DNA Variation, Haplotypes, and Phylogenetic Trees
Scientists use existing sequences in order to determine how they are related to each other.
In this exercise you will:
1) determine variations among six sequences by performing a multiple alignment;
2) determine the six haplotypes represented by these six sequences;
3) deduce the relationships among these six sequences, i.e. how they might be derived
from each other.
1) Variations (SNPs)
Enter Sequence Server  Manage Groups  Sequence sources:  Public
Check SNPs, then click Ok.
Underneath seq 1 click None and select seq 2.
Click None and select seq 3, seq 4, seq 5, seq 6.
Click COMPARE.
2) Status in SNP positions for each sequence (haplotypes)
Record the positions in which the six sequences show variation.
Record for each sequence seq 1 through seq 6 the nucleotides in these positions.
3) How could the sequences be derived from each other (phylogenetic tree)?
Determine how the six sequences might be derived from each other. Only sequences that
differ in one nucleotide can be directly related to each other. Sequences that differ in two
or more nucleotides can only be related to each other through intermediates.
In order to come up with a correct tree you have to follow two rules:


Rule 1: Each branch point can only bear a change in a single nucleotide.
Rule 2: From each branch point only two branches emerge: one branch leads to the
new sequence, the other carries forward the parental sequence. (There is no reason
to assume that the parental sequence would disappear just by the fact that a
mutated sequence occurs.)
Draw a tree representing the relationships among the four sequences. Make sure that you
followed the rules. It is really easy to violate them by introducing two changes at once, or
by having more than one branch emerge from a single branch point. See example below:
Observed sequences: Uwe, Ute, Ule, Ula, Ulla
Tree (potential relationships):
/
Uwe
/ \
Uwe Ute
/
/ \
/ Ute Ule
/
/
/ \
/ Ute Ula \
/
/ \ See
Uwe Ute Ula Ulla Ule