Coop Flashcards
Def. Evolution
Descent with modification; changes in allele freq over time in populations
If mutation rates per base are low what causes large #’s of mutations?
Large # of individuals in population or large genome size
Pairwise diversity
Fraction of sites that differ between two sequences chosen at random
Heterozygosity
Fraction of sites where 1 individual is heterozygous
Hardy-Weinberg assumes
At least 1 generation random mating
Linkage Disequilibrium & equation for D
The non-random association (covariance) of alleles at different sites in the genome in a population.
Dab=Pab-Pa*Pb
What creates LD?
Genetic drift and Hitchhiking
Epistatic selection*
Assortative Mating: Inbreeding – Population structure and admixture – Assortative mating by phenotype*
Example types of neutral alleles (4)
1) A synonymous change in a codon. • 2) A non-‐synonymous change that replaces one amino-‐acid with a funconally similar one.
3) A non-‐synonymous change which produces a large change in a phenotype on which selecon no longer acts
4) not protein coding or important to regulation
Effective pop size Ne
size of an idealized population in which pop size is constant, variance in reproductive success is low, anddriftoccurs at the same rate as that in the actual population of interest
Molecular clock & evidence
The expected number of neutral substitutions = 2T µ i.e. substitutions occur at a linear rate; evidence comes from linear rates of protein evolution across species with different generation times but similar mutation rates
Neutral theory expectation for dN/dS
subst./site nonsynonymous/synonymous:
dN/dS = 1
Expected dN/dS for a gene coding for an important protein (constrained)
Expected dN/dS for a gene Under directional selection; natural example
> 1; vertebrate immune system
Why do you get incomplete lineage sorting?
2 alleles don’t coalesce before the next earliest species divergence… So the gene has a different tree than the species..even when species B and C are more related, A coalesces with B first (less distant past), then C.
What does the Frequency spectrum of alleles look like in a recently expanded population?
Excess of singletons
What does the Frequency spectrum of alleles look like in a recently bottleneckedpopulation?
excess of intermediate frequencies (from mutations in pre-bottleneck branches)
What does the Frequency spectrum of alleles look like in constant size pop evolving neutrally?
Theta/i, eg theta/2 doubles, theta singletons
What is the nearly neutral theory and some evidence to support ?
Levels of constraint aren’t absolute but determined in part by Ne; rodents have larger Ne than primates and so evolve slower
To power studies of demographics through time you want more individuals or loci?
Loci bc they’re inherited independently and most individuals will coalesce rapidly
What was the flaw of the mitochondrial analysis paper stating we were no more than 1/1000 Neanderthal bc 1000 subjects nine had Neanderthal mitochondria
Low power bc modern subjects mitochondrial Dna coalesce quickly in recent past so very small ancient sample. Need more loci to get bigger ancient sample (2%eurasian genome is Neanderthal)
3 components necessary for evolution
1) variation in phenotype
2) fitness differences between phenotypes
3) variation is heritable
Low heritability comes from
Low genetic variance or high environmental variance in phenotype
Natural selection
Nonrandom variation in fitness across individuals with diff. phenotypes
Beta, selection coefficient
Slope of regression between phenotype and fitness, i.e. Covariance of phenotype and fitness over total phenotypic variance
Antagonistic pleiotropy w example
1 gene controls multiple traits where at least one has fitness benefit and another fitness decrease. Derwin’s finches beak length under neg selection but increases due to pleiotropy and positive selection for beak depth
What are three reasons for sexual selection/choosy females?
1) more fit mates = more fit offspring
2) more sexy mates = more sexy offspring ‘sexy sons hypothesis’
3) increase female or offsprings fitness directly, eg by providing resources
How does co-evolution of fisher’s proposed male sexy but ther wise useless signal and female preference?
Males have more offspring because they get additional boost from rare female preference then females who prefer those males assortativelu mate with them, creating genetic covariance between the two traits and female preference rises with increasing male success (sexy sons)
Which reaches fixatin 1st and which rises more quickly? Additive, recessive or dominant beneficial alleles?
Additive has same selection independent of allele frequency and so rises and fixes pretty fast. Dominant rises faster but is slow to fix at the end due to diminishing returns in homozygous context. Recessive alleles are very slow to rise since their neutral when rare/heterozygous
What is overdominance?
Heterozygous advantage.. Results in balanced polymorphism
Balancing selection eg.s
Heterozygous advantage, beneficial when rare (selfing incompatible id allele or plant color morph for flowers offering no rewards to be pollinators)
Additive effect of an allele
effect of an allele averaged across the possible genotypes it could occur in
Evidence against molecular clock
Neutral theory of molecular evolution can not explain a molecular clock measured in years. It predicts a molecular clock measured in generations, which is exactly what we see for changes to synonymous/non-‐coding sites but not what we see for changes to the protein.
How do explain a molecular clock measured in years for protein divergence?
Species with shorter generation time tend to have larger populations and therefore can select on what would be effectively neutral sites in smaller populations (which tend to have longer generation times). This leads to efficient background selection of weakly deleterious alleles in large pops, reducing substitution rates per generation.
What does nearly neutral mean?
Selection acts on same order as drift, effectively neutral if
s ~ 1/(2Ne)
3 reasons there’s so much polymorphism
1) balancing selection (mutation-selection balance is spatially balancing)
2) mutation-selection balance
3) mutation-drift balance (neutral theory)
Def fitness
Expected number of offspring in a specific ecology and environment
T/F: An allele with additive effects has an avg fitness benefit that doesn’t depend on frequency
True! Because it’s additive, it’s fitness effect is the same no matter what it’s paired with
What are all the components contributing to total phenotypic variance?
Environmental, additive genetic, dominance, epistasis (Interactions between loci, Vi)
Do we expect to find more Neanderthal alleles in the human genome at places with higher or lower recombination?
Higher recombination. Neutral Neanderthal alleles that don’t recombine off their mildly deleterious background will get purged from human pop
What is one reason a recent string selection would show a typical sweep signature?
If it starts at 5% or more frequency, not a new mutation, when it’s selected for it will carry multiple hitchhiking backgrounds
Def background selection
Purging of deleterious alleles.. Can also reduce diversity of linked neutral loci
Why do asexual lineages accumulate deleterious mutations and what is the name of that phenomenon?
Muller’s ratchet, can’t recombine off weakly deleterious mutations that hitchhike up in frequency with beneficial mutations
2 advantages and disadvantages to sex:
Advantages: new haplotypes through recombination; can evolve novel solutions in parallel
Disadvantages: cost of raising offspring only 1/2 similar; cost of finding a mate/allee effects; could break up winning combo haplotypes
On avg how many generations does it take a neutral allele to fix?
4Ne
Def species from pop gen
A species is a set of alleles/traits held in linkage disequilibrium through evolution of biological barriers to gene flow
Dobzhansky-‐Muller Incompabilies (DMIs) are examples of
Epistasis. AA and aa both ok but Aa has low fitness - they affect each other’s fitness
What is character displacement and how can it maintain reinforce speciation?
In sympathy one species changes to a phenotype more distinct from the other species even though they’re similar in allopatry. Eg color of flowers or mating rituals, flower timing can reinforce sexual isolation in sympatry
How can inversions be adaptive?
Inversions can lock together successful phenotypes for local adaptation in the face of high migration ; eg butterfly mimicry, mimulus local adaptation,
