population genetics pt.2

Question 1

main steps to quantify population genetics

Answer 1

1. genotype samples
2. calculate genotype freqs
3. calculate expected genotype freqs
4. H0, He Ht
5. F-statistics - FIS, FIT, FST

Question 2

what is heterozygosity

Answer 2

gene diversity
- Heterozygosity is at the centre of population genetics- both mathematically & important to living organisms in general
- Gets much more complicated outside of diploid organisms

Question 3

how does heterozygosity relate to cancer

Answer 3

• Heterozygosity of cell lines
• Loss of heterozygosity (LOH) is a common in cancer development - can result in inactivation of tumor suppressor genes or the activation of oncogenes
• BRCA1 and BRCA2 genes show reduced heterozygosity in breast cancer tumours
• Many diseases associated with increased homozygosity - recessive alleles

Question 4

who developed F-statistics and what are they

Answer 4

• Sewell- Wright (1951)
• Associated with levels of inbreeding
  The F- statistics: FIS FIT FST

Question 5

what is the FIS F-statistics

Answer 5

FIS = (Hs – Hi)/ H
- FIS = inbreeding coefficient (also designated F)
- In diploid species = probability that an individual has two alleles at a particular locus that recently descended from a single common ancestor
- FIS value ranges from 0 (no inbreeding) to 1 (full inbreeding)

Question 6

what is the FIT F-statistics

Answer 6

FIT = (Ht – Hi)/ Ht
- FIT = overall inbreeding coefficient
- compares the heterozygosity of an individual to that of the total population under consideration
- influenced by FIS and FST

Question 7

what is the FST F-statistics

Answer 7

FST = (Ht – Hs)/ H
- FST = probability that two random gametes (or genes), drawn from the same subpopulation, will be identical by descent, relative to gametes taken from the entire population
- AKA measure of genetic differentiation between two separate populations due to genetic drift
- Most common measurement used to describe genetic differentiation of population
- Scale of 0 (complete panmixia) to 1 (complete genetic differentiation in different subpopulations)
- Often (although not always) correctly inferred as surrogate for level between 2 species

Question 8

what guidelines did Wright suggest for interpreting FST values

Answer 8

• 0-0.05: little genetic differentiation (note, if FST is not zero, there is still non-negligible differentiation)
• 0.05-0.15: moderate genetic differentiation
• 0.15-0.25: great genetic differentiation
• > 0.25: very great genetic differentiation
  **This assumes markers are in HWE

Question 9

what is HI, Hs and Ht in the F-statistic equations

Answer 9

• HI = the average observed heterozygosity across subpopulations
• Hs = the average expected heterozygosity across subpopulations
• Ht = the expected heterozygosity of the total population

Question 10

what is I, S and T in the F-statistics

Answer 10

• I = individual
• S = subpopulation
• T = total population
  >FIT = individual + Total population
  >FST = subpopulation + total population
  >FIS = individual + subpopulation

Question 11

reasons Many species avoid inbreeding

Answer 11

• Increase in the frequency of recessive harmful allele
• Increase of homozygosity when heterozygotes have advantage

Question 12

reasons inbreeding isn’t always bad

Answer 12

• Not all individuals have a mate choice - rare / endangered species
• Sometimes if a species has a high enough genetic diversity - not a huge deal
• Sometimes helpful to keep beneficial traits e.g. Seagrass - huge colonies (clone themselves) - already perfectly adapted
• Hymenoptera males only one copy of chromosomes - quickly remove harmful alleles
• Investment in offspring