Chapter 6
Organophosphate insecticides kill insects by inhibiting an enzyme called acetylcholinesterase (AChE1) in the nervous system
used to kill mosquitoes
Some mosquitoes were able to resist stronger doses of the insecticide
C. pipiens carries a gene called Ester, which encodes an enzyme known as esterase
used to break down a wide range of toxins
resistant mosquitoes carried a mutation that altered the expression of Ester to produce more esterase
eventually, the genes of most mosquitoes have changed, giving them resistance to toxic insecticides (evolved)
more prominent in mosquitoes near the coast, rarer for inland mosquitoes
A population is a group of interacting and potentially interbreeding individuals of a species.
made up of individuals that carry alleles
some populations carry large amounts of allelic diversity while others can be identical
Population genetics is the study of allele distributions and frequencies
Because diploid organisms carry two copies of each autosomal chromosome, they can have up to two alleles for each gene or locus.
Individuals carrying two copies of the same allele are homologous at the locus, whereas individuals carrying two different alleles are heterozygous for the locus.
Gregor Mendel discovered how two heterozygous individuals can produce offspring in a 3:1 ratio.
three smooth peas for every wrinkled one
The Hardy-Weinberg theorem states that in the absence of drift, selection, migration, and mutation, allele frequencies at a genetic locus will not change from one generation to the next
Random mating is never really the case, species typically evolve strong preferences about their choice of mates.
When geneticists refer to random mating they mean in terms of alleles.
the wrinkled allele is just as likely to mate with a smooth allele as it is with a wrinkled one
mating is assumed to be random for that genetic locus
When the genetic lotus contains two alternative alleles:
p represents the frequency of one allele
q represents the frequency of the other allele
p + q = 1
The total frequency of all genotypes is the sum of frequencies of individuals with each possible genotype:
1 = f(A1A1) + f(A1A2) + f(A2A1) +f(A2A2)
This principle assumes that populations are infinitely large
Another assumption is that no alleles enter or leave a population through migration
The theorem serves as a null hypothesis under which allele frequencies do not change
Genetic drift → imperfect sampling causes some alleles to be underrepresented relative to others → an allele can be lost
allele frequencies “drift” randomly away from their starting point
purely due to chance, but less familiar than natural selection
Natural selection → environmental factors are unfavorable for certain alleles → those alleles become less common
Migration (gene flow) → individuals with a new allele enter the population → new allele
Mutation → one allele becomes another allele → new genetic variant appears in the population
Hardy-Weinberg equilibrium → random mating, no migration, genetic drift, mutation, or natural selection
Genetic drift is the random, unrepresentative sampling of alleles from a population during breeding
mechanism of evolution because it causes the allelic composition of a population to change from generation to generation
alleles are lost due to genetic drift much more rapidly in small populations than in large populations
if you have a jar of an equal number of jelly beans that are white and red
and you pick a bunch in your hand, you would likely have picked our 50/50 proportion of red and white
but if you only picked out 2, then it wouldn’t be surprising if they were both red
the smaller the number, the more likely you’ll observe large deviations from the original frequency
causes one allele to become fixed → all members carry only that particular allele
given enough time, even large populations will lose alleles due to genetic drift
Genetic bottlenecks are genetic drifts that affect populations that are only temporarily reduced to low numbers
ex. northern elephant seals were slaughtered in huge numbers by hunters
eventually, the entire species was doomed to extinction
through the genetic bottleneck, it lost many of its alleles
if there were 100 jelly bean colors, and as a result of genetic bottlenecks, the population size shrank, then many of the colors might not be present
after the bottleneck, once the population returns to its former size, its genetic variation will remain low as the few colors are the only ones reproducing
if a bottleneck is less severe, more alleles are held
Even brief bottleneck events can lead to drastic reductions in the amount of genetic variation within a population
this loss of allelic diversity can persist for many generations after the event
The founder effect is a loss of allelic variation that accompanies the founding of a new population from a very small number of individuals
founder effects can cause the new population to differ considerably from the source population
when a small number of individuals leave a larger population and colonize a new habitat
ex. plant seeds stick to the feet of migratory birds and are carried somewhere else where they start a population
a type of bottleneck: only a small subset of the genetic diversity of the source populations is likely to be included in the new population → frequencies of alleles differ
Selection occurs whenever genotypes differ in their relative fitness.
depends on the frequency of an allele as well as its effects on fitness
When populations are small, the effects of drift can enhance or oppose the action of selection
for example, by removing harmful alleles that have been driven to low frequency by selection
for example, by removing beneficial alleles
When fitness effects oppose each other, the balance between them will determine the net direction of selection acting on the allele
Natural selection arises when:
individuals vary in the expression of their phenotypes
this variation causes some individuals to perform better than others
Fitness is the reproductive success of a particular phenotype
the fitness of an individual is the product of its entire phenotype (so it could be hard to measure)
Fitness components: survival, mating success, and fecundity
represented by w
describes the relative contribution of all individuals in the population
if individuals with a specific genotype contribute more offspring than individuals with other genotypes, their relative fitness will be greater than 1
if it’s lower, it’ll be less than 1
In other cases, it is measured by comparing all fitnesses with the genotype with the highest fitness of w=1 instead of with the mean fitness
all other genotypes will get a value between 0 and 1
Measuring fitness contributions to a specific allele is more difficult:
for diploid individuals, alleles don’t act alone, they are paired up to form the genotype
if there is a dominance interaction then that will influence the phenotype
selection does not act directly on alleles, it acts on individuals and their phenotypes
Pleiotropy → mutations can have more than one effect on an organism
Antagonistic pleiotropy is when a mutation occurs that will have beneficial effects for one trait but also detrimental effects on other traits
ex. Ester1 that gave mosquitoes resistance to insecticides also gave them a higher probability of getting caught by predator spiders
The net effect of an allele on fitness is the sum of its pleiotropic effects
this would be beneficial for the coastside mosquitoes as they are in more danger and extra esterases would be beneficial even if it makes them more vulnerable to predators
however it would not be beneficial for the inland mosquitoes, so it’ll just lower their overall fitness
Ester4 became selected for later on because it creates esterases (even though it was less protection than the previous one) but it also does not impose a high cost of increased predation
so inlander don’t pay a price for carrying it and coaster benefit from it
Negative selection occurs when alleles that lower reproductive success are selected
Positive selection occurs when alleles that speed up growth and boost survival rate are selected
HMGA2 variant: additive
people who carry one copy will grow half a cm taller than people who lack it
homozygous people (have 2 copies) will get double the effect and grow a cm taller
the effects of the alleles can be predicted simply by summing the number of copies that are present
additive alleles are vulnerable to the action of selection
deleterious additive alleles can be entirely removed from a population
Dominant and recessive alleles are not additive
dominant will overshadow the other allele
the same phenotypic effect will occur when an individual has one copy in a heterozygous or two copies in a homozygous
a recessive allele can only have an effect when paired with another copy of the same recessive allele
Rare recessive alleles are almost always carried in heterozygous individuals
because there would need to be another heterozygous individual that mates with a heterozygous individual (both with the rare trait) for it to possibly pass both rare alleles to a homozygous offspring
Recessive alleles are often hidden from the action of selection because they don’t affect phenotype
Drift alone determines whether recessive alleles persist in a population
if drift occurs, the recessive allele frequency, heterozygotes might become fairly common
the odds are higher that a heterozygote mates with another heterozygote and produces a homozygous recessive offspring
then, selection can begin to act on the recessive allele
With a positive effect from the recessive allele, selection can increase the frequency and the dominant allele decreases in frequency
For deleterious recessive alleles, if drift creates a high frequency of heterozygotes, they will produce recessive homozygotes that will suffer lowered fitness
selections can not remove the recessive allele completely, despite its low fitness
once the frequency drops, it occurs mostly in a heterozygous state where it could once again be hidden from selection
Dominant alleles that are newly introduced to a population will rapidly increase in frequency
if the effects are favorable (average excess of fitness is positive), spreads rapidly
while the allele is still rare (at first), it is present in heterozygous individuals
the rest of the population carries the ancestral allele
as the dominant allele becomes more common, heterozygotes begin to pair with other heterozygotes to produce homozygous offspring
same fitness as heterozygotes and the frequency of the allele continues to increase
as the dominant allele approaches fixation, fewer individuals are heterozygous, and the ancestral allele (now recessive) becomes so rare that heterozygotes rarely mate
the recessive allele is now only present as heterozygotes and since phenotype does not differ between homozygous dominant and heterozygous, the fitness is equal
selection is unlikely to drive the dominant allele to fixation completely as the ancestral trait cannot be eliminated
Rare alleles are almost always carried in a heterozygous state.
When recessive alleles exist in heterozygous individuals, they are invisible to the action of selection.
Selection cannot drive dominant beneficial alleles all the way to fixation because once the alternative (recessive) alleles become rare, they can hide indefinitely in a heterozygous state.
The mutation rate for any specific locus may be extremely low, but it is much higher when considering an entire genome or population. The gradual accumulation of mutations within populations is the ultimate source of heritable genetic variation.
Although the rate of mutation per haploid genome is low, each genome is huge and the rate at which mutations arise in the entire human population is not low.
Cystic fibrosis: genetic disorder in which the lungs build up with fluid, leading to pneumonia
caused by mutations to the CFTR gene which encodes a chloride channel in epithelial cells
Balancing selection actively maintains multiple alleles within a population. Two mechanisms are negative frequency-dependent selection and heterozygote advantage.
Negative frequency dependence occurs if the fitness of an allele is higher when that allele is rare than when it is common.
Heterozygote advantage occurs when the heterozygotes for the alleles in question have higher fitness than either of the homozygotes.
Sometimes, the relative fitness of a genotype is high when it is rare, and low when it is common.
negative frequency-dependent selection
fitness changes as the genotype frequency changes
ex. elderflower orchid
flower in France
in a single population, some have deep purple flowers, while others produce yellow ones
difference in colors are a result of genetic polymorphism (genetic difference among multiple individuals in a population)
orchids produce pollen which is attached to bumblebees that visit the orchids in search of nectar
trick bumblebees by not producing nectar
risk: bumblebees will begin to visit rewardless orchids less
yellow flowers were rare, but they were more fit (delivered more pollen to bees and produced fruits)
but when they were abundant, bees learned to avoid them and favor purple flowers instead
two different colors can coexist in the flower populations
whenever one color starts to disappear, its fitness relative to the other increases until it is common again
when it becomes too common, the other fitness increases and spreads
continuous cycle
Natural selection can maintain allelic variation when heterozygotes have higher fitness than homozygous
heterozygote advantage
selection maintains both alleles in the population
ex. S and A alleles for hemoglobin
in Nigeria, there are few SS genotypes because the S alleles give rise to a deformed form of hemoglobin
RBCs with deformed molecules take a long, curved shape that could contribute to sickle-cell anemia (RBCs die and clump together damaging blood vessels, organs, and joints)
most children with SS die before age 5
yet AA is also uncommon because the S allele also protects people from malaria
makes the infected cells less sticky, reducing clogs and fetal bleeding
so both A and S alleles don’t disappear, heterozygous individuals in regions with malaria have higher fitness than either homozygous genotypes
if malaria was eliminated tomorrow, the S allele would begin to disappear and AS would immediately lose its high fitness advantage
Balancing selection makes the population more resistant overall to malaria
Fitness is not an inherent quality of genotype, it emerges from the relationship of organisms to their environment
a genotype that increases fitness in some environmental conditions may decrease fitness in other conditions
Inbreeding increases the percentage of genetic loci that are homozygous for alleles.
Inbreeding changes genotype frequencies but not allele frequencies and therefore is not a direct mechanism of evolution. Inbreeding can, however, set the stage for strong selection on rare recessive alleles that typically would be masked in heterozygous individuals.
Genetic bottlenecks often go hand in hand with inbreeding and selection if small numbers of individuals establish a new population.
These “founding events” can be important episodes of rapid evolution because genetic drift has noticeable effects, and the increased homozygosity arising from inbreeding exposes recessive alleles to positive and negative selection.
If the new population survives this bottleneck, it may be very different from its parent population.
Sickle-cell anemia illustrates natural selection paradoxically maintaining disease in a population.
Charles II:
he had a host of deformities
by age 30, he looked like an old man
“the Hexed”
his parents had married within their family
marrying relatives kept power within the dynasty, but it had an unfortunate side effect known as inbreeding
Rare recessive alleles can be preserved in large populations because common dominant alleles overshadow them
however, in inbreeding populations, the rare deleterious alleles can become unmasked in homozygotes
parents are closely related and are more likely to share rare alleles two random individuals in a population
the more closely the parents are related, the greater the odds that their children will be homozygous for recessive alleles, including the deleterious ones
Inbreeding does not change the frequency of alleles in a population
it rearranges alleles such that homozygotes for rare recessive alleles become more common
deleterious rare alleles in combination can cause genetic disorders that lower fitness
selection can reduce the frequency of these rare alleles, reducing the genetic variation in the population
The higher the homozygosity, the higher you’d expect rates of lethal genetic disorders to become
High inbreeding tended to be associated with low infant survival rates in the Hapsburg dynasty. As a result, Spanish royalty had few children, and Charles II died without an heir.
Inbreeding coefficient (F): the probability that the two alleles at any locus in an individual will be identical because of common ancestry
can be estimated by measuring the reduction in heterozygosity across loci within the genome of an individual attributable to inbreeding
or it can be estimated by measuring the reduction in heterozygosity at one or a few loci sampled for many different individuals within the population
Inbreeding depression: is a reduction in the average fitness of inbred individuals relative to that outbred
arises because rare recessive alleles become expressed in a homozygous state where they can affect detrimentally the performance of individuals
exacerbates the loss of allelic diversity caused by genetic drift
when populations become small enough, they begin to inbreed
Population subdivision enhances the effects of genetic drift, eroding genetic variation from within local subpopulations and causing allele frequencies to diverge from place to place.
Gene flow counteracts the effects of population subdivision, increasing genetic variation within subpopulations and homogenizing allele frequencies across the landscape.
Landscape genetics accounts for real-world populations
Bighorn sheep:
inhabit a range extending from southern Canada to Baja Penisula in Mexico
but the range is not continuous
they prefer steep rocky cliffs, which tend to be isolated from each other
A sheep from Canada can't wander and mate with a sheep in Mexico
Population structure or subdivision is when the constraints of landscape and distance restrict the movement of individuals from place to place
can affect evolution because it increases the opportunity for genetic drift to change allele frequencies
subdivisions are smaller than entire populations, so even if a sheep were to mate with random alleles within the subpopulation, the frequencies of the alleles in different populations would diverge from each other
drift occurs independently in each of the subpopulations
the longer the populations are separated, the more they should diverge in their respective allele frequencies (the more genetically distant they become)
Fst is a measure of genetic distance between subpopulations
measured the reduction in heterozygotes at a locus attributable to the effects of population subdivision
when values are near zero, then populations have very little genetic structure (allele frequencies are approximately the same from place to place)
when local subpopulations begin to diverge, the value increases
Movement between subpopulations has the opposite effect of divergence
whenever individuals from one local population mate with individuals from other populations, the result will be mixed offspring
the movement of alleles is called gene flow
can counteract the loss of alleles due to drift, restoring genetic variation