Lecture_24.2perpage

Lecture_24.2perpage - 1 Objectives Today (Introduction to...

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Unformatted text preview: 1 Objectives Today (Introduction to Molecular Evolution) Understand Null Hypotheses and Assumptions Understand Molecular Clock (related to above) Understand how to construct a simple 4- gene phylogeny using parsimony Molecular Evolution The evolution of Macromolecules DNA RNA Proteins Reconstructing evolutionary history of genes and organisms Genes trees Species trees (using molecular data) 2 Null Hypotheses and Assumptions Null Hypothesis Simple explanation for comparison to alternatives. Example no relationship between fossil and molec divergence Significant deviation from null An alternative hypothesis might be true Assumption A feature taken as fact to allow us to learn something Null Hypotheses/Assumptions in Molecular Evolution Null Hypothesis No Molecular clock Assumption: Molecular Clock Assumption: Parsimony Null Hypothesis: Neutral Theory (Next Time) 3 Molecular Clock NULL: No relationship between fossil and molecular time estimates Plot fossil divergence time versus molecular differences. Relationship? By ASSUMING a clock: Can extrapolate divergences for groups without fossils Example 1: Hemoglobin Molecular Clock Rejects Null (of no clock) Zuckerkandl and Pauling (1965); Kimura (1968) 4 Assuming a Clock Can estimate divergences w/o fossils If A.A. differences = 0.55, divergence ~= 300MY Example 2 Ramapithicus 14 MY Fossil In 1960s considered closest relative of humans 5 Sarich and Wilson Found: Human, chimp, gorilla albumins 1% different Each differed from Monkeys by 6% Monkeys and apes diverged 30 MYA X = 5 MY Humans only ~5MY diverged from chimps ASSUMES a clock MY x 30 % 6 % 1 = Pre-molecular view of hominoid evolution 6 Molecular Timescale (Based on Albumin Proteins) Inconsistent with Ramapithicus as near humans Gibbons Orangutan Molecular Timescale (Based on Albumin Proteins) Inconsistent with Ramapithicus as near humans Gibbons Orangutan 7 Later Confirmation More Ramapithicus bones indicated it was an ape More molecular data Molecular Clock = Empirical Question Many examples where clock is not supported Some examples where clock is supported Must be tested case by case 8 Parsimony An Assumption We often want to know the relative relatedness of genes or species May ASSUME that simplest explanation is best Parsimony Fewest number of changes represents history Molecular Phylogeny Phylogenies are hypotheses of common ancestry Species have common ancestries Genes have common ancestries Can use genes to infer species history (molecular phylogenetics) 9 Rooted vs. Unrooted Trees Rooted: Makes an Explicit statement about The directionality of time Unooted: Makes NO Explicit statement about The directionality of time Main Steps to Inferring Phylogenies 1. Choose OTUs 2. Choose traits to compare in selected OTUs 3. Choose optimality criterion (e.g. Parsimony) 4. Compare all possible trees 10...
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This note was uploaded on 03/14/2010 for the course EEMB 129 taught by Professor Ajnarivera during the Spring '09 term at UCSB.

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Lecture_24.2perpage - 1 Objectives Today (Introduction to...

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