Lecture 3: A Brief Overview of Molecular Phylogeny - MCD Biology

More documents

Recommendations

Info

6 4. In the case of rRNAs, the high degree of conservation makes the secondary structures important alignment tools – (see secondary structures of rRNAs-available on Class Website). a. Paired regions in the SSU rRNAs are not conjecture based on the occurrence of complements, but are “proven” by covariations in the sequence set that maintain the complementarity. 3. Calculation of trees: there are many ways to do this. As discussed in the Workshop, popular methods include trees based on: • Evolutionary distance • Maximum parsimony • Maximum likelihood A. In each case, a computer-search is used to find “the tree” most consistent with the data set. B. All the methods rely heavily on statistical analysis. One consideration in these calculations or any “discrete number” assessments is “Poisson statistics.” (Biologists need to know about Poisson statistics.)
7 Vignette: Poisson Statistics 1. Poisson Statistics describes distributions of discrete and small numbers. It is often useful in biology and in thinking about the set-up and interpretation of experiments. You probably will see a problem similar to these on Midterm I. 2. P = probability of event: Q = probability of non-event. P+Q = 1 A. Remember also that probabilities multiply: P(x,y) = P(x)•P(y) 3. For small (discrete) numbers: P(x) = mx x! e!m Where: x = number of events m = mean number of events P(x) = probability of x events 4. This expression is useful for all sorts of experimental considerations and problems. e.g.: Problem 1: You are interested in determining the "burst size" of a bacteriophage growing on E. coli. In order to do that, you mix suspensions of phage and E. coli as follows:
Page 1 and 2: 1 Lecture 3: A Brief Overview of Mo
Page 3 and 4: 3 B. Note that seqs from different
Page 5: 5 alignment becomes” straightforw
Page 9 and 10: 1. One ml Eco at 5x10 8 /ml = 5x10
Page 11 and 12: 11 C. This can be estimated (from P
Page 13 and 14: 13 5. Even between the bacterial ph
Page 15 and 16: 15 In this “heuristic” method (
Page 17: 17 set for each tree calculation. T
Page 20 and 21: 20 if you don’t correct for “fa
Page 22 and 23: 22 2. What causes variation in geno
Page 24 and 25: position in sequence* 24 All Arch

Lecture 3: A Brief Overview of Molecular Phylogeny - MCD Biology

Create successful ePaper yourself

Delete template?

Save as template?