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Related Concept Videos

Frequency-dependent Selection01:21

Frequency-dependent Selection

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When the fitness of a trait is influenced by how common it is (i.e., its frequency) relative to different traits within a population, this is referred to as frequency-dependent selection. Frequency-dependent selection may occur between species or within a single species. This type of selection can either be positive—with more common phenotypes having higher fitness—or negative, with rarer phenotypes conferring increased fitness.
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Mutation, Gene Flow, and Genetic Drift01:09

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In a population that is not at Hardy-Weinberg equilibrium, the frequency of alleles changes over time. Therefore, any deviations from the five conditions of Hardy-Weinberg equilibrium can alter the genetic variation of a given population. Conditions that change the genetic variability of a population include mutations, natural selection, non-random mating, gene flow, and genetic drift (small population size).
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Types of Selection01:46

Types of Selection

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Natural selection influences the frequencies of particular alleles and phenotypes within populations in several different ways. Primarily, natural selection can be directional, stabilizing, or disruptive. Directional selection favors one extreme trait and shifts the population towards that phenotype while selecting against individuals displaying alternate traits. Stabilizing selection favors an intermediate trait with a narrow range of variation. Deviation from the optimal phenotype towards an...
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Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.
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What is Population Genetics?01:25

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A population is composed of members of the same species that simultaneously live and interact in the same area. When individuals in a population breed, they pass down their genes to their offspring. Many of these genes are polymorphic, meaning that they occur in multiple variants. Such variations of a gene are referred to as alleles. The collective set of all the alleles within a population is known as the gene pool.
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Gene Flow02:39

Gene Flow

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Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.
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Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.

Fernando Racimo1

  • 1Department of Integrative Biology, University of California, Berkeley, California 94720 fernandoracimo@gmail.com.

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Summary
This summary is machine-generated.

A new method, 3-population composite likelihood ratio (3P-CLR), enhances the detection of ancient selection events by modeling allele frequency changes across three populations. This approach improves upon existing cross-population composite likelihood ratio (XP-CLR) tests for population genetics.

Keywords:
DenisovaNeanderthalcomposite likelihoodpopulation differentiationpositive selection

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Area of Science:

  • Population Genetics
  • Evolutionary Biology
  • Genomics

Background:

  • Detecting natural selection in populations relies on modeling allele frequency changes under selection versus neutrality.
  • The cross-population composite likelihood ratio (XP-CLR) method identifies selection but is limited to recent events and may miss older selective sweeps.
  • Existing methods struggle to differentiate selection occurring before population splits from those occurring afterward.

Purpose of the Study:

  • To develop an advanced method for detecting selection, particularly ancient selective events, that overcomes the limitations of current XP-CLR approaches.
  • To enhance the ability to distinguish between selection that occurred before population divergence and selection specific to individual populations after divergence.
  • To identify novel genomic regions and potential functional mutations associated with selective sweeps in human populations.

Main Methods:

  • Developed an extension of the XP-CLR method, termed the 3-population composite likelihood ratio (3P-CLR), which jointly models allele frequency dynamics in a three-population phylogenetic framework.
  • Applied the 3P-CLR test to population genomic data from the 1000 Genomes Project.
  • Investigated selective sweeps occurring before the split of Yoruba and Eurasian populations, but after divergence from Neanderthals, and sweeps post-Yoruba/Eurasian split.

Main Results:

  • The 3P-CLR method demonstrates superior performance compared to XP-CLR for detecting selection events that predated population splits.
  • Identified genomic regions consistent with previous selection studies and discovered new candidate regions for both recent and ancient selection.
  • Found suggestive functional mutations within some identified regions, potentially explaining the driving forces behind observed selective events.

Conclusions:

  • The 3P-CLR method provides a powerful new tool for detecting ancient selection events and distinguishing their timing relative to population divergence.
  • The application of 3P-CLR to human population data has revealed novel insights into the evolutionary history of modern human phenotypes.
  • This study highlights the utility of advanced population genomic methods for uncovering complex patterns of natural selection.