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BB10007 Genetics > ✅Population Genetics - Paul Craze > Flashcards

✅Population Genetics - Paul Craze Flashcards

1
Q

What are alleles?

A

Alternative DNA sequences at a locus, inherited as a unit

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2
Q

What is a locus?

A

The position in the genome being considered

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3
Q

What are alleles caused by?

A

Single nucleotide polymorphisms and structural differences

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4
Q

What do alleles produce?

A

A genetically based phenotypic differences between individuals

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5
Q

When does a locus not contribute to variation?

A

When all individuals have the same allele

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6
Q

What does phenotypic variation contributed by a locus depend on?

A

The frequencies of alleles

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7
Q

How would the frequency of an allele be calculated?

A

Frequency = number of alleles/total

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8
Q

What are genetic markers?

A

Molecular variants used to differentiate between alleles

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9
Q

The frequency of heterozygotes in a population that is at Hardy-Weinberg equilibrium will…

A

…remain constant

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10
Q

How many alleles will a diploid population of N individuals have?

A

2N

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11
Q

How would the total number of A alleles be calculated?

A

2x number of AA homozygotes + number of Aa heterozygotes

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12
Q

What is evolution?

A

Change in allelic frequencies

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13
Q

What can population differences in allele frequencies be used to understand?

A

Gene flow/migration

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14
Q

How is a genotype frequency calculated?

A

Using the number of individuals with the genotype divided by the total number of individuals

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15
Q

What does the Hardy-Weinberg principle give?

A

The expected genotype frequencies in a model population

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16
Q

What are the Hardy-Weinberg assumptions?

A

Population is very large, random mating, no migration, no selection, no mutation

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17
Q

What is positive assortative mating?

A

Similar individuals tend to mate with each other

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18
Q

What is negative assortative mating?

A

Different individuals tend to mate with each other

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19
Q

What is inbreeding?

A

Individuals tend to mate with relatives

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20
Q

What are offspring of inbreeding more likely to have?

A

Two alleles that are identical by descent (IBD)

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21
Q

What does inbreeding increase?

A

Homozygosity

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22
Q

What is inbreeding measured by?

A

The inbreeding coefficient (F)

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23
Q

What is the inbreeding coefficient?

A

The probability that two alleles are IBD

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24
Q

Where does inbreeding occur most?

A

In self fertilising plant populations

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25
What can inbreeding do to populations?
Decrease the fitness
26
What is genetic drift?
Random changes in allelic frequencies
27
What does Hardy-Weinberg tell you?
That there is no intrinsic force driving allelic change
28
What can changes in allelic frequencies be caused by?
Genetic drift, natural selection, migration
29
What is the expected error in allele frequencies samples in a population?
1/2N
30
What can happen to alleles in small populations?
They can be lost or fixed
31
What happens to alleles in large populations?
They can fluctuate
32
What are founder events?
When a new population is founded by very few individuals and the allele frequencies are different to the original population
33
What is natural selection based on?
The fact that different genotypes have different fitness
34
What is fitness?
The average contribution to the next generation made by an individual or that individual's genome
35
What indicates greater fitness in terms of inheritance?
More copies into the next generation
36
How many alleles does selection favour?
One
37
What is gene flow?
Movement of alleles from one population to another
38
How does time taken to increase in frequency differ between alleles?
DOMINANT - initial increase rapid, but slows as it becomes more common CODOMINANT - reaches fixation most rapidly RECESSIVE - takes longer to increase but reaches fixation quickly once common
39
What factors can increase genetic variation within populations?
Mutation Migration Some types of natural selection
40
What factors can decrease genetic variation within populations?
Genetic drift | Some types of natural selection
41
What factors can increase genetic variation between populations?
Mutation Genetic drift Some types of natural selection
42
What factors can decrease genetic variation between populations?
Migration | Some type of natural selection
43
What are discontinuous trains?
Qualitative, can be categorised into a few classes
44
What are continuous traits?
Quantitative, can vary along a scale of measurement
45
What is polyphenism?
Some characteristics show normal distribution, others show bimodal distribution
46
What are meristic traits?
Are determined by multiple genetic and environmental factors and can be measured in whole numbers. eg litter size
47
What are threshold traits?
Are measured in presence or absence eg susceptibility to disease
48
What kind of distribution is shown by the number of loci against the relative number of progeny?
Normal distribution
49
What is phenotypic variance?
The total amount of variation among individuals in some trait, caused by underlying components of variation
50
What are the components of phenotypic variation (Vp)?
Genetic variance (VG), environmental variance (VE), genotype-environment interaction variance (VGE)
51
How is phenotypic variance calculated?
VG + VE + VGE
52
What is the heritable variation?
Additive genetic variance (VA)
53
What is the non-heritable variation?
Dominance genetic variance (VD), gene interaction (epistatic) variance (VI)
54
How is Genetic variance calculated?
VA + VD + VI
55
What is broad sense heritability?
The proportion of phenotypic variation attributable to genetic differences between individuals
56
How is broad sense heritability calculated?
H^2 = VG/VP
57
What is narrow sense heritablity?
The proportion of phenotypic variation that contributes to the resemblance between parents and offspring
58
How is narrow sense heritability calculated?
h^2 = VA/VP
59
What can heritability be measured by?
Regression, with a linear relationship between phenotype of offspring and phenotype of parents
60
What is genotype-environment interaction?
When the difference between genotypes depends on the environment
61
What can genetic correlations be down to?
Pleiotropy or linkage disequilibrium
62
What is phenotypic correlation?
When the points in the correlation are different individuals
63
What is genotypic correlation?
When the points in the correlation are different genotypes
64
What is linkage disequilibrium?
When there is an association between alleles of different loci, eg if allele A tends to be found with allele B and a with b
65
What is coupling linkage diequilibrium?
When the two dominant alleles associate, and so do the two recessive, eg AB and ab
66
What is repulsion disequilibrium?
When one dominant allele associates with one recessive, eg Ab and aB
67
What is pleiotropy?
Single locus can influence multiple traits at once, which are all inevitably correlated
68
What does pleiotropy tend to result in?
Traits being inherited together
69
What can evolution lead to over time in terms of lineages?
The splitting
70
What is biological evolution?
Genetic (and potentially phenotypic) changes in a group of organisms
71
What is anagenesis?
Evolution taking place in a single group (a lineage) with time
72
What is cladogenesis?
Splitting of one lineage into two, new species arise
73
What types of speciation does cladogenesis include?
Sympatric and allopatric
74
What do species represent on the phylogenetic tree?
The smallest set of organisms that share a common ancestor and can be distinguished from other
75
What is phylogeny?
A representation of the relationship between groups of organisms
76
What is a rooted phylogenetic tree?
Uses distantly related species to infer ancestral state
77
What is an unrooted phylogenetic tree?
No outgroup, relationship between lineages known but not ancestral
78
What is allopatric speciation?
Speciation caused by geographical isolation
79
What is peripatric speciation?
Speciation when a population is peripheral to the main one
80
What is parapatric speciation?
Speciation when populations are not isolated, but adjoining, individuals mate locally
81
What is sympatric speciation?
Describes speciation when populations overlap
82
What are the two categories of reproductive isolating mechanisms?
Prezygotic and postzygotic
83
What are examples of prezygotic isolating mechanisms?
Habitat isolation, behavioural isolation, sperm or pollen not transferred, temporal isolation
84
What are examples of postzygotic isoation?
Zygote dies early in embryogenesis, F1 hybrids are inviable, F1 hybrids are sterile
85
What is secondary contact?
Lineages may split over time but then migration or loss of barriers brings them back into contact
86
What are genetic markers?
Some feature in the genome that allows us to differentiate between alleles
87
What do genetic markers provide?
Information on genetic differences between individuals/populations
88
What are genetic markers used in?
QTL and GWAS studies, forensics, genetic diversity
89
What is RFLP?
Restriction fragment length polymorphism
90
What was used before DNA technology to differentiate between populations?
Alloenzymes
91
How is RFLP done?
Undegraded DNA is cut into fragments using restriction enzymes, and each fragment differs in length due to VNTRs
92
What is RAD sequencing?
Cuts many short fragments and organises them into sequence stacks
93
What are microsatellites?
Short tandem repeats, detected with PCR
94
What is a haplotype?
A small chromosomal block inherited as a unit
95
Why are mitochondrial markers important for population studies?
They have no recombination and uniparental inheritance so each sequence represents the end point of a linkage
96
What can alleles be generated by?
Replication errors

BB10007 Genetics (3 decks)

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