lecture 4

Question 1

what is wrights coefficient of in breed?

Answer 1

• A statistic to estimate the level of inbreeding - how to calculate the inbreeding coefficient

Question 2

what is IBD? what does inbreeding increase?

Answer 2

• IBD- identical by descent - thinking of the alleles and where they are coming from, especially if there is a history of inbreeding in the lineage
  ○ Inbreeding = more homozygosity less hetero
  Looking at how the alleles are distrubuted

Question 3

IBD COEFFICIENT?

Answer 3

The coefficient is F

Question 4

TYPES OF close INBREEDING?

Answer 4

parent child, full sib mating, half sib mating, uncle niece mating, aunt nephew mating

Question 5

types of cousin inbreeding?

Answer 5

first, second, third

Question 6

how to calculate F?

Answer 6

f= (1/2)^I
○ i = the number of individuals that lie in the loop up through the common ancestor and down again not counting the inbred person
* Lower coefficient = lower genetic risk, less inbreeding, more heterozygosity

Question 7

when is F=1? F=0?

Answer 7

• If there are no heterozygotes in the loop = f=1 (the highest it could be)
  In HW equilibrium - F= 0 - bc assumes no inbreeding

Question 8

What if there is more than one loop for inbreeding ?

Answer 8

do sum of F

Question 9

What if ancestors have their own inbreeding coefficient?

Answer 9

F= sum (1/2)^i (1+FA)
○ When common ancestors are inbred, the
inbreeding coefficient increases.
○ FA is the inbreeding coefficient of the common ancestor in any given path,
and these results are summed over all possible paths.

Question 10

• Inbreeding and genotype frequencies?

Answer 10

• Not evolutionarily driven
  
  • We only focused on homozygous for inbreeding

Question 11

what is the proportion of ppluation not inbred?

Answer 11

• 1-F
  
  • Identity by state: the two alleles do NOT come from a common ancestor
  • The probability of having the genotype AA is p^2
    The probability of not being inbred is 1-F

Question 12

probability of getting AA and not being inbred?

Answer 12

p2 (1-F)

Question 13

genotype freq for identity by descent- having the A allele

Answer 13

P2 +pqF

Question 14

inbreeding genotype formulas

Answer 14

Expected frequency of genotype AA = p2 + pqF
Expected frequency of genotype Aa = 2pq(1-F)
Expected frequency of genotype aa = q2 + pqF
When there is no inbreeding (F=O) the equation reduces to Hardy-Weinberg equilibrium.

Question 15

what is effective population size (Ne)

Answer 15

• The breeding population size in an idealized population where a number of conditions (such as equal sex ratio and constancy in population size) apply
  
  • Formulas for effective population size allow deviations from these assumptions to be taken into account estimating the true breeding size of the population
    ○ Ex. Could be used in the study of ancient DNA - did not study every single individual and you cannot make assumptions about the entire population

Question 16

what id heterozygousity

Answer 16

• The proportion of heterozygotes in a population
  
  • when there are only two alleles, the heterozygosity is H=2pq