Exercise 7.2

Pseudogenes Illustrate Functional Constraint and Provide Support for the Neutral Theory of Molecular Evolution

(This exercise is based on Li, W-H., T. Gojobori, and M. Nei. 1981. Pseudogenes as a paradigm of neutral evolution. Nature 292: 237–239.)

(Note: The reference above links directly to the article on the journal’s website. In order to access the full text of the article, you may need to be on your institution’s network [or logged in remotely], so that you can use your institution’s access privileges.)

INTRODUCTION

After gene duplication, one of the gene copies may lose its function, while at least one gene copy remains functional. Such non-functional gene copies are called pseudogenes.

During the early 1980s, several researchers used pseudogenes to test predictions of the neutral theory of molecular evolution. The neutral theory assumes that almost all mutations are either deleterious or neutral, with advantageous mutations being very rare.

QUESTIONS

Question 1. Based on this assumption, would you expect pseudogenes to evolve faster or slower than their functional counterparts? Why?

Use the information in Figure 1 to answer questions 2 through 5.

Figure 1 Plausible phylogenetic tree for three different globin genes. In a classic 1981 study, Wen-Hsiung Li and his colleagues examined the globin genes of mammals, including both functional genes and pseudogenes. Here, O designates the point of gene duplication and X represents the point where the lineages leading to mouse and rat diverged. The transition from the smooth to the dashed line along the lineage leading to A represents the time when the gene lost function and became a pseudogene.

Question 2. Based on the neutral theory and the molecular clock, what should we expect for the rate of evolutionary change along the lineage between O and X and the lineage between O and C? Why?

Question 3. Based on the neutral theory and the molecular clock, what should we expect for the number of nucleotide substitutions along the lineage between O and B and the lineage between O and C? Why?

Question 4. Based on the neutral theory and the molecular clock, what should we expect for the number of nucleotide substitutions along the lineage between O and B and the lineage between O and A? Why?

Question 5. Of the various times, T, Td, and Tn, how long has gene ψα3 been a pseudogene?

Use the information in Table 1 to answer questions 6 through 11.

Table 1 Numbers of nucleotide substitutions per site at the first, second, and third positions of codons between O and A, between O and B, and between O and C, where O is the point of duplication leading to sequences A and B in Figure 1.

Question 6

How many nucleotide substitutions per site occurred between the duplication that led to mouse ψα3 and mouse α1 and human α for the first, second, and third codon positions?

Question 7. In question 6, why is the third position so much different than the first two positions?

Question 8. Is the third position also more divergent for the other O–C comparisons?

Question 9. Which gene has diverged more at the first codon positions since the duplication, mouse ψα3 or mouse α1? How much more?

Question 10. Does the same pattern hold at the third position for this comparison? How can you explain the difference?

Question 11. What general conclusions can be inferred?