Pattern of Polymorphism After

Strong Artificial Selection in a

Domestication EventHidenki Innan and Yuseob KimHidenki Innan and Yuseob Kim

A SummaryBy

William Dotson and Danny Rose

Outline of the Presentation

Background Background InformationInformation

Experimental Experimental Methods and Methods and ResultsResults

Discussion and Discussion and ImplicationsImplications

Background Information

Study ObjectiveStudy Objective– Determine a model for the process of strong Determine a model for the process of strong

artificial selection during a domestication artificial selection during a domestication event.event.

– Artificial SelectionArtificial Selection Differs from advantageous mutant Differs from advantageous mutant

selection selection – i.e. acts on previously neutral allele*i.e. acts on previously neutral allele*

Domestication EventsDomestication Events– Causes fixation of a predetermined Causes fixation of a predetermined

advantageous alleleadvantageous allele i.e. dogs, cows, barley, etc. i.e. dogs, cows, barley, etc.

Background Information Cont.

ApplicationsApplicationsFind domestication genes primarily in Find domestication genes primarily in crops such as corn and ricecrops such as corn and rice Future crop improvementsFuture crop improvements

– Disease modelsDisease models– Greater crop yieldsGreater crop yields

Experimental Theory

Linkage DisequilibriumEquilibrium – 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 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 Measurements of Artificial Selection

– Polymorphism 3 measures of polymorphism in this study

- S variation in segregating site

variation of pairwise nucleotide differences

H homozygosity 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 MethodsSimulation of a Domestication Event – BottleneckSimulation of a Domestication Event – Bottleneck

Neutral Allele in Wild Progenitor

Population (Genetic Drift)

Subset Founder Population and Artificial

Selection Begins (td)

Ancestral Population NAncestral Population N22

Current Population NCurrent Population N11

Experimental Methods

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

Simulation 1

Polymorphism with Selection– Constant population size– 5000 Replications

– Polymorphism is represented as , which is

ideally equal to 4N in 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 1

Standard Selective

Sweep Model

Simulation 2Two 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 2

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 3

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

Simulation 4

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

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