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Detecting Positive Selection

Norman A. Johnson

in Darwinian Detectives: Revealing the Natural History of Genes and Genomes

Published in print:
2007
Published Online:
September 2007
ISBN:
9780195306750
eISBN:
9780199790203
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195306750.003.0004
Subject:
Biology, Evolutionary Biology / Genetics

Positive natural selection, though rare in comparison with negative selection, is the main evolutionary force responsible for adaptive evolutionary change. Using the neutral theory to generate null ... More


A genetic mechanism to link selection to reproductive isolation

Patrik Nosil

in Ecological Speciation

Published in print:
2012
Published Online:
May 2015
ISBN:
9780199587100
eISBN:
9780191810107
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199587100.003.0005
Subject:
Biology, Evolutionary Biology / Genetics

This chapter deals with the conditions under which pleitropy versus linkage disequilibrium can drive ecological speciation. It considers just how tight physical linkage needs to be for linkage ... More


Recombination and linkage disequilibrium in evolutionary signatures

Asher D. Cutter

in A Primer of Molecular Population Genetics

Published in print:
2019
Published Online:
August 2019
ISBN:
9780198838944
eISBN:
9780191874826
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198838944.003.0006
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

Chapter 6, “Recombination and linkage disequilibrium in evolutionary signatures,” explores the role of partial genetic linkage within and between genes in influencing patterns of nucleotide ... More


The Infinitesimal Model and Its Extensions

Bruce Walsh and Michael Lynch

in Evolution and Selection of Quantitative Traits

Published in print:
2018
Published Online:
September 2018
ISBN:
9780198830870
eISBN:
9780191868986
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198830870.003.0024
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

One standard approximation in quantitative genetics is the infinitesimal model, which assumes a large number of loci, each of small effect. In such a setting, the distribution of breeding values in ... More


Multilocus evolution

Glenn-Peter Sætre and Mark Ravinet

in Evolutionary Genetics: Concepts, Analysis, and Practice

Published in print:
2019
Published Online:
July 2019
ISBN:
9780198830917
eISBN:
9780191868993
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198830917.003.0006
Subject:
Biology, Evolutionary Biology / Genetics, Biomathematics / Statistics and Data Analysis / Complexity Studies

Most phenotypic traits are affected by a multitude of genes, which may interact in complex ways. This means that the single locus model explored in chapters 3 and 4 is not always able to capture the ... More


Modeling Linkage Disequilibrium and Performing Association Studies through Probabilistic Graphical Models: a Visiting Tour of Recent Advances

Christine Sinoquet and Raphaël Mourad

in Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics

Published in print:
2014
Published Online:
December 2014
ISBN:
9780198709022
eISBN:
9780191779619
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198709022.003.0009
Subject:
Mathematics, Probability / Statistics, Biostatistics

This chapter offers an in-depth review of recent developments based on probabilistic graphical models (PGMs) and dedicated to two major concerns: the fundamental task of modeling dependences within ... More


Short-term Changes in the Variance: 1. Changes in the Additive Variance

Bruce Walsh and Michael Lynch

in Evolution and Selection of Quantitative Traits

Published in print:
2018
Published Online:
September 2018
ISBN:
9780198830870
eISBN:
9780191868986
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198830870.003.0016
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

Selection changes the additive-genetic variance (and hence the response in the mean) by both changing allele frequencies and by generating correlations among alleles at different loci (linkage ... More


Modeling Linkage Disequilibrium with Decomposable Graphical Models

Haley J. Abel and Alun Thomas

in Probabilistic Graphical Models for Genetics, Genomics, and Postgenomics

Published in print:
2014
Published Online:
December 2014
ISBN:
9780198709022
eISBN:
9780191779619
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198709022.003.0010
Subject:
Mathematics, Probability / Statistics, Biostatistics

This chapter describes the use of decomposable graphical models (DGMs) to represent the dependences within genetic data, or linkage disequilibrium (LD), prior to various downstream applications. ... More


Neutral Evolution in One- and Two-Locus Systems

Bruce Walsh and Michael Lynch

in Evolution and Selection of Quantitative Traits

Published in print:
2018
Published Online:
September 2018
ISBN:
9780198830870
eISBN:
9780191868986
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198830870.003.0002
Subject:
Biology, Evolutionary Biology / Genetics, Biochemistry / Molecular Biology

This chapter reviews the population-genetic theory of neutral alleles in finite populations, examining the probabilities and times to loss or fixation, summary statistics for molecular variation, ... More


Populations in Statistical Genetic Modelling and Inference

Daniel John Lawson

in Population in the Human Sciences: Concepts, Models, Evidence

Published in print:
2015
Published Online:
May 2015
ISBN:
9780199688203
eISBN:
9780191767500
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199688203.003.0004
Subject:
Economics and Finance, Development, Growth, and Environmental

This chapter reviews approaches to how populations of sexually reproducing individuals are defined statistically via genetic criteria. It addresses the question of whether there is a meaningful and ... More


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