FINAL material Flashcards
Lectures 1- /Chapters 1- (29 cards)
Do individuals tend to mate with distantly or closely related sets of populations?
Closely related/same populations due to a type of non-random mating – population structure
Describe Gibbs Sampling
A sampling approach where we assign individuals at RANDOM into K unknown populations:
*K can be thought of as the # of clusters to partition into
- Allele frequencies are estimated at all of the loci in each population
- Those allele frequencies are used to Reassign each individual to a population (k) with a probability of P(Individual|pop. k )
Populations differ in allele frequencies due to….
Genetic drift OR selection being the driving forces behind differentiations across populations.
Describe Bayesian principles
These principles help to model uncertainty and updates the probability for a hypothesis based on new evidence
What is the goal of studying population & quantitative genetics?
To understand the causes and consequences of genetic variation amongst individuals, groups, and populations
*It is the genetic basis of evolutionary change
Describe some important roles of Evolutionary genetics
- Pesticide/insecticide use
- It is the genetic basis of new species
- Species conservation
Describe the differences between populations and quantitative genetics
–> Population Genetics: The study of the causes and consequences of genetic variation within and between populations
- extension of Mendelian genetics to evolving populations
- Basis of evolutionary change and much of the “micro” - evolutionary thought
–> Quantitative genetics:
- extension of population genetics to phenotype (variation) evolution
*Chromosome segregation, recombination, and Mendelian Inheritance provides a strong framework for population and quantitative genetics
Who are the individuals whose ideas helped give a quantitative theory of evolutionary change?
R.A. Fisher, J.B.S Haldane, and Sewall Wright
What is the basic currency in population genetics?
A set of aligned orthologous sequences
*Orthologous: refers to genes in DIFFERENT species that evolved from the same, common ancestral gene
What is meant by the process of descent? How about descent with modification?
The process of going from 1 generation to the next
- Descent plays out over MANY generations
Descent with modification looks at descended alleles which some polymorphism has occurred in the population
Compare a non synonymous vs synonymous mutation
- Nonsynonymous = change in a.a. product
- Synonymous = NO change in a.a. product
What are the 4 summaries of polymorphism?
- Frequency of EACH site
- # of segregating sites
- Heterozygosity
- Pairwise Diversity
How much genetic diversity is seen in Drosophila melanogaster vs. Humans?
*Drosophila melanogaster = 1% (1/100 bases)
*Humans = 0.1% (1/1000 bases)
Equation for A allele frequency given genotype frequencies of A/A, A/G, G/G
2(A/A homozygote freq.) + (1/2 x A/G heterozygote freq.)
What assumptions have to be made when it comes to Hardy-Weinberg Equilibrium (HWE)?
*Have NO evolution:
- Have random mating
- No mutations
- No genetic drift (large population size)
- No migration
- No selection
Define IBD
Sharing of an allele or region of the genome between people due to a shared ancestor
- Can have 1 or both alleles IBD
Approximately how long does it take for a neutral allele to go from being introduced to fixation?
~ 4N generations (same for other alleles)
Under the Neutral Theory of Molecular Evolution, what are the different types of mutations that can occur within a region?
- Highly deleterious mutations
- Neutral mutations
*Rate of substitution: μ(1-C)
What is C?
*C = level of constraint: is the fraction of mutations that are highlighted deleterious
- These CANNOT contribute to substitutions or polymorphisms
- 1-C is the fraction of mutations that are neutral
Describe the how the # of substitutions and alleles can relate
The total # of alleles that were introduced will fixate thus = total # of substitutions in a population where T is longer than the time it fakes to fix a neutral allele.
*T = time in generations that alleles shared common ancestor
Describe the relationship between effective population size and the level of constraint in functional regions
- In SMALL N, genetic drift is fast/high, allowing even weakly deleterious alleles to become fixated by drift –> LOW C
- In LARGE N, genetic drift is slow, there is time for selection to occur so there is a high selective constraint, preventing deleterious alleles from fixating –> HIGH C
- 2Nμ (1-C) is the total number of neutral mutations that enter the population EACH generation
- These mutations have a 1/ (2N) probability of fixating in the population
Describe what a super gene is and how they might arise
A supergene is a type of polymorphism that is balanced by selection due to an inversion or other form of recombination suppression, that locks together multiple alleles
Forms of recombination suppression:
1. Inversion
2.
3.
Why would suppression of recombination arise?
- As selection favors the maintenance of certain allele combinations, recombination may break those alleles away from each other –> making it difficult to maintain the alleles
- This is when selection will selection for suppression of recombination to keep the combo of alleles locked together
