Effective population size and patterns of molecular evolution and variation

@article{Charlesworth2009EffectivePS,
  title={Effective population size and patterns of molecular evolution and variation},
  author={Brian Charlesworth},
  journal={Nature Reviews Genetics},
  year={2009},
  volume={10},
  pages={195-205}
}
The effective size of a population, Ne, determines the rate of change in the composition of a population caused by genetic drift, which is the random sampling of genetic variants in a finite population. Ne is crucial in determining the level of variability in a population, and the effectiveness of selection relative to drift. This article reviews the properties of Ne in a variety of different situations of biological interest, and the factors that influence it. In particular, the action of… 
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Neutral Models of Genetic Drift and Mutation
The Genetic Effective Size of a Population
TLDR
This chapter shows how the population size for such an idealized population can be replaced with an effective population sizes for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision.
Detecting positive selection in the genome
TLDR
Methods that use patterns of between-species nucleotide divergence and within-species diversity to estimate positive selection parameters from population genomic data are discussed.
Effective population size and the rate and pattern of nucleotide substitutions
TLDR
Empirical analyses indicate that variation in substitution rates and patterns caused by differences in Ne is often substantial, however, and must be accounted for in analyses of molecular evolution.
Determinants of genetic diversity
TLDR
Comparative population genomics is on its way to providing a solution to 'Lewontin's paradox' — the discrepancy between the many orders of magnitude of variation in population size and the much narrower distribution of diversity levels.
Quantifying the Variation in the Effective Population Size Within a Genome
TLDR
The amount of variation in the effective population size is quite modest in all species and it is shown that most genes have an Ne that is within a few fold of all other genes, which is sufficient to cause significant differences in the efficiency of natural selection across the genome.
Heterogeneity in effective population size and its implications in conservation genetics and animal breeding
TLDR
The evidence suggests that heterogeneity in Ne can be just as important as heterogeneity in mutation rates in determining levels of genetic diversity throughout the genome, and potential implications for conservation and breeding practices are discussed.
Evolution of the mutation rate.
  • M. Lynch
  • Biology
    Trends in genetics : TIG
  • 2010
Effective sizes and time to migration-drift equilibrium in geographically subdivided populations.
The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection
TLDR
It is shown that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection, and those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for the estimation of human demography.
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References

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TLDR
The general theory of the effective size (Ne) for populations under directional selection is extended to cover linkage and the principles of the theory are also applicable to favorable mutation models if there is a continuous flux of advantageous mutations.
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TLDR
Developments in the prediction equations for the effective size of populations subdivided under various models are reviewed, and extensions are made in several cases.
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TLDR
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TLDR
Predictive equations of effective size under a range of circumstances and some of their implications are reviewed and derivations are made for the simplest cases.
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TLDR
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TLDR
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TLDR
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TLDR
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TLDR
It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X- linked loci relative to autosomal or Y-linked loci.
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TLDR
Results for genes in regions with typical frequencies of crossing over in Drosophila melanogaster suggest that background selection may influence the effective population sizes of different regions of the same gene, consistent with observed differences in codon usage bias along genes.
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