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A Summary By William Dotson and Danny Rose

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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A Summary By William Dotson and Danny Rose

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  1. Pattern of Polymorphism After Strong Artificial Selection in a Domestication EventHidenki Innan and Yuseob Kim A Summary By William Dotson and Danny Rose

  2. Outline of the Presentation • Background Information • Experimental Methods and Results • Discussion and Implications

  3. 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.

  4. Background Information Cont. Applications Find domestication genes primarily in crops such as corn and rice • Future crop improvements • Disease models • Greater crop yields

  5. 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.

  6. 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

  7. 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

  8. 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)

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

  10. 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.

  11. Simulation 1 Standard Selective Sweep Model

  12. 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

  13. Simulation 2

  14. 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

  15. Simulation 3

  16. 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

  17. Simulation 4

  18. 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.

  19. 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

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