Evolutionary Forces Flashcards
How can evolutionary forces be seen
They must be deduced from genetic variation, fitness, phenotype, behaviour
How can evolutionary forces be studied
The forces leave signatures in the genome. This can be studied by looking into
Genetic variation of individuals (e.g. observed heterozygosity, Ho)
Comparing variation across populations (e.g. population differentiation, FST
What are the evolutionary forces
Mutation Random genetic drift Recombination Gene Flow Natural and Sexual selection
What are the effects of the evolutionary force mutation
Increases variation (Ho) and population differentiation (FST)
What are the effects of the evolutionary force random genetic drift
Decreases variation but increase population differentiation
What are the effects of the evolutionary force recombination
Tends to reduce variation and differentiation
What are the effects of the evolutionary force gene flow
Increases genetic variation but reduces population differentiation
What are the effects of the evolutionary forces natural and sexual selection
Depends on the selection coefficients
How do you quantify the effects of evolutionary forces
population genetics - changes in allele haplotype and genotype frequencies
quantitative genetics - changes in fitness, behaviour or phenotype
phylogenetics and macro-evolution - footprints in the genome
How do the evo forces affect natural populations
They reach an equilibrium and researchers study these equilibriums, or experiment and cause deviation
What is a gene
A gene is a piece of DNA located on a particular location of a chromosome (or a locus)
How many alleles on locus on a sexually reproducing diploid organism
There are 2 - one allele originates from the mother the other from the father (except for sex chromosomes)
What is the hardy-weinberg equilibrium model
Useful null model to predict genotype frequencies from allele frequencies
What is a population that is in Hardy-Weinberg equilibrium is called
a panmictic population
What are the assumptions of hardy-weinberg
(1) Organism is diploid
(2) Reproduction is sexual
(3) Generations are non-overlapping
(4) Mating occurs at random
(5) Population size is very large
(6) Migration is zero
(7) Mutation is zero
(8) No natural selection acting gene
What would you conclude if you found an deficit of heterozygotes AB?
32 : 16 : 2 (expected numbers)
40 : 0 : 10 (observed)
(1) Extreme inbreeding (e.g. selfing),
(2) Sampling two separate populations fixed for different alleles, and/or
(3) Underdominance (heterozygotes are less fit), (4) Null alleles
If you would find a significant excess in a particular genotype in H-W, this suggest:
Selection, inbreeding (random genetic drift), gene flow (but not recombination)
What does a mutation do
Changes the DNA, the genetic code
What are the different types of mutations
Point mutations (single nucleotide polymorphisms, SNPs)
DNA replication slippage (microsatellites)
Deletion insertions (indels or frame shift mutations)
Gene duplication and deletion
Transposable elements
What are the fitness effects of mutation
Many mutations are (nearly) neutral (~ 10%, synonymous substitutions ):
Many are detrimental (90% Non-synonymous substitutions)
Very few are beneficial (~ 1-2%)
Why do you think that non-synonymous mutations are often detrimental (or neutral)?
The original genetic code is “tested & proven” over millions of years of evolution. Hence, random improvements are extremely rare!
What symbol is used for base mutation rate?
μ
What is the equation for the probability of an allele to stay unchanged
(1-μ)
What are the equations for the rate of mutation over time
pt = p0(1 - μ)t
pt=p0xe^ut
What is the mutation (genetic) load
it is the reduction in fitness caused by mutations
What is the mutation -selection balance
deleterious mutations are being generated all the time. Bad mutations are removed by selection
Are the majority of mutations recessive or dominant and what is the impact
Recessive
Their (bad) fitness effects are not expressed in the heterozygote genotypes
In heterozygote condition, recessive deleterious mutations cannot be detected
Consequently, recessive mutations generally reach a higher equilibrium frequency
How to estimate mutation rate
DNA sequence divergence and split time of fossil record
Compare genome sequences from children and their parents
Mutation accumulation experiments
What is something extra to consider when estimating mutation rate
the generation time - generation times of female and males may differ
What mutation rate do researchers use in fossil record calibration and why
typically use a mutation rate of 1 × 10−9 mutations per site per year derived from the observed DNA sequence difference of ~1.3% between the human and chimpanzee and an assumed divergence time of 7 Ma based on fossil record
What is the issue with fossil calibration
fraught with its own uncertainty, and the argument is circular
If you “know” the divergence time based on fossils, why bother estimating mutation rates to estimate it?
problem with generation times
two ways to estimate mutation rate
based on parent-offspring comparison
from fossil records
How to estimate mutation rate base on parent-offspring comparison
From the two trios (parents + offspring) the de novo germline base mutation rate µ=10-8 per base pair per generation
Factor 10 different from what people commonly use!
Example of when we got generation time join when considering mutation rate
Previously, researchers assumed 20-25 year human generation time
Currently the estimate is ~29 years (and differs between sexes)
Humans and chimp divergence time recently doubled…!
Why study microsatellite mutation rate of diatoms?
Diatoms are most common type of phytoplankton
100,000 extant species
45% of the total oceanic primary production
Many species are clonal or asexual
What are microsatellites
Repeating sequences
Generally 2 to 6 base pairs
Very common in genomes
What is the mutation rate of microsatellites compared to other neutral regions of DNA
higher rate of mutation
How does the size the of the microsatellite cor change
Slippage mutations tend to extend the size of the core repeat (Single-step mutation model (SMM))
When large, drastic deletions reduce the size (Two-phase model (TPM))
Why are micro satellites an important marker in micro-evolution
Highly polymorphic (many alleles) and high mutation rate
Microsatellites have been used in 189,000 papers in conservation
High resolution, e.g. to distinguish related individuals
High resolution allows you to observe evolutionary change over short periods of time
Describe how microsatelllites have high resolution
Parents tend to have 2 x 2 = 4 distinct alleles
Full-sib offspring have 4 possible genotypes per locus
Using 10 microsatellite loci = >1 million unique genotypes
Why can the high mutation rate of microsatellites be a problem
high mutation rate saturates the number of distinct alleles at a given locus, and causes “size homoplasy
Alleles look the same, but are not identical by descent
An individual may be homozygous at a locus, but its parents could be completely unrelated
What type of marker is replacing microsatellites
SNP markers - but you need many more SNPs than microsatellite loci to get the same resolution
5 conclusions of microsatellite mutation rate is diatoms
Microsatellite mutation rate»_space; base mutation rate (~5 orders of magnitude!)
In diatoms, the rate is relatively high during clonal phase, ca. 3 - 10x higher than in humans
This can generate novel genetic variation in the absence of recombination
Highest rate was observed at start of culturing
Microsatellite mutation rate seems to be unsuitable to calibrate divergence time
What is genetic drift
Chance events leading to a loss of genetic variation
Processes leading to random genetic drift
Small population size (inbreeding)
Founder effects
Population fluctuations
Population bottlenecks
What trait does genetic drift share with mutation
random process
According to the neutral theory of evolution, which forces explain most of the genetic variation
drift and mutation
Who came up with neutral theory
Kimura 1968
What was the main criticism against neutral theory
The average heterozygosity among loci per individual in diverse species, including those with apparently immense population sizes, is mostly restricted to the range 0-20%
(Lewontin, 1974)
What is the symbol for actual population size
Ne/N
What is Ne
genetic effective population size
What is the relationship between Ne and N
Ne<
What causes population size fluctuations
Environmental disturbances
Host-parasite and predator-prey coevolution
Other frequency dependent processes
What reduces Ne/N ratio
Fluctuation in population size Variance in family size Unequal sex-ratio Overlapping generations / age structure Mode of inheritance (Y chromosomes) Selection (balancing selection vs Hill-Robertson effects)
What is a high ratio
when the difference between the numbers is large
What is a low ration
when the difference between the numbers is low e.g. 1:1
What is the common range of Ne/N in natural populations
≈0.0001 - 0.1
What does Ne/N largely depend on and give examples
Largely dependent on taxonomic group
Cod is mass spawner and has small Ne/N
Life bearing mammals relative high Ne/N
What does Vk stand for
Variance in reproductive success
What is the relationship between Vk and Ne/N
when reproductive variance Vk > 2, then Ne/N < 1
Can Ne/Ne be larger than unity
Yes, when Vk < 2, (minimised inbreeding regime)
What equation links Ne/N and Vk
Ne/N (roughly) = 4/Vk+2
What is the harmonic mean population
The long-term effective population size
Across generations, how do we determine the loss of genetic variation
mostly determined but the generation with the smallest Ne
What tends to b bigger, the harmonic mean or the arithmetic mean
harmonic, as it is most influenced by the smallest populations size
What is coalescence time
the time in generations it takes for 2 alleles to coalesce t=2N
Equation for nucleotide diversity
pi = 4Nµ
What is the Wahlund effect
the Wahlund effect is a reduction of heterozygosity (that is when an organism has two different alleles at a locus) in a population caused by subpopulation structure
What are the effects of a post-bottleneck drift after a founder event
It reduces genetic variation (He)
It increase genetic differentiation (FST) between the founder population and the source population
Who developed the F statistic
Wright
Equation explaining the fixation of alleles due to inbreeding and drift
(1 – FIT) = (1 – FIS) (1 – FST)
Loss in Vg = inbreeding x drift
What is the equation for Fis
FIS = 1 – HO/HS
What does Ho stand for
it is the mean observed heterozygosity in subpopulations
What does Hs stand for
it is the mean expected heterozygosity in subpopulations
What is the equation for Fst
FST = 1 – HS/HT
what does Ht stand for
the heterozygosity when considering the subpopulations as a single population (averaging the allele frequencies)
what does Fis and Fst express together
they express how much of the genetic variation is fixed within individuals
Whis F is used to measure how much of the genetic variation is fixed due to inbreeding
Fis (how much is fixed within a genome as homozygosity)
Whis F is used to measure how much of the genetic variation is fixed due to drift
FST (how much is fixed between subpopulations due to population fragmentation)
Why is fixation a problem
Due to fixation, genetic variation is no longer available between individuals, which limits the speed of adaptive evolution
Who introduced nearly neutral theory
Ohta (1970)
Who argued that selection was the most important evolutionary force
Fisher 1958
Who argued drift to be the most important evolutionary force
Wright 1931, 1932
What is Wright’s argument about adaptive topography or adaptive landscape
With constant genotypic fitnesses and random mating, selection causes the gene frequency to change in such a way that the mean fitness of individuals in the population always increases until at equilibrium it reaches a maximum
What are the three phases of wrights shifting balance hypothesis
Random genetic drift
Mass selection
Interdemic selection
Describe Wright’s genetic drift phase
“when the set of gene frequencies drifts at random in the multidimensional space […] around an adaptive peak
Describe Wright’s mass selection phase
when a set of gene frequencies drifts far enough outside the attraction zone of its own peak to become attracted by another peak
Describe Wright’s interdemic selection phase
when migrants from the deme on the highest peak take over other subpopulations
Explain Wright’s shifting balance hypothesis
Genetic drift can be thought of as a process of random exploration of the adaptive zones in a temporarily maladaptive way, on the chance that a new phenotype may be found which will be better adapted.
Describe Kimura’s 1968 neutral theory of molecular evolution
that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants which do not affect fitness
(In genomes of existing species, the vast majority of molecular differences are selectively “neutral“)
Why is neutral theory a cornerstone of population genetics
It states the null model- deviations from it imply selection
Explain Ohta’s nearly neutral theory
Many polymorphisms behave neutrally, where selection is too weak to counter the drift. However, when population size is large, small selective advantages can become fixed by selection
What causes gene flow
Migration can result in gene flow when the migrants successfully reproduce in the recipient population
What does gene flow do to genetic variation
Gene flow tends to increase genetic variation at a local (subpopulation) level and reduces global genetic variation at the metapopulation level by reducingcoalescence time
How are is mutations and geneflow similar
Like mutations, gene flow introduces novel genetic variation that is available to selection
(Reduces inbreeding but disrupts local adaptation )
How is mutations and migration different
migration is a non-random process - it can be phenotype of sex dependent
What are the concerns over genetic rescue in conservation
outbreeding depression/upsetting local genetic adaptation/local purity and provenance,
limited quantitative information on the expected consequences of outcrossing,
lack of clear guidelines,
costs,
risks of disease, pest and parasite spread,
disrupting social systems in some animals,
moving biological material across political jurisdictions,
regulatory barriers
How does gene flow constrain evolutionary change
Darwin emphasised that isolation of populations was one factor promoting evolution.
What was Mayr’s (1996) view on species
That they were ‘real’, not man-made definitions
What was Mayr’s argument about biological species
He argued that a system that prevented unrestricted out-crossing to be superior as it would destroy selective advantages to particular ecological situations
What are the flaws in the biological species concept
It has been disproven several times
can not apply to asexual species as they do not have sex
many recognised species of plant can hyrbridise
gene flow challenges BSC concept as it undermines species identity
What is the BSC definition of a species
species is a group of organisms that can potentially interbreed, or mate, with one another to produce viable, fertile offspring.
How can gene flow be a generating force in evolution
Due to wright’s shifting balance hypothesis and adaptive landscapes:
With natural selection alone, a species would be trapped on one adaptive peak even if there were higher adaptive peaks representing better adapted combinations of characters.
Gene flow allows species to explore the entire adaptive landscape by creating new gene combinations (i.e. epistasis)
What is under-dominance
It is the selection against the heterozygote, causing disruptive selection and divergent genotypes
Will gene flow have a large affect on small of large population when there is underdominance
In a large pop, if a BB migrant enters an AA pop, the inferior heterozygotes are likely to get lost
But in a small pop there is a high chance two inferior heterozygotes will mate and selection then favours the superior BB genotype.
A new adaptive peak is found
Does gene flow have a bigger impact on large or small populations
Small - Due to chance, favourable allele or gene combinations may be generated in small populations
what influences the rate of gene flow
The migration capacity of the species
What is the effect of balancing selection on gene flow?
It increases the effective rate of gene flow by favouring rare genotypes (heterozygotes or rare alleles)
What is a fragmented population called
a meta population
What are the different metapopulation models
Mainland-island
Stepping stone
Levin’s type metapopulations
What needs to be considered in the SLoSS debate
Genetic variation within and between subpopulations F-statistics Effects of gene flow Inbreeding depression Disease outbreak Local extinction Local adaptation
What is gene flows impact on Fst
It reduces it as gene flow homogenises allele frequency across subpopulations
How does population sub-structuring affect coalescence time of alleles
It increases it:
Alleles cannot coalesce if they are in different subpopulations
Hence, more different alleles can be maintained
But these alleles are more likely to be in homozygous state (smaller subpopulation gene pool) Wahlund effect
What does it mean when Fst is zero
There are no subdivisions in the population; complete sharing of genetic material
What does i mean when Fst is 1
There is no sharing a genetic material, extreme differentiation
What does selection do
Alters inheritance of allele and genotype frequencies so that it is no longer neutral
What are the types of selection
Natural selection Balancing selection Positive (Darwinian) selection Negative (purifying) selection Directional selection Disruptive selection Stabilising selection
Does selection increase or decrease genetic varitation and population differentiation
Both- depends on the type of selection
When can selection act
when there is a reproductive excess (more offspring are produced than can survive and reproduce)
How can you calculate selection coefficients
you base them on differences in survival rates
What letter is used to indicate fitness
W (Malthusian fitness
Why does survival need to be associated with a genotype or allele
because you need to identify alleles or genotypes that covey a fitness advantage or disadvantage
What letter is used for the dominance coeffcient
h
If the dominance coefficient h is =0.5 then:
alleles are additive (co-dominant)
If the dominance coefficient h is <0.5 then:
B is recessive (or partially recessive)
If the dominance coefficient h is >0.5 then:
B is dominant (or partially dominant)
What are the equations for working out the respective fitness values
AA = 1 AB = 1-0.5s BB = 1-s
Why do you rarely see deleterious mutations which are dominant or co dominant in large populations
Deleterious dominant mutations will be selected out as soon as they arrive in their heterozygous state
How can deleterious recessive mutations be removed from large populations
The recessive mutatiions first need to increase in frequency due to drift before selection canact upon them
What are the equations for measuring selection with overdominance
AA = 1-s1 AB = 1 BB = 1-s2
Which type of selection does not reduce genetic variation
balancing selection (e.g. overdominance and negative frequency dependent selection) which maintain polymorphism It maintains both A and B alleles in a population
What is the effect of over-dominant selection Fst
It reduces population differentiation as is balances the allele frequencies
Why does overdominance favours rare alleles
because they are more often in a heterozygous state
What is overdominance
heterozygote superiority
What is the classic example of overdominance and what are the fitnesses W
beta hemoglobin in populations in west africa
AA = 0.89
AS = 1
SS = ).2
In what two cases is there not adaptive evolution
when there is no genetic variation or not variation in fitness values
What is the relationship between overdominance and Fst on spatial and temporal scales
At a spatial scale, overdominant selection will reduce the FST
at the temporal scale, overdominant selection increases the FST by promoting the turnover of alleles.
(Every new immigrant allele has a selective advantage, causing alleles to be replaced in rapid succession).
What is the most common selection process
negative (purifying selection)
What other factors can affect temporal Fst
number of alleles per locus, effective migration rate
What is disruptive selection
When the extremes are positively selected
What is pleiotropy
where one gene effects multiples traits
What is genetic hitchhiking
When an allele changes frequency, not because it is under selection, but because it is near another gene undergoing a selective sweep.
What is a selective sweep
WHEN a positively selected mutation occurs and spreads in a population by directional selection, frequency of linked allele (or weakly selected) increases.
What is background selection
loss of genetic diversity at a non-deleterious locus due to negative selection against linked deleterious alleles
What is recombination’s effect on population differentiation
little effect or reduces it (introgression)
What does recombination do
It shuffles genetic variation, increasing genetic variation at a genotypic level
Example of recombination
Homologous recombination (intra-locus recombination)
Non-homologous recombination (inter-locus recombination)
Gene conversion
Chromosomal rearrangements
Introgression (between species)
Horizontal gene transfer (deeply diverged taxa)
Why do siblings look different
Because of recombination
What does recombination happen between
homologous genes (often a consequence of sex), gene paralogous (gene conversion) and between different species (introgression or horizontal gene transfer)
Why is combination important
It separates the good mutations from the bad, speeding up adaptive evolution
Example of the role recombination had in adaptive evolution
Hybrid speciation in Lake Malawi cichlids (Domino Joyce, Hull)
What is introgression
the incorporation (usually via hybridization and backcrossing) of alleles from one entity (species) into the gene pool of a second, divergent entity (species)
What is a fixed allele?
A fixed allele is an allele that is the only variant that exists for that gene in all the population
What is the relationship between Ne and Drift
the magnitude of drift is inversely proportional to effective pop size
What event can dramatically decrease the harmonic mean
a bottleneck event
In terms of an ideal situation, what would the relationship between N and Ne be
N=Ne
What are the requirements for Ne to equal N
equal no. of males and females who can all reproduce
all individuals are equally likely to reproduce
the number of offspring does not vary anymore than expected by chance
Mating is random
The no. of breeding individuals is constant from one gen to the next
What does effective population size mean
it is the size of the population that would lose genetic diversity/lose heterozygosity at the same rate as the actual population
What does different sex ratios decrease Ne
Because not every individual will have an eqaul chance to reproduce
Why could Ne be smaller than N
anything that increases VARIANCE among individuals in reproductive success: unequal sex ratio high variance in family size inbreeding variation in pop size over generations overlapping generations
