Transcript Biology 331 Genetics

Biology 331 Genetics
Population Genetics (Microevolution)
Introduction to Evolution:
Population Genetics (Microevolution):
Evolution occurring at and below the species level
Macroevolution:
Evolution occurring at and above the species level
Outgrowth of agricultural revolution in the 20's40's
Modern importance of
population genetics:
Agriculture
Other genetic engineering
Forensics
Medicine
Conservation
"Pure" Science
speciation, systematics, evolution of behaviors etc.
Variation
Qualitative
Quantitative
Evolution:
What is it?
Means Change
Biological/Organic Evolution Change in an
organism over time
Change in allele frequency over time
Not = Natural Selection
Natural Selection:
How does it work?
More offspring are produced than can survive (Species
could reproduce at an exponential rate)
Most populations have a stable size
Therefore: There is a struggle for existence
Members of a population vary in their characteristics
(short, tall, fast, slow)
Much of this variation is heritable
Therefore: Struggle for existence is not random. It
depends on individual characteristics
(which are heritable)
Natural Selection Continued
Those which are best adapted to the environment
survive and reproduce (Differential Reproduction)
Over time this process brings about changes in
populations with favorable changes accumulating.
Examples:
Cheetah's Speed, Cow's Milk etc.
Fitness:
The ability of an organism to leave offspring in a given
environment
Genetics:
Darwin lacked a method. Mechanism provided by the monk
Gregor Mendel. 1932-1953 modern synthesis
Pepper Moth
Items of note:
Selection on individuals, but individuals do not evolve,
populations do
Natural selection acts on phenotypes but evolution is
change in gene frequency
Natural selection does not "think ahead". Selects
organisms adapted to past environments. But, some
traits may be
favorable in new environments
human bipedalism
Natural Selection acts only on existing traits, variation
is crucial
Natural selection results in organisms better adapted
for an environment...NOT optimally designed
human bipedalism
Hardy-Weinberg:
An introduction
Hardy-Weinberg Theorem:
Allele frequencies stay constant if there is no
selection and it's other assumptions are met
Thus if we have 25% green eye genes, 25%
blue eye genes, and 50% brown eye genes it
will stay that way.
Heterozygosity will also stay the same
Two allele equation:
p2 + 2pq + q2 = 1
p= frequency of allele A
q = Frequency of allele a
p + q = 1.
So p2 = AA, q2 = aa, and pq = Aa
Sophisticated Punnet square:
Genotype frequency
Assumptions:
Random mating
Very large Population size
Diploid
Sexual
Non-overlapping generations
No migration
No mutation
No selection.
So what good is it?
Provides an evolutionary baseline
Calculate deviations from the H.W. Ideal
Hardy-Weinberg and Selection:
Problem #1
Assume a population has two co-dominant
alleles for a gene (B, B')
Assume there are 1000 individuals, 250BB,
500BB', and 250B'B'
So: Freq. B = 500+500/2000 = .5; B'=
500+500/1000 = .5
Assuming H.W. BB = p2 = .25; BB'= 2pq = .5;
B'B'= q2 = .25 (No Change)
Add Selection:
Fitness = Survival (for this example)
BB = 1; BB'= 0.9, B'B'= 0.8
BB = 250; BB'= 0.9(500) = 450; B'B'= 0.8(250)
=200
Frequency BB = 250/900 = .278; BB'= 450/900
= 0.5; B'B'= 200/900 = .222
Frequency B = .278+1/2(.5) = .528, B' = .472
Deviation From H.W.!
Types of selection
Frequency dependant selection
Fitness of an allele depends
upon its frequency
Mutation and Hardy Weinberg:
Assume p has a frequency of 1
What is the frequency of q ?
Now allow a mutation to occur from p to q
Instant evolution!
But is this a "strong" evolutionary effect?
Highest rate of mutation recorded is 0.0007/mutant
cells/cell division
Result....no real effect over one generation
Over time?
Mutation alone is typically a weak evolutionary force
Mutation over time
So why does in matter?
Raw material for evolution
Creates new genes
Mutation selection balance
Migration:
Transfer of alleles from one gene pool to another
One island model:
Assume you have genotypes A1A1, A1A2, A2A2
frequencies p2, 2pq, and q2
A1 is fixed on the continent; A2 is fixed on the island
N on the island is much smaller than on the continent
Migration (m) from the continent to the island is more
important than vice versa (Why?)
m=20% of the island population/generation
A1A1 = 0.2 after migration (was 0)
A2A2 = 0.8 after migration (was 1.0)
Not H.W. equilibrium
Both allele frequencies and genotype frequencies changed
Islands
Long term effect??
The general effect of migration is
homogenization
This effect is proportional to m, and the
difference between Pc and PI
Migration selection balance
Migration as mutation
Gene flow and natural selection
Genetic Drift:
Random variation in allele frequencies due to
sampling error
Yields evolution but not necessarily adaptation
Drift more important in small populations
Coin flipping/beanbag examples
Drift
Absorbing States:
The random fixation of alleles
The frequencies of alleles vary through time
Eventually alleles go to either fixation or loss
Assumes no Migration, mutation, selection etc.
Probability of loss or fixation proportional to
initial frequency
"C" allele example
Loss and Fixation
Drift
What determines probability of loss?
Probability of loss or fixation proportional
to initial frequency
So why does population size matter?
"C" allele example
Speed
Bottle Necks:
"Random" reduction in population size (Disasters)
Only a fraction of the alleles in the initial population
survive
"Instant" Evolution (sampling error)
Small population size after the bottleneck enhances drift
Repeated bottlenecks have huge effect!
European Jews, Lynx, Whales
S. African Cheetahs and Northern Elephant seals almost
"Clones"
Bottlenecks
Bottlenecks
"Instant" Evolution (sampling error)
Small population size after the bottleneck enhances
drift
Repeated bottlenecks have huge effect!
European Jews, Lynx, Whales
S. African Cheetahs and Northern Elephant seals almost
"Clones"
Founder Effect:
Genetic drift in a new colony
May be only one gravid female
Sampling error can result in "instant" evolution
Very much like a bottleneck
Extreme sampling error possible
Founder Effect
Picture Wing Drosophila
Examples
Tristan da Cunha (Classic Example)
Founded by a small number of colonists (15)
Retinitis Pigmentosa (one founder was a carrier)
Amish in PA
Founded by 200 people
1-2 founders have Ellis-van Creveld syndrom
Frequency 0.07 in Amish, 0.001 in the population as
a whole
Village of Salinas:
In the remote mountains of the
Dominican Republic:
One village founder Altagracia Carrasco
Several children with at least 4 women
Large contribution to a small population
Mutant for 5-alpha reductase-2 gene
Low catalytic activity
He was a heterozygote
Enzyme responsible for conversion of
testosterone to DHT
Required for full masculinization of
external genitalia
Results in XY “females”
What happens at puberty?
Guevedoces (penis at twelve)
Effective Population Size:
Theoretical "ideal" population having the same
magnitude of drift as the "Real"(tm) population
Census size:
All the individuals in a population
Assume No selection, No migration, No mutation, Non
overlapping generations, Diploid, Sexual
No population obeys the rules so we need a "fudge
factor"
Effective population size almost always smaller than
the census size
Example:
Assume 500 individuals
250 breeding age
Only 5 "dominant" males breed
EPS = 130
Drift and selection:
Can allow selection to act
"C" allele again!
Nonrandom Mating:
ANY deviation from totally random mating
Inbreeding:
Mating between genetic relatives
Need to calculate the probability that an allele is
Identical By Decent (ibd)
f = probability 2 gametes are ibd beyond
random mating expectaions
Does not require inbreeding in a social sense
F values
Effect of selfing with time:
Increase in number of homozygotes
Why?
Selfing homozygotes yield homozygotes
Selfing heterozygotes yield 50% heterozygotes
and 25% of each homozygote
Increase in homozygosity
Inbreeding continued
Does not affect gene frequencies
Does affect genotype frequencies
Excess homozygotes
Potential affect on evolutionary process?
Effects of inbreeding:
Loss of heterozygosity
What effect might this have?
Inbreeding depression
Due in part to deleterious recessives
Effect of inbreeding depression varies among
lineages
Resistance to inbreeding depression
Inbreeding more likely to be detected in stressed
organisms
Inbreeding affects often show up later in life
• Maternal effects
Effect of low values of "f"
f = 0.0005 (cousin mating)
% of affected individuals from first cousin
mating
18-24% albinism
27-53% tay-sachs
20-26% xeroderma pigmentosa
Positive Assortative mating:
Like breeds with like
Acts like inbreeding but only for selected alleles
Increases homozygosity
Can increase variance in a trait
Short w/ short, tall w/ tall
More variation for selection to act on
Alternative to inbreeding to fix "type"
Negative assortative mating:
Avoidance of like types
To an extent this is the opposite of inbreeding
Does not affect all genes equally
Excess heterozygotes
Avoidance of inbreeding:
Behavior
Dispersal (how far is far enough?)
Not coming into season before dispersal
Social Mores
Mate Choice:
Self incompatibility
MHC rejection
• Why do we want variation at MHC?
Spontaneous abortion/mate choice