I am not certain if I am doing question 5 (i- vii) correctly, need help for question 6 too.

Parts (i) through (vi) challenged you to predict how many times a computer program or application software would be expected to return matrices containing particular characters.

Part (vii) challenges you to state how many distinct most-parsimonious cladograms could be constructed on the basis of all those matrices.

The hint is intended to suggest that the number is small; in other words, all the matrices that you considered for parts (i) through (vi) are similar, so using them to construct most-parsimonious cladograms produces only a few distinct bifurcating branching diagrams.

Part vii- need to consider distinct as referring to topology to provoke appropriate thought for part 6.

Report '1. State {U by whom (e.g., Tony Clitton), {ii} when [e.g., 1934], and (iii) in what form {e.g., online program source or book reference or ...] the bootstrap resampling procedure rst and formally was introduced to phylogenetic systematic analysis. i- Jweph mam ii. 1935 iii. Computer analysis Evolution Journal published: W J. [1985}. Condcocc limits on phylogcnics: an approach using the bootstrap. Evolution, 39(4), TEE79] . 1111p:a\"fill.."il.."il.r.jstcr.org;f stablcAD-EETE} 2. Describe the steps {i.e., at least three} involved in determining bootstrap proportions for a phylogenetic systematic analysis. i. Plot your original data set ii. Produce bootstrap replicates using Articial data sets from the original data set using the computer Sample at random, with replacement, from original characters iii. Estimate the phylogeny from each bootstrap replicate Sample at random, with replacement, from original characters iv. Draw a tree Majority-rule consensus phylogeny Contains all the moncphyletic groups that appear in at least haif of our bootstrap replicate Label the node at the base of the clade with the percentage of replicates in which it appeared The bootstrap support for the clade - The number estimates the confidence we can have that the presence of the clade in our reconstruction would hold up to modest changes in the characters sampled - High bootstrap support indicates that the clade is a strong winner across our entire data set 3. For a phylogenetic systematic analysis containing three characters, state the probability for obtaining any particular matrix among all those possible through bootstrap resampling [if necessary, you may assume that the weighting associated with sampling each character is identical and that character order in each matrix matters, so that x y z is different from 2 y it]; show yourcachlation. probability: \"2? The probability is getting any latter three times, (1!?!) \"3 = \"2? mmmmmmmsmmmmmmmmmmmm 2%. IE; as. m. m m. mm 4. Imagine that you were asked to perform a phylogenetic systematic analysis with the following taxcn-character matrix. HUI} 5:44\" Frcduce the mcst-parsimcnicus cladcgram{s] above, at the right. 5. Suppose that you were asked to perform 2? bcctstrap replicates for the phylogenetic systematic analysis in part 4 (if necessary, you may make the same asSum ptions as those descri bed in part 3). {i} State hDW many times you would expect a computer program or application software to return a matrix containing only character x (i.e., x xx}; show your reasoning. One time for only character x {xxx} x x A T D B T 1 C D 1 {ii} Use your response tc part {i} to state how many times you would expect a computer program or application software to return a matrix containing only character y or only character One time for only character y {y} and Cine time for only character 2 {3;} lm} 445:\": DhH": AND\": Gm]:- A'HDN DLLN AtDN {iii} State how many times you would expect a ccrnputm program or application softwe to return a malrix with two columns containing character y and one column containing character 2; show your calculation or reasoning. Six times with two column of y Twelye times with one column of z B ll" A U 1 C 1 7- 3" 1 D 1 1 El 1 {iv} Use your response to part (iii) to state how many times you would expect a computer program or application software to retum a matrix with two columns containing character 2 and one column containing characterx or two columns containing character x and one column containing character y. Six times with two columns of 2 Twelve times with one column of x Six times with two columns of x Twelye times with one column of y DUE} 4.1.3:: (3.14%: gambit {'4} Use your responses to parts (iii and iv} to state how many times you would expect a coinputer program or application scware to return a matrix with two columns containing character 2 and one column containing character y or ttyc columns containing character x and one column containing character: or two columns containing character y and one column containing character x. 5,115,116.12 = six times {Hi} State how many times you would expect a computer program or application software to return a malJ'ix containing all three characters; show your calculation cr reasoning. Six times with all three characters x y z A i] 1 D B 'I 1 'i C 1 El 1 {vii} Considering responses to parts {i} through {vi}, produce all the possible distinct most- parsimonious cladograms that could result from 2? bootstrap replicates (hint: the number is far fewer than 2?). E. If you have invested thought generally in the bootstrap resampling procedure as it applies to phylogenetic systematic analysis and specically in the foregoing exercises, then you might have noticed a potential problem with a m part 2 and the accurate response to part 5 vii. State as concisely as you can the problem: The problem would become more serious with greater taxon and character numbers; you will be challenged to identity in the literature the rst attempt to avert the problem with a particular change to one step in part 2 with Cocktail Party Criterion Test 02