USING POPULATION GENOMICS TO DETECT SELECTION IN NATURAL POPULATIONS: KEY CONCEPTS AND METHODOLOGICAL CONSIDERATIONS. (Q34469723)

2 August 2017

title

USING POPULATION GENOMICS TO DETECT SELECTION IN NATURAL POPULATIONS: KEY CONCEPTS AND METHODOLOGICAL CONSIDERATIONS. (English)

1 reference

2 August 2017

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Paul A Hohenlohe

1

1 reference

2 August 2017

Patrick C Phillips

series ordinal

2

1 reference

2 August 2017

William A Cresko

series ordinal

3

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2 August 2017

language of work or name

English

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publication date

1 November 2010

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International Journal of Plant Sciences

2 August 2017

published in

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2 August 2017

volume

171

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2 August 2017

issue

9

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2 August 2017

page(s)

1059-1071

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Linkage and association mapping of Arabidopsis thaliana flowering time in nature

2 August 2017

cites work

1 reference

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6 July 2018

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The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation

6 July 2018

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A composite of multiple signals distinguishes causal variants in regions of positive selection

6 July 2018

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Detecting positive selection from genome scans of linkage disequilibrium

6 July 2018

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Genome-wide scans for footprints of natural selection

6 July 2018

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Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data

6 July 2018

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Molecular networks as sensors and drivers of common human diseases

6 July 2018

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Genetics in geographically structured populations: defining, estimating and interpreting F(ST)

6 July 2018

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Detecting loci under selection in a hierarchically structured population

6 July 2018

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The role of geography in human adaptation

6 July 2018

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Constructing genomic maps of positive selection in humans: where do we go from here?

6 July 2018

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Human genetic variation and its contribution to complex traits

6 July 2018

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Estimation of allele frequencies from high-coverage genome-sequencing projects

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Divergent selection and heterogeneous genomic divergence

6 July 2018

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Personal genomes: The case of the missing heritability

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Next-generation DNA sequencing

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Effects of spatially varying selection on nucleotide diversity and linkage disequilibrium: insights from deer mouse globin genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

A population genomic approach to map recent positive selection in model species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Linkage disequilibrium under genetic hitchhiking in finite populations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Linkage disequilibrium--understanding the evolutionary past and mapping the medical future

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Genome-wide detection and characterization of positive selection in human populations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

EVOLUTION IN MENDELIAN POPULATIONS

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The molecular genetics of crop domestication

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Soft sweeps III: the signature of positive selection from recurrent mutation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Genomic signatures of positive selection in humans and the limits of outlier approaches

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Positive natural selection in the human lineage

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Adaptation and speciation: what can F(st) tell us?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

How reliable are empirical genomic scans for selective sweeps?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Balancing selection and its effects on sequences in nearby genome regions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Soft sweeps II--molecular population genetics of adaptation from recurrent mutation or migration

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

A map of recent positive selection in the human genome

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The hitchhiking effect on linkage disequilibrium between linked neutral loci

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Molecular signatures of natural selection

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Genomic scans for selective sweeps using SNP data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Testing hypotheses regarding the genetics of adaptation.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Using genome scans of DNA polymorphism to infer adaptive population divergence

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Soft sweeps: molecular population genetics of adaptation from standing genetic variation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Molecular population genetics and the search for adaptive evolution in plants

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Pattern of polymorphism after strong artificial selection in a domestication event

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The genealogy of sequences containing multiple sites subject to strong selection in a subdivided population.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Hitchhiking mapping--functional genomics from the population genetics perspective

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Detecting recent positive selection in the human genome from haplotype structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The coalescent in an exponentially growing metapopulation and its application to Arabidopsis thaliana

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Genetic drift in an infinite population. The pseudohitchhiking model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Variation and selection at the CAULIFLOWER floral homeotic gene accompanying the evolution of domesticated Brassica oleracea

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Measures of divergence between populations and the effect of forces that reduce variability.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Properties of statistical tests of neutrality for DNA polymorphism data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Statistical tests of neutrality of mutations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The effect of deleterious mutations on neutral molecular variation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Evolutionary Rate at the Molecular Level

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

A test of neutral molecular evolution based on nucleotide data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Adaptive protein evolution at the Adh locus in Drosophila

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Evolution of the ancestral recombination graph along the genome in case of selective sweep.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Population genomics of the Arabidopsis thaliana flowering time gene network.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Detecting selective sweeps: a new approach based on hidden markov models.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Sizing up human height variation

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

From genotype to phenotype: systems biology meets natural variation

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Soft selective sweep near a gene that increases plant height in wheat

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The structure of linkage disequilibrium around a selective sweep

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Geographical variation in selection, from phenotypes to molecules.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Accurate inference and estimation in population genomics

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The effects of artificial selection on the maize genome

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Identifying adaptive genetic divergence among populations from genome scans.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

DetSel 1.0: a computer program to detect markers responding to selection

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

Insecticide resistance in the mosquito culex pipiens: what have we learned about adaptation?

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3016716

The power and promise of population genomics: from genotyping to genome typing

27 October 2018

1 reference

12 December 2020

The signature of positive selection on standing genetic variation

1 reference

12 December 2020

Inbreeding coefficients and coalescence times

1 reference

12 December 2020

Who believes in whole-genome scans for selection?

1 reference

12 December 2020

Natural distributions of mitochondrial sequence diversity support new null hypotheses

1 reference

12 December 2020

Coalescent under the evolution of coadaptation

1 reference

12 December 2020

Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives

1 reference

12 December 2020

ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE.

1 reference

12 December 2020

The effect of linkage on limits to artificial selection

1 reference

12 December 2020

The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations

1 reference

12 December 2020

Identifiers

DOI

10.1086/656306

1 reference

2 August 2017

1 reference

2 August 2017

1 reference