Integrative Biology 200A “PRINCIPLES OF PHYLOGENETICS” Spring 2006 University of California, Berkeley Kipling Will- 27 April 06 Biogeography--Why things are where they are.-- The field that attempts to document and understand the spatial patterns of organisms in the past and present and develop process explanations for variation in distribution. I. Ecological Biogeography A. Typically deals with relatively recent patterns and interactions with an ecological and phonological emphasis. 1. From this view questions addressed might be like “What allows a species to occur in one area and prevents it from expanding into other areas?” B. Community based. C. Can involve paleontological data, so is not restricted to currently extant populations. D. Studies often involve the impact of human activities; succession theory; the dynamics of communities and populations; fire ecology; restoration ecology; invasive species; species pulses or waves; island biogeography. e.g., Elias, S.A., Berrnan, D., Alfimov, A. 2000. Late Pleistocene Beetle Faunas of Beringia: Where East meets West. Journal of Biogeography. 27:1349-1~63. II. Phylogeography A. The attempt to take into account the geographic distribution of species/populations in establishing their phylogeny/divergence, and to understand the geographic patterns that may result from divergence, ultimately leading to speciation. 1. Focus on species boundaries. 2. Often looks at gene trees or genealogies. 3. Shares methodology with phylogenetics. e.g., Gody. J.A., Negro, J.J. Hiralodo, F., Donázar, J.A. 2004. Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L.) as revealed by mitochondrial DNA. Molecular Ecology. 13:2 p. 371. III. Historical Biogeography A. Usually involves older patterns inferred by looking at clades (often as species and higher taxa) B. Focus on why lineages are represented in certain areas and not others and why is a pattern of distributions frequently repeated in different lineages. C. Typically area relationships and general patterns of diversity are emphasized over single taxon distributions. e.g., Marshall, C. J., Liebherr, J.K. 2000. Cladistic biogeography of the Mexican transition zone. Journal of Biogeography. 27( 1 ):203-216. IV. Brief Historical overview of “periods” and discoveries A. At the time of a limited view of dynamics and diversity 1. Creation myths, dispersal from Noah's ark, etc. 2. Little understanding beyond local flora/fauna B. Age of exploration 1. 17th century led to discovery of too many species for the Ark 2. Realization that environmentally similar but distantly isolated regions have distinct assemblages of organisms (Buffon's Law) 3. Islands have lower diversity 4. Similar floristic zonation (Humbolt) C. 19th century, advances in geology and evolutionary theory 1. Lyell, Darwin, Wallace, Sclater, Hooker, etc. 2. Abandonment (by most) of the idea of static distribution and immutability of species. 13. Landbridges/megacontinents (e.g. Hooker, Wallace) vs. dispersal (e.g. Darwin) D. 20th century 1. Continental drift (Wegener 1912)- but not really accepted until 1960s- (Dietz & Holder 1966) Persistent dispersalists like Mayr and Darlington maintained that even of continents moved dispersal was still more important. 2. -Panbiogeography of Croizat, phylogenetics of Hennig and implementation Brundin (1966) for a trans-Gondwanan group of flies 3. Vicariance biogeography fully developed by Platnick & Nelson (1978) V. Generally used current methods of Historical (Vicariance) Biogeography >> -Similar systems like parasites and their hosts can use the same or similar methods. Host -- Associate organism -- paralogous gene host organism -parasite organism geographic area - organism >> A. Historical explanation for disjunct patterns can be either dispersal or fragmentation of a continuous range (vicariant). B. Vicariance biogeography usually considers dispersal to be an ad hoc explanation that could be used to account for any pattern. C. Implied process assumptions in pattern methods, which are more explicit in event-based methods 1. allopatric speciation is relative more common 2. dispersal is relatively less common than stasis 3. current distributions generally reflect ancient events D. The basics 1. You need monophyletic groups that occur in three or more areas a. Requires that you assume the phylogeny is correct 2. Replace the OTU names with area names to make taxon-area cladograms a. Requires you assume the known ranges are adequate 3. Summarize the set of taxon-area cladograms to make a general area cladogram that shows the congruent vicariant pattern a. Assumption of simplicity or at least that the majority of taxa respond the same most of the time 4. "Missing", widespread taxa and redundant areas are problems. a. Areas may be absent in groups because i. no member ever occur in the area ii. sampling error iii. extinction b. Taxa may occur in more than one area because i. non-response to a vicariant event ii. sympatric speciation iii. dispersal (secondary sympatry) 3. Redundant distributions in two taxa i. dispersal in one or both taxa VI. A priori methods- Derive general biogeographic patterns from shared cladistic patterns and distributional data. No secondary or "total evidence" analysis. A. Component Analysis. TAC, FAC, RAC, GAC: Use taxon area cladograms (TAC) to derive reduced area cladograms (sometimes called fundamental area cladograms (FAC)) from phylogenetic hypotheses and distributional data under Assumptions 0, 1, 2 (Platnick & Nelson 1978). General Area cladograms (GAC) are the intersection of reduced area cladograms (RAC) from two or more sets of trees. 2Assumption 0: assumes that widespread taxa are the result of non-response to only the most recent vicariant event (can we know if this was not a dispersal event?), so that areas that are occupied by widespread taxa are interpreted as being most closely related. Clearly, the existence of more than one widespread taxon, each occupying overlapping but not identical sets of areas are conflicting evidence for area relationships. The conflict is resolved for these redundant areas for the most apical cladistic position. Assumption 1: assumes that widespread taxa are the result of non-response to the most recent OR earlier vicariant event (dispersal event?). Redundant area representations are all considered valid. The assumption will often produce more
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