GENETICS 633 Lecture Notes - Lecture 2: Nucleotide Diversity, Genotype Frequency, Heterozygote Advantage

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8 Sep 2016
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September 6, 2016 – Introductory Lecture
- Applications of Population Genetics
oConserving wildlife
oIdentifying and distinguishing individuals
oReconstructing genealogical history
oUnderstanding the spread of infectious disease
oIdentify genetic causes of trait variation
-Heterozygote advantage: when the heterozygote in a population confers an evolutionary
advantage and is selected for, even if the homozygote confers a disadvantage
-Nucleotide diversity: the chance that, at any specific site, the bases of that site will differ from
another member of the population. Humans have a nucleotide diversity of roughly 0.1%, which
is abnormally low.
otheories for why our species has such a low nucleotide diversity include population size,
recent bottlenecks, and the relatively short time our species has existed
September 8, 2016 – Describing genetic variation; patterns of variation in natural populations
- Basic definitions of genetic variation at a single site
oAllele: a distinguishable version of a polymorphism
oGenotype: a particular combination of alleles
oAllele frequency: the population frequency of an allele
oGenotype frequency: the population frequency of a particular combination of alleles
oPopulation: a group of interbreeding individuals that exist together in time and space
oScientific model: an intentional simplification of nature that makes testable predictions
regarding natural phenomena
- First genetic model
oStipulations
Two sexes
Diploidy
Large population
Non-overlapping generations
All individuals capable of mating
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Random mating
Large number of gametes
oAllele and genotype frequencies notation
Autosomal locus with two alleles, A1 and A2
p = freq of A1
q = freq of A2
p + q = 1
P = freq of A1A1
Q = freq of A2A2
H = freq of A1A2
P + Q + H = 1
n = number of sequences sampled
N = number of individuals sampled
oRelating allele and genotype frequencies: Hardy Weinberg with 2 or more alleles
pi = frequency of the ith allele
Pii = freq of genotype ii
Pij = freq of genotype ij
Pi = pi2
Pij = 2pipj
pi = pii + 0.5 [n](sigma)[j = 1] {Pij}
oHardy-Weinberg consequences
Can predict genotype frequencies from allele frequencies, and vice versa
These predictions are generated after just 1 generation of random mating
Comparing allele and genotype frequencies can detect inbreeding
Rare alleles are mostly found in heterozygotes
Heterozygotes are most commonly observed at intermediate allele
frequencies (1/3 to 2/3)
Homozygotes are most commonly observed when allele frequencies are
not intermediate
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