1. Asymmetric Sequence Divergence of Duplicate Genes Experimented By: Gavin Conant and Andreas Wagner Presented By: Jennifer Case and Jonathan Hobbs

2. What are Gene Duplications? Duplication: More than one copy of a particular chromosomal segment in a chromosome set

3. Why Study Duplications? Why are they important? What can duplications tell us?

4. Divergence Divergence is an important process for driving evolutionary changes.

5. Necessary Vocabulary K a - amino acid (non-synonymous) substitutions K s - silent (synonymous) substitutions P - probability of reoccurrances happening by chance alone X 2 - a goodness-of-fit test r - a statistical association s - a statistical association

6. Methods Considered Nucleotide-based tests Amino Acid-based tests Codon-based tests

7. Purpose of this experiment 1. Test the number of pairs with asymmetric Ka values that can be explained by the 5% error rate of our individual hypothesis tests. 2. Test to see if asymmetric a.a. divergence is coupled to greater functional divergence in one of two duplicate genes.

8. First Hypothesis “…the number of pairs with asymmetrical Ka values could be explained by a 5% error rate…”

9. Methods for Hypothesis 1 Codon Model--allows for the possibility that duplicate genes evolve independently. 2 duplicate genes and one outgroup gene are found

10. Methods for Hypothesis 1 Likelihood Ratio Test x 2 analysis P (probability) significance

11. [Ka] asymmetrical in 5% error Everything that was more significant than 5% supports the hypothesis, everything 5% or under rejects it.

12. Results for Hypothesis 1 Special results:  Fission Yeast Outgroup gene is very distant from duplicates  Fruit Fly Lysozyme D Gene Family Chitanase  Worm 7-helix transmembrane chemoreceptor domains

13. Results for Hypothesis 1 Unsaturated nucleotide sequence- Sites that have not begun to back mutate.

14. Discussion for Hypothesis 1 An average genome contains at least 20% of gene duplicates that diverge asymmetrically.  Larger numbers with larger data (ex. worm and fruit fly) Differs from other studies  different approaches  different models

15. Second Hypothesis “…tested the hypothesis that asymmetric amino acid divergence is coupled to greater gene expression divergence in one of two duplicate genes.”

16. Methods for Hypothesis 2 2 questions were asked in this part of the experiment  1.) Is there association between sequence asymmetry and expression divergence? 2.) Is there association between sequence asymmetry and asymmetry of expression divergence?

17. Methods for Hypothesis 2 To answer first question:  Only used the two duplicates because of lack of sequence data.  Used eleven different experimental conditions for data acquisition.  Found log 2 -transformed ratios  Compared normalized difference to the different in the transformed ratios.

18. Methods for Hypothesis 2 To answer 2nd question:  gene under-expression by at least two-fold  Compared Found value to the normalized value

19. Results for Hypothesis 2 mRNA microarray data  no significant correlation between degree of asymmetry and divergence in expression level calculated statistical association between asymmetry in expression level and asymmetry in K a  Found no significant association

20. Discussion for Hypothesis 2 What is the significance of having no significant correlation between sequence asymmetry and:  expression divergence  asymmetry of expression divergence

21. Selection Process 2 Forces can drive asymmetric divergence  relaxed selective constraints sequence divergence is neutral  directional or positive selection the rate of K a /K s is greater than 1 advantageous mutations play a key role in divergence.

22. Results for Selection Process Statistical association between asymmetry in amino acid divergence and evolutionary constraints on duplicate pairs. (K a /K s )

23. Results for Selection Process They found:  in yeast weakly significant correlation between asymmetry and selective constraints  in fruit fly and worm highly significant correlation between asymmetry and selective constraints

24. To Test for Positive Selection Triplet-based Method vs. Pairwise Method

25. Discussion for Selection Process It appears as though relaxed selective constraints may be largely responsible for asymmetric divergence Not necessarily the case!  Positive Selection acts fast and in a small area so it can be difficult to detect.  Need more than just the sequence to tell if positive selection has taken place.  Probably BOTH are largely responsible depending on which gene is in question