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BIO235 > population genetics > Flashcards

population genetics Flashcards

1
Q

what is population genetics

A

the genetic structure of a population

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2
Q

define population

A

a group of individuals from the same species that interbreed

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3
Q

what does population genetics describe

A

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

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4
Q

what does genetic structure explore (2 pieces of info)

A

gene (allele) frequencies and genotype frequencies

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5
Q

why is loss of genetic variability hard to measure

A

usually occurs after over various generations

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6
Q

what is heterozygosity

A

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

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7
Q

how are heterozygosity and fitness related

A

positively

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8
Q

under Hardy-Weinberg, how are heterozygotes represented

A

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

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9
Q

under Hardy-Weinberg, how are homozygotes represented

A

2pq

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10
Q

what is allelic diversity (richness)

A

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

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11
Q

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

A

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

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12
Q

what are the 2 HW equations

A

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

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13
Q

what are the assumptions of the HWE

A

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

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14
Q

what are outliers

A

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

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15
Q

what type of markers are likely to be in HWE

A

neutral markers that infer no fitness advantage

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16
Q

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

A

markers infer fitness which may lead to divergent selection among populations

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17
Q

what are neutral markers useful for studying

A

gene flow, migration or dispersal

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18
Q

what are adaptive markers useful for studying

A

adaptation, sexual selection and evolution

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19
Q

what is sexual reproduction (at molecular level)

A

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

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20
Q

what occurs during meiosis

A

duplication of genetic material and production of haploid gametes

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21
Q

what is recombination

A

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

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22
Q

what happens in random mating

A

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

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23
Q

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

A

25% AA
65% Aa
10%aa

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24
Q

what is panmixis

A

complete interbreeding

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25
Q

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

A

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

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26
Q

what is assortative mating

A

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

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27
Q

give an example of assortative mating

A

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

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28
Q

what is inbreeding

A

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

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29
Q

what is inbreeding depression

A

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

30
Q

what are 2 effects of inbreeding depression

A

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

31
Q

why are mutations rare

A

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

32
Q

do all proteins mutate at the same rate

A

no

33
Q

what happens in natural selection

A

alleles which enhance survival and reproduction will increase in frequency

34
Q

define migration

A

movement of individuals between populations or subpopulations

35
Q

what is the relevance of migration to allele populations

A

can potentially bring new alleles into a population

36
Q

what does N represent in effective population size

A

total number of individuals in a population

37
Q

what is the issue with using N

A

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

38
Q

what does Ne represent

A

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

39
Q

what is the minimum Ne

A

the minimum number of individuals needed to maintain genetic variability

40
Q

explain the 50/500 rule for the minimum Ne

A

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

41
Q

who came up with the 50/500 rule and when

A

Franklin, 1980

42
Q

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

A

100/1000 rule
Frankham 2014

43
Q

what is He

A

expected heterozygosity

44
Q

what is Ar

A

allelic richness

45
Q

what is Ne

A

effective population size

46
Q

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

A

the population is out of Hardy Weinberg equilibrium

47
Q

what is Ho

A

heterozygosity observed

48
Q

what is Phwe

A

the probability of conformance to HWE

49
Q

what does heterozygosity mean in terms of gene diversity

A

heterozygosity = gene diversity

50
Q

what is loss of heterozygosity (LOH) often associated with

A

cancer development

51
Q

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

A

the genes show reduced heterozygosity

52
Q

what is Fis and define

A

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

53
Q

what is the range of values that Fis can take on

A

0 (no inbreeding) - 1 (full inbreeding)

54
Q

what is Fit and define

A

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

55
Q

what is Fst

A

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

56
Q

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

A

Fst

57
Q

what is the scale for Fst values

A

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

58
Q

what is Hi

A

average observed heterozygosity across subpopulations

59
Q

what is Hs

A

average expected heterozygosity across subpopulations

60
Q

what is Ht

A

expected heterozygosity of total population

61
Q

how do you calculate Fis

A

= (Hs - Hi) / Hs

62
Q

how do you calculate Fit

A

= (Ht - Hi) / Ht

63
Q

how do you calculate Fst

A

= (Ht - Hs) / Ht

64
Q

when is inbreeding not so important

A

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

65
Q

who came up with F statistics

A

Sewall Wright, 1951

66
Q

what does an Fst of 0 mean

A

no differentiation

67
Q

what does an Fst of 1 mean

A

fixation for different alleles in different subpopulations

68
Q

what are the Fst values for moderate genetic differentiation

A

0.05-0.15

69
Q

what are the Fst values for great genetic differentiation

A

0.15-0.25

70
Q

what are the Fst values for very great genetic differentiation

A

> 0.25

71
Q

do adaptive markers often have high or low Fst

A

high

BIO235 (12 decks)

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