chapter 6 the ways of change: drift and...
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Chapter 6
The ways of change: drift and selection Population genetics
Study of the distribution of alleles in
populations and causes of allele frequency
changes
Key Concepts
Diploid individuals carry two alleles at every
locus
Homozygous: alleles are the same
Heterozygous: alleles are different
Evolution: change in allele frequencies from
one generation to the next
Hardy-Weinberg equilibrium
Population allele frequencies do not change
if:
Population is infinitely large
Genotypes do not differ in fitness
There is no mutation
Mating is random
There is no migration
Predictions from Hardy-Weinberg
Allele frequencies predict genotype frequencies
p2 + 2pq + q2 = 1
Key Concepts
Hardy-Weinberg theorem proves that allele
frequencies do not change in the absence of
drift, selection, mutation, and migration
Mechanisms of evolution are forces that
change allele frequencies
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Populations evolve through a variety
of mechanisms Key Concept
Hardy-Weinberg serves as the fundamental
null model in population genetics
Genetic Drift
Peter Buri started 107 cultures with 8 males and 8
females all heterozygous for bw75 red eye and for bw
white eye
bw / bw75 heterozygous orange parents
All H-W assumptions met except large population size
19 generations – each generation started with:
Randomly selected: 8 males and 8 females
Many populations had alleles that went to
Extinction
Fixation Other populations ranged between two extremes
What happened?
Genetic drift causes evolution in finite
populations
Genetic drift causes
evolution in finite
populations
Genetic drift results from random
sampling error
Sampling error is higher with smaller sample
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Drift reduces genetic
variation in a population
Alleles are lost at a faster
rate in small populations
Alternative allele is fixed
Key Concepts
Genetic drift causes allele frequencies to
change in populations
Alleles are lost more rapidly in small
populations
Evolutionary biologists have debated the
importance of natural selection and
genetic drift
R.A. Fisher
Natural Selection
and
Statistics
Sewel Wright
Genetic Drift
Important
Motoo Kimura
also emphasized
Genetic Drift
Bottlenecks reduce genetic variation Northern Elephant Seals – killed for tusks (ivory)
and then for museums!
A bottleneck causes genetic drift
Rare alleles are most likely to be lost
during a bottleneck Founder Effect Mutiny on the Bounty –Pitcairn Islands
Founder effects cause genetic drift
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High incidence of migraine headaches
attributed to founder effects on Norfolk Island
in Pitcairn Islands
Genotypes, Phenotypes and
Selection
Alleles are selectively neutral if they have no
effect on the fitness of their bearers. This
phenomenon often occurs when genetic
variation at a locus does not effect the
phenotype of an individual.
Selection acts on whole phenotypes of
individuals.
Key Concept
Even brief bottlenecks can lead to a drastic
reduction in genetic diversity that can persist
for generations
Key Concept
Alleles are selectivity neutral if they have no
effects on the fitness of their bearers. This
phenomenon often occurs when genetic
variation at a locus does not affect the
phenotype of an individual.
Selectively neutral
S = selection coefficient used to express how
much genotypes differ in fitness
Selection acts on whole phenotypes of
individuals So must affect fitness
The concept of fitness
Fitness: the reproductive success of an individual with a particular phenotype
Components of fitness:
Survival to reproductive age
Mating success
Fecundity
Relative fitness: fitness of a genotype standardized by comparison to other genotypes
Selection Changes Allele Frequencies
Average excess fitness: difference between
average fitness of individuals with allele vs.
average fitness of those without
Use this to predict how the frequency of the
allele will change from one generation to the
next
Change in frequency
due to selection p is
frequency of A1 allele
Average fitness of the
population p is frequency of A1
allele
Average excess of fitness
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Natural selection more powerful in
large populations
Drift weaker in large populations
Selection weaker in small populations
Small advantages in fitness can lead to large
changes over the long term
Pleiotropy may constrain evolution
Pleiotropy: mutation in a single gene affects
many phenotypic traits
Can be antagonistic
Net effect on fitness determines outcome of
selection
Pesticide resistance and pleiotropy
• Ester1 - mosquitoes resistant to insecticide, but more vulnerable to
spider predation. Ester1 higher fitness on coast; away from coast much
lower fitness (no insecticide)
• Ester+4 less protection from mosquitoes at coast, but more common
than Ester1.. Higher fitness inland because less cost of predation. BUT
higher costs due to overproduction of esterases.
• Antagonistic Pleiotropy
Pesticide resistance and pleiotropy
Antagonistic Pleiotropy
Effects of mutation have opposite effects on
fitness
Ester1 has benefit along the coast but
Inland, benefit declines because there are
fewer mosquitoes, and cost increases due to
increased chance of predation by spiders
Key Concept
Hardy-Weinberg serves as the fundamental
null model in population genetics
Condition that we try to falsify
Test populations to see if they are in H-W equil.
These are the null model frequencies
Ex: Hemoglobin (Box 6.3)
Cavalli-Sforza - Nigeria
Hg A and S (based on difference in β-globin)
Results: More SA and AA and fewer SS than
H-W would predict
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Why are there so many hemoglobin
A alleles in the population?
Heterozygote Advantage
S = sickle cell disease hemoglobin
SS = sickle cell disease
Low fitness
A = normal hemoglobin
AA = Susceptible to malaria
Low fitness
AS
Protected from malaria
Protected from sickle cell disease
Survive and reproduce – higher fitness
Testing the Null Model
Cavalli-Sforza, 2007
Heterozygote advantage and sickle-
cell anemia Founder effect
Amish of Lancaster, PA
Ellis-van Creveld Syndrome:
mutation causes dwarfism
and polydactylism
General population at levels
less than 0.1%,
Lancaster Amish the allele’s
level is approximately 7%.
Absence of upper
incisors and conical
lower incisors
Ellis-van Creveld
Inherited disorder of bone growth:
Very short stature (dwarfism).
Short forearms and lower legs
Narrow chest with short ribs.
Extra fingers and toes (polydactyly),
Malformed fingernails and toenails
Dental abnormalities.
More than half of affected individuals are born
with a heart defect, which can cause serious
or life-threatening health problems.
Founder effect
Nonrandom Mating
sibling matings - Inbreeding
reduces variation
Fig Wasps
Naked Mole rats
Human Eyebrow Mites
(Demodex folliculorum)
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Experimental evolution
provides important
insights about selection
• Richard Lenski started 1988
• Started culture with 1 E. coli cell
• Started 12 cloned populations
• Grow in 10 mL cultures with
small amount of glucose
Natural selection in action
Alleles that lower fitness experience Negative Selection
Alleles that increase fitness experience Positive Selection
Results
All cultures adapted to low glucose availability
Accumulated adaptations that made them
more efficient at growing under the
experimental conditions
Rate of increase in fitness has slowed but still
condinues to rise after 60K generations
Comparison of wild and adapted
strains
Transfer segments of DNA from one cell of
generation 10K into ancestral cultures of the
same line
Then mixed each line of engineered bacteria
with unmanipulated ancestral bacteria
Results:
Saw increased fitness with one particular
engineered line DNA segment
Help synthesize cell membrane
Transferred one nucleotide into ancestral
bacteria and increased fitness by 5%
Comparison of wild and adapted
strains
Tested generation 500 for mutation – not
present
Tested generation 1000 and found that
mutation was present in 45% of population
Generation 1500 97% of bacteria had it
This rapid spread is typical of a mutation that
enhances fitness
Mutation may allow cell to make thinner
membranes while reproducing faster
Found epistatic genes (interact with other
alleles)
Relationships among alleles at a locus
Additive: allele yields twice the phenotypic
effect when two copies present
Especially vulnerable to selection
Favorable alleles can go to fixation if additive
allele is present
Fitness order: Heterozygotes – homozygotes –
those without the allele
Deleterious alleles can go extinct
Fitness order:– homozygotes -those without the
allele – heterozygotes - homozygotes with the
allele
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Relationships among alleles at a
locus
Dominant and recessive alleles are not
additive
Dominance: dominant allele masks presence
of recessive allele in heterozygote
Dominant allele has same effect whether
present in one or two copies
Effects of selection on different types
of alleles
Mutation generates variation
Mutation rates for any given gene are low
But, considering genome size and population
size many new mutations arise each
generation
Estimate in humans: 8.5 billion new mutations
Source of variation for selection and drift to
act on
Mutation-selection balance
Equilibrium frequency reached through tug-
of-war between negative selection and new
mutation
Explains persistence of rare deleterious
mutations in populations
Balancing selection
Some forms of selection maintain diversity in
populations:
Negative frequency-dependent selection
Fitness is high when phenotype is rare
Fitness is low when phenotype is common
Heterozygote advantage
Negative frequency-dependent
selection
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Key Concepts
Selection occurs when genotypes differ in
fitness
Outcome of selection depends on frequency
of allele and effects on fitness
Population size influences power of drift and
selection
Drift more powerful in small population
Selection more powerful in large population
Key Concepts
Alleles may have pleiotropic effects
When fitness effects oppose each other
environment determines direction of selection
Laboratory evolution studies reveal how
alleles rise and spread through populations
Rare alleles almost always carried in a
heterozygous state
Recessive alleles invisible to selection
Selection cannot drive dominant to fixation
Key Concepts
Mutations are the source of new genetic
variation in populations
Can be many in a large population
Balancing selection maintains multiple alleles
in populations
Negative frequency-dependent
Heterozygote advantage
Inbreeding and the Hapsburg dynasty
Inbreeding coefficient
Probability that two alleles are identical by descent
Inbreeding depression results in reduced
fitness- inbreeding and selection
Rare deleterious alleles more likely to combine
in homozygotes
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Key Concepts
Alleles are identical by descent if they both
descended from a single mutational event
Inbreeding increases percentage of loci that
are homozygous for alleles identical by
descent
Genetic bottlenecks often go hand in hand
with inbreeding and selection
Recessive alleles exposed to selection
How Genetic Variation is Lost
Effects of Population size
Genetic Drift: fixation or loss of alleles
Population bottlenecks
causes
habitat destruction or fragmentation
introduced competitors or predators
disease
affects Mendelian (discontinuous) characters
more severely than quantitative (continuous)
characters
Genetic Drift
ex. Cheetahs Acinonyx jubatus
Large scale climate change about 10,000 years ago
Most populations of cheetahs went extinct in North America,
Europe, Asia, and much of Africa
Current animals are the result of inbreeding among the
surviving few animals (perhaps a single preganant female?)
Little genetic variability especially among immune system
genes
Genetic Drift
Habitat encroachment and poaching have
further reduce cheetah numbers,
consequently snuffing out even more genetic
variation and leaving cheetahs even more
vulnerable to extinction.
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10,000ya
Slides excerpted from:
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Cheating Cheetahs
2007 study, female cheetahs seem to be at least as
promiscuous as their male counterparts.
Females frequently mate with several different
males while they are fertile and are then likely to
bear a single litter of cubs fathered by multiple
males making many of the cubs within a single
litter only half-siblings.
This discovery has important implications for the
conservation of these endangered animals.
Though it conflicts with the idea that cheaters
never prosper, evolutionary theory suggests
that, in this case, cheating may be beneficial
Cheating Cheetahs
Three hypotheses for evolution of cheating
1. Even if several of her cubs were killed by a new
disease, succumbed to a novel environmental
stress, or just didn't have what it took to make a
living in the Serengeti, a female with a variable litter
could still hope that one of her cubs would have "the
right stuff" to survive.
Biologists refer to this as "bet-hedging" — not
putting all your eggs (or in this case, cubs) in one
basket.
Cheating Cheetahs
2. Perhaps, multiple mating is really a strategy to avoid
expending extra energy fending off would-be
suitors. In other words, maybe females mate
multiple times not because it ensures genetic
variation in offspring, but because it's so much
easier than fighting off males right and left.
Web info from Berkeley evolution education site
http://evolution.berkeley.edu/evolibrary/news/07070
1cheetah
Cheating Cheetahs
3. Perhaps multiple mating evolved as a way to deter
infanticide. In some big cats (and in many other species),
males try to kill cubs that are not their own. However, if a
mother mates with many different males, it is more difficult
for a male to tell whether or not a cub is his own — and the
male would likely be deterred from killing the cub. This third
hypothesis suggests that multiple mating was favored by
natural selection because it discouraged infanticide against
a female's cubs, not because it increased the litter's genetic
variation.
This third hypothesis fits with the observation that wild
cheetah males seem to rarely (if ever) commit
infanticide, though it is common in lions and other big
cats.
Cheating Cheetahs
Gottelli, D., Wang, J., Bashir, S., and Durant, S. M.
(2007). Genetic analysis reveals promiscuity among
female cheetahs. Proceedings of the Royal Society B
274(1621):1993-2001.
http://dx.doi.org/10.1098/rspb.2007.0502
Menotti-Raymond, M., and O'Brien, S. J. (1993). Dating
the genetic bottleneck of the African cheetah.
Proceedings of the National Academy of Sciences
90(8):3172-3176.
http://www.pnas.org/content/90/8/3172.abstract
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Natural Selection
Individuals vary in the expression of their
phenotypes
This variation causes some individuals to
perform better than others
Natural Selection happens when there is
differential fitness
Modern definition: Natural Selection
The differential survival or reproduction, on the
average, of different phenotypes in a population
Will lead to changes in frequencies of those
phenotypes within a generation, that is,different
age classes will have different phenotype
frequencies.
Within a generation - Darwin thought of many
generations
Evolution happens between generations
Note: NS does not have to lead to evolution!
The concept of fitness
Fitness: the reproductive success of an individual with a particular phenotype Ability to get genes into future generations
Components of fitness: Survival to reproductive age
Mating success
Fecundity
Relative fitness: fitness of a genotype standardized by comparison to other genotypes
Measuring Fitness
Difficult, rarely possible to
Record lifetime reproductive success
Record how many of those offspring survive to
reproduce themselves
Other problems
Can’t follow organisms for long time
Complex relationship b/w genotype and phenotype
Fitness is product of entire phenotype
Proxies for fitness
Probability of surviving to reproductive age
Measure number of offspring in a season
Fitness
t and t+1 = generations
Fecundity = ability to produce gametes
Contribution to the next generation = fitness
If different phenotypes are due to different genotypes,
and have different fitnesses, then natural selection
will act and the phenotype and genotype frequencies
will change.
Zygote adult gametes zygotes
t t t t+1
Survival Fecundity Mating
Fitness
Absolute fitness of a genotype = average
reproductive rate of individuals with that genotype
Absolute Fitness = W
Subscripts = genotypes
A1A1 W11
A1A2 W12
A2A2 W22
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Fitness
Absolute fitnesses determine whether a population
will increase or decrease in size
If average absolute fitness of all individuals in the
population is >1 then population increases in size
If average absolute fitness is <1 then population
decreases in size
Fitness
Population geneticists use value W
W = all fitness components: survival, mating
success and fecundity
Describes relative contribution of individuals
with one genotype compared with the average
contribution of all individuals in the population
Relative Fitness
Average excess fitness: difference between
average fitness of individuals with allele vs.
those without Δp = p x (aA1/ϖ)
Contribution of alleles to fitness
Average excess fitness can be used to
predict how the frequency of the allele will
change from one generation to the next