population genetics

Question 1

what is population genetics

Answer 1

the genetic structure of a population

Question 2

define population

Answer 2

a group of individuals from the same species that interbreed

Question 3

what does population genetics describe

Answer 3

how genetic transmission happens between a parent and offspring - the relationship between the genotype of the parents and the offspring in a population

Question 4

what does genetic structure explore (2 pieces of info)

Answer 4

gene (allele) frequencies and genotype frequencies

Question 5

why is loss of genetic variability hard to measure

Answer 5

usually occurs after over various generations

Question 6

what is heterozygosity

Answer 6

proportion of individuals carrying different alleles at each of one (or several) loci

Question 7

how are heterozygosity and fitness related

Answer 7

positively

Question 8

under Hardy-Weinberg, how are heterozygotes represented

Answer 8

p^2 + q^2 (pp + qq)

Question 9

under Hardy-Weinberg, how are homozygotes represented

Answer 9

2pq

Question 10

what is allelic diversity (richness)

Answer 10

the number of different alleles in the population adjusted by sample size

Question 11

example HWE:
co-dominant alleles: a=white, A = purple
genotypes: aa = white, Aa = light purple, AA = purple
plants: 200 white, 500 light purple, 300 purple
work out allele frequencies

Answer 11

500 + 300 + 200 = 1000 genotypes, 2000 alleles
genotype freq: aa = 0.2, Aa = 0.5, AA = 0.3
allele freq: a = 200 + 200 + 500 = 900 / 2000 = 0.45
A = 300 + 300 + 500 = 1100 / 2000 = 0.55

Question 12

what are the 2 HW equations

Answer 12

p + q = 1
p^2 + q^2 + 2pq = 1

Question 13

what are the assumptions of the HWE

Answer 13

diploid system,
sexual reproduction only,
random mating with all other individuals in the population,
no mutations of the alleles being considered,
no natural selection of the alleles being considered,
no migration with other populations,
the population is infinitely large

Question 14

what are outliers

Answer 14

markers that appear to be under selection (high FST), not in HWE

Question 15

what type of markers are likely to be in HWE

Answer 15

neutral markers that infer no fitness advantage

Question 16

why are non-neutral / adaptive markers likely to be out of HWE

Answer 16

markers infer fitness which may lead to divergent selection among populations

Question 17

what are neutral markers useful for studying

Answer 17

gene flow, migration or dispersal

Question 18

what are adaptive markers useful for studying

Answer 18

adaptation, sexual selection and evolution

Question 19

what is sexual reproduction (at molecular level)

Answer 19

production of haploid gametes (meiosis) followed by union of 2 gametes from 2 different parents to form new diploid offspring (syngamy)

Question 20

what occurs during meiosis

Answer 20

duplication of genetic material and production of haploid gametes

Question 21

what is recombination

Answer 21

crossing over of chromatids to exchange genetic material in the reshuffling of genes so gametes contain different set of alleles than either of the original parent chromosomes

Question 22

what happens in random mating

Answer 22

mating pairs will form as if there were random collisions between genotypes

Question 23

if a population was made up of 25% AA, 65% Aa and 10% aa then (according to random mating) what will be the genotypes of the females that a male could mate with

Answer 23

25% AA
65% Aa
10%aa

Question 24

what is panmixis

Answer 24

complete interbreeding

Question 25

mating can be random with respect to certain genes but not with respect to others, give an example

Answer 25

people may mate randomly with respect to blood type, but not in respect of hair colour

Question 26

what is assortative mating

Answer 26

individuals may choose to mate with genetically similar individuals (positive assortative mating) or with genetically dissimilar individuals (negative assortative mating)

Question 27

give an example of assortative mating

Answer 27

mice prefer too mate with mice with a different body odour from themselves

Question 28

what is inbreeding

Answer 28

non-random mating of individuals ore closely related than expected by chance, dependent on population size

Question 29

what is inbreeding depression

Answer 29

decline in the value of a trait related to fitness as a direct consequence of inbreeding

Question 30

what are 2 effects of inbreeding depression

Answer 30

increase in freq of recessive deleterious allele increase of homozygosity when heterozygotes have advantage

Question 31

why are mutations rare

Answer 31

DNA repair mechanisms are efficient most mutations are deleterious, only mutations not deleterious will persist

Question 32

do all proteins mutate at the same rate

Answer 32

no

Question 33

what happens in natural selection

Answer 33

alleles which enhance survival and reproduction will increase in frequency

Question 34

define migration

Answer 34

movement of individuals between populations or subpopulations

Question 35

what is the relevance of migration to allele populations

Answer 35

can potentially bring new alleles into a population

Question 36

what does N represent in effective population size

Answer 36

total number of individuals in a population

Question 37

what is the issue with using N

Answer 37

simplistic representation as not all individuals may produce offspring (e.g. juveniles)

Question 38

what does Ne represent

Answer 38

the size of an ideal theoretical population that would show the same rate of increase in inbreeding as the population in question

Question 39

what is the minimum Ne

Answer 39

the minimum number of individuals needed to maintain genetic variability

Question 40

explain the 50/500 rule for the minimum Ne

Answer 40

50 = minimum short-term Ne to avoid inbreeding effects 500 = minimum Ne to avoid loss of genetic variability and evolutionary potential

Question 41

who came up with the 50/500 rule and when

Answer 41

Franklin, 1980

Question 42

what is the revised Ne rule and who / when was it established

Answer 42

100/1000 rule Frankham 2014

Question 43

what is He

Answer 43

expected heterozygosity

Question 44

what is Ar

Answer 44

allelic richness

Question 45

what is Ne

Answer 45

effective population size

Question 46

what does it show if the heterozygosity expected is much higher than the heterozygosity observed

Answer 46

the population is out of Hardy Weinberg equilibrium

Question 47

what is Ho

Answer 47

heterozygosity observed

Question 48

what is Phwe

Answer 48

the probability of conformance to HWE

Question 49

what does heterozygosity mean in terms of gene diversity

Answer 49

heterozygosity = gene diversity

Question 50

what is loss of heterozygosity (LOH) often associated with

Answer 50

cancer development

Question 51

what is true of BRAC1 and BRAC2 genes (regulate cell growth) in breast cancer

Answer 51

the genes show reduced heterozygosity

Question 52

what is Fis and define

Answer 52

inbreeding coefficient = probability that an individual has 2 alleles at a particular locus that recently descended from a single common ancestor

Question 53

what is the range of values that Fis can take on

Answer 53

0 (no inbreeding) - 1 (full inbreeding)

Question 54

what is Fit and define

Answer 54

the overall inbreeding coefficient = compares heterozygosity of an individual to that of the total population under consideration; influenced by Fis and Fst

Question 55

what is Fst

Answer 55

the probability that 2 random gametes (or genes) drawn from the same subpopulation will be identical by descent, relative to gametes taken from the entire population

Question 56

what is the most common measurement used to describe the genetic differentiation of populations

Answer 56

Fst

Question 57

what is the scale for Fst values

Answer 57

0 (complete panmixia) - 1 (complete genetic differentiation)

Question 58

what is Hi

Answer 58

average observed heterozygosity across subpopulations

Question 59

what is Hs

Answer 59

average expected heterozygosity across subpopulations

Question 60

what is Ht

Answer 60

expected heterozygosity of total population

Question 61

how do you calculate Fis

Answer 61

= (Hs - Hi) / Hs

Question 62

how do you calculate Fit

Answer 62

= (Ht - Hi) / Ht

Question 63

how do you calculate Fst

Answer 63

= (Ht - Hs) / Ht

Question 64

when is inbreeding not so important

Answer 64

when there is no mate choice e.g. endangered species, if a species has incredibly high genetic diversity, can be beneficial to keep some traits e.g. seagrass is huge colony of perfectly adapted plants

Question 65

who came up with F statistics

Answer 65

Sewall Wright, 1951

Question 66

what does an Fst of 0 mean

Answer 66

no differentiation

Question 67

what does an Fst of 1 mean

Answer 67

fixation for different alleles in different subpopulations

Question 68

what are the Fst values for moderate genetic differentiation

Answer 68

0.05-0.15

Question 69

what are the Fst values for great genetic differentiation

Answer 69

0.15-0.25

Question 70

what are the Fst values for very great genetic differentiation

Answer 70

>0.25

Question 71

do adaptive markers often have high or low Fst

Answer 71

high