Pop Gen

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mutation

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ultimate source of genetic variation

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mutation includes

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includes a change in the nucleotide sequence of a single gene as well as the formation of a new chromosome rearrangement

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transpsable elements

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DNA sequence that is able to replicate and insert into any of a large number of sites in the genome
Barbara Mclintock

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transpoable elements II

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if a transposable element is inserted in/near a gene, it can alter the level/pattern of gene expression. it can also alter recombination btwn transposable elements, which leads to chromosome rearrangment

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Irreversible mutation

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initial freq is low in a lg pop, a single mutant allele in a diploid pop of size n = 1/(2n)

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recurrent mutation

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alone, increases the freq mutant allele in a pop very slowly
gen 1 = 1(2n)
gen 2 = 2/(2n)
gen 3 = 3/(2n)

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mutation pressure

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tendency for allele freq to change as a result of recurrent mutations

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HWE = violation

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no mutations, but mutations have no influence on natural selection. however mutation must be irrevesible

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chemostat

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used for maintaining a pop of bacteria in continuous culture

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reversible mutations

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mutation pressure on the allele frq pushes in both directions, eventually will reach an equilibrium where the freq of p remains constant from gen to gen

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Neutral Theory of Molecular Evolution

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many genetic polymorphisms result from sevectively neutral alleles maintained by a balance between effects of mutation and random genetic drift

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selection in haploid organism

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`selection acts on phenotype, not the genotype
`selection is realized as differential pop growth
`doesnt matter if it is discrete or continuous

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discrete model

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darwinian fitness

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Continuous model

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Malthusian fitness

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Selection in a Diploid Organism

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Viability, sexual selection, meiotic drive, gametic selection, and fecundity selection

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Viability

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diff genotypes can have diff rates of development and diff probabilities of survival to adulthood

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Sexual selection

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adults must be able to attract mates, diff in genotypes

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Meiotic drive

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when heterozygotes produce gametes that may not use mendelian segragation

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Gametic selection

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differential survival of haploid cell

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Fecundity selection

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once mated, genotypes can produce diff # of offspring

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assumptions of natural selection

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infinite size, no mutations, no migrations, random mating, fitness is constant, selection only takes place through differential zygote survival of diploid genotypes

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relative fitness

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relative fitness of genotypes choosen as standard comparison will be equal to 1

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locally stable

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allele freq moves closer and closer to equilibrium in subsequent generations

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globally stable

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allele freq move toward equilibrium no matter where they started

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balanced polymorphisms

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polymorphisms w/a stable equilibrium

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unstable

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initailly close equilibrium but then in moves away

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semistable

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no tendency to change

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overdominance

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heterozygous genotypes have a higher fitness than either homozygote

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heterozygote inferiority

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fitness of heterozygote is less than that of both homozygotes

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Pleitropy

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gene having multiple effects

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differential selection in the sexes

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some genes may have diff effects in the two sexes

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freq dependent selection

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this is when fitness is a function of either allele freq or genotypic freq. fitness of each decreases in proportion to its freq

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Density dependent selection

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fitnesses are functions of pop sizes

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fecundity selection

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deff in fitness between the genotypes results from the differeing abilites of mating pairs to produce offspring. # of fitness parameters equals # of distinct kinds of mating pairs

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heterogeneous environments

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models in which relative fitness is changed according to the environment, changes can be spacial or temporal

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marginal overdominance

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each homozygous is favored in a diff subset of environments

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cline

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geographical trend in allele freq. result of migration or selection

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gametic selection

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when haploid phase of the life cycle is exposed to selection

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epistasis

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genetic effects of diff loci that contribute to a phenotypic thrait are not additive

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kin selection

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relatives have genes in common

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inclusive fitness

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taking in account not only your an organisms fitness, but its relatives fitness

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Neutral theory

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Kimuura suggested that most polymorphims observed at the molecular level are selectively neutral

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Theoretical principles of neutral theory

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kimuura knew mutations could have an effect on fitness. he thought that they could be eliminated or deleterious or invery rare cases-favorable and then become fixed

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neutral theory main principles

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1. pop has neutral allele w/freq of P0, prob allele becomes fixed = P0, initial freq = P0 = 1/(2n)
2. neutral mutation rate = m
3. ave time that occurs between nuetral substitutions = 1/m
4. on ave nuetral mutations will become fixed over a long period of time but if they are to be lost, they will be lost very quickly
5. infinite alleles model-model of mutation in which each new allele is novel

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rate of amino acid replacement

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several substitutions/yr/genome

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molecular clock

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the ave. rate of molecular evolution. it is usually uniform throughout long periods of evolutionary time

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variation among genes in the rate of the molecular clock

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molecular clock ticks diff for diff genes some protiens are very tolerant of substitutions whereas others can have deletorious effects from even 1 to a few changes genes who are buffered from the environmnet usually have a slower rate of mutation

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Generation time effect

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molecular clock data is usually constant over a time scale measured in years, not generations. exceptions rodents have faster clock than primates

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gene genealogies

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tress can be constructed from the sequences of genes from diff species and from sequences of alleles form a single species gene genealogie