Prof. Kelsey's Flashcards
Population structure?
= spatial structure divided into smaller local populations.
F(IS) = (Hs - Hi)/Hs ?
= measures the reduction of heterozygosity within a subpopulation.
R = h²S ?
= determines the amount of selection due to evolutionary change.
R = response to selection.
h² = heritability.
S = selection differential.
Inbreeding coefficient?
= determines how much of inbreeding is occurring in populations.
● F = (Ho - H)/Ho
Ho = expected heterozygosity = 2pq.
H = actual observed heterozygotes.
F 0 —> 1 for inbreeding coefficient?
Suggests inbreeding.
Selective agent?
= environmental cause of fitness differences among organisms with different phenotypes.
Eg. Seeds eaten by Darwin’s finches.
w = fitness of individual/average fitness
= relative fitness of individual in the population in terms of selection.
F(ST) = Ht - Hs (with dash on top) / Hs (with dash on top) ?
• measures differentiation among subpopulations.
- gives you a # 0<x<1
- close to or = to zero, little difference.
- close to one, more differentiated.
• tells you how different the subpopulations are from one another.
F(IT) = Ht - Hi (dash) / Ht
• reduction in individual hetero relative to metapopulation.
Hi (dash) = average reduction of heteroz in one individual.
Ht = reduction heteroz in total metapopulation.
Absolute fitness
Relative fitness
• average number of offspring produced by a genotype over its lifetime.
0 < w < 1 will die most fit
• (w) relative difference between genotypes.
w = absolute fit of interest/ absolute fit of most fit genotype
Indirect selection?
• takes place on correlated traits
- one trait target of selection, 2nd is not target, but may appear to be due to correlation with target.
• changes in correlated trait not affecting fitness.
Beta?
= selection gradient.
• measure of direct selection.
• partial regression of slopes.
• when positive: direct selection active.
• + or - depicts + or - slxn.
Ne = 4NmNf / Nm+Nf
Nm + Nf = Na
• determines magnitude of genetic drift when or more assumptions are violated (¹ #sexes; ² no sex/nat slxn; ³ subpop same in next generation).
Nm = males.
Nf = females.
Population genetics?
= study of naturally occurring genetic differences between organisms and populations.
Migration
m
• homogenizes the population.
• increases allelic variation.
- movement of individuals between populations.
- proportion of individuals that move between populations in a generation.
Mutation?
• ultimate source of genetic variation.
• changes allele frequency because it can change actual allele.
• 4 kinds of mutation.
How do you identify selection agent based on selection gradients?
• partition fitness into various fitness components.
• look at fitness components & see what selection is acting on.
Adaptive radiation?
= evolution of ecological diversity within ecological habitats.
• closely related species evolving to live in varying habitats.
Selection vs Migration?
• local adaptation from local selection; variation among subpopulations.
• relative activity of each can mean the difference of homogenizing a population or adaptation.
Frequency of alleles?
= proportion of alleles present in a population.
Target of selection?
= trait that helps the organism deal with challenge in the environment, i.e., selective agent.
• phenotypic traits that selection acts directly upon.
Genetic drift?
= fluctuations in allele frequency that are due to random chance.
- important in small populations.
Increases variance among subpopulations.
Decreases variation within subpopulations.
Evolution requirements of natural selection?
- Phenotypic variation for a trait.
- Consistent relationship between phenotypic variation & variation in fitness.
- Must be heritable trait.
Directional selection?
= selection acting in positive or negative direction.
• moves mean left or right.
• width of curve decreases.
• changes the diversity, i.e., homogenizes.
Non random mating
Negative assortment mating
- dissimilar phenotype mating.
Result : High heterozygosity.
Five factors that effect/criteria of Hardy-Weinberg?
- Random mating.
- No slxn.
- Large population size (no drift).
- No migration.
- No mutation.
Molecular clocks?
• main assumption: sub. rate constant across lineages.
• allows use of molecules to date species events (i.e., divergence).
Migration vs Drift?
• migration can balance drift according to:
FsubST = 1/(1+4NeM)
• can use to calculate migration with allele frequency…but does have problems.
Hardy-Weinberg Principle?
= non changing population (equilibrium)
• allele frequency should be constant over time.
Selection vs Drift?
• selection will have an effect on genotype frequencies.
S > 1/2Ne
if not true, drift has greater effect
Consequences of genetic drift in a subpopulation
• decrease allelic variation.
• increase homozygotes.
Negative frequency dependent selection
• more common.
• genotype fitness decreases as frequency decreases.
- fitness of rare genotypes is higher (fewer individuals there are, higher the fitness).
- maintains a balance between alternative phenotypes in a population.
Inbreeding
Non-random mating
• mating among individuals closely related.
Result:
• more likely to share genes.
• affect multiple loci.
• increase homozygosity.
• offspring similar with multiple characters.
Consequences of genetic drift in a metapopulation?
• average allele frequency does not change.
• increase homozygosity.
Test for equilibrium
• determine if genotypes in a population differ significantly from expected with HW.
• if it does differ, can lead to what is causing evolutionary change.
Disruptive selection
• intermediate trait is minimum for fitness.
• non linear fitness function.
• means stays same.
• increase in # of individuals with trait values are decreased.
• can lead to speciation.
Positive frequency dependent selection
• genotype fitness increases as frequency increases.
I.e., Mimicry - often leads to fixation of the increasing genotype frequency.
Direct selection
• causal relationship of genotype & phenotype.
• trait (target of slxn) interacts with selective agent which directly influences fitness.
Selection
• leads to differential reproductive success of certain phenotypes.
• acts on phenotypes.
Non random mating
Positive assortative mating
• mating among similar phenotype.
Result:
• Increases homozygosity (only for trait looking at).
• Decreases heterozygosity by 1/2 each generation.
Polymorphic
= population has multiple genes present in population for a given gene.
Stabilizing selection
• intermediate is optimum for fitness, i.e., intermediate trait increases fitness.
• non linear function.
• decreases variance of individuals.
• does not move mean.
Chi squared
• determines if HW holds or not.
chi² = (obs - exp)² / exp.
obs = observed allele frequency.
exp = expected allele frequency.
Codon usage bias
• if a gene is highly expressed; one codon over another may be chosen and if that gene frequency is selected for, that codon will increase in #.
Mutation rate (μ)
• chance of a mutation happening at any given gene.
10⁴ - 10⁶ per generation.
Selection coefficient (s)
• measures strength of selection against a genotype.
s = 1 - w
when:
s = 1 selected against.
s = 0 is normal.
Correlation selection
• occurs when 2 traits interact to determine fitness.
- certain combinations of traits have a higher fitness.
• similar to epistasis.
Fitness function
• describes the relationship of phenotype and fitness based on slope.
• indicative of directional selection.
• slope = strength of selection.
4-fold degenerate codon
• can change to any of the 4 nucleotides, the amino acid stays the same.
I.e., Proline, Leucine, Ala, Val.
Codominance
• equal effect on fitness.
A1A1 = 1
A2A2 = 0.5
A1A2 = 0.75 (= .5/2 + ½ = 0.25+0.5 = 0.75)
All arbitrary.
Overdominance
• fitness of heterozygote is higher than homozygous.
• balancing selection occurs to lead to 50-50 allele frequency.
A1A1 = 1-s
A1A2 = 1
A2A2 = 1-s
All arbitrary.
dS
synonymous sites/ #sites *
- = # 4 fold degenerate sites + ⅓ of 2 fold deg.
• gives you rate of sub type/site/sequence.
dN
nonsynonymous sites/ # sites °
• only relative to # of sites where you could have a nonsyn. sub.
° # sites that could have occurred at (# nonden. + ⅔ of 2 fold deg.)
• rate of variation basically due to slxn.
What can cause rate variation among lineages?
• positive selection on one lineage.
• purifying selection on one lineage.
• if using a coding region, you could get around this by just using synonymous sites.
Mutation-selection balance
• slxn removes deleterious alleles.
• mutation introduces deleterious alleles.
• balance between this is that deleterious alleles are maintained through mutation.
Relative Selective Codon Usage (RSCU)
RSCU <1 RSCU> 1
of occurrences of codon / # of expected to occur
(at random)
• more frequent than expected at random (RSCU <1)
• less frequent than expected at random (RSCU >1)
Experimental manipulation
• determine experimentally what is causing correlation or what traits affect fitness.
- tests if your target of selection hypothesis holds true or not.
