Pattern of Polymorphism After Strong Artificial Selection in a Domestication Event
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Pattern of Polymorphism After Strong Artificial Selection in a Domestication Event Hidenki Innan and Yuseob Kim. A Summary By William Dotson and Danny Rose. Outline of the Presentation. Background Information Experimental Methods and Results Discussion and Implications.

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Pattern of Polymorphism After Strong Artificial Selection in a Domestication EventHidenki Innan and Yuseob Kim

A Summary

By

William Dotson and Danny Rose


Outline of the presentation
Outline of the Presentation a Domestication Event

  • Background Information

  • Experimental Methods and Results

  • Discussion and Implications


Background information
Background Information a Domestication Event

Study Objective

  • Determine a model for the process of strong artificial selection during a domestication event.

  • Artificial Selection

    • Differs from advantageous mutant selection

      • i.e. acts on previously neutral allele*

    • Domestication Events

      • Causes fixation of a predetermined advantageous allele

        • i.e. dogs, cows, barley, etc.


Background information cont
Background Information Cont. a Domestication Event

Applications

Find domestication genes primarily in crops such as corn and rice

  • Future crop improvements

    • Disease models

    • Greater crop yields


Experimental theory
Experimental a Domestication EventTheory

Linkage Disequilibrium

Equilibrium – the genotype of a chromosome at one locus is independent of its genotype at the other locus

  • Disequilibrium- there is a nonrandom association between a chromosome’s genotype at one region and its genotype at the other region

    • Selection*

    • Genetic drift

    • Population admixture

  • Can be calculated as a numerical value.


Experimental theory1
Experimental a Domestication EventTheory

Selection and Linkage Disequilibrium

  • Artificial selection puts unequal pressure on a what was likely previously a neutral allele

    • When the allele is selected for, it carries a random selection of surrounding genes with it

      • Genotypes from region to region in each generation are no longer independent of each other

      • These quantifiable effects are used as signatures for selected genes

        • Example – young allele at high frequency


Experimental methods
Experimental Methods a Domestication Event

  • Measurements of Artificial Selection

    • Polymorphism

      • 3 measures of polymorphism in this study

        - qS variation in segregating site

        -qpvariation of pairwise nucleotide differences

        -qHhomozygosity of the derived allele per site

      • Low amounts of polymorphism suggest the influence of selection (signature)

  • Using history of frequencies of the allele classes, a model and simulation were developed


Experimental methods1
Experimental Methods a Domestication Event

Simulation of a Domestication Event – Bottleneck

Current Population N1

Ancestral Population N2

Neutral Allele in Wild Progenitor Population (Genetic Drift)

Subset Founder Population and Artificial Selection Begins (td)


Experimental methods2
Experimental Methods a Domestication Event

  • Basis model used for experimental simulations to investigate patterns of DNA polymorphism after domestication with and without selection.


Simulation 1
Simulation 1 a Domestication Event

Polymorphism with Selection

  • Constant population size

  • 5000 Replications

  • Polymorphism is represented as qp, which is ideally equal to 4Nmin a constant size population

  • Several initial frequencies were studied and compared with the standard selective sweep model

  • Different strengths of selection were compared in the second figure.


Simulation 11
Simulation 1 a Domestication Event

Standard Selective Sweep Model


Simulation 2
Simulation 2 a Domestication Event

  • Two simulations were used to determine the joint effects of selection and population bottleneck

    • The severity of the bottleneck differs in each case.

    • The level of polymorphism is reduced by the bottleneck regardless of the effect of selection

    • The qualitative effect of p is almost identical in both models


Simulation 21
Simulation 2 a Domestication Event


Simulation 3
Simulation 3 a Domestication Event

Measured the effects of

  • different values for initial time of selection (td)

  • ancestral population size (N2)

  • and current population size (N0) on the expected level of polymorphism


Simulation 31
Simulation 3 a Domestication Event


Simulation 4
Simulation 4 a Domestication Event

  • Individual Polymorphisms in 8 different simulations

  • Polymorphism decreases as you get further away from the target site

  • Target site is at 0.5


Simulation 41
Simulation 4 a Domestication Event


Experimental methods3
Experimental Methods a Domestication Event

Statistical Tests for Selection

  • Tajima’s (D)

  • Fay and Wu’s (H)

  • Hudson – Kreitman – Aguade (HKA)

    These statistical tests were used to analyze the simulations to detect a signature of selection.

    These tests supported the theoretical model in that it followed the patterns of polymorphism and selection.


Discussion and implications
Discussion and Implications a Domestication Event

  • Models were developed to measure the level of polymorphism and subsequently detect genes that were selected for through domestication events.

  • Initial frequencies of alleles greatly affects the likelihood that evidence for selection can be detected from patterns of polymorphism.

    • Difficult to detect many genes involved in domestication

  • It is likely that these patterns will be used to detect domesticated genes in future studies, but a more robust model will be needed in cases when the initial p is high.

  • Implication previously discussed

    • Crop yields

    • Diseases


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