Frequent occurrence of WGD during evolution

For more info about our services contact : help@bestpfe.com

Table of contents

List of Figures
List of Tables
Abbreviations & Denitions
I Introduction
1 Preamble
1.1 Thesis summary
1.2 Organization of the thesis
1.3 Publications resulted/forthcoming from this thesis
2 Evolution by gene duplication
2.1 Evolution through WGD and SSD
2.1.1 Mechanisms of gene duplication
2.1.2 Frequent occurrence of WGD during evolution
2.1.3 Antagonist retention pattern of SSD and WGD duplicates
2.1.4 Critical role of WGD in evolution
2.2 Evolutionary fate of gene duplicates
2.2.1 Neo-functionalization
2.2.2 Subfunctionalization
2.2.3 Buering against deleterious mutations
2.2.4 The dosage balance hypothesis
2.3 Dominant deleterious mutations
2.3.1 The great expansion of dominant deleterious gene families
2.4 Objectives
II Materials & Methods
3 Population genetics approach
3.1 Hypothesis: a qualitative model recently proposed
3.2 Population genetics models: a deterministic approach
3.2.1 Simple haploid deterministic model
3.2.2 Extension to diploid models
3.3 Population genetics models: a stochastic approach for small populations
3.3.1 General approach for K alleles
3.3.2 Stochastic simulations
4 Mediation Analysis approach
4.1 Pearl’s Causal Mediation Analysis
4.1.1 Total, direct and indirect eects
4.1.2 An example: the simple binary case
4.2 Application of the Mediation Analysis to genomic data
4.3 Extensions of the Mediation Analysis to more than three variables
4.3.1 First approach: the distinction between mediators and covariates
4.3.2 A general approach: the parents of X and Y
4.4 Relationship to Maathuis’s approach
III Results
5 Population genetics results
5.1 Deterministic solutions of the haploid model for neutral subfunctionalization
5.2 Analysis of gene duplicates xation through stochastic simulations
5.2.1 Fixation rates for neutral subfunctionalization
5.2.2 Finite size eects on the xation of gene duplicates
5.2.3 Extension to adaptive subfunctionalization for SSD duplicates
5.3 Application to the prevalence of human oncogenes with WGD vs SSD duplicates
6 Mediation Analysis results
6.1 The extended Mediation Analysis on genomic data
6.1.1 Genomic properties related to ohnolog retention
6.1.2 Inferred causal graph for ohnolog retention
6.1.3 Application of the extended Mediation Analysis to genomic properties
6.2 Direct causes of ohnolog retention
IV Discussion & Perspectives
7 Discussion and Perspectives
V Appendices
A Population genetics: a general stochastic approach
A.1 General stochastic models using a master equation
A.2 Four-allele deterministic models of SSD vs WGD duplicates retention
A.3 Exact results for two-allele stochastic models
B Pearl’s theory of the do-calculus
B.1 Basic concepts of the do-calculus
B.1.1 Markovian models
B.1.2 General models
B.1.3 The do-calculus and the Mediation Analysis
Bibliography