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Lecture_Notes_1 - Evolutionary Trees Fredrik Ronquist 1...

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Evolutionary Trees Fredrik Ronquist August 29, 2005 1 Evolutionary Trees Tree is an important concept in Graph Theory, Computer Science, Evolutionary Biology, and many other areas. In evolutionary biology, a tree is a branching diagram used to illustrate the divergence over time of evolutionary lineages (species) or of genetically encoded traits (such as DNA or protein sequences) of those lineages. The former trees are sometimes called species trees and the latter gene trees , with the word gene loosely referring to any genetic component or genetically determined trait of an organism. The word phylogeny is usually used as a synonym of species tree. In organisms that reproduce asexually, gene trees and species trees are essentially the same thing but organisms that reproduce sexually, including most multicellular organisms, mix genes with different ancestry every time they reproduce. Therefore, sexually reproducing organisms diverge more slowly than their genes, and this introduces several potential sources of mismatch between gene and species trees, as we will see later during the course. Generally speaking, however, gene trees and species trees tend to be largely congruent. We will, during the course, cover both Population Genetics and Phylogenetics, in particular the ways in which they use evolutionary trees. Population Genetics focuses on individual or closely related evolutionary lineages and the genetic structure within them. This information, contained in gene trees, is used to describe the present, infer the recent past, or predict the immediate future of evolutionary lineages (populations). Phylogenetics is the study of species trees and their implications concerning the evolution over longer time scales. There is an interesting divide between Population Genetics and Phylogenetics, among other things evident in the fact that evolutionary lineages are referred to as populations in the former field and species in the latter. The critical difference appears to be in the life span of the lineages: the term species implies a longer life span 1
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BSC5936-Fall 2005-PB,FR Computational Evolutionary Biology than the term population . A lineage that lasted or is predicted to last some critical amount of time (say 10,000 to 100,000 years or more) is typically referred to as a species, whereas a lineage with shorter life span is called a population and not a species. There is also some anthropocentrism involved, so we tend to call lineages closely related to us separate species (eg. Neanderthals) whereas similar amounts of divergence would probably be understood as population-level differentiation in invertebrates. An evolutionary tree is typically drawn with the root at the bottom (Fig. 1) unlike other types of trees, such as those used in Computer Science, which by convention are drawn with the root at the top. The evolutionary tree (or any other tree for that matter) consists of two components: the divergence points and the lines connecting them. Biologists typically refer to the divergence points as nodes
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Lecture_Notes_1 - Evolutionary Trees Fredrik Ronquist 1...

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