Chapter 1
1 Introduction
2 Algorithms
2.1 Probabilistic global alignment
2.2 Probabilistic local alignment
3 Statistics of hybrid alignment
3.1 Score landscape and islands
3.2 Large-score statistics
3.3 Island peak scores
3.4 Sequence length correction
4 Numerics
5 Summary
Acknowledgments
6 Appendix A: Consistency of our approximations
7 Appendix B: Z and W
References
Chapter 2
1 Introduction
2 Optimization criteria
3 Approximations and convergence
4 Evaluating tree alignment as a model for MSA
5 Biological validation of MSA
6 Conclusion
Acknowledgements
References
Chapter 3
1 Introduction to the code
1.1 Anticodon redundancy and degeneracy
2 Translational parasitism
2.1 Translation, redundancy and degeneracy
2.2 Population dynamics
2.3 Evolutionary dynamics of single parasite and host
2.4 Evolutionary dynamics of two pairs of host and parasites
3 Adaptive modification of tRNA base composition
4 Long term trends in codon usage
5 Summary and conclusions
Acknowledgements
References
Chapter 4
1 Evolution experiments in vitro
2 Molecular evolution including phenotypes
3 The RNA model
4 Computer simulation of RNA evolution
5 Transitions, continuity, and statistical neighborhoods
6 An exercise in probabilities
7 Molecular evolution in the post-genomic age
Acknowledgements
References
Chapter 5
Introduction
Principles of molecular evolution
Finite populations and the neutral theory
Eigen’s theory of quasi-species
Applications to Proteins
Molecular evolution and the thermodynamic hypothesis
Conclusion
Acknowledgments
References
Chapter 6
1 Introduction
2 Maximum parsimony and long branch attraction
3 The need for models and the maximum likelihood method
4 Anonstationary model of DNA evolution
5 The thermophilic nature of the common ancestor
References
Chapter 7
1 Introduction
2 Terminology
2.1 Phylogenetic networks
3 Cophylogeny
3.1 Cophylogenetic events
3.2 Recovery of events
3.3 “Missing the boat” and extinction
3.4 Pandora’s box: Sampling, ghosts, sources and sinks
4 The cophylogeny mapping
5 Problems
5.1 Existence
5.2 The number of cophylogenetic maps
5.3 What are the statistical properties of cophylogeny maps?
6 Optimality
7 Existing methods of finding cophylogeny maps
7.1 Page’s “reconciled trees”
7.2 Brooks’ parsimony analysis
7.3 Ronquist’s solution
8 Jungles and scary creatures
8.1 A new jungle construction
9 Examples
9.1 A simple three taxon case
9.2 Lizards and malaria in the caribbean
10 Discussion
Acknowledgements
References
Chapter 8
1 Introduction
2 Markov-chain Monte Carlo methods
3 Bayesian statistics and the MCMC approach to phylogenies
4 MCMC and phylogenetic-comparative methods
5 Application to the evolution of lichen formation
5.1 MCMC phylogenetic tree sampling
5.2 Reconstruction of gains and losses, and ancestral states
5.3 Convergence of the Markov-chain
5.4 Rates of gains and losses of lichenization
5.5 Probable phylogenetic position and number of gains and losses
6 Conclusions and discussion
Acknowledgements
References
Chapter 9
1 Introduction
2 Terminology
3 The Yule model
4 Depth of a most recent common ancestor (MRCA)
4.1 Distance of MRCA from root
5 Probability distribution for cherries
5.1 Yule Model
5.2 Uniform model
5.3 An example
6 Rooting an unrooted tree
6.1 Maximum likelihood estimation of the root edge
6.2 Probability of locating the root edge
6.3 Exact asymptotic value of epsilon(n)
7 Extending the Yule model
7.1 Two classes of models
Acknowledgement
References
Chapter 10
1 Introduction
2 Configuration spaces
2.1 Move sets
2.2 Transition matrices
2.3 Configuration space topologies
3 Basic properties of landscapes
3.1 Local optima
3.2 Basins
3.3 Gradient walks and adaptive walks
3.4 Barriers
3.5 Depth
3.6 Correlation
4 Spectral landscape theory
5 Concluding remarks
Acknowledgements
References
Chapter 11
1 Introduction and motivation
2 The strong selection limit
3 Evolutionary trajectories
4 Distribution of evolution times
5 Comparison to record dynamics
6 Outlook
Acknowledgements
References
Chapter 12
1 Introduction
2 Multilevel evolution: Pattern formation, phylogenetic trees and punctuated equilibria
2.1 Dynamics of meso-scale patterns shape of micro-scale replicators through evolution: A review
2.2 Interplay between pattern formation and the shape of phylogenetic trees
3 Multilevel morphogenesis: Coordination, evolution and re-inventions along phylogenetic trees
3.1 A model for multilevel morphogenesis
3.2 Mechanisms of Morphogenesis
3.3 A case study of the development and evolution of a morphotype
4 Conclusions
Acknowledgements
References
Chapter 13
1 Introduction
2 Models of basic evolutionary strategies
2.1 Darwin strategy
2.2 Boltzmann strategy
2.3 Mixed Boltzmann-Darwin strategy
2.4 Tournament – nonlinear strategies
3 Stochastic modeling of mixed strategies
4 Simulations – the dependence on search parameters
5 Control of the mutation/selection rate
6 Discussion
Acknowledgment
References
Chapter 14
1 Introduction
2 Penna model
3 Main results
4 Applications
5 Summary
6 Appendix: A simpler alternative
References
Chapter 15
1 Introduction
2 Evolution of competing phenotypes
3 States of the system
4 Evolutionary pathways
5 Discussion
Acknowledgements
References
Chapter 16
1 Introduction
2 Population dynamics
3 Evolutionary dynamics
4 Food web properties and co-evolution
5 Discussion
Acknowledgment
References
Chapter 17
1 Introduction
2 Modelling species networks
2.1 Species interactions and population dynamics
2.2 Network dynamics
3 The shape of a species network
3.1 A single food chain
3.2 A single trophic layer
3.3 The full network
4 The local structure and .uctuations
5 Conclusion
Acknowledgment
References
Chapter 18
1 Macroevolution and extinction
2 Coevolution on a rugged fitness landscape
3 Network model of macroevolution
4 Extinction in layered networks
5 Discussion
Acknowledgements
References