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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
  • Background Information
  • Experimental Methods and Results
  • Discussion and Implications
background information
Background Information

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.

Applications

Find domestication genes primarily in crops such as corn and rice

  • Future crop improvements
    • Disease models
    • Greater crop yields
experimental theory
Experimental Theory

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 Theory

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
  • 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

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
  • Basis model used for experimental simulations to investigate patterns of DNA polymorphism after domestication with and without selection.
simulation 1
Simulation 1

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

Standard Selective Sweep Model

simulation 2
Simulation 2
  • 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 3
Simulation 3

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 4
Simulation 4
  • Individual Polymorphisms in 8 different simulations
  • Polymorphism decreases as you get further away from the target site
  • Target site is at 0.5
experimental methods3
Experimental Methods

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
  • 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