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Sem 2: Evolutionary biology > Week 3 > Flashcards

Week 3 Flashcards

1
Q

What is evolution?

A

Change in heritable traits of biological organisms over generations

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2
Q

What is genetic drift?

A

Random fluctuations in allele frequencies occur as a
result of ‘sampling error’ between generations in finite populations

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3
Q

What can be impacted by genetic drift?

A

All loci/alleles subject to genetic drift - but all are not necessarily subject to selection (at any given time/place)

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4
Q

What is the outcome of genetic drift?

A

Can lead to replacement of old alleles by new alleles (and sometimes the trait they confer) - non-adaptive evolution

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5
Q

What is genetic drift in the potential outcomes of evolution?

A

Genetic drift = null hypothesis for evolutionary change

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6
Q

What can be an alternative cause of genetic drift?

A

Sampling error alone can cause frequency of alleles to go up or down

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7
Q

How can you work out the random variance in allele frequency between one generation and the next?

A

V = p (1-p) / 2N
V = variance
p = allele frequency
2N = 2 x number of individuals (number of gene copies in a population)

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8
Q

What has the greatest impact on variance?

A

Higher variance in smaller populations (mathematical property!)

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9
Q

What does genetic drift have the most impact on?

A

Genetic drift is most important in small populations

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10
Q

Why does genetic drift impact smaller populations?

A

They have a greater variance every generation for allele frequency meaning it is more likely that by random chance two allele A1 are in the embryo compared to A1A2 or A2A2. Larger populations have greater security from this as more individuals can heterzygous or more likely to meet homozygous of the other varient

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11
Q

What does genetic drift mean for heterozygosity?

A

As allele frequency drifts towards fixation or loss, the frequency of heterozygotes decreases

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12
Q

What does Hardy-weinberg principle state?

A

Hardy-Weinberg theory states: p2+ 2pq + q2 = 1 …
Where p = freq of allele A1 q = freq of allele A2

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13
Q

Where is herterozygous at its biggest?

A

Frequency of H is highest when p = 0.5 ( 2 x 0.5 x 0.5 = 0.50)
As freq of A1 moves towards 0 or 1 the freq of H falls ( e.g. 2 x 0.9 x 0.1 = 0.18 )

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14
Q

How can you predict the frequency of heterozygosity in fututre generations?

A

Hg1 = Hg [1- 1/(2N)]
Averaged across populations, the frequency of heterozygotes (H) obeys the relationship
Where Hg+1 is heterozygosity in the next generation
N = number of individuals in the population (2N = number of gene copies)
Hg is heterozygosity in the present generation

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15
Q

What is the value of [1 - 1/2N]?

A

The value of [1 - 1/2N] is always between 0.5 (when N = 1) and 1 (when N = infinite)

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16
Q

What does the [1 - 1/2N] number mean for heterozygosity?

A

So expected H in the next generation is always less than in current generation
If N is large the decrease in H is small - if N is small the decrease in H is large

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17
Q

What does bottlenecks mean with drift and variation?

A

Big decrease in population size – a specific case of drift.
Usually results in loss of genetic variation

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18
Q

What is the founder effect?

A

If a new population is formed by a small number of colonists, the genetic drift ensues

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19
Q

What is the consequence of the founder effect?

A

A colony formed by a small number of founders will suffer loss of genetic variation – rare alleles are likely to be lost

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20
Q

What happens to heterozygosity if a colony is founded by 2 people?

A

A colony founded by just a pair, N = 2 then H1 = H [1-1/4] = H1 (0.75)
Heterozygosity, on average, reduced by 25% per generation

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21
Q

How impactful is genetic drift?

A

Genetic drift is the predominant force at the genetic and phenotypic level

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22
Q

What is the difference between genetic drift and natural selection?

A

Genetic drift, unlike natural selection, acts on genetic variation in a predictable manner, in relation to past and present population size

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23
Q

What is important in using genetic drift of non selected genes?

A

So if we can measure variation at genes not under natural selection, we can compare patterns of DNA variation from current populations to reconstruct their population history

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24
Q

What is an experiment where they demonstrated genetic drift on real life population?

A

107 experimental populations of D. melanogaster heterozygous for eye colour (A1 A2). In all populations the starting frequency of Allele A2 was 0.5
Selected 8 males and 8 females randomly from each population in each generation to start the next generation of that population

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25
What was the outcome of the experiment on genetic drift on Drosophula melanogaster?
By generation 19: 30 populations lost allele A2 29 had fixed allele A2
26
What is an example of wildlife being impacted by genetic drift?
Berthelot’s pipit, Anthus berthelotii, colonisation of the macaronesian islands
27
What was the outcome of Anthus berthelotii colonisation of macaronesia islands?
Founder (bottleneck) effects explain 60% variation at neutral genes Bottlenecks- better predictor of morphological variation than the environment
28
What did Anthus bethelotti colonisation show about the strength of genetic drift?
Drift can (often!) be stronger than selection
29
How can genetic drift be applied to evolutionairy history?
Genetic drift enables us to reconstruct population history
30
What is an example of genetic drift being used to show population history?
Seychelles warbler (Acrocephalus sechellensis)
31
How was the Seychelles warbler population history traced by genetic drift?
Endangered when discovered Compared DNA between 26 museum and contemporary specimens Used simulations to model genetic drift over time and reconstruct population history Seychelles warblers existed in 10,000’s across the region a few hundred years ago
32
What is census size?
Number of individuals in a population
33
Why is genetic drift and loss of heterozygosity will be greater than expected?
Genetic drift and loss of heterozygosity will be greater than expected because not all individuals contribute genetically to the next generation The population is effectively smaller than it really is
34
What is Ne?
Ne = effective population size
35
What is effective population size?
The size of an ideal theoretical population that would lose heterozygosity at the same rate as the actual population
36
What can impact effective population size?
Variation in the number of progeny Overlapping generations Unequal numbers of males and females Fluctuations in population size
36
What can impact effective population size?
Variation in the number of progeny Overlapping generations Unequal numbers of males and females Fluctuations in population size
37
How does variation in the number of progeny impact effective population size?
If some individuals have more offspring than others, Ne will be reduced
38
How does overlapping generations impact effective population size?
Individuals mate over multiple generations Offspring may mate with parents They carry identical copies of the same genes, so the effective number of genes in the population is reduced
39
How does unequal numbers of males and females impact effective population size?
You can use forumla: Ne = 4(Nm x Nf) / (Nm + Nf)
40
What is the effective population of 100 individuals with 50:50 ratio?
4(50 x 50) = 10,000 50 + 50 = 100 10,000 / 100 = 100
41
What is the effective population of 100 individuals with 20 males : 80 females ratio?
2(20 x 80) = 6400 20 + 80 = 100 6400 / 100 = 64
42
How can flucutating population size impact effective population?
All populations fluctuate in size – the rate of genetic drift is higher in small populations, so Ne is more strongly affected when population is small Calculate using harmonic mean
43
What is the forumula of effective population size?
nh = k / ((1/n1) + (1/n2) ...... (1/nk)) k = number of generations 1/nx = the number of breeding adults at a generation
44
What is an example calculation of 5 sucessive generations?
Ne = 5 / ((1/100) + (1/150) + (1/25) + (1/150) + (1/125)) = 70
45
What is the costs of small Ne?
Loss of heterozygosity Loss of genetic diversity
46
What are the associated benefits of heterozygosity?
Hz advantage Hiding deleterious mutations
47
What is inbreeding and how likely is it?
Mating between related individuals A degree of inbreeding is inevitable in small populations – members of the population share ancestors
48
What is F in inbreeding?
F= coefficient of inbreeding Probability that two alleles in an individual are identical by descent (descended from the same allele with a single ancestor)
49
What is the function of the inbreeding coefficient?
Inbreeding coefficient can be predicted as a function of the population size
50
What happens with inbreeding coefficient over time?
Inbreeding coefficient increases more rapidly in small populations than in large populations
51
What is the formula of change in inbreeding coefficient?
ft+1 = (1/2N) + (1 - 1/2N)ft
52
What is inbreeding depression?
Inbreeding reduces reproduction and survival
53
What are the consequences of inbreeding depression?
Reduces heterozygosity Exposes rare deleterious recessive alleles (as a homozygote) Loss of genetic diversity (reducing adaptive potential)
54
What are the consequences of reduces genetic diversity?
Inability to adapt to new challenges - e.g. new diseases Population level effect – not an individual effect
55
What is an example of inbreeding depression?
Florida panther, Puma concolor coryi Tail kink, Cryptorchidism in males, deformed sperm, disease susceptibility
56
What are the similarities between inbreeding and genetic drift?
Both related to population size Both have similar effects in reducing genetic diversity Both increase risk of extinction in small populations This is why genetic diversity is a global priority for the IUCN Both key forces in evolution, especially in small populations
57
What is an extinction vortex?
Small population --> inbreeding and/or genetic drift --> Loss of genetic variability --> reduction in individual fitness and population adaptability --> lower reproduction and higher mortality --> smaller population
58
What prevents populations going extinct?
Other evolutionairy forces introduce new genetic variation
59
What is an example of genetic rescue?
1995 Florida Panther N≈25 with inbreeding depression 95% likelihood of extinction in 20 years… 1995 – Eight pumas introduced from Texas
60
What was the consequence of the Florida panther genetic rescue?
Hz increases! Survivorship increases! Inbreeding traits decrease! Population recovers!
61
What allows for genetic rescue to occur?
Genetic rescue due to gene flow
62
How are most populations structure?
Very few species exist as single, panmictic populations – they are structured
63
What are underlying causes structured populations?
Natural aggregations Fragmented habitats
64
What are the consequences of natural aggregations?
Causes population subdivision which leads to genetic differentiation among subpopulations
65
What causes random evolutionairy changes?
GENETIC DRIFT and MUTATION & RECOMBINATION
66
What causes deterministic changes?
SELECTION and GENE FLOW
67
How do genetic processes genetic population structure?
Influence GENETIC POPULATION STRUCTURE Allele frequencies vary in time and space across groups of individuals this can, in turn, affect evolutionary processes e.g. diversification, speciation
68
What is the definition of population?
Geographically distinct groups of individuals of a species
69
What is an example of a evolutionary divergance in nearby populations?
Spring tail (Lepidocyrtus) – populations just 10km away diverged for 10 million years
70
What is an example of a mutation being selected for by the same species living in different environments?
Beach mouse, Peromyscus polionotus – intraspecific colour polymorphism caused by single amino acid difference - selected in different habitat types
71
What scale should evolution be applied?
Evolutionary processes must be considered across the entire species range rather than within single populations
72
What can cause deviations in hardy-weinberg expectations?
Deviation from Hardy Weinberg expectations can result from substructure
73
What is the Wahlund effect?
A reduction of heterozygosity in a population caused by subpopulation structure
74
How can you quantify population structure?
Population structure can be quantified using Wrights F (fixation) statistics
75
What does wrights F (fixation) mean?
F equals the loss of heterozygosity relative to that expected if all individuals (across the entire sample) were randomly mating (i.e. they are in one single panmictic population)
76
How do you calculate wrights F (fixation)?
F = (Hexp – Hobs)/Hexp where Hexp is heterozygosity expected under HWE = (2pq) and Hobs is the heterozygosity actually observed
77
What reduces the Heterozygosity observed (Hobs)?
Lower Hobs is produced by subdivision into smaller populations - diverging through genetic drift or selection (and/or non random mating)
78
What does a high wrights F (fixation)?
A larger F means there is greater population subdivision (breeding within populations)
79
How can you measure F(inverse^)IS?
F(inverse^)IS measures - population structure (inbreeding) in individuals relative to subpopulations, FIS = (HS - HI)/HS
80
How can you measure F(inverse^)IT?
F(inverse^)IT measures - population structure (or inbreeding) in individuals relative to total population, FIT = (HT - HI)/HT
81
How can you measure F(inverse^)ST?
F(inverse^)ST measures - population structure (or inbreeding) subpopulations relative to the total population, FST = (HT - HS)/HT
82
When measuring F:IS, IT or ST what does HT, HT, HS mean?
HI = observed heterozygous HS and HT = expected heterozygous under HWE in total or subpopulations
83
How does genetic structure increase over time with no migration?
With no migration, genetic structure will increase over time due to genetic drift because drift acts more rapidly in small populations, genetic structure (F(inverse^)ST) accumulates fastest between small populations
84
How can you calculate F(inverse^)ST?
FST = 1 – (1 – 1/2N)^t N = the effective population size, t = time in generations
85
What is the difference between F(inverse^)ST and population structure?
You’ll often see “population structure” and “FST” used synonymously in literature
86
What is a key feature of population structure?
Population structure is a dynamic process
87
What is gene flow?
Movement of gametes or individuals among populations
88
Why is gene flow important?
Important factor determining level of population structure Gene flow - opposes the effect of genetic drift
89
What are models of gene flow?
Isolated population distribution – Island Models Continuous population distribution – Isolation-by-distance Model
90
What is the overvoew of isolated population distrubution model?
Discrete populations with individuals migrating from one population to another with equal probability (p): p1=p2=p3 Model is not realistic in natural populations
91
What is the overview of continuous population distribution – Isolation-by-distance Model?
Even distribution of individuals Can be thought of a series of continuous overlapping populations Individuals less likely to migrate to more distant sites Closer parts of the population more genetically similar Realistic - used in computer simulations
92
What is the use of models?
Models we can determine the effect of gene flow on allele frequencies e.g. Island model
93
What can determine the magnitude of gene flow?
The magnitude of gene flow can be determined by the migration rate (m)
94
How can you measure expected change in allele frequency (per generation) due to gene flow (∆p?
∆p1 = m(p2 - p1)
95
What does p1, m and p2 mean?
p1 = allele frequency in recipient population p2 = allele frequency in donor population m = proportion of alleles entering a population through immigration
96
How can you measure m?
% migrated per generation eg 1% = m of 0.01
97
Starting with p1 = 1 and p2 = 0, and M = 0.01 ∆p1 = m(p2 - p1) Over 1 generation g1 p1^g1 = p1 + m (p2 - p1) = p1 + 0.01 (0 - 1) = 0.99 Over 2 generations g2 p1^g2 = p1^g1 + m (p2 - p1’) = 0.98
98
What happens over time with migration and change in gene frequencies?
Change is rapid initially….. but as gene frequencies between populations get more similar i.e. (p2 - p1), the rate of change slows. The homogenisation of allele frequencies
99
What is an overview of gene flow?
Gene flow is a powerful evolutionary process High migration over a few generations can have a massive effect on allele frequencies Gene flow over a small number of generations does not necessarily reflect long term population processes
100
What are the differences between gene flow and genetic drift?
Migration introduces new alleles into each population Genetic drift and migration are opposing forces Population differentiation depends on population size and (effective) migration rate…which can be very high when recipient pop is small (n = small) Given enough time, populations reach migration-drift equilibrium
101
What did Wright show with F(inverse^)ST and migration rate?
Wright showed that under an island model of migration at equlibrium, FST is linked to migration rate
102
What is the equation for working out F(inverse^)ST by migration rate?
FST = 1 / (4Nm + 1) m is the fraction of immigrants in the population (migration rate) N = population size Nm = number of immigrants each generation
103
What impacts differentiation between populations?
Differentiation between populations depends on the product of population size and migration rate = Nm
104
What does different Nm impact F(inverse^)ST mean?
f Nm = 0 (no migration); FST = 1 (different alleles fixed) - divergence! If Nm = 1 (1 migrant per generation); FST = 0.2, drift is counterbalanced by migration (no divergence or convergence!) = Equilibrium If Nm > 1 populations will homogenise - convergence
105
How much gene flow can counter gene flow?
Effects of genetic drift can be counteracted by (little) gene flow
106
How can F(inverse^)ST be used as an estimation tool?
Due to the expected relationship between F(inverse^)ST and Nm, F(inverse^)ST has been used to estimate migration / gene flow
107
What is an example of a animal with little population subdivision?
Mytilus edulis - mollusc F(inverse^)ST = 0.006 with an Nm of 42.0
108
What is an example of a animal with a large population subdivision?
Plethodon dorsalis - salamander F(inverse^)ST = 0.714 with an Nm of 0.1
109
What is an example of estamating gene flow with F(inverse^)ST?
Mountain sheep points = Fst between pairs of sampled locations Black dots = pairwise Fst and geographical distance on different mountain ranges Open Triangles = pairwise Fst and locations for locations on same mountain range Shows clear pattern of Isolation-by-distance within and among mountain ranges Red arrow – indicates higher Fst (less gene flow) across mountain ranges than within
110
What is the definition of F(inverse^)ST?
The fraction of genetic variation in a group of populations that results from differences between the populations
111
What is an example of gene flow: Isolation-by-adaptation?
Neochlamisus bebbianae leaf beetles 2 types: Maple-associated population and willow-associated population Genome-wide structure between populations on different host plants is stronger (i.e. FST is higher) than between geographically distant populations on the same plant Suggests local adaptation to different plants, which causes a barrier to gene flow

Sem 2: Evolutionary biology (11 decks)

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