genetics

f2

raw material of evolutionary change

problem of darwin’s mechanism of natural selection

mechanisms of natural selection needed a heredity model that preserves variation rather than diluting it

scientific paradigms

a theory (natural selection) becomes powerful when paired with a compatible mechanism (genes that segregate and assort) that makes quantitative prediction possible

darwin’s postulates

1. Individuals vary

2. some of the variations are passed to offspring

3. variants differ in survival/reproduction

natural selection

individuals who survive and go on to reproduce are those with the most favorable variations

transmission genetics (eukaryotes)

population can be explained by how alleles are packaged into gametes and passed to offspring

blending inheritance

law of segregation

each parent only passes on one allele

law of independent assortment

locus

information stored by DNA

depends on copying mechanism that has high fidelity and occasional mutation

raw material of evolutionary change

alleles

heritable variation + differential reproductive success —>

predictable change in allele frequencies over generations

mutation vs substitution

single mutation changes gene frequencies, substitution is when mutation rises to 100% frequency in the population

transitions and transversions

transition: purine ←> purine

transversion: purine ←> pyrimidine

synonymous

changes codon without changing amino acid

non-synonymous

changes amino acid

nonsense mutation

introduces premature stops

SNPs

single nucleotide polymorphism

single-base differences

hapmap project

• measure SNP frequencies

• chose sites and gene mapped people from there

• looks at geographic/ancestral distributions and correlations with nearby SNPs

• allows us to make inferences from patterns

insertions

adding bases in multiples of 3

deletions

removes bases in multiples of 3

frameshift

adding/deleting bases in not groups of 3

microsatellites

short tandem repeat whose length can change by slippage

more likely than SNPs

copy number variants

chromosomal segments are duplicated or deleted

unequal crossing over (missing or added some info)

whole genome duplication

• meiosis doenst happen properly

somatic vs germline mutations

• somatic rates can be higher than germline rates

• germline mutations contribute directly to evolutionary change across generations

population thinking

• mutations are rare on an individual level but are numerous on the population scale

intra vs inter-specific variation

intraspecific: differences within a single species, necessary for evolutionary change

interspecific: differences between 2+ species, outcome of evolutionary change

why continuous variation?

• multiple polymorphic loci in a population

• many loci with allelic variation produces continuous variation

• environmental variation in the population

variance partitioning

• partitioning variance into different sources

• can find phenotypic variance

phenotypic variance (Vz)

genetic variance (Vg) + environmental variance (Ve)

what influences a phenotype

Genetics

• alleles and their independent/additive effects (Va)

• combination of alleles at a locus (dominance, Vd)

• combination of alleles between loci (epistasis, Vi)

Environment

• diff environments can cause diff phenotypes to develop (Ve)

Vz=[Va+Vd+Vi]+Ve

*assumption: parents pass alleles, not whole multilocus genotypes

additive genetic variance

• component of genetic variance that “shows up” next generation

• selection acts on phenotypic variance (response to selection depends on how much is due to additive genetic effects)

heritability

h²=Va/Vz

• proportion of phenotypic variance that is attributed to additive genetic effects

• proportion of variance that “shows up” next generation

• if h² = 0, evolution won’t occur (requires heritable variation)

h²

• heritability ranges between 0 and 1 (proportion)

• measured with parent-offspring regression

• sleeper slopes imply more additive variance relative to total variance

breeder’s equation

R=h²S

change in z = h²S

• even strong selection (large S) produces little change if h² (heritable variation) is small, because most variance is not transmitted

will traits that have been evolving under a history of strong natural selection show high heritability or low heritability

low heritability because selection reduces genetic variation

evolution

change in allele frequencies

hardy weinberg

p² + q² + 2pq = 1

idea population assumptions

• No natural selection of the gene

• No genetic drift or random allele frequency changes

• No gene flow (no new alleles added or lost through immigration/emigration; all alleles from original gene pool)

• No mutations

• Random mating with respect to gene in question

→ allele frequency won’t change under ideal conditions

allele frequency dynamics

p value will move to the right (0.4)

does crossing over change allele frequency?

won’t do anything to a single locus (if A is independent to B)

probability: AND

multiply the probabilities

probability of rolling 1 and a 2

(1/6)(1/6) + (1/6)(1/6) = 2/36

can tell mating is random from allele frequency because…

p², 2pq, q² all correspond