Population Genetics Flashcards
Aristotle – Main Ideas
- examined natural world for evidence of divine order
- can understand the world by looking at physical biological objects – reveal reality by observing the natural world
- Scala naturae (Chain of Being) – fixed
Aristotle
What is the idea of Scala naturae (Chain of Being)?
- hierarchical arrangement of forms
- species arranged linearly along a scale (God → man → mammals → egg-laying animals → insects → plants → non-living matter)
- formed basis for Western belief in fixity of species, each of which has a typical form
Carolus Linnaeus – Main Ideas
- binomial system
- proposed a nested system of relationships (as opposed to Scala naturae)
- Linnaean system
- defined species by focusing on reproduction
- believed in balance of nature
- eventually acknowledged limited formation of new species by hybridization
Carolus Linnaeus
What is the binomial system?
classification system for organisms
each organism a specific name and generic name
ie. humans → Homo sapiens
Carolus Linnaeus
What is the Linnaean system?
nested system of relationships (as opposed to Scala naturae)
groups organisms into:
kingdom – ie. animalia phylum – ie. chordata class – ie. mammalia order – ie. primates family – ie. Hominidae genus – ie. Homo species – ie. sapiens
Carolus Linnaeus
How did he define species by focusing on reproduction?
recognized fundamental difference between:
- interbreeding organisms (within a species)
- non-interbreeding organisms (different species)
Carolus Linnaeus
What were his beliefs in the balance of nature?
- each species has its place in a divine plan
- species would not change or go extinct
Comte de Buffon – Main Ideas
- degeneration
- change only happens within families
Comte de Buffon
What was his idea of degeneration?
believed Linnean hierarchy reflected common descent with divergence over time
- physical environment (somehow) changes organic particles
- new species form when animals migrate
- new environment then causes change to the species
Comte de Buffon
How did he describe his idea that change only happens within families?
- each family conforms to an internal mold
- species can change over time, but are limited to their original mold
Erasmus Darwin – Main Ideas
- wrote about laws of organic life
- transformation or transmutation
- all of life consists of ‘one living filament’ connecting all living forms to common ancestor
Erasmus Darwin
What was his idea of transformation or transmutation?
believed organisms constantly attempted to improve themselves by adapting to their environment
Erasmus Darwin
Was there a mechanism for transmutation?
no
- could have been mutations
- could have been environment inducing mutations
Jean-Baptiste Lamarck – Main Ideas
- first to put mechanism to evolutionary change – inheritance of acquired characters
- theory of transformism
- evolution is a perfecting process
- suggested a mechanism for this organic progression
Jean-Baptiste Lamarck
What is the theory of transformism?
- organisms progress through hierarchy of advancing forms (almost Scala naturae in reverse)
- nature has gradually complicated their structure – producing in succession every species of animal, beginning with the least perfect (or simplest) and ending with the most perfect
- at base of hierarchy, ‘simple’ organisms constantly arise by spontaneous generation
Jean-Baptiste Lamarck
What was the mechanism that he suggested for the organic progression of species?
first law: use or disuse of a structure leads to its development or diminishment
second law: acquired characters can be passed onto offspring
Thomas Malthus – Main Ideas
principle of overproduction
Thomas Malthus
What is the principle of overproduction?
- most organisms produce far more offspring than can possibly survive
- even when resources are plentiful, populations tend to grow geometrically until they outrun their food supply
- poverty, disease, and famine are inevitable, leading to ‘struggle for existence’
Charles Lyell – Main Ideas
- principles of geology
- uniformitarianism
- applied his views to the living world
Charles Lyell
What are the principles of geology?
(had major influence on Darwin and Wallace)
- believed earth is constantly changing
- processes that molded earth’s surface can be understood by modern-day events
Charles Lyell
What is uniformitarianism?
earth is subject to gradual, continuous change – but without progress or development, earth remains at steady state
Charles Lyell
How did he apply his views of the Earth to the living world?
initially believed that some members of all classes of organisms existed throughout the history of Earth
- BUT the change that occurred was abundance and location of species, and exact form of each species
- species have a real existence in nature, and at the time of its creation, each was endowed with attributes and organization by which it is now distinguished
Charles Darwin – Main Ideas
natural selection
Charles Darwin
What were his critical facts on natural selection?
- variability exists within species
- variant traits may be inherited (Darwin didn’t know how)
- composition of populations must change over time → evolution by natural selection
- as natural selection acts on geographically isolated populations, they become increasingly different from each other, leading to formation of first varieties within a species → separate species → genera, etc. (ever-branching process)
Charles Darwin
What did he draw from Malthus’s Principle of Overproduction?
- the principle implies that many individuals must die or fail to reproduce
- individuals slightly better suited to their environment must be more likely to survive
- therefore, some variants will be preserved over time more than others
Alfred R. Wallace – Main Ideas
- natural selection co-discovered
- (drawing from Lyell and Malthus) realized that self-acting process of natural selection would necessarily improve the race, because in every generation the inferior would inevitably be killed off and the superior would remain – fittest would survive
What is evolution?
change in form and/or behaviour of organisms between generations
descent with modification (Darwin definition)
What is change?
origin and alteration over generations of (ideas within society)…
- frequencies of genotypes within populations
- proportion of differentiated populations within species
- proportion of species with different traits within a lineage
What is natural selection?
process by which some individuals contribute more offspring to next generation as a consequence of carrying trait(s) favourable to survival or reproduction
What are some reasons why evolutionary change can occur?
chance bursts of reproduction, deaths and mutation
natural selection explains how undirected change can improve match between organism and its environment
What are the 3 things required for evolution by natural selection?
- individuals vary in some trait (variance)
- individuals with some trait values are more likely to live and/or reproduce (selection)
- parents have offspring with similar trait values (heritability)
What is selection?
differential survival or reproduction of different entities
- only time when there is variation in fitness (ability to survive and reproduce)
- some individuals are better able to survive than others
What is fitness?
average contribution per parent to next generation, including survival and reproduction
What contributes to changes in allele frequencies?
differences in fitness (W)
What do changes in allele frequencies do?
alleles cause individuals to survive at different rates
can measure these rates by fitness, which automatically leads to change
How does allele frequency change before and after haploid selection?
frequency after selection takes into account fitnesses of the alleles
Haploid Selection
What happens to allele frequencies if there is no selection?
allele frequencies are expected to remain the same after gametes come together (gamete union), and after they fall apart again (meiosis)
Haploid Selection
What does the equation for allele frequency after one generation assume?
- haploidy – only has one copy of each gene (A or a)
- only two alleles
- nothing else is going on – no mutation, or selection in diploid phase, etc.
What does it mean to reproduce asexually?
doesn’t have alternations between haploid and diploid – only has haploid selection regime
What are the differences between the equations for evolutionary change for sexual and asexual haploids?
identical equations, as long as there is no selection in diploid phase
Evolution by Natural Selection: Long Term
What are we assuming?
- environment is staying the same
- relative fitness of the two alleles are constant over time
How do we measure fitness when considering the spread of a new beneficial allele (A) in a population of wildtype alleles (a)?
typically measure fitness relative to the wildtype:
Wa = 1 WA = 1 + s
What is the selection coefficient (s)?
proportional increase in fitness caused by replacing allele a with A
- need to define reference, and measure all fitnesses relative to that value, before calling it a selection coefficient
- find selection curve by fitting data
What is selection?
proportional change of relative fitness
Is mean fitness always positive?
yes
Is mean fitness in offspring or parent generation higher?
offspring
What is mean fitness?
sum of fitness of each individual times its weighted frequency in population
If evolution were so easy and effective, why isn’t everything the same?
- organisms vary
- environments differ – fitnesses would be different, would be selected in different directions
- world is changing – not having same fitness when it started
What are methods of evolution NOT by natural selection?
- mutations arise – prevents from rising to perfection
- chance plays a role
- sex and recombination alter
- alleles favoured for effects on some traits may affect other traits (pleiotropy)
- neighbouring alleles in genome can be dragged with selected alleles (hitchhiking) – genes are not selected in isolation
What does the spread of a beneficial allele look like on a graph?
always follows S-shaped curve – increasing slowly when allele is rare and also when it is common (understand why this is)
What does it mean to be a weakly favoured allele?
difference in fitness between an allele and a relative allele is low
Does evolution work better with more or less variability?
more
When does natural selection act in haploids?
haploid stage
no selection in diploid stage
When does natural selection act in diploids?
diploid stage
Diploid Selection in Asexuals
How does mean fitness change over time?
increases over time (or stays the same)
Diploid Selection in Sexuals
Key Point
sex (segregation) can undo genetic associations built by selection
change due to selection is the same, but meiosis breaks apart and reassorts the diploid genotypes
When do we assume Hardy-Weinberg proportions?
(assuming random mating among gametes)
during gamete union
What is assortative mating?
A only mates with A sperm
What is sexual selection?
some eggs preferentailly mate with one type than another
What are some cases where gametes don’t combine randomly?
- assortative mating
- sexual selection
(usually not random mating in organisms)
Diploid Sexuals without Selection
Key Point
with random mating and no selection, allele frequencies do not change (from one generation to the next) and diploids are immediately in Hardy-Weinberg proportions
Diploid Sexuals without Selection
Assumptions
- random combination of gametes from gamete pool
- no differences in fitness among genotypes
- very large population (no chance effects changing genotype frequencies at any step)
- no mutation or migration altering variants in population
if populations of adults are not at Hardy-Weinberg proportions, it indicates that one of our assumptions is wrong (ie. there may be selection or non-random mating)
Diploid Sexuals without Selection
Why might there be fewer heterozygotes observed in a population than at HW?
- due to selection
- due to non-random mating
- due to assortative mating
- maybe something is occurring in a neighbouring gene
- recent immigration of one of the homozygotes
- fitness disadvantage of heterozygotes
- combination of these factors
Diploid Sexuals with Selection
Key Point
with random mating and selection, allele frequencies do change
- while diploids are at Hardy-Weinberg proportions at birth, they may not be after selection
- if W are different, p in one generation is different from p in next generation
Diploid Selection in Sexuals
What is a polymorphism?
neither allele goes to 100% frequency (more than one type in population)
Diploid Selection in Sexuals
Why can evolution move populations away from the most fit genotype (ie. heterozygote disadvantage)?
- even though a is favoured over A, A can get selected if you start right
- evolution does not see the fact that there’s a better genotype
- evolution is myopic – works with genotype in population, which determines how allele frequencies change from one generation to the next
Diploid Selection in Sexuals
What is an equilibrium?
point of a system that when started at that point, system no longer changes
found by identifying when p[t] equals p[t+1]
Diploid Selection in Sexuals
What is an unstable equilibrium?
points nearby are repelled away from the equilibrium
Diploid Selection in Sexuals
What is a stable equilibrium?
points nearby approach the equilibrium
Diploid Selection in Sexuals
What is the selection coefficient (s)?
measures fitness of one homozygote (AA) relative to the other (aa)
Diploid Selection in Sexuals
What is the dominance coefficient (h)?
measures how dominant A is with respect to fitness
How does mean fitness change in diploid sexuals?
always increases (or stays the same)
Is selection generally slower in haploids or diploids? Why?
diploids
because mutations are partially ‘masked’ in heterozygotes
when heterozygotes are exactly intermediate (‘additive case’,
WAa = (WAA + Waa) /2 ), mean fitness rises half as fast as was seen in haploids
Diploid Selection
Describe the S-shaped curve of the spread of a beneficial allele.
- always follows S-shaped curve
- increases slowly when allele is rare or common
- curve is flatter at first for recessive (partially to fully) beneficial alleles
- curve is flatter near fixation for dominant (partially to fully) beneficial alelles
- very little room if you’re starting near fixation
Diploid Selection
What are the proportions of frequencies immediately after random union of gametes?
Hardy-Weinberg proportions are reached (p2, 2pq, q2)
Diploid Selection
What are the proportions of frequencies after selection?
- selection can lead to departures from Hardy-Weinberg among adults, even with random mating
- selection builds favourable allele combinations that are broken apart by sex – overall, mean fitness increases over time or stays the same
Diploid Selection
What are the proportions of frequencies after selection?
- selection can lead to departures from Hardy-Weinberg among adults, even with random mating
- selection builds favourable allele combinations that are broken apart by sex – overall, mean fitness increases over time or stays the same
Diploid Selection
Mean fitness increases over time or stays the same in a one locus diploid model of selection. Does this mean it is optimal?
NO – mean fitness rises over time but stops at (ie. 1.1), cannot reach its optimal (ie. 1.2)
If the frequency of allele A at locus A is 1.0 in a population, what processes could lead to a change in allele frequency? Select all that apply.
- mutation
- migration
- drift, hitchhiking, and selection will not result in evolutionary change because allele ‘A’ cannot change in frequency when it is the only allele present (it will stay at 100%)
True or False: Evolution by natural selection will occur whenever there is variation in a trait that results in individuals with different fitnesses, regardless of the cause of the variation.
false
if the variation is not genetic, then evolutionary change will not occur by natural selection
ie. when we prune the plants in our gardens (or other animals eat our plants), the result is variation in the size of plants, but that variation isn’t inherited.
What processes can lead to a decline in mean fitness across one full generation of a life cycle?
- mutation
- selection at two loci with recombination – can lead to the breaking apart of linkage disequilibrium that can cause declines in fitness over time
- selection at one locus with drift – can lead to a decrease in fitness (ie. even leading to the fixation of deleterious alleles by chance)
mean fitness rises from one generation to the next with either haploid selection (only) or diploid selection (only)
-
in diploids, meiosis and random mating can lead to a decrease in fitness, while selection leads to a rise in fitness, but the net result is that mean fitness either rises or stays the same across a full generation
-
Is selection more efficient with a smaller or larger population size?
larger
- less chance involved
- less drift
Mutation-Selection Balance
while selection reduces frequency of deleterious alleles, mutation continually reintroduces them
Mutation with Selection – Haploids
Key Point
if mutation repeatedly generates deleterious alleles, then they will persist in populations despite their negative effects
selection will act to remove mutant alleles, but mutation will reintroduce them, with these two forces balancing over time
How does mean fitness change with mutation?
with mutation and selection, mean fitness can decline over evolutionary time
mean fitness continues to decrease over time (as new mutations arise) until it eventually stabilizes
mean fitness can decline when majority are deleterious
What is mutation load?
reduction in fitness due to mutations (μ)
mutations reduce fitness on average by an amount that depends only on the mutation rate, and combination of mutation and selection can lead to declining fitness
more severe mutations will equilibrate at lower frequency, and less severe mutations will equilibrate at higher frequency
but number of deaths will depend only on mutation rate
-
Are mutant alleles expected to be found at higher frequency when recessive or when they affect heterozygous fitness?
recessive
What is genetic drift?
change in allele frequencies that results from random sampling processes that take place within populations over generations
Why is drift always acting?
because all populations are finite, drift is always acting – produces small or large changes in allele frequencies and affecting loci throughout the genome
Changes in allele frequencies from one generation to the next are expected to be ____ in smaller populations.
greater
Populations remain polymorphic for longer, on average, with _____ population size.
increasing
What are effects of drift driven mainly by?
population size
therefore, all else being equal, drift acts similarly across all of the loci in the genome
Genetic Drift
In diploid populations, what is the probability that a neutral (no selection) allele fixes?
its initial frequency (p)
Genetic Drift
What is expected heterozygosity?
probability that two alleles drawn at random are different alleles
can be calculated to measure loss of genetic variability due to drift
Genetic Drift
When we sample two alleles at time ‘t’, what are the two possibilites?
sampled alleles descended from same parent allele
- probability = 1/(2N)
sampled alleles descend from different parent alleles
- probability = 1 - 1/(2N)
Genetic Drift
Ignoring mutation, what is the only way for the alleles to differ at time t?
if they descended from different parent alleles, which occurs with probability 1-1/(2N)
Genetic Drift
How much does genetic variability decline in every generation?
genetic variability declines by 1/(2N) every generation in a population of N diploids
Genetic Variation
Is expected heterozygosity faster with smaller or larger populations?
smaller
Genetic Variation
What is expected homozygosity?
probability that two alleles drawn at random are the same allele
What does expected homozygosity describe?
describes the increase in homozygosity when alleles have recently descended from the same ancestor in a finite population (“inbreeding”)
small populations, in particular, become “inbred” with little genetic variation remaining due to drift
What are founder effects?
effects that occur when a new population is founded by a small number of individuals from a larger source population
What is a genetic bottleneck?
severe reduction in the number of individuals in a population, which results in the loss of genetic variation in the surviving population
loss of genetic diversity in nature is more likely to limit a population’s ability to cope with environmental change, reducing its evolutionary potential and, thereby, increasing extinction risk
With few surviving lineages…..
with few surviving lineages, chance that the two alleles in an individual recently shared a common ancestor is much higher (= “inbreeding”), increasing the frequency of homozygous recessive diseases (= “inbreeding depression”)
When might the impact of drift be less noticeable?
if selection is strong enough and the population size large enough
In a large population, what is the probability of fixing a new mutation?
(Haldane’s fixation probability)
twice its selective advantage when rare (2s in haploids, 2hs in diploids)
What is the fate of an allele determined more by?
determined more by selection than drift in diploid populations when 2hs > 1/(2N)
Can slightly deleterious mutations fix?
yes, due to drift
drift acts similarly across all of the loci in the genome
-
If two loci were evolving independently…
knowing the allele at A would not say anything about which allele is present at B
What is disequilibrium (linkage disequilibrium)?
measures genetic associations among two loci, indicating which alleles tend to be found together at two loci
*linkage disequilibrium is terribly named – it can be found between unlinked loci (ie. between sites on different chromosomes) and can persist at equilibrium
Positive vs. Negative Disequilibrium
positive: when two alleles occur together more often than expected
negative: when two alleles occur together less often than expected
What is recombination?
occurs during meiosis in sexual organisms to generate gametes carrying new combinations of alleles
genetic distance between two loci on a chromosome – how likely they will recombine during meiosis
What is recombination rate (r) between two loci?
probability of cross-over between them, creating non-parental gametes
parental chromosome combinations are produced at total rate 1–r (each being the one inherited in the gamete with probability ½)
non-parental chromosomes are produced at total rate r, with each of the two types of recombinant chromosomes occurring ½ of the time
Why might we find disequilibrium?
several processes generate associations among loci:
- drift
- mutation
- migration
- selection
Why would drift lead to disequilibrium?
chromosome combinations rise or fall in frequency, by chance
Why would mutation lead to disequilibrium?
new mutations appear on particular genetic backgrounds
Why would migration lead to disequilibrium?
movement of individuals mixes different chromosomes
Why would selection lead to disequilibrium?
some chromosome combinations are fitter than others
When does linkage disequilibrium decay over time, and at what rate?
without processes of mutation, drift, migration, or selection (which causes disequilibrium to rise), disequilibrium decays over time at a rate proportional to recombination
D[t+1]=(1-r) D[t]
What is genetic hitchhiking?
linkage disequilibrium between a selected and a neutral locus can cause alleles at neutral locus to change in frequency
With selection in both loci, how can linkage disequilibrium be generated?
by fitness interactions (epistasis)
combinations that are more fit will become more common through linkage
