Asymmetric Sequence Divergence of Duplicate Genes

Asymmetric Sequence Divergence of Duplicate Genes

Experimented By: Gavin Conant and Andreas Wagner

Presented By: Jennifer Case and Jonathan Hobbs

What are Gene Duplications?What are Gene Duplications?

• Duplication:

More than one copy of a particular chromosomal segment in a chromosome set

Why Study Duplications?Why Study Duplications?

• Why are they important?

• What can duplications tell us?

DivergenceDivergence

• Divergence is an important process for driving evolutionary changes.

Necessary VocabularyNecessary Vocabulary

• Ka - amino acid (non-synonymous) substitutions

• Ks - silent (synonymous) substitutions • P - probability of reoccurrances happening by

chance alone• X2 - a goodness-of-fit test• r - a statistical association• s - a statistical association

Methods ConsideredMethods Considered

• Nucleotide-based tests

• Amino Acid-based tests

• Codon-based tests

Purpose of this experimentPurpose 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.

First HypothesisFirst Hypothesis

• “…the number of pairs with asymmetrical Ka values could be explained by a 5%

error rate…”

Methods for Hypothesis 1Methods for Hypothesis 1

• Codon Model--allows for the possibility that duplicate genes evolve independently.

• 2 duplicate genes and one outgroup gene are found

Methods for Hypothesis 1Methods for Hypothesis 1

• Likelihood Ratio Test

• x2 analysis

• P (probability) significance

[Ka] asymmetrical in 5% error[Ka] asymmetrical in 5% error

• Everything that was more significant than 5% supports the hypothesis, everything 5% or under rejects it.

Results for Hypothesis 1Results 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

Results for Hypothesis 1Results for Hypothesis 1

Organism # of Gene Triplets # of UnsaturatedTriplets with

asymmetry in Ka

Percent ofAsymmetry in Ka

Baker’s Yeast 22 6 27Fission Yeast 14 3 21

Fruit Fly 44 13 30Worm 164 46 28

Unsaturated nucleotide sequence- Sites that have not begun to back mutate.

Discussion for Hypothesis 1Discussion 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

Second Hypothesis Second Hypothesis

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

Methods for Hypothesis 2Methods 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?

Methods for Hypothesis 2Methods 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 log2-transformed ratios

Compared normalized difference to the different in the transformed ratios.

Methods for Hypothesis 2Methods for Hypothesis 2

• To answer 2nd question:

gene under-expression by at least two-fold

Compared Found value to the normalized value

Results for Hypothesis 2Results 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 Ka

Found no significant association

Discussion for Hypothesis 2Discussion for Hypothesis 2

• What is the significance of having no significant correlation between sequence asymmetry and:

expression divergence

asymmetry of expression divergence

Selection ProcessSelection Process

• 2 Forces can drive asymmetric divergence

relaxed selective constraints• sequence divergence is neutral

directional or positive selection• the rate of Ka/Ks is greater than 1

• advantageous mutations play a key role in divergence.

Results for Selection ProcessResults for Selection Process

• Statistical association between asymmetry in amino acid divergence and evolutionary constraints on duplicate pairs. (Ka/Ks)

Results for Selection ProcessResults 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

To Test for Positive SelectionTo Test for Positive Selection

• Triplet-based Method vs. Pairwise Method

Discussion for Selection ProcessDiscussion 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