支序分类学派vsPhenetic.PPT

Modeling 2 In general, substitutions are more frequent between bases that are biochemically more similar. In the case of DNA, the four types of transition (A → G, G → A, C → T, T → C) are usually more frequent than the eight types of transversion (A → C, A → T, C → G, G → T, and the reverse). Such biases will affect the estimated divergence between two sequences. A C A C T A C C G A C A C A C T A C T T A C A C T A C A A A T T C single substitution convergent substitution convergent substitution multiple substitution coincidental substitution parallel substitution conservation ATGCTGTTAGGG ATGCTCGTAGGG MetLeuLeuGly * * ATGCT-GTTAGGGXX ATGCTCGT-AGGGXX MetLeuValArgXxx Character-state weight matrices have usually been estimated more or less by eye, but they can also be derived from a rate matrix. For example, if it is presumed that each of the two transitions occurs at double the frequency of each transversion, a weight matrix can simply specify, for example, that the cost of A-G is 1 and the cost of A-T is 2. Specification of the relative rates of substitution among particular residues usually takes the form of a square matrix; the number of rows/columns is four in the case of bases, 20 in the case of amino acids (e.g., in PAM and BLOSUM matrices), and 61 in the case of codons (excluding stop codons). A R N D C Q E G H I L K M F P S T W Y V A 2 R -2 6 N 0 0 2 D 0 -1 2 4C -2 -4 4 -5 4 Q 0 1 1 2 -5 4 E 0 -1 1 3 -5 2 4 G 1 -3 0 1 -3 -1 0 5 H -1 2 2 1 -3 3 1 -2 6 I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6 S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 3 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -2 0 1 3 W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1