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Introduction to Human Genetics > Population Genetics > Flashcards

Population Genetics Flashcards

1
Q

Define population genetics

A

The study of diversity within and across populations along with its causes and implications

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2
Q

What is population genetics required for?

A

For establishing the evolutionary relationships between populations and thus, human population diversity.

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3
Q

What 5 things does population genetics incorporate?

A

Migration patterns (local, regional, global), relatedness of different populations, mating patterns, admixture, natural selection

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4
Q

What is admixture?

A

Genetic admixture occurs when individuals from two or more previously separated populations begin interbreeding.

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5
Q

What are the consequences of admixture?

A

Admixture results in the introduction of new genetic lineages into a populations..

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6
Q

How does admixture affect adaptation?

A

Admixture slows down local adaptation by introducing foreign, unadapted genotypes (gene swamping). It also prevents speciation by homogenizing populations.

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7
Q

T/F: Gene frequencies for traits/ diseases may be present in different freqeucnies within populations.

A

True

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8
Q

What does population genetics enable us to do?

A

To map susceptibility factors of a disease onto the genome and offers advantages in genetic counselling and forensics.

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9
Q

What three factors influence genetic diversity?

A

Genetic mechanisms, evolutionary forces, population characteristics.

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10
Q

What are the genetic mechanisms influencing genetic diversity?

A

Mutation and recombination

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11
Q

What are the evolutionary forces influencing genetic diversity?

A

Natural selection and genetic drift

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12
Q

What are the population characteristics?

A

Population size, geographic distribution, mating patterns and migration.

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13
Q

Where is the A allele predominantly distributed?

A

Europe

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14
Q

Where is the B allele predominantly distributed?

A

There is a block of high distribution extending from northern central Russia to the Indian subcontinent.

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15
Q

Where is the O allele predominantly distributed?

A

South America, central America

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16
Q

How was the distribution of the ABO alleles discovered?

A

Using genetic markers which are loci that are frequently heterozygous in a population.

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17
Q

What is the MAF of genetic markers?

A

> 1-5%

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18
Q

How can maternal lineage be traced?

A

Through using mtDNA

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19
Q

How can paternal lineage be traced?

A

Through Y-chromosome haplotype

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20
Q

T/F mtDNA is linear

A

False

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21
Q

How many genes are found on mtDNA?

A

37 genes, required for normal mitochondrial function.

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22
Q

13 mitochondrial genes encode for…

A

enzymes involved in oxidative phosphorylation

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23
Q

Why is mtDNA exclusively inherited maternally?

A

All spermatozoan mitochondria are metabolised upon fertilisation of the oocyte.

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24
Q

T/F: the majority of mtDNA is non-coding

A

False; the majority is coding, however the non-coding region has a high mutation rate and does not recombine.

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25
Q

How can mtDNA be used in gene mapping?

A

The high mutation rate and lack of recombination result in these mutations accumulating on the haplotype, thus enabling related haplotypes to form haplogroyps

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26
Q

What are haplogroups?

A

These are groups of mutations found on mtDNA which share defining variants at key sites.

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27
Q

T/F: The Y chromosome recombines with the X chromosome

A

Neither; only the telomeric pseudoautosomal regions recombine with the X chromosome.

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28
Q

Why is the Y chromosome male specific?

A

The Y chromosome is the chromosomal determinant of males in humans, as their sex chromosomes are XY.

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29
Q

What can mtDNA and Y chromosome haplogroups be used for?

A

To reconstruct the relationship among haplotypes through using mutations. The geographic distribution of lineages can then provide information on the history of populations such as population origin, population age.

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30
Q

How does population age affect mutation number?

A

The number of mutations increases with the age of lineages.

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31
Q

T/F: markers with different mutation rates are informative for different time periods

A

True

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32
Q

What type of mutations are inherited?

A

Germ-line mutations

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33
Q

How are new alleles produced?

A

Mutation

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34
Q

What is mutation pressure?

A

The changing of allele frequencies through mutation

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35
Q

How can haplotype diversity be increased?

A

Meiotic recombination; creates new combinations of alleles on chromosomes, i.e. new haplotypes.

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36
Q

What is Muller’s ratchet?

A

The observation that asexually reproducing species and non-recombining portions of the human genome are prone to degeneration.

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37
Q

Name a genetic advantage of sexual reproduction.

A

In sexual reproduction it takes less time to assemble the fittest genotype as alleles can be combined in parallel whereas in asexual reproduction only one allele can prevail and so combination must occur serially.

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38
Q

T/F: Under independent assortment, the frequency of combined alleles should be equal to the product of the two allele frequencies.

A

True

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39
Q

Name four factors of linkage disequilibrium.

A

Recombination, selection, migration/admixture, genetic drift

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40
Q

Which project utilised LD in creating association maps?

A

The HapMap project

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41
Q

Why would one population have a greater number and size of linkage blocks compared to another?

A

The older population the more recombination has occurred in the genome resulting in less and smaller linkage blocks.

42
Q

Define Genetic Drift

A

The random change in allele frequencies

43
Q

Why is effective population size important?

A

It allows us to compare the amount of genetic drift experienced by different populations. It allows us to calculate the probability and fixation for a new allele in the absence of selection and mutation.

44
Q

Each generation represents….

A

a finite sample from the previous one and so the magnitude of genetic drift relates to population size.

45
Q

What are the differences in allele frequency between a population of N=20 and N=1000?

A

In N=20, the allele rapidly becomes either fixed or lost from the population however when N=1000 both alleles persist in the population.

46
Q

What are the two main processes of genetic drift?

A

Bottlenecks and the founder effect.

47
Q

How does population size affect genetic drift?

A

Genetic drift is stronger in smaller populations, reducing population heterozygosity.

48
Q

`What is the founder effect?

A

the founder effect occurs during the colonisation of a new territory, forming a new population with only a subset of the genetic diversity present in the original population.

49
Q

What are population bottlenecks?

A

Bottlenecks are the reduction in size of a single, previously larger population resulting in a loss of diversity.

50
Q

How do bottlenecks occur?

A

The occur due to a natural disaster, famine or epidemic.

51
Q

What are population isolates?

A

These are small populations isolated from other populations by geography or social reasons.

52
Q

Population isolates perform which genetic diversification process?

A

The founder effect

53
Q

T/F: the founder effect results in a reduced genetic heterogeneity?

A

True

54
Q

What 5 forms of information can population isolates confer?

A

Population-specific disease spectrum, population specific disease alleles, degree of linkage disequilibrium, mendelian disease, complex disease.

55
Q

Name a country where population isolates can be found.

A

Finland.

56
Q

T/F: in Finland is there a reduced Y chromosome diversity?

A

True

57
Q

What four diseases are rare in Finland but prevalent in the rest of Europe?

A

Cystic Fibrosis, Phenylketonuria, Galactosemia, Maple Syrup disease

58
Q

What are the three main “enriched” diseases of Finland?

A

Aspartylglucosaminuria, late infantile neuronal ceroid lipofuscinosis and progressive epilepsy with mental retardation.

59
Q

In Finland 1 mutation is responsible for what percentage of disease alleles?

A

75-98%

60
Q

`How can the differences in allele frequencies be measured?

A

They are measured as differences in heterozygosity using the fixation index.

61
Q

What is the fixation index?

A

Fst is a measure of population differentiation due to genetic structure of a population.

62
Q

What is assumed whilst calculating Fst?

A

That the population is in Hardy-Weinberg equilibrium

63
Q

What does an Fst = 0 indicate?

A

There is no genetic differentiation

64
Q

What does Fst=1 indicate?

A

There is complete genetic differentiation where there is a fixation of alternate alleles.

65
Q

What does Fst indicate?

A

The proportion of genetic variance that is due to population differentiation.

66
Q

Can Fst be used as a measure of genetic distance?

A

Yes, between pairs of populations.

67
Q

What is the Darwinian definition of natural selection?

A

The differential reproduction of genotypes in succeeding generations.

68
Q

How does natural selection manipulate diversity?

A

through selecting: survival into reproductive age, success in attracting a mate, the ability to fertilise, the number of progeny.

69
Q

Define fitness.

A

The ability of an individual genotype to survive and reproduce, partly dependent on the environment.

70
Q

What is negative selection?

A

This is the selection against variants that put their carriers at a disadvantage. This acts against change as it is essential to maintain efficient gene function as it is. This selection is seen in metabolic processes; stabilising.

71
Q

What is positive selection?

A

This is the selection for variants that put their carriers at an advantage which therefore acts in favour of change. Spreads novel adaptations.

72
Q

T/F: Positive selection leaves signatures on the genome?

A

True

73
Q

Name two ancient adaptations which are species specific?

A

Bipedalism and speech

74
Q

Name recent adaptations which are population specific

A

Resistance to infectious disease, skin colour, lactose tolerance and adaptations to altitude

75
Q

What is genetic hitch-hiking and the consequences thereof?

A

As an allele increases in frequency, variants at a nearby location, with an absence of recombination, also increase in frequency. This results in an excess of rare variants compared to other populations.

76
Q

What is another name for hitchhiking?

A

Selective sweeping

77
Q

Name the consequence of selective sweeping.

A

This alters the typical pattern of genetic variation in a region, resulting in the rapid increase of the advantageous variant.

78
Q

Positive selection of a trait…

A

creates a signature consisting of a genomic region with reduced diversity and an excess of rare alleles.

79
Q

What is selective sweeping dependent on?

A

This is dependent on the strength of the selection pressures and therefore the time taken to complete the sweep.

80
Q

What are ancestral alleles?

A

Those which are present in the common ancestor

81
Q

What are derived alleles?

A

Those which are non-ancestral, arising from recent mutations

82
Q

Derived alleles arise because of

A

mutation

83
Q

What can you conclude if a derived allele is found at high frequency?

A

As these alleles are rare to start with, if they are found at a high frequency in a population then this is indicative of a selective sweep.

84
Q

Give an example of a derived allele.

A

The Duffy blood group shows an excess of high frequency derived alleles at the Duffy red cell antigen gene (the FY gene)

85
Q

When did population differences first arise in human populations?

A

less than 50-75000 years ago

86
Q

Name two population differences observed in humans

A

Lactose tolerance and skin colour

87
Q

Why did the LCT locus show a rapid increase in frequency?

A

There was not enough time for haplotype breakdown through recombination resulting in an increase of LD around the LCT region.

88
Q

Where does the melanin pathway occur?

A

Melanocytes

89
Q

What is tyrosine oxidised to first?

A

dopaquinone

90
Q

What are the two possible products of the melanin pathway?

A

Eumelanin or pheomelanin

91
Q

Which is the brown/black pigment of the melanin pathway?

A

Eumelanin is the brown/ black pigement

92
Q

Which is the red/yellow pigment?

A

Pheomelanin

93
Q

Which melanin pigment is found in higher concentrations in African populations?

A

Eumelanin

94
Q

T/F: Caucasians produce pheomelanin

A

False

95
Q

What was the selection pressure to reduce melanin production in Caucasians?

A

As humans migrated into cloudy, sunless regions, there was a reduction in melanin production but plasma vitamin D levels increased profoundly as the lack of sunlight made vitamin D production more efficient.

96
Q

What are the two models on human origins and which is the correct one?

A

Multiregional and Out of Africa. Out of Africa is the correct model.

97
Q

What does the multiregional model state?

A

Modern Homo sapiens evolved regionally with gene flow between each of these regional populations

98
Q

What does the Out of Africa model state?

A

That modern Homo sapiens originated in Africa and then emigrated, replacing local hominids.

99
Q

Why is the out of Africa model supported?

A

Humans lack diversity, reflecting a recent origin in a small localised population. Evidence also supports that global diversity is a subset of African diversity

100
Q

The subset of African diversity implies…

A

that there was a founder effect or bottleneck event.

101
Q

What is the relationship between LD and distance from Africa?

A

LD increases with increased distance from Africa as the older African populations have had more recombination events

Introduction to Human Genetics (4 decks)

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