Computational Evolutionary Biology

Lecture Notes

This section provides outlines and questions for a few of the lecture sessions. Additional lecture notes are forthcoming.

Questions

Before and after every lecture, questions for further discussion and reflection were provided. Questions for lecture 1 and lecture 2 are given below:

Lec #1: Introduction - Rice: Chapter 1

1. 1.Why do organisms require evolutionary theory? What is it about organisms that requires an evolutionary accounting?
2. 2.Do all historical processes require a selectionist account?
3. 3.What are the major features of organic diversity?
4. 4.What other classes of objects, besides organisms, are conditioned by history?
5. 5.Describe the organization of morphospace. How is it clustered?
6. 6.How is individuality (variation within each type) like/unlike that found in minerals?
7. 7.What about the distribution of forms in morphospace encourages an historical explanation?
8. 8.Does perfection of organic design require evolutionary explanation?
9. 9.What is the principle of historical inference?
10. 10.How are the "quirks" within adaptations "signs of the past"?
11. 11.Distinguish transformational and variational evolution.
12. 12.How are changes in an ensemble different in biological evolution than in stellar evolution?
13. 13.Why is sieving useless without heritability of traits?

Additional Readings:

 Gould, S. J. The Panda's Thumb: More Reflections in Natural History. Reissue ed. New York, NY: W.W. Norton and Company, 1992. ISBN: 9780393308198 .

Lec #2: Population Genetics - Rice: Chapter 1 and 2

1. 1.Describe the way variation, heritability and differential reproduction convert individual variation to population variation.
2. 2.Why does every population have differential reproduction? Does this always imply natural selection?
3. 3.How do we find out if variation is heritable? Why is this especially difficult with animal behavior?
4. 4.Are chromosome number and shape invariant in a population? (Discuss supernumerary chromosomes, inversion loops,...)
5. 5.How much protein variation is there for sexually reproducing species? What are poly-morphic loci?
6. 6.How big does a population have to be to realize Hardy Weinberg assumptions?
7. 7.Contrast continuous and discrete population growth models.
8. 8.Compare fitness as defined in terms of contribution to the succeeding generation and fitness in terms of optimality.
9. 9.What are Mendel's laws? In what way are theylaws?
10. 10.Is simple dominance common? Do all loci assort independently?
11. 11.Describe segregation distortion. How is the t-allele retained by the population?
12. 12.Define endogamy, planktonic mating, gene frequency (allele frequency), and gamete distribution.
13. 13.How do we move from phenotypic to genotypic frequency.
14. 14.Derive the Hardy-Weinberg equilibrium. What assumptions must be made?
15. 15.What does the following table illustrate? Focus on the assumptions that have to be made to apply this model.
    
    

Allele frequencies.

1. 16.What happens to the allele frequency after one round of random mating? How does this show that heritable variation is conserved?
2. 17.Can simple blending be simulated by having a trait that is the result of many loci? How does this difference reinvigorate Darwin's whole argument? (This is a critical point, make sure you can answer this.)
3. 18.Discuss the relationship between environment, genetics and development.
4. 19.In what ways is DNA 'self-reproducing'?
5. 20.Discuss the following:21.Define allele, genotype, fitness, relative fitness, absolute fitness, mean population fitness, marginal fitness, viability selection, sexual selection, fertility selection, adaptive landscape, Darwinian extinction, mutation-selection equilibrium, mutational load, segregation load, outcrossing, additive genetic variance, fundamental theorem of natural selection, norms of reaction.
   1. oDifferential reproduction is not equivalent to natural selection.
   2. oNatural selection operating at various levels (e.g. group and kin selection with respect to altruism).
   3. oHow does vegetative growth make the evaluation of fitness by "counting heads" difficult?
   4. oWhat are some causes of differential reproduction?
   5. oDiscuss the fitness of phenotypic classes and the fitness of genotypic classes.

Labs

Lab 1: Forces of Evolution

Part 1(PDF)
Part 2 (PDF)

Lab 2: Evolution, Polymorphism and the Coalescent

Part 1 (PDF)
Part 2 (PDF)

Supporting files for Lab 2 (Part 1):

5-sequence-data.txt (TXT)
PiS-awk.txt (TXT)
sites-testdata.txt (TXT)

Supporting files for Lab 2 (Part 2):

ms is from Professor Richard Hudson at University of Chicago. The following compiled binaries and source files are provided courtesy of Richard Hudson, and used with permission.

msmac.tar.gz (GZ) (The GZ file contains: params, clms, migmat, col1, ms, stats, sample_stats, seedms, ._.DS_Store, and .DS_Store.)
mslinux.tar.gz (GZ) (The GZ file contains: clms, col1, seedms, ms, stats, and sample_stats.)
mslinuxsource.tar.gz (GZ) (The GZ file contains: 9 .c files, 1 .h file., clms, col1, migmat, params, readme, and seedms.)
msmacsource.tar.gz (GZ) (The GZ file contains: 10 .c files, ._.DS_Store, .DS_Store, clms, migmat, params, readme, seedms, and 1 .h file.)
mssource.zip (ZIP) (The ZIP file contains: 9 .c files, clms, col1, migmat, params, readme, seedms, and 1 .h file.)
ms - A Program for Generating Samples under Neutral Models (PDF)

Lab 3: Detecting Selection

Part 1 (PDF)
Part 2 (PDF)

Supporting files for Lab 3 (Part 1):

falciparum.fas (FAS)
pf11_0344.fasta (FASTA)
Pfa3D7_chr11ORFs50.fasta (FASTA)

Supporting files for Lab 3 (Part 2):

PAML Description (PDF)
paml-exercise1.ctl (CTL)
codonmlpair.ctl (CTL)
mhc.phy (PHY)
codonmlsites.ctl (CTL)
codonmllineage.ctl (CTL)
paml_gstd1_seqfile.txt (TXT)

Lab Supporting Files

The supporting files are needed to complete the lab exercises. Each lab explains the files and procedures needed to perform the various exercises and comparative tests in PAML, the software used in the course. In order to use PAML, users must provide a control (.ctl) file which specifies the particular model and estimation method to use and a data sequence (.phy) file given in the proper format.

The Population Genetics and Evolution Simulation

The Populus Java® computer program, version 5.3 that is needed to complete Lab 1 is available at the University of Minnesota Web site. Make sure you have checked for Java® compatibility according to the instructions on that page. A PDF file of instructions for all modules is available here. (PDF - 5.2 MB)