ALTERNATIVE ASSESSMENT 1.

Note: Submit your output in PDF. An output submitted, not in PDF, will not be scored.

I. Complete the following statements. Each item carries 1 point.

1. It was initially thought that the Ramapithecus was the most recent ancestor of Homo
sapiens, as it diverged from non-human primates. However, the study of Sarich and Wilson
on the protein serum albumin debunked this hypothesis.

2. The Jukes-Cantor Model is the simplest of the 5 distance correction models. It only
assumes two basic principles, (a) the 4 bases have the same frequencies and (b) the rate
of substitution is equal.

3. Distance methods rely heavily on fossil records to compute how long organisms of
interest have evolved from each other.

4. The GTR Model is the distance method that is more commonly used because it takes into
account the differing evolutionary rates between sequences and not just ultrametric branch
lengths.

5. Through molecular analysis of HIV and SIV sequences, Patient Zero of the 1981 AIDS
pandemic was traced to have existed in Chimpanzees back in the early 1900’s.

II. Answer the questions briefly and completely. Each question carries 3 points: 2 pts.
for integration of concepts, and 1 point for organization of concepts.
1. If you will construct several phylogenetic trees of mammalian species using protein
sequences from cytochrome c, hemoglobin, and fibrinopeptides which trees would have a
more or less similar tree topology? Which trees would look very different from each other?
Why is this so?
Cytochrome c and Hemoglobin would have more similarities because of their
slower rates of amino acid changes, whereas Fibrinopeptides would look much
more different compared to both, especially Cytochrome c, since it has a much
faster rate of amino acid changes.

2. Why is UPGMA an unreliable method in tree construction?

First of all, the UPGMA uses ultra-metric data, which is not realistic. Secondly, it
relies too much on its ultrametricity for it to be organized.

III. Listen to the podcast and answer the questions that follow. Each question carries 3
points: 2 pts. for integration of concepts, and 1 point for organization of concepts.

Podcast: Molecular Clock, Pt.1: Mitochondrial DNA | Curious Minds

https://www.cmpod.net/the-real-adam-and-eve-the-molecular-clock-part-i/
1. How is rolling a dice comparable to the genetic mutations between two different organisms
(example: ape and human)?
The process by which rolling a dice and mutations occur seem to produce
random results, but after looking at it repeatedly you see a pattern that follows
statistical rules.

2. Based on the podcast, why were biologists initially apprehensive in utilizing the molecular
clock in identifying the origin of different organisms?
Biologists were apprehensive because of the lack of technological capabilities
behind this type of research and that the data they could collect were too
 random and could end up very wrong. There were too many variations that
scared biologists on the accuracy of their findings.

3. Identify one alleged full proof way to ensure that a molecular clock is credible.
Treating the mutations as a statistical pattern solidifies the methods used in
molecular clock theory. Fossil findings also help justify the credibility of the
results.

4. Who is Mitochondrial Eve and how did science help in uncovering the mystery behind her?
Mitochondrial Eve is the ancestral mother to all humans, a common ancestor
that lived in Africa long, long ago. Science helped uncover her through Rebecca
Cann’s research involving the molecular clocks based on our mitochondrial DNA.

5. What is your personal take on Mitochondrial Eve? How can you relate it to the debate
between creationism versus evolution? Elaborate your answer.
Mitochondrial Eve to me, is the most common and most recent ancestor
between all us humans. This prehistoric mother contained the source code that
defines our mitochondria and all its mutations. Knowing this, I assume that Eve
may also have an ancestor with which it retained its mitochondrial traits.
Knowing this, I believe that it is one of the starts in the evolutionary history of
humans.