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Special Topics in Evolution Questions

Bring on the tough stuff

1. Explain the difference between homology, orthology, and paralogy.

2. You find two species that have the same gene, X. The nucleotide difference between the two is 35 substitutions, and their last common ancestor is 10 million years ago. You find gene X in two more species that had a common ancestor 40 million years ago. What would be the expected number of differences between the two gene X's? Assume a universal molecular clock applies.

3. There are two species of monkeys in an isolated forest in South America; one species has red noses, while another has blue noses. They are both most closely related to each other, but only the blue-nosed species is resistant to Monkey Virus X. What is the relationship between Monkey Virus X resistance and blue-nosed monkeys?

4. You find a new species of flightless bird called the "Shmoop" on an island in the Atlantic that is most similar to a pigeon. Describe the process of evolution for that bird on that island. How would your conclusion be different if you found that the Shmoop was most closely related to a penguin?

5. Why is the Linnean taxonomical system of nomenclature not a good system to determine relationships of various species?

6. Based upon the phylogenetic tree from Practice Test #3, what is the relationship (homology-wise) between LEP, Lepa, Lepa1,and Lepa2?

7. Are humans a species of chimpanzee?

8. Scientists studying the Shmoop discover that it is resistant to avian influenza, a disease that is highly prevalent on the island. They noticed that the gene that regulates the development of wings is adjacent to the gene that is responsible for influenza resistance. What is the relationship between these two genes?

9. Describe the type of speciation that would occur if an earthquake splits a big lake into two smaller lakes.

10. What are some key gaps in the RNA World hypothesis explanation of the origin of life?

Possible Answers

1. Explain the difference between homology, orthology, and paralogy.

Homology is any similar trait that is shared in function or structure between two species and is shared in a common ancestor. Orthology and paralogy are specific versions of homology, describing the relationship of the trait. Orthologous traits are the equivalent homologous trait in two related species. Paralogous traits are duplicate traits that were produced in one ancestral species after a gene duplication event. For instance, the alpha-globin and beta-globin genes would be considered paralogous. The alpha-globin gene in mice and in rats would be considered orthologous. All related globin genes in rodents would be considered homologous.

2. You find two species that have the same gene, X. The nucleotide difference between the two is 35 substitutions, and their last common ancestor is 10 million years ago. You find gene X in two more species that had a common ancestor 40 million years ago. What would be the expected number of differences between the two gene X's? Assume a universal molecular clock applies.

If you assume a universal molecular clock, the calculated rate here is 3.5 substitutions/(site*million years). So, if the two species had a common ancestor 40 million years ago, you would expect approximately 140 substitutions between the two genes.

3. There are two species of monkeys in an isolated forest in South America; one species has red noses, while another has blue noses. They are both most closely related to each other, but only the blue-nosed species is resistant to Monkey Virus X. What is the relationship between Monkey Virus X resistance and blue-nosed monkeys?

You would need more information to answer this question, but the simplest explanation is that genes encoding development of blue-noses also confers resistance to Monkey Virus X. However, it is unlikely that development of blue-nose has any physiological fitness benefit, and is purely a sexually selected trait. So, the selection of resistance against Monkey Virus X must also be conferred with the selection for blue noses. So, virus resistance is a genetic hitchhiker to blue-nosed development (and vice versa).

4. You find a new species of flightless bird called the "Shmoop" on an island in the Atlantic that is most similar to a pigeon. Describe the process of evolution for that bird on that island. How would your conclusion be different if you found that the Shmoop was most closely related to a penguin?

We know that pigeons fly, so it is likely that an ancestor of this flightless bird and the pigeon arrived on this island some time ago. Because there was no need to maintain the ability to fly, the birds' wings became vestigial. If we found that the closest relative was a penguin, and knowing that penguins do not fly, we would assume that the bird arrived on the island by means of a raft or ancient land bridge (or by swimming). Either way, conditions on the island favor loss of flight, which is why the bird is incapable of flying.

5. Why is the Linnean taxonomical system of nomenclature not a good system to determine relationships of various species?

The Linnean taxonomical system was a useful technique to name organisms and broadly group them together into kingdoms, phyla, etc. However, recent phylogenetic evidence suggests that these are not good groupings based upon genetic information. It is more likely that organisms with similar genetic sequence are related to each other than with similar phenotypic features (see birds and bats wings), so when relationships are unresolved, most scientists lean towards genetic information (molecular evolution) to resolve relationships. Therefore, Linnean taxonomy is losing favor in the scientific community. Sorry, Carolus.

6. Based upon the phylogenetic tree from Practice Test #3, what is the relationship (homology-wise) between LEP, Lepa, Lepa1,and Lepa2?

LEP, Lepa, Lepa1, and Lepa2 are all homologous genes found in different species of fish and land animals. While LEP and Lepa are orthologous genes, Lepa1 and Lepa2 are paralogous genes found in goldfish, salmon, and the common carp. These genes were likely formed from a duplication of Lepa in the common ancestor of goldfish, salmon, and the common carp.

7. Are humans a species of chimpanzee?

Humans are not a species of chimpanzee, and neither is a chimpanzee a species of humans. Chimpanzees are related to humans in that we share a common ancestor (which dates back around 5-6 million years ago). Many times people say that humans are not monkeys, and technically we are not. Monkeys are a group of animals that share a common ancestor with the Great Apes (of which humans are a part) around 28 million years ago. This is where phylogenetics and taxonomy clash somewhat. Humans are primates in that their taxonomical classification lists them in the order Primata, but they are not monkeys, as they have very distinct features from monkeys. Chimpanzees and humans are collectively apes (based upon taxonomical classification), but they are two independent species that are similar to each other.

8. Scientists studying the Shmoop discover that it is resistant to avian influenza, a disease that is highly prevalent on the island. They noticed that the gene that regulates the development of wings is adjacent to the gene that is responsible for influenza resistance. What is the relationship between these two genes?

It is likely that the development of wings is a genetic hitchhiker to influenza resistance. While there is no selection for flight, there is a strong selection for influenza resistance for the Shmoop. So, while the bird doesn't need wings anymore, it still makes them because the gene for wing development is so close to that for influenza resistance.

9. Describe the type of speciation that would occur if an earthquake splits a big lake into two smaller lakes.

Assuming a big lake becomes divided into two smaller lakes, this will create two separate geographic niches. This is essentially allopatric speciation. However, it is possible that there might be some space for movement from one lake to another, if they are linked in any way (by water). Therefore the types of speciation would be parapatric (which allows for movements between niches) or possibly even sympatric (depending on how easily movement occurs from one lake to another). Peripatric is unlikely, as for this to occur, a species not present in one half of the lake would have to migrate from the other half of the lake and then speciate after separation. This species would have to be incapable of going back to the original half of the lake that it was found.

10. What are some key gaps in the RNA World hypothesis explanation of the origin of life?

While there are several lines of evidence that supports the RNA World hypothesis, there are many gaps that don't completely prove it. For instance, the Miller-Urey experiment did not produce all of the essential biomolecules for life, the formation and structure of cells still seems unclear (although the role of clay to regulate replication of lipids and vesicles seems promising), and no evidence of metabolic ribozymes have been found. Also, most of the metabolites that were believed to be formed in early Earth should be broken down faster than they could be incorporated into proto-cells.

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