Quest 4 Flashcards
The Law of Large Numbers
Actual frequencies mirror expected frequencies when samples sizes are very large
The Wright-Fisher model
Just like HW but relaxes the infinite population size assumption.
Genetic drift
The process of random fluctuation in allele frequencies due to sampling effects in finite populations
3 consequences of genetic drift
- In finite pops, all allele freqs fluctuate over time, even in the absence of natural selection
- Some alleles are fixed others are lost n fractions of heterozygotes in the pop decreases over time
- Separate populations diverge in their allele freqs, and in terms of which alleles are present
What is Ne?
Effective population size. The population size that is reproducing and contributing to population.
Population bottleneck
Cuts the population size dramatically leading to shifts in allele frequency simply by chance.
What is He?
Heterozygote population
Kimura (Selection or drift)
When pop size is large and selection is strong, selection determines allele frequencies.
When pop size is small and/or selection is weak, drift determines allele frequencies
If s> 1/2Ne
selection coefficient is greater than 1/2 effective population
Selection wins
If s< 1/2Ne
selection coefficient is less than 1/2 effective population
Drift wins
Leading edge expansion
a form of drift via founder effects leading to reduced genetic diversity in a newly colonized area
Neutral Theory of Molecular Evolution
Looks at the genotype, not phenotype.
Fine scale view to nucleotide changes over time, which push phenotypic changes.
2 points of the variation in population
- Most variation in a population is selectively neutral
- Most changes in the DNA are selectively neutral
Substitution
When a base changes due to mutation and is subsequently fixed in the population
Usually measured by substitutions/generation.
Substitutions vs mutations
Substitutions are not mutations.
Sub. are neutral
Most mutations are deleterious
Synonymous substitutions
Change in base pairs that encodes same protein
Purifying selection
A type of natural selection that removes harmful mutations from a population, preserving the function of essential genes over generations.
Positive selection
A type of natural selection that favors beneficial mutations, increasing their frequency in a population and driving adaptive evolution.
Ka =
number of nonsynonymous subs / nonsynonymous sites
Ks =
number of synonymous subs / synonymous sites
Ka/Ks <1
Purifying selection
Ka/Ks >1
Positive selection
Pseudogenes
Non-functional DNA sequences that resemble functional genes but have lost their ability to code for proteins due to mutations. They arise from gene duplication or retro-transposition and accumulate mutations without selective pressure.
Neutralist vs selectionist
Neutralists - drift is most important for evo
Selectionist - selection is most important for evo
Molecular clocks
can look at mutations and estimate how old a clade is
The genetic equidistance principle
suggests that if molecular changes occur at a constant rate across lineages the members of any given clade should be equidistant from the members of an outgroup
Founders effect
a type of genetic drift that occurs when a small group of individuals becomes isolated from a larger population, leading to reduced genetic diversity and a gene pool that may not be representative of the original population.
Are molecular clocks useful?
They are when comparing a single locus over a short time for closely related organisms.
As time passes saturation becomes and issue.
The Nearly Neutral Theory of molecular evolution
Smaller populations have longer generations, smaller pops have higher sub rates due to drift
Coalescent Theory
How gene copies spread through finite pops over time
Gene tree
Species tree
H0w is the gene tracked without selection it is a random process
Coalescent time
The number of generations that we must go back for a population to be reduced to 2 parental lineages. (~ 2N generations)
What is the largest factor of coalescent time?
population size
polygenic traits
traits that are influenced by multiple genes, often along with environmental factors, resulting in a continuous range of variation, such as height, skin color, and eye color in humans
Additive gene effects
Occur when multiple genes contribute to a trait, and each allele’s effect is cumulative, meaning their combined influence determines the phenotype in a predictable way
Latent variation
Not new variation but a new assortment of previously occurring Mendelian variation when multiple genes control “one” trait
Revealed by selection
Epistasis
Two or more alleles interact in non-additive ways
Haplotype
A set of alleles inherited together on the same chromosome
Genotype
The allele identity whole organism
Physical linkage
When loci are close together on the same chromosome and thus are segregated together
In absence of recom, a double heterozygote produces only two gamete types
Linkage disequilibrium
The non-random association of alleles at different loci in a given population.
The frequency of association of their different alleles is higher or lower than expected
Influences of linkage disequilibrium
- selection
- rate of recombination
- mutation rate
- genetic drift
- system of mating
- pop structure
- genetic linkage
Linkage equilibrium
When the genotype of a chromosome at one locus is independent of its genotype at another locus.
What does a D = 0 mean?
Linkage equilibrium
What does a nonzero D mean?
Linkage disequilibrium
4 causes of LD
- new mutation
- selection
- migration
- drift in a small pop
How is LD lost in a population?
meiosis with crossing over and outbreeding (sexual repro)
Genetic hitchhiking
Occurs when a neutral or even slightly deleterious allele increases in frequency because it is linked to a beneficial allele undergoing positive selection.
Background selection
A process in which negative (purifying) selection against deleterious mutations in a genome region leads to a reduction in genetic variation at nearby neutral sites.
Selective Sweeps
The process where a beneficial genetic mutation rapidly increases in frequency within a population, reducing genetic variation near the mutation due to strong natural selection.
Why is selective sweeps more consequential in haploid oganisms
They have no crossing over
Genetic draft
neutral alleles follow strong selection on a close allele
What causes genetic draft?
Hitchhiking
Genetic drift vs genetic draft
Both reduce overall diversity
drIft is more powerful in small populations
drAft is independent of population size
Big take away of Drift and Draft
drIft - pos alleles are more likely fixed and neg are more likely lost AS POP SIZE INCREASES
drAft- opposite, mildly beneficial more likely lost and mildly deleterious more likely fixed AS N INCREASES
Two main points on Linkage and Selection
- Alleles can increase in frequency due to selection because they code for good traits, or because they are linked to genes that code for good traits
- Natural selection (good or bad) decreases genetic variation at loci to the selected allele
What are the 2 hallmarks for genetic drift?
- Low genetic diversity within populations
- High genetic diversity between populations
