Exam 4: Chapters 20-21 Flashcards
Population Genetics
What does population genetics study? What is it?
The transmission of genetic variation in populations
- An extension of Mendel’s basic principles
- Tool to learn about biological function, evolutionary mechanisms, and human history
What is a population?
A group of interbreeding individuals of a single species living in the same time and place
What is a gene pool?
The total of all alleles carried in all members of a population
What is a sample?
A number of individuals used to make inferences about the entire population
What is phenotypic frequency?
What is genotypic frequency?
Example?
Pheno: Proportion of individuals in a population that have a particular phenotype
Geno: Proportion of individuals in a population that carry a particular genotype
Ex. population of 20, gene with 2 alleles (A and a)
12 (AA), 4 (Aa), 4 (aa)
Pheno frequency: A_ = 16/20 = 0.8 aa = 4/20 = 0.2
Geno frequency: AA = 12/20 = 0.6, Aa = 4/20 = 0.2, aa = 4/20 = 0.2
What is allelic frequency? How is it calculated?
Proportion of gene copies in a population that are of a given allele type
Ex. 20 people, 40 alleles
12 AA –> 24 A alleles
4 Aa –> 4 A alleles and 4 a alleles
4 aa –> 8 a alleles
Frequency of A = (24+4)/40 = 0.7
Frequency of a = (8+4)/40 = 0.3
or
Frequency of A = f of AA + 1/2 f of Aa
Frequency of a = f of aa + 1/2 f of Aa
What are Hardy-Weinberg equilibrium five assumptions?* What is the HWE?
1) The population has an infinite number of individuals
2) Individuals mate at random
3) No new mutations appear
4) No migration into or out of the populations
5) Genotypes have no effect on ability to survive and transmit alleles to the next generation
HWE: allele and genotype frequencies will not change unless one of the above conditions is violated
(Independently developed by these men in 1908)
What are the two important outcomes of sexually reproducing diploid organisms with equal segregation and random mating? (Under the HWE)
1) Allelic frequencies should be same in adults as in gametes
2) Allele frequencies in gametes can be used to calculate expected genotype frequencies in zygotes in the next generation (predicting genotype frequencies in next generation)
How can the Hardy-Weinberg proportions be expressed as a binomial equation?
- in HWE: p^2 + 2pq + q^2 = 1 (AA + Aa + aa = 1)
p = allelic frequency (A) - dominant
q = allelic frequency (a) -recessive - Graph: one set of allele frequencies corresponds to one set of genotype frequencies
p + q = 1 (allele frequencies)
p^2 cannot be phenotypically distinguishable from pq - largest value for heterozygous: 50/50 p/q frequencies
What happens to a population not at HWE?
- one generation of random mating can reshuffle alleles into equilibrium (back to HWE)
– allele frequency remains constant
– genotype frequency changes
(except for sex-linked traits, that take a little longer)
Ex: - Generation 1: b (blue eye allele) = 0.5 - all Bb with brown eyes
- Generation 2: b (blue eye allele) = 0.5 - 25% BB, 50% Bb, 25% bb (p^2, 2pq, q^2)
What happens with sex-linked genes and HWE?
(X-linked)
- these genes require several generations to reach HWE
- first generation 100% males aY & females AA, second 100% AY and Aa, then oscillate: takes 6 generations or so to equilibrate at HWE
* important in endangered species
How does humans relate to HWE?
- many human loci are near HWE
- random mating may seem unrealistic, however, humans are not mating based on a specific genotype
- many loci do not affect phenotype and are used in solving crimes and identifying human remains
What are the geographic differences in proportions of blue eyes in Europe?
- HWE predicts allele frequencies are forever unchanging: they should be the same everywhere (NOT what we see)
- Blue-eyes recessive to brown and arose 6,000-10,000 years ago
- Trait common in Europe but rare outside of Europe
- Globe is not evenly distributed with the OCA2 eye color gene
What does Hardy-Weinberg provide for modeling population deviations?
A starting point/foundation
- Natural populations rarely meet simplified assumptions of H-W
– New mutations at each locus arise occasionally
– No population infinitely large
– Migrates of small groups of individuals does occur
– Mating not random
– Genotype-specific differences in fitness
- H-W use: estimating population changes through a few generations: not as useful for predicting long-term changes
What is the Monte Carlo simulations?
- A method to model long-term changes in allele frequencies
- Uses computer program to model possible outcomes of randomly chosen mating over a designated number of generations
– Starting population: defined number of individuals homozygous and heterozygous
– mating pairs chosen through random-number generating program
– Offspring genotypes of each generation based on probabilities
What happens at each generation in a Monte Carlo simulation? Then what?
- At each generation:
– Total offspring number and parental population size are equal
– Parental generation is discarded and offspring serve as parents of next generation (works for humans) - Multiple, independent simulations are performed
- Each simulation represents a possible pathway of genetic drift
– change in allele frequencies as a consequence of randomness in inheritance due to sampling error from one generation to the next
What do we see in Monte Carlo and genetic drift?
- There are different sizes of genetic drift
- 6 Monte Carlo simulations run with two initial populations of heterozygous individuals and
- in these simulations there was no selection
- Smaller population leads to greater genetic drift (allele may fall out/be lost {bottom of chart} and or become fixed {top of chart})
- Larger population leads to less genetic drift
What is fixation, what causes it, and how long does it take?
- Fixation: when only one allele in a population has survived and al individuals are homozygous for that allele
– no further change can occur (without migration) - At each generation, changes in allele frequencies are relatively small
- Over many generations, there can be large changes in allele frequency
- Populations with 2 alleles of equal frequencies: median number of generations to fixation is roughly equal to the total number of gene copies in breeding individuals
(Population of 10, median fixation time 20 generations)
What accelerates genetic drift?
1) Founder effects: a few individuals separate from a larger populations and establish a new population
2) Population bottlenecks: large proportion of individuals die (ie from environmental disturbances)