GENETICS 633 Lecture Notes - Lecture 4: Molecular Evolution, Single-Nucleotide Polymorphism, Chromosome

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20 Sep 2016
September 20, 2016 – examining simulations
- Simulations in population genetics
oExamine how a statistic responds to an evolutionary parameter
oTest the null hypothesis (for example, neutral evolution with demography
oEstimate parameters (for example, approximate Bayesian computation
oForward simulations: includes every individual in every generation. Flexible but
computationally slow
oCoalescent (backwards) simulations: Considers only the sample’s history. Limited
options, but very fast
- Simulations in this class
oRead instructions from the syllabus and the manuals for the programs being used:
ms, by Hudson 2002, which is neutral selection only
msms, by Ewing and Hermisson 2010, which adds positive selection
oIf using a PC, may need to install “Strawberry Perl”, as well as install the simulation file
from Learn@UW in a place that is easy to access from command prompt
oAll the inputs and outputs are documented on the syllabus and on Learn@UW
- Reviewing the homework
oThe expected time for the first question is 118 generations
oThe expected time for the second question is 3933.33 generations
oWhen discussing whether the estimate above is accurate, we touched on how the
assumptions for the simulation would need to be adjusted in order to more improve the
accuracy. We also indicated that the variance would have to be lower, and that using
actual sequence data would improve the accuracy
oWhen discussing whether smaller populations would experience a faster or slower rate
of coalescent events than larger populations, we agreed that smaller populations would
have faster coalescent events since random chance is a greater determinant in their
genetic changes than in larger populations
Mutation and Population Genetics
-Mutation is the ultimate source of all genetic variation
oMutation: the permanent incorporation of random errors in DNA that results in
differences between ancestral and descendant copies of DNA
- Kinds of mutation
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