Lecture 5- Population genetics I

Question 1

what is population genetics

Answer 1

the study of genetic diversity within a population, usually within a species

Question 2

what is a genetic marker

Answer 2

genomic regions which are useful for investigating and measuring variation

Question 3

at what point is a population deemed to be polymorphic?

Answer 3

when there is variation at an allele in ~1-5% of the population

Question 4

measures of sequence diversity that can be used

Answer 4

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

Question 5

variable h

Answer 5

fraction of individuals expected to be heterozygous, equivalent to the probability that 2 alleles at a randomly sampled point will be different

Question 6

h equation

Answer 6

1-(sum of allele frequencies)^2

Question 7

what does ‘average heterozygosity (h)’ represent

Answer 7

proportion of loci that are heterozygous in an average individual

Question 8

what is HW equation useful for

Answer 8

predicting genotype frequencies from allele frequencies

Question 9

some assumptions of HW (there’s 9 here- don’t need to name them all)

Answer 9

○ 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

Question 10

how do you interpret a HW result?

Answer 10

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

Question 11

mutation levels vs genome size

Answer 11

mutation levels inversely proportional to genome size- higher genome size > lower mut rate

Question 12

what does linkage disequilibrium mean for inheritance

Answer 12

inheritance of genes on the same chromosome is not independent due to nonrandom inheritance of genes in closer contact

Question 13

how does LD change across generations

Answer 13

becomes less impactful due to recombination and random assortment of these recombined chromosomes

Question 14

why can inbreeding be bad

Answer 14

increases the frequency of homozygotes- can lead to inbreeding depression where this homozygosity extends to deleterious, recessive alleles

Question 15

example of where inbreeding depression can be seen

Answer 15

dogs- australian shepherds have a lower survival rate

Question 16

impact of drift on homozygosity

Answer 16

often leads to fixation of a homozygous allele, especially in small populations

Question 17

what is the founder effect

Answer 17

reduction in genetic diversity when a new subset of a population splits off from a larger one

Question 18

examples of the founder effect

Answer 18

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

Question 19

what is effective population size (Ne)

Answer 19

number of individuals which contribute genetically to a population, likely to be different from the census size

Question 20

what is an ‘island model’

Answer 20

model of how migration impacts gene flow, generally leading to more diversity within- but less among- populations. alleles will likely converge under these

Question 21

fixation index (FST)

Answer 21

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

Question 22

what are clustering algorithms + example

Answer 22

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