Week 3 Flashcards
What is evolution?
Change in heritable traits of biological organisms over generations
What is genetic drift?
Random fluctuations in allele frequencies occur as a
result of ‘sampling error’ between generations in finite populations
What can be impacted by genetic drift?
All loci/alleles subject to genetic drift - but all are not necessarily subject to selection (at any given time/place)
What is the outcome of genetic drift?
Can lead to replacement of old alleles by new alleles (and sometimes the trait they confer) - non-adaptive evolution
What is genetic drift in the potential outcomes of evolution?
Genetic drift = null hypothesis for evolutionary change
What can be an alternative cause of genetic drift?
Sampling error alone can cause frequency of alleles to go up or down
How can you work out the random variance in allele frequency between one generation and the next?
V = p (1-p) / 2N
V = variance
p = allele frequency
2N = 2 x number of individuals (number of gene copies in a population)
What has the greatest impact on variance?
Higher variance in smaller populations (mathematical property!)
What does genetic drift have the most impact on?
Genetic drift is most important in small populations
Why does genetic drift impact smaller populations?
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
What does genetic drift mean for heterozygosity?
As allele frequency drifts towards fixation or loss, the frequency of heterozygotes decreases
What does Hardy-weinberg principle state?
Hardy-Weinberg theory states: p2+ 2pq + q2 = 1 …
Where p = freq of allele A1 q = freq of allele A2
Where is herterozygous at its biggest?
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 )
How can you predict the frequency of heterozygosity in fututre generations?
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
What is the value of [1 - 1/2N]?
The value of [1 - 1/2N] is always between 0.5 (when N = 1) and 1 (when N = infinite)
What does the [1 - 1/2N] number mean for heterozygosity?
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
What does bottlenecks mean with drift and variation?
Big decrease in population size – a specific case of drift.
Usually results in loss of genetic variation
What is the founder effect?
If a new population is formed by a small number of colonists, the genetic drift ensues
What is the consequence of the founder effect?
A colony formed by a small number of founders will suffer loss of genetic variation – rare alleles are likely to be lost
What happens to heterozygosity if a colony is founded by 2 people?
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
How impactful is genetic drift?
Genetic drift is the predominant force at the genetic and phenotypic level
What is the difference between genetic drift and natural selection?
Genetic drift, unlike natural selection, acts on genetic variation in a predictable manner, in relation to past and present population size
What is important in using genetic drift of non selected genes?
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
What is an experiment where they demonstrated genetic drift on real life population?
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
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
What is an example of wildlife being impacted by genetic drift?
Berthelot’s pipit, Anthus berthelotii, colonisation of the macaronesian islands
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
What did Anthus bethelotti colonisation show about the strength of genetic drift?
Drift can (often!) be stronger than selection
How can genetic drift be applied to evolutionairy history?
Genetic drift enables us to reconstruct population history
What is an example of genetic drift being used to show population history?
Seychelles warbler (Acrocephalus sechellensis)
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
What is census size?
Number of individuals in a population
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
What is Ne?
Ne = effective population size
What is effective population size?
The size of an ideal theoretical population that would lose
heterozygosity at the same rate as the actual population
What can impact effective population size?
Variation in the number of progeny
Overlapping generations
Unequal numbers of males and females
Fluctuations in population size
What can impact effective population size?
Variation in the number of progeny
Overlapping generations
Unequal numbers of males and females
Fluctuations in population size
How does variation in the number of progeny impact effective population size?
If some individuals have more offspring than
others, Ne will be reduced
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
How does unequal numbers of males and females impact effective population size?
You can use forumla: Ne = 4(Nm x Nf) / (Nm + Nf)
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
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
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
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
What is an example calculation of 5 sucessive generations?
Ne = 5 / ((1/100) + (1/150) + (1/25) + (1/150) + (1/125)) = 70
What is the costs of small Ne?
Loss of heterozygosity
Loss of genetic diversity
What are the associated benefits of heterozygosity?
Hz advantage
Hiding deleterious mutations
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
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)
What is the function of the inbreeding coefficient?
Inbreeding coefficient can be predicted as a function of the population size
What happens with inbreeding coefficient over time?
Inbreeding coefficient increases more rapidly in small populations than in large populations
What is the formula of change in inbreeding coefficient?
ft+1 = (1/2N) + (1 - 1/2N)ft
What is inbreeding depression?
Inbreeding reduces reproduction and survival
What are the consequences of inbreeding depression?
Reduces heterozygosity
Exposes rare deleterious recessive alleles (as a homozygote)
Loss of genetic diversity (reducing adaptive potential)
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
What is an example of inbreeding depression?
Florida panther, Puma concolor coryi
Tail kink, Cryptorchidism in males, deformed sperm, disease susceptibility
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
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
What prevents populations going extinct?
Other evolutionairy forces introduce new genetic variation
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
What was the consequence of the Florida panther genetic rescue?
Hz increases!
Survivorship increases!
Inbreeding traits decrease!
Population recovers!
What allows for genetic rescue to occur?
Genetic rescue due to gene flow
How are most populations structure?
Very few species exist as single, panmictic populations – they are structured
What are underlying causes structured populations?
Natural aggregations
Fragmented habitats
What are the consequences of natural aggregations?
Causes population subdivision which leads to genetic differentiation among subpopulations
What causes random evolutionairy changes?
GENETIC DRIFT and MUTATION & RECOMBINATION
What causes deterministic changes?
SELECTION and GENE FLOW
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
What is the definition of population?
Geographically distinct groups of individuals of a species
What is an example of a evolutionary divergance in nearby populations?
Spring tail (Lepidocyrtus) – populations just 10km away diverged for 10 million years
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
What scale should evolution be applied?
Evolutionary processes must be considered across the entire species range rather than within single populations
What can cause deviations in hardy-weinberg expectations?
Deviation from Hardy Weinberg expectations can result from substructure
What is the Wahlund effect?
A reduction of heterozygosity in a population caused by subpopulation structure
How can you quantify population structure?
Population structure can be quantified using Wrights F (fixation) statistics
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)
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
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)
What does a high wrights F (fixation)?
A larger F means there is greater population subdivision (breeding within populations)
How can you measure F(inverse^)IS?
F(inverse^)IS measures - population structure (inbreeding) in individuals relative to subpopulations, FIS = (HS - HI)/HS
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
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
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
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
How can you calculate F(inverse^)ST?
FST = 1 – (1 – 1/2N)^t
N = the effective population size,
t = time in generations
What is the difference between F(inverse^)ST and population structure?
You’ll often see “population structure” and “FST” used synonymously in literature
What is a key feature of population structure?
Population structure is a dynamic process
What is gene flow?
Movement of gametes or individuals among populations
Why is gene flow important?
Important factor determining level of population structure
Gene flow - opposes the effect of genetic drift
What are models of gene flow?
Isolated population distribution – Island Models
Continuous population distribution – Isolation-by-distance Model
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
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
What is the use of models?
Models we can determine the effect of gene flow on allele frequencies e.g. Island model
What can determine the magnitude of gene flow?
The magnitude of gene flow can be determined by the migration rate (m)
How can you measure expected change in allele frequency (per generation) due to gene flow (∆p?
∆p1 = m(p2 - p1)
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
How can you measure m?
% migrated per generation eg 1% = m of 0.01
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
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
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
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
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
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
What impacts differentiation between populations?
Differentiation between populations depends on the product of population size and migration rate = Nm
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
How much gene flow can counter gene flow?
Effects of genetic drift can be counteracted by (little) gene flow
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
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
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
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
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
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
