Bioinformaticians, Can You Pass That Exam?

Bioinformaticians, Can You Pass That Exam?

Good knowledge of molecular evolution is essential to perform any research in bioinformatics and computational biology. Unlike the difficult 8th grade questions from early 19th century popping up over the internet, today’s question paper on molecular evolution exam is only a week old. Larry Moran, the author of the highly informative sandwalk blog, posted the exam questions of his undergraduate course on molecular evolution at the University of Toronto. See whether you can clear it !!


Here’s the final exam in my course. Students have to answer the first two questions and three of the next five questions. How would you do?

1. Choose a subtopic from your essay and explain it better than you did in your essay and/or rebut the comments and criticisms made by the marker/grader.

2. Michael Lynch says in The Origins of Genome Architecture ….

Nothing in Evolution Makes Sense Except in the Light of Population Genetics

Evolution is a population genetic process governed by four fundamental forces, which jointly dictate the relative abilities of genotype variants to expand through a species. Darwin articulated a clear but informal description of one of those forces, selection (including natural and sexual selection), whose central role in the evolution of complex phenotypic traits is universally accepted, and for which an elaborate formal theory in terms of changing genotype frequencies now exists. The remaining three evolutionary forces, however, are non-adaptive in the sense that they are not the function of the fitness properties of individuals: mutation (broadly including insertions, deletions, and duplications) is the fundamental source of variation on which natural selection acts; recombination (including crossing-over and gene conversion) assorts variation within and among chromosomes; and random genetic drift insures that gene frequencies deviate a bit from generation to generation independently of other forces. Given the century of theoretical and empirical work devoted to the study of evolution, the only logical conclusion is that these four broad classes of mechanisms are, in fact, the only fundamental forces of evolution. Their relative intensity, directionality, and variation over time define the way in which evolution proceeds in a particular context.

Do you agree with Lynch that Nothing in Evolution Makes Sense Except in the Light of Population Genetics? If so, why isnt population genetics taught in introductory biology courses? If not, why not?

3. Imagine that identical female twins were born to a woman in 1000 AD. Imagine that you could find a direct descendant of each twin in 2015. If you sequence the complete genomes of the descendants, approximately how many differences would you expect to find? How do these compare to the differences between any two randomly selected individuals from the same part of the world? Explain your reasoning and describe any assumptions you make. Think carefully before you answer. The second question is the most important one. (Human mutation rate = 130 mutations per generation. Haploid genome size = 3.2 109 bp.)

4. Why do some scientists think that there is no unique tree of life?

5. Many people believe that recombination evolved because it increases genetic variation in a population and this provided a selective advantage over species that didnt have recombination. Do you agree with this explanation for the evolution of recombination? Why, or why not? What are the other possibilities?

6. What is evolvability and why could it be important in evolution? Why are some scientists skeptical of this claim?

7. Richard Dawkins once wrote,

Even the most ardent neutralist is quite happy to agree that natural selection is responsible for all adaptation. All he is saying is that most evolutionary change is not adaptation. He may well be right, although one school of geneticists would not agree. From the sidelines, my own hope is that the neutralists will win, because this will make it so much easier to work out evolutionary relationships and rates of evolution. Everybody on both sides agrees that neutral evolution cannot lead to adaptive improvement, for the simple reason that neutral evolution is, by definition, random, and adaptive improvement is, by definition, non-random. Once again, we have failed to find any alternative to Darwinian selection, as an explanation for the feature of life that distinguishes it from non-life, namely adaptive complexity.

Richard Dawkins (1986) The Blind Watchmaker. p. 304

Can you describe situations in Richard Lenskis ongoing evolution experiment where neutral or deleterious alleles were essential for adaptive change?

The exam is already creating waves around the blogosphere. Comment section of the post has grown to nearly 90 replies. Also, Arlin Stoltzfus, a researcher working on mutationism, wrote a large blog post to present his views on one of the questions.

Over at Sandwalk, Larry Moran posted some interesting bits from his molecular evolution class exam, including a passage from Mike Lynch arguing for his claim that nothing in evolution makes sense except in the light of population genetics. In this passage, which Ill quote below, Lynch says that evolution is governed by 4 fundamental forces.

The idea that evolution is governed by population-genetic forces is common but fundamentally mistaken. I wish we could just put this to rest.

Enjoy !!

Written by M. //