this model (**a**) and a time-calibrated phylogeny with molecular estimates for lineage divergence times (**b**, adapted from Pereira and Baker (#ref-CR51)), it is possible to reconstruct the spatio-temporal evolution of the group (**c**) by using a parametric biogeographic method such as Dispersal--Extinction--Cladogenesis (Ree et al. (#ref-CR58)). The parametric reconstruction (**c**) shows the most likely range inheritance scenario at each cladogenetic event; that is, how the ancestral range became divided between the two descendants at speciation; for example, "NZ/Gondwana" indicates diversification within New Zealand when this area was still part of East Gondwana (formed by AFR, NZ, SAM, AUS, and NG), while "NZ/AUS-NG" indicates vicariance between NZ and Australia-New Guinea. Abbreviations as in Fig. (#Fig1) **Compared to previous approaches, these methods offer several advantages (Sanmartín 2010). The most obvious is that the frequency (rate) of events can be estimated from the data, instead of assigned a cost a priori using ad hoc criteria, as in event-based biogeographic methods. There are also additional advantages:** **Rather than considering only the most parsimonious, "minimum change" reconstruction like parsimony, parametric methods can evaluate every possible ancestral area in terms of its "likelihood" (probability) of explaining the data. Therefore, they are better in integrating the uncertainty in the reconstruction of ancestral ranges in the phylogeny ("mapping uncertainty"). In addition, Bayesian parametric approaches can estimate the parameters over every possible tree topology and combination of branch lengths, so they can account for the uncertainty associated with the phylogenetic inference itself ("phylogenetic uncertainty").** **Parametric methods also provide an appropriate statistical approach to compare alternative biogeographic hypotheses or scenarios. Each scenario is formulated in terms of different parametric models, which can be compared on the basis of how well they fit the data. Because the parameters of each alternative model are biogeographic processes, one can identify the processes that best explain the biogeographic patterns by identifying the "best-fitting" model, for example, by using likelihood-based statistical tests. This contrasts with the use of random permutation tests in event-based biogeography, in which observed patterns can only be compared with those expected by chance (Fig. 3d).** **The most important advantage of parametric methods is their ability to integrate into the biogeographic inference estimates of the evolutionary divergence between lineages or the time since cladogenesis, which are represented by the length of branches in the phylogeny (Fig. 4b). For example, Fig. 4c shows that the giant moas of New Zealand diverged from the other ratites in the Early Cretaceous, when New Zealand was still part of Gondwana. In contrast, kiwis and African ostriches (Struthio) are of more recent origin (Late Cretaceous), when Africa and New Zealand had begun to rift apart from Antarctica and Australia. Since these are flightless birds, it raises the intriguing possibility that their ancestors could fly and lost this ability to adapt to the new insular environments, once the southern continents became isolated by oceans.** **Parametric methods are still in their infancy and only a few approaches have been developed (see Ree and Sanmartín 2009; Sanmartín 2010 for a review). The most popular is the Dispersal--Extinction--Cladogenesis (DEC) likelihood model developed by Richard Ree and colleagues (Ree et al. 2005; Ree and Smith 2008). This allows estimating by maximum likelihood rates of range expansion (dispersal) and contraction (extinction), and range inheritance scenarios at cladogenetic events from a time-calibrated phylogeny with terminal lineage distributions (Ree and Smith 2008). The second method is the Bayesian island biogeography (BIB) model developed by Sanmartín et al. (2008), which uses Bayesian inference to estimate areas' carrying capacities and rates of dispersal between islands from phylogenetic and distributional data of multiple co-distributed groups. It can be used to infer general biogeographic patterns by using a Bayesian approach that accommodates for differences in age, evolutionary rate, and dispersal capability across lineages (Sanmartín 2010). This approach has recently been used in continental biogeography to infer rates of biotic exchange between ecological and geographically isolated regions in Africa (Sanmartín et al. 2010).** **As with event-based methods, parametric methods have been criticized for their reliance on a particular biogeographic model, which is seen as a limitation. Biogeographical models, however, are best seen not as constraints over the data but as alternative hypotheses to explain the data (Sanmartín et al. 2008). A more important limitation is how to balance the complexity of biogeographic models with the inferential power of the method (Ree and Sanmartín 2009). The number of possible ranges and parameters to estimate increases with the number of areas (Fig. 4a), so it is important to think carefully about the model; i.e., the more parameters in the transition probability matrix, the less data available to estimate each parameter. One advantage of the parametric approach is that one can make use of alternative sources of evidence to decrease the size of the parameter matrix. For example, one can disallow certain ancestral ranges based on biological implausibility, e.g., areas that are not geographically adjacent. Another possibility is to disallow certain transitions between geographic states. An advantage of parametric approaches over parsimony-based methods is that they allow external evidence other than the tree topology and lineage distributions to inform the biogeographic model. This can be done by either adding new parameters to the transition matrix, or by scaling a global dispersal or extinction rate according to abiotic factors like geographic distance, the availability of land connections, or the strength of wind and ocean currents (Buerki et al. 2011). For example, in island systems like the Canary Islands, one may wish to constrain dispersal to follow the island chain by making the rate of dispersal between non-adjacent islands in the chain equal to zero (Sanmartín et al. 2008). Whether these constraints are biologically realistic or not depends on each particular scenario.** **Finally, a present limitation of the parametric approach is that it assumes that range evolution is uncoupled with lineage diversification. In parametric methods, range evolution is modeled as a process that evolves along the branches of a phylogenetic tree, but the biogeographic model itself does not influence the birth--extinction stochastic process that determines tree growth, branch lengths, and topology (Ree and Sanmartín 2009). Yet some studies have demonstrated that dispersal into new areas can lead to an increase in the rate of diversification (e.g., Moore and Donoghue 2007), which suggests that there is a relationship between the rate of cladogenesis and biogeographic evolution. Goldberg et al. (2011) recently expanded the DEC model of Ree et al. to incorporate range-dependent diversification, in which speciation and extinction parameters are dependent on the size of ancestral geographic ranges; for example, widespread ancestral lineages would have a higher rate of allopatric speciation and a lower rate of extinction than ancestral lineages endemic to a single area. These methods hold great promise, but even the simplest implemented two-area models are parameter-rich (Goldberg et al. 2011), and the inferential power of more complex multiple-area models remains to be tested.** 6. **Integrating Ecological Processes: Ecological Vicariance and Niche Modeling** **Integrating ecological processes into the reconstruction of biogeographic scenarios has been a long-term aim in historical biogeography (Morrone and Crisci 1995). But until recently there has been no real effort to combine these two aspects of the discipline into a common analytical framework. This has become possible through the development of ecological niche modeling techniques (ENMs). According to the concept of niche conservatism (Wiens 2004; Wiens and Donoghue 2004), lineages tend to conserve their ecological niche through time, the set of environmental conditions in which lineages can reproduce and maintain viable populations. Vicariance is considered the outcome of any environmental change that causes a division in a species geographic range (Wiens 2004). ENMs (Peterson et al. 1999; Kozak et al. 2008) use the association between distribution data (species occurrences) and environmental variables (e.g., temperature, precipitation) to predict the range within which a species could occur. Assuming that niches are preserved over time ("niche conservatism"), and given information about past climates, one can project back the ecological niche for different points in time to reconstruct past species distribution patterns (Yesson and Culham 2006), or to find areas that were in the past within the environmental tolerance of the species and could have acted as dispersal corridors across regions that are now uninhabitable (Weaver et al. 2006). Smith and Donoghue (2010) were the first to combine parametric biogeographic methods with paleoclimate data and ecological niche models of extant taxa as a way to understand how past climates and land connections have shaped the biogeographic distribution of lineages over time. Similarly, Stigall and Lieberman (2005, 2006) pioneered the integration of ENM models into paleobiogeographic analysis, through the combination niche models with the fossil record of extinct lineages (e.g., Maguire and Stigall 2009). The advantage of this approach over ENM models based on extant taxa (Smith and Donoghue 2010) is that fossil-based ENM reconstructions do not assume that ecological niches are stable over time (this might be true for ecological time scales but not over geological scales of millions of years), so these models can be used to track patterns of niche conservatism and evolution over longer time scales (Stigall 2012).** **1.2 SUMMARY** Biogeography is the scientific study of the distribution of species and ecosystems across space and time. It seeks to understand the patterns and processes that have shaped the Earth\'s biodiversity. The historical development of biogeography can be divided into several key stages, and the field has also branched out into various sub-disciplines over time. Here\'s an overview of the historical development and branches of biogeography: **Historical Development of Biogeography:** 1. **Early Observations (Ancient Times to 18th Century):** Biogeography has ancient roots, with early observations of the distribution of plants and animals recorded by explorers, naturalists, and philosophers like Aristotle and Pliny the Elder. However, systematic scientific study began in the 18th century with the work of Carl Linnaeus and Georges-Louis Leclerc, Comte de Buffon. 2. **Voyage of Charles Darwin (19th Century):** Charles Darwin\'s voyage on the HMS Beagle (1831-1836) was a pivotal moment in the history of biogeography. His observations of different species on the Galápagos Islands and elsewhere contributed significantly to the development of the theory of evolution by natural selection. 3. **Alfred Russel Wallace (19th Century):** Alfred Russel Wallace independently developed the theory of evolution by natural selection and made significant contributions to biogeography. His work on the Wallace Line, a boundary separating Asian and Australian flora and fauna, is particularly noteworthy. 4. **Colonization and Island Biogeography (20th Century):** The 20th century saw advancements in the understanding of island biogeography, driven by research on the colonization and extinction dynamics of species on islands. This work was pioneered by ecologists like Robert MacArthur and E.O. Wilson. 5. **Modern Biogeography (Late 20th Century to Present):** Modern biogeography has incorporated advances in molecular biology, genetics, and geographic information systems (GIS) technology. Researchers use phylogenetic methods and historical biogeography to explore the evolutionary history and distribution of species. **Branches of Biogeography:** 1. **Ecological Biogeography:** This branch focuses on the distribution of species in relation to their environment. It examines the ecological factors that influence the distribution of organisms, including climate, habitat, and competition. 2. **Historical Biogeography:** Historical biogeography seeks to reconstruct the historical processes that have shaped the current distribution of species. It often involves the use of phylogenetics to infer evolutionary relationships and historical biogeographic events. 3. **Island Biogeography:** Island biogeography examines the unique patterns and processes associated with species on islands. It explores factors like island size, distance from the mainland, and the dynamics of colonization and extinction. 4. **Paleobiogeography:** This branch studies the distribution of organisms in the geological past by analyzing fossil evidence. It helps us understand how Earth\'s landmasses and climates have changed over time. 5. **Conservation Biogeography:** Conservation biogeography applies biogeographic principles to conservation efforts. It helps identify areas of high biodiversity and prioritize conservation strategies to protect vulnerable species and ecosystems. 6. **Marine Biogeography:** Marine biogeography focuses on the distribution of species in the world\'s oceans. It examines factors like ocean currents, temperature gradients, and the presence of underwater features that influence marine life. 7. **Macroecology:** Macroecology investigates large-scale patterns in species distribution and abundance. It often employs statistical and modeling approaches to understand global biodiversity patterns. 8. **Human Biogeography:** This branch explores the influence of human activities, such as habitat destruction, introduction of invasive species, and climate change, on the distribution of species. Biogeography continues to evolve as an interdisciplinary field, with researchers from various scientific backgrounds collaborating to address complex questions about the distribution of life on Earth and its conservation. Top of Form **1.3. Approaches in Biogeography** **History of Biogeography** The study of biogeography gained popularity with the work of Alfred Russel Wallace in the mid-to-late 19th Century. Wallace, originally from England, was a naturalist, explorer, geographer, anthropologist, and biologist who first extensively studied the [Amazon River](https://www.thoughtco.com/amazon-river-overview-1435530) and then the Malay Archipelago (the islands located between the mainland of Southeast Asia and Australia). During his time in the Malay Archipelago, Wallace examined the flora and fauna and came up with the Wallace Line---a line that divides the distribution of animals in Indonesia into different regions according to the climates and conditions of those regions and their inhabitants\' proximity to Asian and Australian wildlife. Those closer to Asia were said to be more related to Asian animals while those close to Australia were more related to the Australian animals. Because of his extensive early research, Wallace is often called the \"Father of Biogeography.\" Following Wallace were a number of other biogeographers who also studied the distribution of species, and most of those researchers looked at history for explanations, thus making it a descriptive field. In 1967 though, Robert MacArthur and E.O. Wilson published \"The Theory of Island Biogeography.\" Their book changed the way biogeographers looked at species and made the study of the environmental features of that time important to understanding their spatial patterns. As a result, island biogeography and the fragmentation of habitats caused by islands became popular fields of study as it was easier to explain plant and animal patterns on the microcosms developed on isolated islands. The study of habitat fragmentation in biogeography then led to the development of conservation biology and [landscape ecology](https://www.thoughtco.com/what-is-landscape-archaeology-171551). 1. **Historical Biography** Today, biogeography is broken into three main fields of study: historical biogeography, ecological biogeography, and conservation biogeography. Each field, however, looks at phytogeography (the past and present distribution of plants) and zoogeography (the past and present distribution of animals). Historical biogeography is called paleobiogeography and studies the past distributions of species. It looks at their evolutionary history and things like past climate change to determine why a certain species may have developed in a particular area. For example, the historical approach would say there are more species in the tropics than at high latitudes because the tropics experienced less severe climate change during glacial periods which led to fewer extinctions and more stable populations over time. The branch of historical biogeography is called paleobiogeography because it often includes paleogeographic ideas---most notably plate tectonics. This type of research uses fossils to show the movement of species across space via moving continental plates. Paleobiogeography also takes varying climate as a result of the physical land being in different places into account for the presence of different plants and animals. 2. **Ecological Biogeography** Ecological biogeography looks at the current factors responsible for the distribution of plants and animals, and the most common fields of research within ecological biogeography are climatic equability, primary productivity, and habitat heterogeneity. Climatic equability looks at the variation between daily and annual temperatures as it is harder to survive in areas with high variation between day and night and seasonal temperatures. Because of this, there are fewer species at high latitudes because more adaptations are needed to be able to survive there. In contrast, the tropics have a steadier climate with fewer variations in temperature. This means plants do not need to spend their energy on being dormant and then regenerating their leaves or flowers, they don't need a flowering season, and they do not need to adapt to extreme hot or cold conditions. Primary productivity looks at the [evapotranspiration](https://www.thoughtco.com/geography-4133035) rates of plants. Where evapotranspiration is high and so is plant growth. Therefore, areas like the tropics that are warm and moist foster plant transpiration allowing more plants to grow there. In high latitudes, it is simply too cold for the atmosphere to hold enough water vapor to produce high rates of evapotranspiration and there are fewer plants present. 3. **Conservation Biogeography** In recent years, scientists and nature enthusiasts alike have further expanded the field of biogeography to include conservation biogeography---the protection or restoration of nature and its flora and fauna, whose devastation is often caused by human interference in the natural cycle. Scientists in the field of conservation biogeography study ways in which humans can help restore the natural order of plant and animal life in a region. Often times this includes reintegration of species into areas zoned for commercial and residential use by establishing public parks and nature preserves at the edges of cities. Biogeography is important as a branch of geography that sheds light on the natural habitats around the world. It is also essential in understanding why species are in their present locations and in developing protecting the world\'s natural habitats. Biogeography is the study of the geographic distribution of plant and animal species and ecosystems over space and time. Its scope is the entire biosphere from the beginning of life. Organisms and biological communities often vary in a regular fashion along geographic gradients of latitude, elevation, isolation and habitat area. Biogeography as a science is the synthesis of concepts and information from geology, physical geography, evolutionary biology, and ecology. As our climate changes and the sixth great extinction transpires, vital biogeographic research reveals changing dispersal patterns of species and any physiological and ecological constraints on their movement. Biogeography also provides better understanding of evolutionary time frames and global spatial scales involved in climate changes throughout geologic time. **1.3 SUMMRY** Biogeography is the study of the distribution of species and ecosystems across geographic space and through geological time. It seeks to understand the processes and patterns that shape the distribution of life on Earth. There are several approaches in biogeography, each of which focuses on different aspects of this field. Here are some key approaches in biogeography: 1. **Historical Biogeography**: - Historical biogeography focuses on the study of how species and ecosystems have evolved and dispersed over geological time. It often involves reconstructing the history of species\' distributions using phylogenetic trees and geological evidence. - Concepts like vicariance (splitting of a population by geological events) and dispersal (movement of species to new areas) are central to historical biogeography. 2. **Ecological Biogeography**: - Ecological biogeography emphasizes the study of present-day distribution patterns of species and ecosystems and the ecological factors that influence these patterns. - It considers factors such as climate, habitat, competition, predation, and human activities in explaining the distribution of organisms. 3. **Island Biogeography**: - Island biogeography is a specialized subfield that focuses on the distribution of species on islands and how island size, isolation, and habitat diversity influence species diversity. - The theory of island biogeography, developed by Robert MacArthur and E.O. Wilson, has been influential in understanding species diversity on islands. 4. **Molecular Biogeography**: - Molecular biogeography uses genetic data, such as DNA sequencing, to investigate the historical and contemporary distribution of species. It can reveal information about migration patterns, population histories, and genetic diversity. - Molecular phylogenetics and phylogeography are common techniques in this approach. 5. **Paleobiogeography**: - Paleobiogeography focuses on the study of past distributions of species using fossil evidence. It can provide insights into ancient ecosystems, climate change, and the movement of species over geological time scales. 6. **Macroecology**: - Macroecology examines large-scale patterns of species distribution and biodiversity. It often involves analyzing large datasets to identify global or regional trends in species diversity and abundance. - This approach can help answer questions about the factors driving species richness and the distribution of species across different regions. 7. **Conservation Biogeography**: - Conservation biogeography combines principles from biogeography with conservation science. It aims to identify areas of high biodiversity and prioritize conservation efforts in those regions. - Conservation biogeographers work to protect ecosystems, prevent species extinctions, and preserve genetic diversity. 8. **Cultural Biogeography**: - Cultural biogeography explores the influence of human culture, history, and migration on the distribution of species and the spread of agricultural practices and domesticated species. - It considers how human activities have shaped the distribution of plants, animals, and pathogens. These various approaches in biogeography often overlap and complement each other, helping scientists gain a comprehensive understanding of how life is distributed on Earth and how it has evolved and changed over time. Top of Form **1.4. Importance of Biogeographic studies** If we accept that the field of biogeography is the study of living things and especially the association of living things, the next question, which poses itself, is for what reason or purpose does a geographer study biogeography? One simple answer to this question of course will be that: A geographer studies biogeography in order to understand and solve biogeographic problems. Other reasons we study biogeography are: 1. Biogeography enables us to identify [biodiversity patterns](https://www.jotscroll.com/forums/3/posts/290/biodiversity-conservation-types-loss-importance.html) in the past and present, to identify the expansion of organisms while it enables us to study about the relationship between living and non-living factors influence organisms to exist. 2. It enables us to identify the environmental diversities of Biogeography and the fluctuations of diversities and the problems arising in the environment. 3. We study biogeography to find out why resources are not evenly distributed on the Earth 4. It also helps us to find out what is where and why it is there 5. Biogeography provides evidence of evolution A biogeographer is a person who studies the **geographic distribution of plants and animals** on the earth. The study of biogeography became popular due to the work of Alfred Russel Wallace, an England exploraer (1823-1913). Alfred Russel Wallace is regarded as the father of biogeography. Wallace was a naturalist, explorer, geographer, anthropologist, and a biologist who was recorded as the first geographer to extensively study the Amazon River and then the Malay Archipelago (the islands located between the mainland of Southeast Asia and Australia). During his time in the Malay Archipelago, Wallace studied the flora and fauna and came up with the Wallace Linea line that divides the distribution of animals in Indonesia into different regions according to the climates and conditions of those regions and their inhabitants' proximity to Asian and Australian wildlife. Those closer to Asia were said to be more related to Asian animals while those close to Australia were more related to the Australian animals. Aside Wallace, there were a number of other biogeographers who also studied the distribution of species, and most of those researchers looked at history for explanations, thus making it a descriptive field. **SUMMRY** Biogeographic studies are crucial for understanding the distribution of life on Earth, the processes that have shaped it, and the implications for conservation, ecology, and evolutionary biology. Here are some key reasons why biogeographic studies are important: 1. **Biodiversity Conservation**: Biogeographic research helps identify areas of high species diversity and endemism (species found only in specific regions). This information is vital for designing effective conservation strategies and protected areas to safeguard unique and threatened ecosystems and species. 2. **Understanding Evolution**: Biogeography provides insights into the historical processes that have driven the evolution of species and the formation of biotic communities. It helps answer questions about when and how different species diverged and spread across the planet. 3. **Invasive Species Management**: Biogeographic studies help track the movement of invasive species, which can have devastating effects on native ecosystems. Understanding the natural ranges of species can aid in predicting and preventing invasions. 4. **Climate Change and Habitat Shifts**: With climate change altering the distribution of habitats and species, biogeography plays a critical role in predicting how these shifts will impact ecosystems and informing adaptive management strategies. 5. **Island Biogeography**: Islands often host unique ecosystems and are valuable laboratories for studying the processes of speciation, extinction, and colonization. Biogeographic research on islands has led to key insights in ecology and evolution. 6. **Historical Biogeography**: By analyzing the historical distribution of species, researchers can reconstruct past geological events and climatic changes. This knowledge helps us understand how Earth\'s continents and biotas have evolved over millions of years. 7. **Phylogeography**: This subfield of biogeography focuses on the genetic diversity and distribution of species. It helps uncover patterns of historical migration, gene flow, and adaptation, which are important for understanding the dynamics of biodiversity. 8. **Ecosystem Services**: Biogeographic studies contribute to our understanding of the services ecosystems provide, such as pollination, water purification, and carbon storage. This knowledge is vital for sustainable resource management and human well-being. 9. **Biosecurity**: Governments and organizations use biogeographic data to develop biosecurity measures to protect agriculture, forestry, and public health from pests and diseases that may be introduced by global trade and travel. 10. **Conservation Planning**: Conservation practitioners use biogeographic information to prioritize areas for protection and restoration efforts. Conservation planning tools often incorporate biogeographic data to maximize the conservation impact with limited resources. In summary, biogeographic studies are essential for unraveling the complex patterns of life on Earth, guiding conservation efforts, understanding evolutionary processes, and addressing contemporary challenges like climate change and invasive species. They provide a foundation for informed decision-making in ecology, conservation, and natural resource management.