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| <meta name="generator" content="pandoc"> | ||
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| <title>Population Genetics Notes</title> | ||
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| <h1> | ||
| Population Genetics Notes | ||
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| <p> | ||
| <strong>Graham Coop</strong><br/> | ||
| Department of Evolution and Ecology & Center for Population Biology<br/> | ||
| University of California, Davis<br/><br/> | ||
| This work is licensed under a <a href="https://creativecommons.org/licenses/by/3.0/us/">Creative Commons Attribution 3.0 Unported License</a><br/> | ||
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| <h2>Table of Contents</h2> | ||
| <ul> | ||
| <li><a href="chapter-01.html#allele-and-genotype-frequencies">allele and genotype frequencies</a><ul> | ||
| <li><a href="chapter-01.html#allele-frequencies">allele frequencies</a></li> | ||
| <li><a href="chapter-01.html#hardyweinberg-proportions">hardy–weinberg proportions</a></li> | ||
| <li><a href="chapter-01.html#coefficient-of-kinship">coefficient of kinship</a></li> | ||
| <li><a href="chapter-01.html#inbreeding">inbreeding</a></li> | ||
| <li><a href="chapter-01.html#calculating-inbreeding-coefficients-from-data">calculating inbreeding coefficients from data</a></li> | ||
| <li><a href="chapter-01.html#summarizing-population-structure">summarizing population structure</a></li> | ||
| </ul></li> | ||
| </ul> | ||
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| <ul> | ||
| <li><a href="chapter-02.html#genetic-drift-and-neutral-diversity">Genetic Drift and Neutral Diversity</a><ul> | ||
| <li><a href="chapter-02.html#LossofHet">Loss of heterozygosity due to drift.</a></li> | ||
| <li><a href="chapter-02.html#DriftMutationBalance">Levels of diversity maintained by a balance between mutation and drift</a></li> | ||
| <li><a href="chapter-02.html#the-effective-population-size.">The effective population size.</a></li> | ||
| <li><a href="chapter-02.html#neutral-diversity-and-population-structure">Neutral diversity and population structure</a></li> | ||
| <li><a href="chapter-02.html#other-approaches-to-population-structure">Other approaches to population structure</a><ul> | ||
| <li><a href="chapter-02.html#assignment-methods">Assignment Methods</a></li> | ||
| <li><a href="chapter-02.html#principal-components-analysis">Principal components analysis</a></li> | ||
| </ul></li> | ||
| </ul></li> | ||
| </ul> | ||
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| <ul> | ||
| <li><a href="chapter-03.html#correlations-between-loci-linkage-disequilibrium-and-recombination">Correlations between loci, linkage disequilibrium, and recombination</a></li> | ||
| </ul> | ||
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| <ul> | ||
| <li><a href="chapter-04.html#the-phenotypic-resemblance-between-relatives">The phenotypic resemblance between relatives</a><ul> | ||
| <li><a href="chapter-04.html#additive-genetic-variance-and-heritability">Additive genetic variance and heritability</a></li> | ||
| <li><a href="chapter-04.html#the-covariance-between-relatives">The covariance between relatives</a></li> | ||
| <li><a href="chapter-04.html#the-response-to-selection">The response to selection</a></li> | ||
| </ul></li> | ||
| </ul> | ||
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| <ul> | ||
| <li><a href="chapter-05.html#one-locus-models-of-selection">One-locus models of selection</a><ul> | ||
| <li><a href="chapter-05.html#fitness">Fitness</a></li> | ||
| <li><a href="chapter-05.html#haploid-selection-model">Haploid selection model</a></li> | ||
| <li><a href="chapter-05.html#diploid-model">Diploid model</a><ul> | ||
| <li><a href="chapter-05.html#diploid-directional-selection">Diploid directional selection</a></li> | ||
| <li><a href="chapter-05.html#heterozygote-advantage">Heterozygote advantage</a></li> | ||
| </ul></li> | ||
| <li><a href="chapter-05.html#mutationselection-balance">Mutation–selection balance</a><ul> | ||
| <li><a href="chapter-05.html#inbreeding-depression">Inbreeding depression</a></li> | ||
| </ul></li> | ||
| <li><a href="chapter-05.html#migrationselection-balance">Migration–selection balance</a><ul> | ||
| <li><a href="chapter-05.html#some-theory-of-the-spatial-distribution-of-allele-frequencies-under-deterministic-models-of-selection">Some theory of the spatial distribution of allele frequencies under deterministic models of selection</a></li> | ||
| </ul></li> | ||
| </ul></li> | ||
| </ul> | ||
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| <ul> | ||
| <li><a href="chapter-06.html#stochasticity-and-genetic-drift-in-allele-frequencies">Stochasticity and Genetic Drift in allele frequencies</a><ul> | ||
| <li><a href="chapter-06.html#stochastic-loss-of-strongly-selected-alleles">Stochastic loss of strongly selected alleles</a></li> | ||
| <li><a href="chapter-06.html#the-interaction-between-genetic-drift-and-weak-selection.">The interaction between genetic drift and weak selection.</a><ul> | ||
| <li><a href="chapter-06.html#the-fixation-of-slightly-deleterious-alleles.">The fixation of slightly deleterious alleles.</a></li> | ||
| <li><a href="chapter-06.html#Section:fixation_weakly_sel">A Sketch Proof of the probability of fixation of weakly selected alleles</a></li> | ||
| </ul></li> | ||
| </ul></li> | ||
| </ul> | ||
| <ul> | ||
| <li><a href="chapter-07.html#genetic-drift-and-neutral-alleles">Genetic drift and Neutral alleles</a><ul> | ||
| <li><a href="chapter-07.html#the-fixation-of-neutral-alleles">The fixation of neutral alleles</a></li> | ||
| <li><a href="chapter-07.html#the-coalescent-and-patterns-of-neutral-diversity">The Coalescent and patterns of neutral diversity</a></li> | ||
| <li><a href="chapter-07.html#the-coalescent-process-of-a-sample-of-alleles.">The coalescent process of a sample of alleles.</a></li> | ||
| <li><a href="chapter-07.html#comparing-polymorphism-and-divergence">Comparing polymorphism and divergence</a></li> | ||
| <li><a href="chapter-07.html#deviations-from-the-constant-population-model.">Deviations from the constant population model.</a></li> | ||
| </ul></li> | ||
| </ul> | ||
| <ul> | ||
| <li><a href="chapter-08.html#the-effect-of-linked-selection-on-patterns-of-neutral-diversity">The effect of linked selection on patterns of neutral diversity</a><ul> | ||
| <li><a href="chapter-08.html#a-simple-recurrent-model-of-selective-sweeps">A simple recurrent model of selective sweeps</a></li> | ||
| </ul></li> | ||
| </ul> | ||
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