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Purpose of phylogenetics :

Purpose of phylogenetics : Try to find the genealogical ties between organisms, reconstructing the evolutionary relationship between species. Backtrack characterizations of ancestors Estimate the time of divergence between two organisms since they last shared a common ancestor.

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Purpose of phylogenetics :

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  1. Purpose of phylogenetics : • Try to find the genealogical ties between organisms, reconstructing the evolutionary relationship between species. • Backtrack characterizations of ancestors • Estimate the time of divergence between two organisms since they last shared a common ancestor.

  2. node : a node represents a taxonomic unit. This can be a taxon (an existing species) or an ancestor. • branch : defines the relationship between the taxa in terms of descent and ancestry. • topology : is the branching pattern. • branch length : often represents the number of changes that have occurred in that branch. • root : is the common ancestor of all taxa.

  3. There are three major groups of analyses to examine phylogenetic relationships between sequences :

  4. Cladistic methods : trees are calculated by considering the various possible pathways of evolution and are based on parsimony methods. The resulting tree is called a cladogram. Cladistic methods use each alignment position as evolutionary information to build a tree.

  5. Phenetic methods : trees are calculated by similarities of sequences and are based on distance methods. The resulting tree is called a dendrogram and does not necessarily reflect evolutionary relationships. Distance methods compress all of the individual differences between pairs of sequences into a single number.

  6. Probabilistic methods : this method uses probability calculations to find a tree that best accounts for variation in a set of sequences. (i.e. maximum likelihood and Bayesian inference

  7. character state isdetermined by using an outgroupand could be ancestral or derivate. Symplesiomorphies and autapomorphies O a b c d O atctg a atatc b atatg C acatg d acatg

  8. Maximum parsimony The principle of maximum parsimony searches for tree that requires the smallest number of evolutionary changes to explain the differences observed among the OTUs (Operative Taxonomic Units) under study. Such a tree is called a maximum parsimony tree.

  9. Informative sites

  10. Informative sites

  11. Trees on the forest !

  12. Note: Some figures and concepts were taken from: http://allserv.rug.ac.be/~avierstr/principles/phylogeny.html http://microbio.fciencias.unam.mx/evolucion/Maxima_parsimonia.htm http://cgi.sfu.ca/~amooers/cgi-bin/Data/lecture9a.pdf Elliott Sober (1988) Reconstructing the Past, Parsimony, Evolution, and Inference. The MIT Press, USA Li, Wen-Hsiung (1997) Molecular Evolution. Sinauer Associates, USA

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