Apr17_Reticulation - Integrative Biology 200A...

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University of California, Berkeley B.D. Mishler April 17, 2008 . Phylogenetic trees VIII: Below the "species level;" phylogeography; dealing with reticulation A. The fractal nature of the Tree of Life. The tree of life is inherently fractal-like in its complexity, which complicates the search for answers to these questions. Look closely at one lineage of a phylogeny (remember: defined as a diachronic connection between an ancestor and a descendent) and it dissolves into many smaller lineages, and so on, down to a very fine scale. Thus the nature of both the terminal units (OTUs -- the "twigs" of the tree in any particular analysis) and the characters (hypotheses of homology, markers that serve as evidence for the past existence of a lineage) change as one goes up and down this “fractal” scale. Ontologically speaking, larger-scale lineages are usually composed of smaller lineages nested inside them, and the choice of which lineage to represent in a particular analysis depends on the questions begin asked. Furthermore, the lineages at these different levels potentially have different histories; in other words the smaller lineages are not always proper subsets of the larger ones. This is sometimes called the gene tree / species tree distinction (Maddison and Maddison 1992), but that distinction is far too simplified; there are many nested levels of potentially incongruent lineages, not just two. Besides, there is no a priori "species tree" to compare gene trees to; on the contrary the "species tree" has to be inferred from gene trees! B. Is there a difference between genealogy and phylogenetics? or: Is there an important break at the "species level"? Rosenberg and Nordborg (2002) say that there is a difference, and many workers (primarily zoologists) do make a distinction between reconstructing trees at the population level (genealogies) and at the species level and above (phylogenies). The same workers would distinguish phylogeography from phylogenetic biogeography, and separate out study of coalescence ("gene trees") from branching evolution ("species trees"). A bit if history: population genetics has always placed special emphasis on identity of genes by descent -- why? It goes back to the concept of replication we discussed previously. To study a process of natural selection, you need to know what the replicators are, as well as the interactors. So knowing identity of genes isn't enough, you need to know that they are related, Knowing how things are related is essential to testing functional hypotheses. Population geneticists developed important methods to study gene trees, independently from the methods developed by systematists to study species trees. But the two traditions have themselves exhibited hybrid vigor in the last decade! A
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This note was uploaded on 08/01/2008 for the course IB 200 taught by Professor Lindberg,mishler,will during the Spring '08 term at University of California, Berkeley.

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Apr17_Reticulation - Integrative Biology 200A...

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