Ch10_MolEvo

Ch10_MolEvo - An Introduction to Bioinformatics Algorithms

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www.bioalgorithms.info An Introduction to Bioinformatics Algorithms Molecular Evolution

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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Outline Evolutionary Tree Reconstruction “Out of Africa” hypothesis Did we evolve from Neanderthals? Distance Based Phylogeny Neighbor Joining Algorithm Additive Phylogeny Least Squares Distance Phylogeny UPGMA Character Based Phylogeny Small Parsimony Problem Fitch and Sankoff Algorithms Large Parsimony Problem Evolution of Wings HIV Evolution Evolution of Human Repeats
An Introduction to Bioinformatics Algorithms www.bioalgorithms.info CHANGES Neighbor Joining Algorithm –ADD – introduce the notion of molecular clock – ADD – description of NJ algorithm Additive Phylogeny – ADD ANIMATION TO ALGORITHM – IN the “RECONSTRUCTING TREES FROM ADDITIVE MATRICES” draw an edge of length k as k-vertex edge – will be easier to show the shortening process. UPGMA –REWRITE – VERY CONFUSING – CHECK DIFFERENCES WITH THE BOOK Fitch and Sankoff Algorithms – VERY CONFUSING – REDO ADD – Large Parsimony Problem

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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Early Evolutionary Studies Anatomical features were the dominant criteria used to derive evolutionary relationships between species since Darwin till early 1960s The evolutionary relationships derived from these relatively subjective observations were often inconclusive. Some of them were later proved incorrect
An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Evolution and DNA Analysis: the Giant Panda Riddle For roughly 100 years scientists were unable to figure out which family the giant panda belongs to Giant pandas look like bears but have features that are unusual for bears and typical for raccoons, e.g., they do not hibernate In 1985, Steven O’Brien and colleagues solved the giant panda classification problem using DNA sequences and algorithms

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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Evolutionary Tree of Bears and Raccoons
An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Evolutionary Trees: DNA-based Approach 40 years ago: Emile Zuckerkandl and Linus Pauling brought reconstructing evolutionary relationships with DNA into the spotlight In the first few years after Zuckerkandl and Pauling proposed using DNA for evolutionary studies, the possibility of reconstructing evolutionary trees by DNA analysis was hotly debated Now it is a dominant approach to study evolution.

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An Introduction to Bioinformatics Algorithms www.bioalgorithms.info Emile Zuckerkandl on human-gorilla evolutionary relationships: From the point of hemoglobin structure, it appears that gorilla is just an abnormal human, or man an abnormal gorilla, and the two species form actually one continuous population.
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Ch10_MolEvo - An Introduction to Bioinformatics Algorithms

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