Population Genetics Flashcards
define Evolution
the change in form and/or behaviour of organisms between generations
define Natural Selection
the process where some individuals produce more offspring than others, carrying forward their “better” traits that are more favourable to survival and reproduction
Natural Selection occurs when there is…
Variance, Selection and Heritability of traits
Aristotle (384-322 AD)
looked for evidence of “divine order”. came up with hierarchical arrangement of forms—species arranged linearly along a scale with 1=God, 2=Man, etc.
Carolus Linnaeus (1707-1778 AD)
- proposed the nested system of relationships for organisms
- recognized fundamental difference b/w interbreeding within a species vs. non-interbreeding (diff species)
- believed in balance of nature (species had a specific place and would not change or go extinct)
Comte du Buffon (1707-1788 AD)
- believed Linnean hierarchy of species relationships, but that there could be divergence over time due to changes in environment AND change could only happen within families
Erasmus Darwin (1731-1802 AD)
- believed organisms could improve and adapt to better suit their environment (did not propose a mechanism for this)
- all life consists of “one living filament” connecting all organisms to one common ancestor
Jean-Baptiste Lamarck (1744-1829 AD)
- proposed mechanism for inheritance of acquired characteristics
1st law: use/disuse of a structure leads to its development or diminishment
2nd law: these acquired traits are heritable
traits better suited to the environment are favoured and rise in frequency over generations.
Thomas Malthus (1766-1834 AD)
principle of overproduction - most organisms produce more offspring than can survive
- populations grow geometrically until they outstrip their food supply and resources.
- major influence on Darwin and Wallace
Charles Lyell (1797-1875 AD)
proposed “Uniformitarianism”: the earth is subject to gradual, continuous change but without progress or development (remains at a steady state)
Charles Darwin (1809-1882 AD)
Theory of Natural Selection:
- variability exists within species
- variant traits must be inherited
- individuals more suited to their environment will more likely survive
- said that natural selection acting on isolated populations causes them to become increasingly different from each other.
Alfred R. Wallace (1823-1913 AD)
discovered Natural Selection independently of Darwin
- realized that natural selection inevitably occurs due to inferior individuals being killed off and the superior ones remaining and reproducing i.e. survival of the fittest
Selection
differential (or preferential) survival and/reproduction of individuals with certain genotypes
Fitness
the average contribution per parent to the next generation, including survival and reproduction
Long term effects: WA = Wa
A allele freq. (p[t]) remains at its initial frequency (p[0])
“neutral”
Long term effects: WA > Wa
A allele freq. (p[t]) goes to 1
“Directional Selection” favouring A
Long term effects: WA < Wa
A allele freq. (p[t]) goes to 0
“Directional Selection” favouring a
selection coefficient
”s” it is the proportional increase in fitness caused by replaced a with A
What does the curve look like for the spread of beneficial allele A?
follows an S-shape curve, slowly at first when allele is rare AND when it is common
how do weakly favoured alleles spread?
slowly, because they are not strongly favoured
Heterozygous Advantage
when heterozygotes (Aa) have 5x the relative fitness compared to homozygotes
diploid model without selection
Diploids allele frequencies remain at Hardy-Weinberg proportions in populations with random mating and no selection
Polymorphism
when there are multiple different alleles of a single locus existing in a population.
is reached when heterozygous advantage occurs in a population
Hardy-Weinberg Equilibrium definition & formulas
a principle stating that genetic variation in a population will remain constant from one generation to the next in the absence of disturbing factors (selection, mutation, drift, etc).
p^2 + 2pq + q^2 = 1
dominance coefficient
“h” = measures how dominant A is with respect to fitness
types of mutations
- point mutations
- structural mutations
- genomic mutations
average mutation rate in eukaryotes
rate = 10^(-8) ~ 10^(-10) per basepair per generation
“u” (miu)
- symbol for mutation disturbing the wildtype function
- “mutation load” being the reduction in fitness due to mutation
“v” (nu)
- mutation restoring wildtype function
- increase in fitness due to mutation
q when h>0
not recessive
q=u/hs
q when h=0
recessive
q=sqrt(u/s)
Diploid fitness (mutation with selection)
WAA = 1
WAa = 1 - hs
Waa = 1 - s
if h = 0
mutation is recessive
if h = 1
mutation is dominant
define Genetic Drift
- the change in allele frequencies that results from random sampling processes that take place in populations over generations
- drift is always acting on populations (so long as they are finite)
- drift results in the loss or fixation of an allele, even in large populations
is genetic drift a random process?
Yes, however some of its behaviours are predictable.
does population size influence rate of genetic drift?
Yes
in smaller populations, changes in allele frequencies from one generation to the next are greater
as population size increase, allele frequencies are expected to remain polymorphic for longer
i.e. larger populations are better able to retain genetic variation
in a diploid population, what is the probability that a neutral allele fixes?
the probability that a neutral allele A will fix is equal to its initial frequency p
what is the amount of time it takes for a single allele to fix?
2N generations with N number of haploid individuals
4N generations with N number of diploid individuals
defin Coalescence time
how far you must go back in time to find the most recent common ancestor for a shared allele
define Expected Heterozygosity
the probability that two alleles drawn at random are different alleles (in both haploids and diploids).
H[t] = 2p[t]q[t] = 2pq
how does H[t] (expected heterozygosity) change over time due to drift?
H[t] = (1-1/(2N))H[t-1]
define Founder Effects
effects that occur as a result of a new population being founded by a small number of individuals from a larger population
- small set of genes in the genetic pool for the population to be built on
define Population Bottleneck
a severe reduction in the number of individuals in a population, resulting in a loss of genetic variation in the surviving population
- can result in inbreeding, with there being few individuals the chance that two alleles recently shared a common ancestor is much higher
what is the probability of fixing a new mutation in a large population?
2s in haploids
2hs in diploids
- the fate of an allele in a diploid population is determined more by selection than by drift.
define (Linkage) Disequilibrium
measures the genetic associations among two loci, indicating which alleles tend to be found together in an individual
D = XABXab - XAbXaB
*note that the loci do not need to be physically linked, they can be on different chromosomes
if D>0
positive disequilibrium means its more common to see in individuals of A with B, a with b.
if D<0
negative disequilibrium means its more common to see individuals of A with b, a with B
define Recombination Rate
“r” = rate between two loci that determines the probability of a cross-over event between them, creating non-parental gametes
also the distance between two loci (very hard to determine)
what causes Linkage Disequilibrium?
several processes cause associations between loci including
- Drift
- Mutation
- Migration
- Selection
if there’s no selection, mutation, or drift can allele frequencies still change?
Yes, if there are genetic associations between alleles (D). Evolutionary change occurs due to mixing of alleles because of recombination.
Genetic associations decay by a factor of (1-r)
how do genetic associations decay?
Genetic associations decay by a factor of (1-r).
They persist for longer if loci sites are closer (low r)
how does selection effect sites that are in disequilibrium?
- selection on one gene site causes changes to other nearby sites linked to that gene.
- if selection is stronger, the selected allele rises in frequency faster and brings its associated gene loci with it (until they’re separated by recombination).
if both sites are under selection, how does fitness change?
- mean fitness can decline over time due to the combined effects of selection and recombination
what is genetic hitchhiking?
- when neighbouring alleles in the genome are dragged with selected alleles in increased or decreased fitness due to selection (alleles that are in linkage disequilibrium).
- when there is Linkage Disequilibrium between a selected locus and neutral locus, causing the neutral allele to change in frequency.
