Week 1: Evolution: Geological Time, Primate and Human Evolution, and Molecular Evolution

I. Geological and Evolutionary Timeline

Earth is approximately 4,600 million years old (equivalent to 4.6 billion years old). The major events of the evolution of life on Earth are summarized in Table 1, and together with the activity that follows are adopted (with modification) from Barrow (2016). Your instructor might ask you to read Barrow’s article “Picturing Evolution through Geologic Time” before coming to the lab.

Activity 1: Representation of Evolutionary Timeline

1. Using string (thread) and a tape measure or long ruler (see Figure 1), measure a piece of string 4.6 meters long. Lay it flat on the bench. This represents a timeline of Earth’s 4.6 billion year history.

2. Calculate what each unit of the ruler represents in the number of years. For example:

If 4.6 m = 4.6 billion years, then 1 m = 1 billion years.

1 m = 1 billion years

1 cm = _____ years

1 mm = _____ years

3. Using masking tape, place a thin piece of tape on the string at the appropriate distance to indicate each evolutionary event from Table 1 on the string. On the tape indicate the date and the event. Do this until you have marked all the events on the string. Please note that in order to mark the events to scale as required, you will need to use the conversion factors you calculated in the previous step. For example, if you are marking the origin of the prokaryotes to scale, you need to know how far 3400 million years would be from 4600 million years (the beginning of your timeline). You can solve it using algebra.

[latex]\frac {3400 \text { million}}{4600 \text { million}} = \frac {x}{4.6 \text {m}}[/latex]

You can solve for x algebraically as follows:

[latex]x = \frac {3400 \text { million * } 4.6 \text { m}}{4600 \text { million}}[/latex]

The units “million” cancel, and your final answer is in meters (m).

This tells you how many meters to measure from 0 (the end of your timeline, or the present day). That is the point where you will place the event “prokaryotes.” Calculate the other events in Table 1 in a similar manner.

4. Answer the following questions.

a. What patterns if any did you notice in the timeline? In other words, what did you notice or what surprised or interested you about the spacing of the events?

b. What proportion (in %) of Earth’s life history does each event represent? Complete your work in a table like Table 2 below. Show your calculations.

II. Primate and Human Derived Characteristics

Primates are the order of mammals that includes all monkeys and apes. The apes include gorillas, orangutans, chimpanzees, and humans. Characteristics of both primates and humans can be found in Table 3.

An indication of the larger brain size is evidence found from cranial bones in skull fossils of different taxa. Here are some representatives.

Activity 2: Skull Fossil Exercise

Pre-lab

Your instructor might direct you to view this short video from the American Museum of Natural History before lab.

In the lab

It is estimated that the chimpanzees diverged from the lineage that gave rise to the human lineage about 6 mya (including Australopithicenes such as Lucy and later, other Homo species such as Homo neanderthalensis, the Neanderthals). Modern humans (Homo sapiens) evolved approximately 200,000 years ago (0.2 mya). Examine the replica skulls on the demonstration table closely, which are similar to the ones in Figure 2. View the cranial bones as well as the facial bones. Consider the following attributes:

1. the length of the jaw
2. the size of the cranium
3. the morphology of the bridge of the nasal bone
4. the morphology of the eyebrow ridge
5. teeth number and specialization

What patterns do you notice for i–v from the most primitive to the advanced organism? Refer to Figure 2, which is organized from the most primitive (left) to advanced (right), to help your analysis. Record your observations in a table like Table 4 below.

Answer the following questions.

a. What can you conclude from your observation of the size of the cranium?

b. What can you conclude about the differences observed in the number and morphology of the teeth?

III. Molecular Evolution

Molecular data can be used to delineate relationships among organisms. The more DNA identity (similarity), the more closely two species are; that is, the more recent their common ancestry and point of divergence. The more DNA difference (dissimilarity), the more distantly related two organisms are considered to be. It is therefore of value to calculate how similar or dissimilar conserved sequences of DNA are.

For example, look at the following two sequences (N2 and N1), representing short DNA sequences belonging to two different species (Figure 3). They have been aligned using bioinformatics software. Consider the first 100 nucleotides. How many of the nucleotides are identical between species N2 and N1?

Figure 3: DNA alignment of two simulated DNA from two hypothetical species, N1 and N2. Alignment and figure by F. Tamari

Using the same software, the differences can be highlighted. Here’s a snapshot of this simple analysis (Figure 4).

Figure 4: DNA alignment of two simulated DNA from two hypothetical species, N1 and N2. Alignment and figure by F. Tamari

For the first 100 nucleotides:

% difference = {100% [asciimath]xx[/asciimath] (# changed nucleotides)} / total number of nucleotides considered

= [asciimath]100% xx frac{3}{100}[/asciimath]

= 3%

% identity = {(100%) * (# unchanged nucleotides)} / total number of nucleotides considered

= 100% * 97 / 100

= 97%

Consider the following alignment for two other species, N3 and N4 (Figure 5).

Figure 5: DNA alignment of two simulated DNA from two hypothetical species, N3 and N4. Notice that the total number of nucleotides is not 100 as before! Alignment and figure by F. Tamari

Calculate both % difference and % identity. Show all your work.

% difference =

% identity =

Activity 3: Molecular Evolution Exercise

This activity was written by Dr. Craig Hinkley, with data gathered from the DNA Learning Center at Cold Spring Harbor.

Procedure

1. Work in groups of four students.

2. Each group has four DNA sequence comparisons to examine. These DNA comparisons are between a modern human and either another modern human, a Neanderthal, a chimpanzee, or a dog.

3. In a table similar to Table 5 below, record the ID (location name/number) of the specimen of modern human DNA your group is comparing and the ID (location name/number) of the four specimens to which it is being compared.

4. Each student in a group should work with one DNA sequence comparison.

5. For each comparison, the differences between the two sequences are highlighted. Dashes (–) indicate a mutation that is due to either an insertion or deletion in one of the sequences.

6. Count the number of differences between your two sequences.

a. Count each nucleotide difference as one difference (including single insertions or deletions).

b. Count each insertion or deletion containing more than one difference (two or more dashes in a row) as one difference.

7. State hypotheses about which DNA sequences will show the most or least similarity.

8. In a table similar to Table 6 below, record the total number of DNA nucleotide differences and the total number of DNA nucleotides that were compared.

a. Calculate the percentage of DNA nucleotide differences between the sequences and record the percentage difference in your copy of Table 6.

b. In your copy of Table 6, record the data for the other three DNA comparisons from your group.

Data analysis

1. Examine the data you recorded in your copy of Table 6. In other words, try to look for trends or patterns in your data. Record what you find.

2. Arrange the sequences from the smallest number of nucleotide differences to the largest number of differences.

3. Arrange the sequences from the smallest percentage of nucleotide differences to the largest percentage of differences.

4. Is there any difference between the order of the sequences you wrote down in #2 and #3 above? If so, why do you think there is a difference?

5. Which is better to use for the comparisons, the total number of nucleotide differences or the percentage of nucleotide differences? In 2–3 sentences, explain why you think so.

Conclusion

In 3–4 sentences, write a conclusion that states whether the data supports or does not support the hypotheses you formed in #7 of the procedure above. Include at least one piece of data that supports this conclusion.

Work Cited

Barrow, L. H. (2016). Picturing evolution through geologic time. The American Biology Teacher, 78(2), 137–140. https://doi.org/10.1525/abt.2016.78.2.137