Rapidly evolving genes and genetic systems 1st Edition by Rama S Singh, Jianping Xu, Rob J Kulathinal ISBN 0199642273 9780199642274

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ISBN 10: 0199642273 
ISBN 13: 9780199642274
Author: Rama S Singh, Jianping Xu, Rob J Kulathinal

Rapidly evolving genes and genetic systems 1st Table of contents:

1 Introduction
1.1 A gradualist history
1.2 Mechanisms of rapid and episodic change
1.2.1 Unconstrained neutral space
1.2.2 Horizontal gene transfer
1.2.3 Developmental macromutations
1.2.4 Evolution by gene regulation
1.2.5 Coevolutionary forces
1.2.6 Sexual selection and sexual arms races
1.2.7 Population demography and genetic revolutions
1.2.8 Adaptive radiation
1.3 Punctuated equilibrium within a microevolution framework
1.4 Tempo, mode, and the genomic landscape
1.5 ‘Rapidly evolving genes and genetic systems’: a brief overview
1.6 Future prospects

Part I From Theory to Experiment
2 Theoretical perspectives on rapid evolutionary change
2.1 Introduction
2.2 When is strong selection strong?
2.3 Does strong selection differ in kind from weak selection?
2.4 Concluding thoughts

3 Recombination reshuffles the genotypic deck, thus accelerating the rate of evolution
3.1 Introduction
3.2 Simulating selection on multilocus genotypes
3.3 Discussion
3.4 Conclusions

4 Heterogeneity in neutral divergence across genomic regions induced by sex-specific hybrid incompatibility
4.1 Introduction
4.1.1 Detecting incompatibility factors
4.1.2 Within-species polymorphisms for incompatibility factors with sex-limited transmission
4.2 Genealogical migration rate
4.2.1 Definition
4.2.2 Non-sex-specific incompatibility
4.2.3 Sex-specific incompatibility
4.3 Applications
4.3.1 Mitochondrial introgression
4.3.2 Interpreting region-specific FST
4.4 Conclusions

5 Rapid evolution in experimental populations of major life forms
5.1 Introduction
5.2 Features of experimental evolution
5.3 Types of experimental evolution
5.3.1 Directional selection
5.3.2 Adaptation
5.3.3 Mutation accumulation
5.4 Rapid change and divergence among mutation accumulation population lines
5.4.1 Microbial growth rate
5.4.2 Other microbial traits
5.4.3 Plants and animals
5.5 Adaptation and directional selection experiments
5.5.1 Adaptation of E. coli populations
5.5.2 Adaptation of viral populations
5.5.3 Adaptation and directional selection in fruit flies
5.5.4 Adaptation in yeast
5.5.5 Directional selection in mammals
5.5.6 Correlated changes between traits
5.5.7 Acquisition of novel phenotypes
5.6 Genomic analysis of experimental evolution populations
5.7 Conclusions and perspectives

Part II Rapidly Evolving Genetic Elements
6 Rapid evolution of low complexity sequences and single amino acid repeats across eukaryotes
6.1 Introduction
6.2 Rapid evolution of low complexity sequences
6.2.1 Mutational processes
6.3 Rapid divergence of LCRs and their impact on surrounding sequences
6.3.1 LCRs as indicators of regions of lowered purifying selective pressures
6.3.2 Mutagenic effect of LCRs
6.4 Low complexity sequences under selection
6.4.1 Deleterious effects of LCR size variation
6.4.2 DNA composition
6.4.3 LCR distribution
6.4.4 Phenotypic effects of LCR size variation
6.4.5 Selection for low information content
6.5 Perspectives

7 Fast rates of evolution in bacteria due to horizontal gene transfer
7.1 Introduction
7.2 Quantifying horizontal gene transfer
7.3 Understanding the variation of gene gain and loss
7.4 Horizontal gene transfer in duplicated genes
7.5 Pseudogenization of horizontally transferred genes
7.6 Mobile sequences and gene movement
7.7 Gene exchange goes fine-scale
7.8 Conclusions

8 Rapid evolution of animal mitochondrial DNA
8.1 Introduction
8.2 Mitochondrial replication, strand bias, and evolutionary rates
8.3 The change in genetic code and evolutionary rate
8.4 The change in tRNA genes and evolutionary rate
8.5 Conclusions

9 Rapid evolution of centromeres and centromeric/kinetochore proteins
9.1 Centromeres in ‘the fast lane’
9.2 Rapidly evolving centromeric histones
9.3 Bewildering centromeric DNA complexity and evolution
9.4 The ‘centromere paradox’: conflict, not coevolution
9.5 Support for the centromere drive model
9.6 Taxonomic differences in susceptibility to centromere drive
9.7 Rapid evolution of other centromeric proteins
9.8 Centromere drive and postzygotic isolation between species
9.9 Future directions

10 Rapid evolution via chimeric genes
10.1 Introduction
10.2 Mechanisms of formation
10.3 Selection
10.4 Genomic stability
10.5 Function
10.6 Non-coding DNA
10.7 Future directions

11 Evolutionary interactions between sex chromosomes and autosomes
11.1 Introduction
11.2 Gene traffic between sex chromosome and autosomes
11.2.1 Gene traffic in Drosophila
11.2.2 Gene traffic in mammals
11.2.3 The cause and consequence of gene traffic
11.3 The generality of gene traffic out of the X in the genus Drosophila
11.3.1 Gene traffic in Drosophilidae and RNA-based and DNA-based duplication
11.3.2 Independent tests of gene traffic
11.4 Mechanisms underlying gene traffic out of the X: the detection of meiotic sex chromosome inactivation
11.4.1 Evolutionary genetic models
11.4.2 Molecular mechanistic models
11.5 The X-recruitment of young male-biased genes and gene traffic out of the X chromosome
11.5.1 Age-dependence in Drosophila
11.5.2 Age-dependence in mammals
11.5.3 The slow enrichment of X-linked female genes
11.6 Concluding remarks

12 Evolutionary signatures in non-coding DNA
12.1 Introduction
12.2 Challenges to studying the evolution of non-coding DNA
12.2.1 Identifying functional non-coding DNA
12.2.2 Estimating the neutral evolutionary rate
12.2.3 Limitations of identifying rapid evolution in non-coding DNA
12.3 Patterns of evolution in non-coding DNA
12.3.1 Selection in conserved non-coding sequences?
12.3.2 Detecting selection in promoters and TFBSs
12.3.3 Emerging trends in microRNA binding sites
12.3.4 Coding versus non-coding
12.4 Future prospects

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Tags: Rama S Singh, Jianping Xu, Rob J Kulathinal, genes, genetic systems