While you analyze the data that you are given to identify similarities and differences, be sure to use specific data to draw your comparisons, hypotheses, and discussions from.
It is especially helpful to quantitatively compare data. Be careful, though, about the conclusions you draw — if species B and C each have 5 differences from species A, then they could have anywhere from 0 to 10 differences with each other! If you only have a few animals with data to analyze in part C, you could simply make this comparison for every pair. If you have 6 or 7 animals, then you could pick just a few pairs to compare. There are other legitimate ways to form quantitative data — for instance, you could focus on specific locations where most animals have the same amino acid, but some are different.
These types of analysis tend to be harder to interpret, though. If you choose to use them, I suggest that you still complete at least some of the above types of analysis as well. Use the chart to compare the amino acid sequences for the organisms. Do this in a way that lets you obtain quantitative numerical data; see above for suggestions. Hypothesize about how closely related the different organisms are, based on the amino acid data in the chart. In particular, focus on organisms that are also found on your phylogenetic tree, but you may choose to discuss others, too.
That would be especially helpful if you used only three or four of the organisms that are also in the chart, or if one or more organisms that you did not include in your tree jump out at you as being especially similar or especially different from the ones you did include. Discuss how this analysis compares to the relationships that were shown on your phylogenetic tree. Remember that "discuss" means more than simply identifying whether the relationships are the same or different as what is shown.
You can also suggest why they're likely the same, or what possible differences could imply, if anything. Please be aware that Step 3 should be written as a short essay, not a list or set of questions and answers. You may include a chart or table for the quantitative data you identified, but the key findings should also be written in sentence form.
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