population genetics

Question 1

what is Population genetics

Answer 1

• The genetic structure of a population (a group of individuals from the same species that interbreed)
• describes how genetic transmission happens between a parents and offspring, i.e. the relationship between the genotype of the parents and the offspring in a population

Question 2

what is Genetic structure a combination of

Answer 2

gene (allele) + genotype frequencies
- Frequencies change in time + space – results in variation in population structure

Question 3

Heterozygosity definition

Answer 3

the proportion of individuals carrying different alleles at each loci - can be positively correlated with fitness

Question 4

Allelic diversity / richness definition

Answer 4

number of different alleles in the population adjusted by sample size
* more sensitive of population bottlenecks + loss of genetic diversity

Question 5

why is Estimating genetic diversity difficult

Answer 5

Loss of genetic variability is usually difficult to measure - takes place over various generations

Question 6

how is homozygosity and heterozygosity shown in the equation under Hardy Weinberg equilibrium

Answer 6

F(A)=p F(a)=q (aleles)
Homozygotes p2, q2
Heterozygotes 2pq

Question 7

Allele frequency definition

Answer 7

the number of each allele in the population

Question 8

how are genotype and allele frequencies denoted when Describing genetic diversity

Answer 8

algebraically
- genotype freq : P, Q, R (AA = P, Aa = Q, aa = R)
- allele (single letter) : p, q (A = p, a = q) - p + q = 1

Question 9

calculate gene/allele frequencies from genotype frequencies

Answer 9

p= P + ½Q
q = R + ½Q

Question 10

example of how to calculate genotype + allele frequency from simple info

Answer 10

• Alleles: a=white A=purple (co-dominant)
• Genotypes: aa=white AA=purple Aa=light purple
• 1000 plants: 200 white, 300 purple, 500 light purple
  Genotype freqs:
  >aa=200/1000=0.2 - Aa=500/1000=0.5 - AA=300/1000=0.3
  Allele freqs: (2000 alleles - diploid organism)
  >a=400+500/2000=900/2000=0.45
  >A=600+500/2000=1100/2000=0.55

Question 11

example 2 of how to calculate Allele frequency from genotype frequency

Answer 11

• Genotype frequency: AA Aa aa
  Frequency of AA = 3/8 = 0.375 (P)
  Aa = 3/8 = 0.375 (Q)
  aa = 2/8 = 0.25 (R)
• allele frequency:
  Frequency of A = 9/16 = 0.5625
  a = 7/16 = 0.4375

Question 12

how do genotype frequencies need to be to conform to Hardy-Weinberg equilibrium

Answer 12

under random mating & in the absence of selection

Question 13

what is Hardy-Weinberg equilibrium

Answer 13

genotype frequencies in the population have reached a stable condition

Question 14

what is Hardy-Weinberg model

Answer 14

a neutral model we fit to our data set - its assumptions in reality are rarely met - some are impossible - would violate laws of thermodynamics

Question 15

what is the assumption of HWE

Answer 15

A single generation of random mating establishes genotype (and allele) frequencies which remain stable in future generations (HW equilibrium)

Question 16

what are the 7 assumptions that variation is maintained with in the HWE

Answer 16

1.Diploid system
2. Sexual reproduction
3. Random mating with all other individuals in the population
4. No mutation of the alleles under consideration
5. No natural selection on the alleles under consideration
6. No migration with other populations
7. The population is infinitely large
**describes an ideal population

Question 17

what are outliers

Answer 17

markers that appear to be under selection - high FST
values, not in HWE etc
**FST test assumes HWE - so violate the assumptions

Question 18

what are neutral genetic markers

Answer 18

• infer NO fitness advantage (often, but not always in HWE)
• Useful investigating processes such as gene flow, migration or dispersal

Question 19

what are non-neutral genetic markers

Answer 19

• DO infer fitness (dis)advantage may lead to divergent selection among populations (likely to be out of HWE).
• Useful for studying adaptation, sexual selection, evolution etc
• probably the stuff you all find more exciting

Question 20

explain the sexual reproduction assumption in HWE

Answer 20

Sexual reproduction at the molecular level = production of haploid gametes (meiosis), followed by the union of two gametes from two different parents to form a new diploid offspring (syngamy)

Question 21

meiosis definition

Answer 21

duplication of genetic material and production of haploid gametes

Question 22

recombination definition

Answer 22

crossing over of chromatids to exchange genetic material - results in the reshuffling of genes so gametes contain a different set of alleles than either of the original parental chromosome

Question 23

explain the random mating assumption in HWE

Answer 23

• mating pairs will form as if there were random collisions between genotypes
  E.g. if a population was made up of 25% AA, 65% Aa and 10% aa, then among the females that a male could mate with: 25% will be AA, 65% will be Aa and 10% will be aa

Question 24

Panmixis meaning in mating systems

Answer 24

Panmixis = complete interbreeding
Note: mating can be random with respect to certain genes but not with respect to others
E.g. people may mate randomly with respect to blood type, but not with respect to hair colour

Question 25

what is Assortative mating in mating systems

Answer 25

• positive assortative mating = individuals may choose to mate with genetically similar individuals
• negative assortative mating = individuals may choose to mate with genetically dissimilar individuals
  E.g. mice prefer to mate with mice with a different body odour from themselves

Question 26

what is Inbreeding

Answer 26

non-random mating of individuals more closely related than expected by chance - depends on population size

Question 27

what is Inbreeding depression

Answer 27

decline in the value of a trait related to fitness as a direct consequence of inbreeding
- Increase in the frequency of recessive harmful allele
- Increase of homozygosity when heterozygotes have advantage

Question 28

explain the mutation assumption in HWE

Answer 28

• New variation is produced by mutation
• mutation is rare for 2 reasons:
  >DNA repair mechanisms are efficient
  >Most mutations are harmful - only mutations not harmful (or weakly harmful) will persist
• Different proteins have different rates of change (mutation) & are under different selective constraints
• Mutation alone will change allele frequencies only very slowly

Question 29

explain the natural selection assumption in HWE

Answer 29

• Natural selection = alleles that enhance survival and reproduction will increase in frequency
• For most ecological applications information from genetic loci which are not under strong selective forces is required - i.e., “neutral molecular markers”

Question 30

explain the migration assumption in HWE

Answer 30

• Migration = movement of individuals between populations or subpopulations - potentially brings new alleles into a population
• Migration has a homogenizing effect between populations — if individuals reproduce! (gene flow)
• Gene flow limits among population genetic differences

Question 31

explain the infinitely large population size assumption in HWE in terms of Effective population size (Ne)

Answer 31

• N = total number of individuals in a population - Simplistic representation since not all individuals may produce offspring (e.g. many may be juveniles)
• Ne of a population = the size of an “ideal” (i.e one that meet HWE assumptions) population that would lose heterozygosity (i.e inbreed) at a rate equal to the observed population
• Minimum Ne = minimum number of individuals needed to maintain genetic variability
• Traditionally: 50/500 rule
  >50 refers to minimum short term Ne to avoid inbreeding effects
  >500 refers to minimum Ne to avoid the loss of genetic variation and evolutionary potential
  >Revised: 100/1000

Question 32

what can be used to describe Population’s genetic diversity

Answer 32

He (expected heterozygosities)
Ar (allelic richness)
Ne (size of an “ideal” theoretical population)