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BIOL 405

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Spring 2014 TuTh 9:45 – 11:00 008 Mueller


Instructor: Dr. Kateryna Makova 305 Wartik Lab Office hrs: 8:30-9:30-TuTh 


TA: Ms. Rebeca Campos Sanchez 510 Mueller Office hrs:11:30-12:30-TuTh



Fundamentals of Molecular Evolution, 2000, by D Graur and WH Li (Sinauer) 


Supplemental readings will be assigned throughout the semester.

Other books that might be useful:

Molecular Evolution: A Phylogenetic Approach, 1998, by RDM Page and EC Holmes (Blackwell Science)

Molecular Evolution, 1997, by WH Li (Sinauer)



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Lecture notes will be available the day before the lecture 




in-class exams              (2 @ 25 points each)    50 points

homework assignments   (2 @ 10 points each)    20 points

final project                  (1 @ 30 points)           30 points

Total                                                          100 points


In-class exams (closed-book) will include material from lectures, reading assignments, and homework assignments. There will be questions about material from the book (but not covered in lectures), so read the book! The last in-class exam will serve as a final (there will be no final during finals period). Sample problems will be provided.


Homework assignments will consist of problems, including the use of molecular evolution analysis software (MEGA). The students will be given 1 week to turn the home assignments in. Home assignments will be collected before the start of the class on the due dates. Late assignments will not be accepted.

Final project will require the student to synthesize the concepts from the lectures and the book, to analyze the biological data of interest, and to present data in the format of a scientific paper. Undergraduate students are encouraged to work on this project in pairs (two students working together on the project can turn in one paper). Projects can be turned in late, but 5 points will be deducted for each late day.


Grades: 95-100 (A); 90-94 (A-), 85-89 (B+); 80-84 (B); 75-79 (B-); 70-74 (C+); 65-69 (C); 60-64 (C-); 55-59 (D+); 50-54 (D); <50 (F).



BIOLOGY 405 MOLECULAR EVOLUTION Lecture Schedule (Spring 2014)










p. 1-4




Gene structure

p. 5-24





p. 25-38




Dynamics of genes in a population

p. 39-42, 47-53




Dynamics of genes in a population

p. 41-47, 53-57




Diversity and databases

p. 57-59





p. 86-98




Substitution models

p. 67-79

Ass. given



Coding substitution models

p. 79-86




Introduction to phylogenetic trees

p. 165-182, 217-220

Ass. due



Distance matrix methods

p. 182-184, 189




Parsimony methods

p. 189-197




Maximum likelihood methods

p. 198-199




exam 1





Tree reliability: bootstrap

p. 208-211




Phylogenies: problems and examples

p. 212-246




How to build phylogenies? MEGA tutorial

Suppl. readings



Gene duplication; new genes; pseudogenes

p. 249-304




Repetitive elements and evolution by transposition

p. 225-228,323-359

    Pr. topic due



Variation in substitution rates

p. 99-115, 123-132

   Ass. given



Molecular clock

p. 139-155




Molecular Signatures of Selection

p. 110-117,119-123

    Ass. due



Molecular Signatures of Selection

p. 57-64




Sex chromosomes

p. 117-119




Codon bias

p. 132-139




exam 2





Concerted evolution and horizontal gene transfer

p. 304-322, 359-366




Human genome and comparative genomics

Suppl. readings

Project due



Discussion of individual projects





Discussion of individual projects





Lecture topics are tentative


Molecular Evolution
Final Project Guidelines


The final project is designed to be an assignment that integrates the concepts that you have learned during the semester and builds on what you accomplished in all assignments.  The main goal of the final project will be to analyze a set of nucleotide or protein sequences using the techniques of molecular evolutionary analysis.  There are several directions that one could take in this assignment, but do not feel constrained by these types of projects:

1. Analysis of nucleotide or protein sequences of a multigene family from within a species genome to infer the mechanisms of expansion or the evolutionary history of the expansion within the genome.

2. Analysis of nucleotide sequences from one or more loci within one or more species to determine the genetic mechanisms that have acted on the gene loci.

3. Analysis of homologous genes or proteins among different species to infer the phylogenetic relationships among species.


Feel free to set up an appointment to discuss the possible directions that your project might take.  The project will be a combination of written and statistical analyses that will include the following elements:


1. Background to the Problem.  Why did you choose to examine this problem with molecular evolutionary analysis?  What other work has tried to examine this problem (provide references to the previous work that you cite)?  Why do you think your analysis may provide breakthrough information about the biological problem that you have tackled?

2. Description of the Data.  What sequences did you collect for your analysis?  What are the GenBank Accession numbers for the sequences that you used?  What is the origin of the sequences?  Who generated the data?  You can present this information in tabular form, but you must include a written description of the data.

3. Description of the Data Analysis.  How did you analyze the data and why did you choose the methods that you used?

4. Results of the Data Analysis.  What inferences can you draw from the data analysis?  This should be a description of your phylogenetic trees and the general tendencies that you observed in the trees.  What do your statistical analyses say about the robustness of the analyses?

5. Discussion.  What is the biological meaning of the data that you collected?  


I will grade the final project based on two broad criteria:

1. Technical.  Were the analyses appropriate?  Were they correctly presented and interpreted?  

2. Integration and Creativity.  How well did the project integrate the information from Molecular Evolution to examine the biology of a genetic or organismal phenomenon?  How creatively did the student examine this problem?


Undergraduate students are encouraged to work on the project in pairs. The first page of the project should clearly state the specific contribution of each of the two co-authors to the project (it is expected to be equal).

The final project will be due before the beginning of the class on 24 April 2014.


There is no separate final exam in this class.