BCH 447 lecture 1
We created a phylogenetic tree. Conceptually, we look at the differences in
the amino acid sequences of the same protein in different species and compare
the difference. Using the difference factor we can create a phylogenetic
tree. This is shown in the notes for lecture one.
This is a stochastic problem.
We look at the difference between species and create a phylogenetic tree
based on their distance from each other with the distance being based on
genetic difference number... Once more are seen. Note that it is okay to wing
it a little as long as the numbers are relatively the same. In our tree we
see that caw is more distant from humans than monkeys are. We also see that
the chicken is more related to the cow than to the humans.
Note that the chicken should be equidistant from mammals, but it is rather
hard for us to get the numbers to represent that, so instead, we have a 14
nucleotide difference between humans and chickens and a 12 nucleotide
difference between chickens and cows.... Our chicken in this case though,
likely has a sequence problem.
Once more, the tuna should be equidistant also.
Look at the drawn sample
The first paper was written in 1963. The sequence here was determined through
protein sequencing... A technique pioneered by Sanger.
Always keep in mind that sequences may not be completely accurate, secondly
we are dealing with very minor numbers and there is noise in the data.
Finally it would be better to run a larger protein because we get rid of more
noise and increase accuracy.
Bacteria are very different from eukaryotic differences. Note how both ends
of the tree from bacteria to another sector have the same distance. That's
how we guessed the luca number... This is called inferring the root.
As described above... Our branches from luca are roughly the same length. It
suggests that there is a persistent rate of change that is occuring over time.
Which is weird because we are all under different selective pressures. But
The reasoning has to do with the polymerases mistakes. The reason they are
persistent is because of mutations in non selected regions of proteins.
Selection maintains regions that are important but regions that are not, will
mutate at a persistent rate that is directly dependent on the flaws that dna
polymerase has, every 1/1billion nucleotides... Since the mutations are
neutral they do not effect the organism and get carried onto progeny without
There are two mechanisms of fixation. One is natural selection and the other
is random genetic drift (by accident... Neutral mutation). By chance
unimportant allelles get eliminated while the other becomes fixed. These
mutations aren't recognized by natural selection and therefore are under a
constant rate of mutation. 99.9% of evolution comes from random genetic
drift... Not natural selection.
In the cytochrome C sequences it must be noticed that the regions with the largest variant nucleotides ar