4. Consider the following multiple sequence alignment (spaces included for ease
ID: 213118 • Letter: 4
Question
4. Consider the following multiple sequence alignment (spaces included for ease of reading) for the proto-insulin gene: Human: ATGGCccTGT GGATGCGCCT CCTGCCCCTG CTGGCGCTGC TGGCCCTCTG Sheep: ATGGCCATGT GGACACGCCT GGTGCCCCTG CTGGCCCTGC TGGCACTCTG Chick: ATGGCTCAT GGACACGCCT TCTGCCTCA GGCCCTGC TAGcccG a) (4pt) You are considering the Jukes-Cantor model of sequence evolution, which is a single parameter model of evolution (typically described simply as a). Given only the comparison between Human and Sheep as training data, what is your best estimate of a? b) (3pt) Would the mutation rate be greater or less than the observed substitution rate for mammals? Why? c) (3pt) From the standpoint of constructing a phylogenetic tree, how many positions (columns) in this alignment are informative?Explanation / Answer
In these multiple sequences alignment you can see there are four nucleotides, A, G, C and T.these four states at a single nucleotides site if we just use raw number of differences between two species DNA sequenceswe can get misleading results. In jukes-cantor model its easy to estimate and correct for the total number of changes that have occured, which may not be visible. but with the help of jukes - cantor model we will be visible to us.
(a) 1. we can see the C nucleotide change into T nucleotide in first position so these models are closely related.
2. Nucleotides can occur at different frequencies.
3. each nucleotide pair has a different rate. In other words,A changes into T with the same rate that T changes into T. sequences evolution have been proposed These substitution models differ in terms of the parameter used discribe the rate at which one nucleotide replaces another during evolution its a single parameter model of evolution .
4. in mammals seem to show high levels of variation.
(b) 1. we have find the mutation rate is approximately constant per year and largely similar genes.the rate at which changes mutation rate and the rate at which these changes become into the species shared mutation rate.
2. Mutation rate varies between the species, if the neucleotidea are damage that changs the sequences mostly these type of damage occur in animals so we can say the mutation rate greater in mammals in cimparision of other species.
3.Source of mutation is DNA replication the genome is copied and may be small chance of an error and this error change the base sequence.this may be occur in vertebrate, species with shorter generation and this also effect to the plants.so its prooves that mammal have high mutation rate in the comparision of other species.
(c)1. A phylogenetic and evolutional tree showing evolution relationships between biological species, these relationships are called the phylogeny of the species.
2. Position of alignment are, Pairwise sequences alignment, multiple sequence alignment.
in pairwise one change into other nucleotides and change at place as C change into T. and in multiple alignment changes in more than one nucleotides .
2. In contructing a phylogenetic tree DNA is more informative in the case of protein analyzing. because of there is evolutionary time is too much and its not reflect its occur the actual mutation.
3. In general the tree based on DNA sequences is more informative and alignment many not closely related species, the DNA sequence carry more rich information than aminoacid sequence. but DNA and protein are present in reaction, and proteins are having 20 aminoacids that contains more information, but its the less the because AA sequences brings more information. so informative alignments are AA, four nucleotides, aminoacids T. almost more informative DNA,AA.
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