Classification and Phylogeny 2

Now some choices how to infer a phylogeny distance

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Unformatted text preview: mmon ancestor, rather when the gene duplicated. The average rate of gene duplication: 1 in a million The average mutation rate: 1 in a billion Alignment When you are comparing, read within a column. The column must deal with homologous characters. Now some choices: how to infer a phylogeny Distance methods Parsimony methods Statistical methods Maximum likelihood These differ in the kinds of data they accept and the way they produce the estimate of the tree. A distance method: UPGMA Species 1- 4, 10 nucleotides. Don’t care that are nucleotides. Condense to numbers. Count up differences between, say, species 1 and 2 (5, so 5 is the distance) Count all 6 distances. Pairwise comparisons (distances) between all taxa in the sample A smaller distance seems to infer a more recent common ancestor Arrange distances in a matrix Similarities recorded there may reflect the history of lineage splitting events Crank through an algorithm for producing a tree The shortest distance: 2,3 are a clade 1 is the next most similar to 2 and 3. And finally 4. The modus operandi of UP...
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