Determinants of Genetic Variation in Genomes (Mutation (Fixation…
Determinants of Genetic Variation in Genomes
the effect of mutation on fitness, relative to the fitness of WT individuals.
the process of evolutionary change involving the random sampling of genes from the parental generation to produce the offspring generation, causing the composition of the offspring and parental generations to differ
measures the extent to which the fitness of a heterozygote carrier of a mutation is affected, relative to the effect of the mutation on homozygous carriers.
selection that favours one allele over all other alleles of a gene. The frequency of this beneficial allele can rise of can be held in check by recurrent mutations.
a type of natural selection that favours intermediate phenotypes, such as when the population is close to its fitness optimum with respect to the trait.
standing genetic variation
allelic variation that is currently segregating within a population from old mutation events, as opposed to alleles that just arose by new mutation events.
natural selection against deleterious alleles that arise in a population, preventing their increase in frequency
Effective population size
random fluctuations through time in the allele frequencies of a population cause by sampling effect that is strongest in small populations. Drift can overwhelm the determisnistic effects of natural selection if the selective differences between alleles are small
a panmictic population lacks subdivision according to spatial location of genotype, sot hat all parental genotypes potentially contribute to the same pool of offspring.
used to simplify calculations of effective population size, by assuming that the rate of
Poisson distribution: limiting case of the binomial distribution, valid when the probability of an event is very small. The mean and variance of the number of events are then equal.
oalescence is slower than the rate at which alleles switch between different compartments of a structured population as we trace them back in time
a method of reconstructing the history of a sample of alleles from a population by tracing their genealogy back to their most recent common ancestral allele.
coalescence: the convergence of a pair of alleles in a sample to a common ancestral allele, tracing them back in time.
fitness-class coalescent: a version of structured coalescent models of evolution that traces how individuals descend by mutations through different fitness classes, rather than through time.
effect of inbreeding
mode of inheritance/ neutral diversity: variability arising from mutations that have no effect on fitness
age and stage structure
change in population size
stochastic fluctuations in allele frequencies in a population caused by repeated hard selective sweeps. Hypothesized to be the primary source of stochastic variation in allele frequencies in large populations, in which the sampling effects of genetic drift are relatively weak compared with smaller populations.
marked reductions in population size followed by the survival and expansion of a sample of the original population. it often results in the loss of genetic variation and a skewed site frequency spectrum
the effect of selection on variation at one location in the genome and on evolution at other genetically linked sites.
fixation of a single new beneficial mutation
fixation of selectively equivalent alleles that occur at intermediate frequency in the population at the onset of selection.
partial sweep (polygenic selection)
adaptation by polygenic selection causes an increase in the frequency of alleles at many loci, but selection does not necessarily drive fixation at any given locus.
the process by which selection against deleterious mutations also eliminates neutral or weakly selected variants at closely linked sites in the genome
when recombination fails to break down linkage disequilibrium between alleles at selected loci, the ability of selection to act on these alleles tends to be reduced.
the process by which a neutral, or in some cases deleterious, mutations may change in population frequency owing to linkage with a selected mutation.
also known as nonsynonymous sites, these are any nucleotides within a gene at which a point mutation can alter the encoded amino acid sequence. models of molecular evolution account for different possible degeneracies of such sites in codons.
a measure of whether alleles at two loci coexist in a population in a nonrandom fashion. Alleles that are in linkage disequilibrium are found together on the same haplotype more often than would be expected under free recombination