Lecture 5- Population genetics I Flashcards
what is population genetics
the study of genetic diversity within a population, usually within a species
what is a genetic marker
genomic regions which are useful for investigating and measuring variation
at what point is a population deemed to be polymorphic?
when there is variation at an allele in ~1-5% of the population
measures of sequence diversity that can be used
proportion of variable sites- or number of distinct sequences
average pairwise difference between all possible pairs of individuals in your sample
-can also calculate difference per site
variable h
fraction of individuals expected to be heterozygous, equivalent to the probability that 2 alleles at a randomly sampled point will be different
h equation
1-(sum of allele frequencies)^2
what does ‘average heterozygosity (h)’ represent
proportion of loci that are heterozygous in an average individual
what is HW equation useful for
predicting genotype frequencies from allele frequencies
some assumptions of HW (there’s 9 here- don’t need to name them all)
○ Diploid organism w sexual reproduction, random, independent chromosome transmission
○ Non-overlapping generations
○ Infinite population size w no genetic drift
○ Random mating
○ M and F have same closed pop w no migration
○ M and F equal allele frequencies
○ No migration
○ No mutation
No selection
how do you interpret a HW result?
equilibrium is reached quite readily in the absence of evolutionary force, if there is disequilibrium, there is probably an evolutionary force acting on the population
mutation levels vs genome size
mutation levels inversely proportional to genome size- higher genome size > lower mut rate
what does linkage disequilibrium mean for inheritance
inheritance of genes on the same chromosome is not independent due to nonrandom inheritance of genes in closer contact
how does LD change across generations
becomes less impactful due to recombination and random assortment of these recombined chromosomes
why can inbreeding be bad
increases the frequency of homozygotes- can lead to inbreeding depression where this homozygosity extends to deleterious, recessive alleles
example of where inbreeding depression can be seen
dogs- australian shepherds have a lower survival rate
impact of drift on homozygosity
often leads to fixation of a homozygous allele, especially in small populations
what is the founder effect
reduction in genetic diversity when a new subset of a population splits off from a larger one
examples of the founder effect
higher disease prevalences in some human populations (Amish- genetic syndrome causing polydactyly, heart defects, short stature)
some wild felids- issues with bottlenecks, more vulnerable to extinction
what is effective population size (Ne)
number of individuals which contribute genetically to a population, likely to be different from the census size
what is an ‘island model’
model of how migration impacts gene flow, generally leading to more diversity within- but less among- populations. alleles will likely converge under these
fixation index (FST)
fraction of genetic diversity related to differences among populations
FST = 0- no divergence and frequent migration
FST = 1- complete divergence, likely no migration
proportional to- and therefore can be calculated using- heterozygosity levels
what are clustering algorithms + example
algorithms used to help identify subgroups of a population using genetic data
STRUCTURE program- was used to split an endangered tree into populations, useful information for conservation
