Bio 322 Quiz 4- Questions and Correct Answers

Method for construction of gene phylogenies choose gene of interest - identify homologs - align sequences - calculate gene tree OTU: operational taxonomic unit the terminal nodes in a phylogenetic tree - the quantitative or qualitative criteria to define them can vary - a common definition in bacteria is all genes sharing a given % identity in their DNA sequence (usually 97-99%) Sequence databases to identify homologs -genbank -EMBL nuceotide sequence database -DDBJ (DNA data bank of japan) DNA substitution matrix A C G T A 1 0 0 0 C 0 1 0 0 G 0 0 1 0 T 0 0 0 1 Calculate gene tree: Parsimony possible trees are compared and eachis given a score that is a reflection of the minimum number of character state changes that would be required over evolutionary time to fit the sequences into that tree. the optimal tree is considered to be the one requiring the fewest changes Calculate gene tree: Distance the optimal tree is generated by first calculatinf the estimated evolutionary distance between all pairs of sequences. these distances are then used to generate a tree in which the ranch patterns and lengths best represent the distance matrix Calculate gene tree: maximum likelihood this mehtod is similar to parisomy methods is that possible trees are compared and given a score. the score is based on how likely the given sequences are to have evolved in a particular tree given a model of amino acid or nuceotide substitution probabilities. teh optimal tree is considered to be the one that has the highest probability Calculate gene tree: bayesian a variant of maximum likelihood in which the likelihood of a tree itself is calculated Substitution matrix A C G T A 0 2 1 2 C 2 0 2 1 G 1 2 0 2 T 2 1 2 0