Overview of Historical Biogeography: Taxon & Area Biogeography, Models, Techniques, Assignments of Biology

Download Overview of Historical Biogeography: Taxon & Area Biogeography, Models, Techniques and more Assignments Biology in PDF only on Docsity! Historical Biogeography Fredrik Ronquist November 16, 2005 1 Introduction Historical biogeographers and phylogeographers study very similar problems even though the time scales and spatial scales are typically larger in historical biogeography. Phylogeographers decided early on to ignore much of the existing literature in historical biogeography and the two disciplines still develop largely independently today. Historical biogeography can be divided into two subdisciplines: taxon biogeography and area bio- geography. In the former we are interested in reconstructing the geographic distribution history of a particular group of organisms. Questions we may be interested in answering include: Where did the organisms originate? How did they colonize the areas in which they live today? When did they first come to a particular area? How prone to dispersal is the lineage? In area biogeography, the focus is on general phenomena that affect many groups of organisms. Typical research questions in- clude: How was a particular community assembled? What is the explanation of commonly observed disjunct distributions? What are the most important geographic dispersal barriers that affect or affected the distributions of organisms in a particular region of the world? Are differences in species diversity between two regions best explained by differential speciation or differential extinction? In terms of quantitative methods, historical biogeography is still dominated by parsimony or opti- mization techniques. There is an overwhelming number of approaches that have been discussed in the literature. They can be classified into pattern-based and event-based ; the former approaches are simple numerical recipes whereas the latter identify some biologically interesting events, associate these events with costs, and then find the minimum-cost solutions. In recent years, there has also been a few papers discussing likelihood approaches to problems in historical biogeography, but the development of these methods is still in its infancy. 1 BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology 2 Area models Before discussing the techniques used in taxon and area biogeography, it is useful to describe the different models or scenarios that are used to describe how organism distributions evolve over time. The simplest model is the island model. Geographic areas are represented as islands that remain constant through time (Fig. ??). Important processes that shape the distribution of lineages include dispersal between islands and speciation within islands. The use of island models is certainly not restricted to true islands. Many types of geographic situations can be described in terms of islands. For instance, patches of particular habitat like mountaintops, freshwater lakes, or rivers can all be thought of as islands. Figure 1: Different area models used in historical biogeography The vicariance model starts with a large geographic area, which is split into smaller and smaller parts by the appearance of dispersal barriers (Fig. ??). Organism lineages that respond to the appearance of a dispersal barrier by speciating produce a vicariance pattern in which sister groups have complementary distributions, together corresponding to a larger ancestral distribution. 2 BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology Figure 3: The areasum optimization technique. unit areas. However, if speciation occurs in an ancestor occupying a single unit area, both daughter lineages are assumed to occur in the same area. Both of these events have zero cost. Lineages can then colonize new unit areas or go extinct in previously occupied unit areas; a unit cost is used for each addition or deletion of a unit area from a distribution. The resulting technique will in some cases favor an island colonization history and in some cases a vicariance history (Fig. ??). Note that the vicariance events need not conform to a general pattern; one lineage can be reconstructed as having a vicariance history involving a completely different sequence of geographical splitting than its sister lineage. This also means that, in principle, dispersal-vicariance optimization can reconstruct reticulate distribution histories. Before ending this section, it is worth pointing out that results from area biogeography approaches, such as general estimates of dispersal rates, could be used in taxon biogeography to increase the precision of the reconstructions of past distributions for single organism groups. However, this is still rarely done. 5 BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology Figure 4: The dispersal-vicariance optimization technique. 4 Area biogeography The simplest approach to generalities in historical biogeography is to use one of the taxon biogeog- raphy techniques and then simply summarize the results across organism groups. For instance, we could apply Fitch optimization over the same set of islands for a large set of organism groups and then summarize the number of dispersals between particular islands to get an estimate of the rel- ative frequency of different types of dispersal events. We might, for instance, discover asymmetric dispersal between some islands, perhaps showing the effects of prevailing winds or ocean currents on long-distance dispersal. For an example involving dispersal-vicariance optimization and the his- torical biogeography of terrestrial animals in the northern Hemisphere, see the paper by Sanmartin, Ronquist, and Enghoff (2001). They used dated phylogenies to be able to separate biogeographic events temporally and thus address a reticulate geological history. A disadvantage with the above approach is that we lose some information by ignoring the presence of generalities when reconstructing the distribution history of each individual group. For instance, if we have a choice between explaining a particular pattern in one organism group as the result of 6 BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology event A or event B, it might be helpful to know that across a larger set of organisms, event A is common and event B rare. To take such information into account, we need techniques that try to identify general events and put a premium on using these in explaining the distribution history of individual groups of organisms. Most of the work on such methods has focused on parsimony techniques based on the vicariance model, and it exemplifies the more general problem of tree fitting, which we will examine in more detail in the next lecture. If the vicariance model is true, then we can describe the history of areas in terms of branching diagrams, which are called area cladograms or sometimes general area cladograms. Each split in the area cladogram corresponds to the appearance of a particular geographic area splitting one ancestral area into two smaller daughter areas. If all organisms had a perfect vicariant history, then the area cladogram could be found by simply replacing the organisms with their distributions in any of the phylogenies of organisms inhabiting the areas. However, if processes such as random dispersal and extinction occur on top of a generally vicariant history, we need more sophisticated techniques for measuring the fit between a particular area cladogram and one or more organism phylogenies. The first step in describing such a method is to identify the events. Typically, there are four types of events that are considered in parsimony-based approaches to finding general area cladograms (Fig. ??). These are vicariance, duplication (speciation within an area), sorting (partial extinction), dispersal (speciation-associated), extinction, and non-speciation dispersal. In vicariance, a lineage of organisms responds to the appearance of a general dispersal barrier by speciating. Duplication within one area can result either from sympatric speciation or from allopatric speciation in response to a temporary local dispersal barrier. A sorting event results when an organism lineage, in response to the appearance of a general dispersal barrier, either goes extinct in one of the daughter areas or fails to make it to one of the areas (missing the boat). Finally, a dispersal event is typically modeled as being associated with speciation. True extinction and dispersal associated with extinction in the original area are difficult to consider in parsimony methods because they completely erase the information about past distributions. Therefore, they are typically ignored. Assuming a model with these four events, the next step is to identify a cost for each. In other contexts were parsimony methods are used, it is possible to use the same cost for all events. A simple example is the standard four-by-four model of DNA substitution, where Fitch parsimony uses the same cost for all transitions. However, in the biogeographic context this is not possible, at least not if we wish to reconstruct vicariance scenarios. Consider a simple example in which 7