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Welcome to Spring Semester 2013
Introduction to Genetics and Evolution
Mohamed Noor
A whirlwind introduction to evolution and genetics, from basic principles to current applications, including how disease genes are mapped and how we leverage evolutionary concepts to aid humanity.
This week we will take a look at issues of population genetics. These are the
class materials we'll work with this week.
Problem Set: This week is the fifth graded problem set: Population Genetics Problem Set, Week 6.
This assignment should be completed at least once before the Nov. 19th, 12:00 pm EDT deadline. Please read the grading policy (if you haven't already done so) before completing the problem set, to better understand the requirements for the course.
There is also a set of practice problems available. The download links for the problems and their solutions is available to the right of lecture #6 in week 6. These problems are not graded nor are they required for understanding the assigned problem set. They are purely for the benefit of students that wish to have additional material to work through and check their understanding of the class topics.
Don't forget to check your graded problem set from Week 5, also in the wiki page for Problem Sets and Exams! Also, please post in the Problem Set Week 5 forum if you got a correct answer for one of the problems, in the threads provided (the "How Did You Correctly Solve..." series), so that all students can see the line of thinking that reached a correct answer!
Lecture: Allele and genotype frequencies
Problem Set: This week is the fifth graded problem set: Population Genetics Problem Set, Week 6.
This assignment should be completed at least once before the Nov. 19th, 12:00 pm EDT deadline. Please read the grading policy (if you haven't already done so) before completing the problem set, to better understand the requirements for the course.
There is also a set of practice problems available. The download links for the problems and their solutions is available to the right of lecture #6 in week 6. These problems are not graded nor are they required for understanding the assigned problem set. They are purely for the benefit of students that wish to have additional material to work through and check their understanding of the class topics.
Don't forget to check your graded problem set from Week 5, also in the wiki page for Problem Sets and Exams! Also, please post in the Problem Set Week 5 forum if you got a correct answer for one of the problems, in the threads provided (the "How Did You Correctly Solve..." series), so that all students can see the line of thinking that reached a correct answer!
Lecture: Allele and genotype frequencies
- Calculating genotype frequencies from counts
- Calculating allele frequencies from genotypes
- Joint probability to determine genotype frequencies from allele frequencies
- Self-perpetuates!
Lecture: The Hardy-Weinberg (HW)
equilibrium
- Allele & genotype frequencies stay stable with some assumptions
- Can always calculate genotype frequencies from genotype counts
- Can always calculate allele frequencies from genotype frequencies
- Cannot always calculate genotype frequencies from allele frequencies
- But can if “boring” population-- many assumptions
- By seeing HOW natural populations deviate from the HW expected genotype frequencies, we infer what interesting evolutionary forces are operating
- Mathematical tests for deviation from HW expectation
Lecture: Deviation from Hardy Weinberg Equilibrium:
Wahlund Effect
- See deviation from HW when pool two populations that are individually at HW
- Deviation from random mating assumption
- Deviation called “Wahlund effect”
GWAS assumes HW, so very important to test for it
- Often not done
- Example where did test but didn’t interpret correctly
Lecture: Differences between populations:
Origins and quantifying
- Differentiation can be from unique mutations or differences in frequencies
- Measure differentiation in frequencies between populations not individuals
- Fst measures differentiation basically as extent of Wahlund effect
- Example Fst values for human populations
- Assumptions (often violated) in Fst
Lecture: Effects of gene flow
- Makes allele frequencies converge among populations
- Continent-island model
- Assumed to be one-way
- Island model
- Assumed to be symmetric
- Relevant parameters for effect: rate and difference in gene flow
Lecture: Inbreeding
- Effects similar to Wahlund since also non-random mating
- Reduces proportion of heterozygotes
- Measure also similar-- Wright’s inbreeding coefficient (F)
- Example measures in humans
- Why inbreeding is bad
- Not intrinsically bad, but exposes recessive bad alleles by making them homozygous
Optional Suggested Readings:
- Evolutionary Analysis, 4/e, Freeman & Herron, pages 169-182, 223-232, 264-275
- Introduction to Genetic Analysis, 10/e Griffiths et al, pages 644-648
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