Transcript lecture 02 - selection on the gene, genome, trait and phenotype

Evolution by natural selection
The Modern synthesis restated Darwin’s 4 postulates:
(1) Individuals in a population are variable for most traits,
because mutation creates new alleles and sexual
reproduction creates new allele combinations in every
generation
(2) Individuals pass their particular alleles to their offspring
(3) More offspring are produced than can survive
(4) Individuals that survive, or reproduce the most, have
allele combinations that best adapt them to their
environment
Natural selection & fitness
Natural selection is the sole process that produces adaptation to
the environment
- an adaptation is a trait that makes you better suited to your
ecological niche, and increases your fitness
Alleles or allele combinations, and the traits they produce, determine
fitness of an individual: # of offspring that survive to reproduce
- if you live forever but produce no offspring, your fitness = 0
Allele combinations resulting in higher fitness are passed to more
offspring, and thus those alleles rise in frequency over time
(becoming more common)
-
Natural selection & fitness
Two general points to consider:
1) there is a trade-off between offspring size and number
- the same amount of resources can be divided into more but
smaller offspring, or fewer, bigger offspring
maternal
energy
(e.g., available
egg yolk)
If life is easy, and offspring survival
rates are high, which strategy do
you predict selection will favor?
Natural selection & fitness
Two general points to consider:
1) there is a trade-off between offspring size and number
- the same amount of resources can be divided into more but
smaller offspring, or fewer, bigger offspring
- measuring “fitness” is not trivial; it’s not always just # of
babies made
2) an individual’s fitness is determined by lifetime reproductive
output, not just the # of offspring laid in a given year
Lack’s hypothesis: How many offspring?
Assume the more eggs you lay,
the lower the odds of surviving
are for each individual offspring
Multiplying # of offspring
(= clutch size) by odds of each
offspring’s survival gives the
optimal clutch size
(Lack’s hypothesis)
Life-history evolution: How many offspring?
Data from study on birds showed that the mean # of surviving
baby birds was highest for clutches of 12 eggs
However, birds laid 8-9 eggs per clutch in any given year, to
save energy for future reproduction
Natural selection acts at many levels
In a given environment, natural selection may act strongly on:
1) one genetic locus (physical spot on chromosome)
2) multiple, adjacent loci
molecular evolution
3) one trait in isolation
phenotypic evolution
4) the correlation between two or more traits
Selection on one locus
Selection favoring one allele at a given locus is termed
purifying selection
- “purifying” because at this level, selection acts against all but
the most favorable allele
- will decrease genetic polymorphism at that locus
if selection strongly favors “C” allele of the C gene...
A
B
C
D
E
F
a
b
c
d
e
f
a
b
c
d
e
f
a
b
c
d
e
f
Selection on one locus
Selection favoring one allele at a given locus is termed
purifying selection
- “purifying” because at this level, selection acts against all but
the most favorable allele
- will decrease genetic polymorphism at that locus
Purifying selection reduces polymorphism at the C gene, by
removing other alleles from the population
A
B
C
D
E
F
A
B
C
D
E
F
A
B
C
D
E
F
A
B
C
D
E
F
A
B
C
D
E
F
A
B
C
D
E
F
Indirect selection on nearby loci
Selection favoring one allele at a given locus is purifying selection
Case 1: Bacteria (~ no recombination during reproduction)
What effect will purifying selection on the C gene have on
level of polymorphism at the D gene?
A
B
C
D
E
F
a
b
c
d
e
f
a
b
c
d
e
f
a
b
c
d
e
f
Indirect selection on nearby loci
Selection favoring one allele will also tend to drag alleles at nearby
or linked loci to high frequency
if selection strongly favors “big C” allele of the C gene...
A
B
C
D
E
F
a
b
c
d
e
f
...it will also tend to favor “B” and
“D” alleles, if they happen to be
linked to “C” on a chromosome
 in asexual organisms, alleles get inherited as a team due to
linkage; what’s good for one allele is good for its neighbors
 genetic hitch-hiking: neighboring alleles benefit from
purifying selection, even if they aren’t under selection at all

Indirect selection on nearby loci
Case 1: Bacteria (~ no recombination during reproduction)
if selection strongly favors “big C” allele of the C gene...
A
a
B
b
C
c
D
E
F
Q
d
e
f
q
What effect will purifying selection on the C gene have on
polymorphism at the distant Q gene?
Selective sweeps
Bacteria (and mitochondria, their descendants) have
circular chromosomes and limited recombination
A
B
C
D
E
F
Are therefore prone to selective sweeps
1) purifying selection favors one allele of one gene, pushing it
to fixation (100% frequency in the population)
2) at the same time, selection reduces polymorphism at all
genes throughout the genome
3) whole population ends up with reduced (if any)
polymorphism, until mutation or migration introduces new
alleles
Indirect selection on nearby loci
Selection favoring one allele will also tend to drag alleles at nearby
or linked loci to high frequency
if selection strongly favors “big C” allele of the C gene...
A
B
C
D
E
F
a
b
c
d
e
f
...all these alleles will be lost,
unless they can get onto the
“winning team”  i.e., any
chromosome with a C allele
Indirect selection on nearby loci
Selection favoring one allele at a given locus is purifying selection
Case 2: Eukaryotes (recombination during reproduction)
What effect will purifying selection on the C gene have on
level of polymorphism at (1) the D gene?... (2) the F gene?
A
B
C
D
E
F
A
B
C
D
E
F
a
b
c
d
e
f
a
b
c
d
e
f
Indirect selection on nearby loci
recombination allows linked loci to escape the effects of
purifying selection on nearby genes
 crossing over “breaks up the team”
Even if selection strongly favors C allele... alleles of other
genes can cross over onto C chromosomes
A
B
C
D
E
F
a
b
c
d
e
f
A
B
C
d
e
A crossing over event can rescue the “d” allele by moving it
next to the winning “C” allele, favored by purifying selection
f
Indirect selection on nearby loci
Selection favoring one allele at a given locus is purifying selection
Case 2: Eukaryotes (recombination during reproduction)
A
B
C
D
E
F
a
b
c
d
e
f
A
B
C
D
E
f
However, a crossing over event becomes more likely as you
move farther away on the chromosome
 “f” is more likely to get recombined onto a “C” chromosome
than “d” because the F gene is farther away

Natural selection acts at many levels
In a given environment, natural selection may act strongly on:
1) one genetic locus (physical spot on chromosome)
2) multiple, adjacent loci
molecular evolution
3) one trait in isolation
phenotypic evolution
4) the correlation between two or more traits
Modeling selection on quantitative traits
50
45
40
35
30
25
20
15
10
5
0
0
5
10
15
20
25
30
weight
How would you model the relationship between weight
and fitness, given these data?
Modeling selection on quantitative traits
50
45
y = 1.6(x) - 1.9
40
35
30
25
20
A model is an equation expressing
the relationship between a trait
and some measure of fitness
15
10
5
0
0
5
10
15
20
25
30
weight
For each unit increase in body size (weight), you get ~1.6 offspring
- the slope (coefficient associated with trait value) tells you how
strongly that trait affects fitness
Modeling selection on quantitative traits
50
45
y = 1.6(x) - 1.9
40
35
30
25
20
A model is an equation expressing
the relationship between a trait
and some measure of fitness
15
10
5
0
0
5
10
15
20
25
30
weight
How would you expect this trait (size) to evolve over time?
Directional selection
50
45
y = mx + b
40
A linear relationship between
the value of a trait and fitness
is termed directional selection
35
30
25
20
15
The model is the equation of the
best-fit line through the data
10
5
0
0
5
10
15
20
25
30
trait
“fitness” is generally estimated as probability of adult survival, or
# of offspring produced over some interval (ideally, lifetime)
The mean value of a trait under directional selection should evolve
in one direction over time...
- mean value should increase if slope (m) is positive
Directional selection
Directional selection can also be
inferred when the distribution of
trait values in a population shifts
in one direction over time
# of individuals
25
20
15
Remember: directional selection
10
a) changes the mean value of
a trait (+ or -)
5
0
0
5
10
15
20
# of value
individuals
trait
25
b) decreases the variance around
the mean value of a trait
(trims one tail off the distribution)
Directional selection
Directional selection can also be
inferred when the distribution of
trait values in a population shifts
in one direction over time
# of individuals
25
20
15
Remember: directional selection
10
a) changes the mean value of
a trait (+ or -)
5
0
0
5
10
15
20
# of value
individuals
trait
25
b) decreases the variance around
the mean value of a trait
(trims one tail off the distribution)
Stabilizing selection (non-linear)
25
y = -0.1x2 + 2.3x + 1.4
20
Stabilizing selection favors
individuals with trait values
close to the population mean
15
10
5
0
0
5
10
15
20
25
30
weight
Model is non-linear, meaning not a straight line (curved)
Quadratic equation includes (a) the trait value (x), and also
(b) the square of the trait value (x2), which is what makes it
a non-linear relationship
Stabilizing selection (non-linear)
Stabilizing selection maintains
trait values over generations
close to the same mean
# of individuals
25
20
Remember: stabilizing selection
15
a) no change to mean value of
trait
10
b) decreases variance
5
(trims both tails off distribution)
0
0
5
10
15
20
trait
# of value
individuals
25
Stabilizing selection (non-linear)
Stabilizing selection maintains
trait values over generations
close to the same mean
# of individuals
25
20
Remember: stabilizing selection
15
a) no change to mean value of
trait
10
b) decreases variance
5
(trims both tails off distribution)
0
0
5
10
15
20
trait
# of value
individuals
25
Disruptive selection (non-linear)
30
y = 0.1x2 - 2.3x + 27
25
Disruptive selection favors
individuals with trait values
far from the population mean
20
15
10
5
0
0
5
10
15
20
25
30
weight
Model is also a quadratic equation, but now:
(a) coefficient associated with the trait value (x) is negative (-2.3)
(b) coefficient of squared term (x2) is positive (0.1)

Disruptive selection (non-linear)
Disruptive selection splits one
group into two sub-groups of
different ecotypes or specialists
# of individuals
25
20
Remember: disruptive selection
15
a) no change to mean value of
trait
10
b) increases variance
5
(shifts distribution towards tails)
0
0
5
10
15
20
value
#trait
of individuals
25
Disruptive selection (non-linear)
Disruptive selection splits one
group into two sub-groups of
different ecotypes or specialists
# of individuals
25
20
Remember: disruptive selection
15
a) no change to mean value of
trait
10
b) increases variance
5
(shifts distribution towards tails)
0
0
5
10
15
20
value
#trait
of individuals
25
Disruptive selection (non-linear)
Disruptive selection is of special interest as a potential agent of
ecological speciation
# of individuals
25
20
15
10
5
0
0
5
10
15
20
25
# trait
of individuals
value
A generalist species of bird will feed on seeds of many sizes
If the most common plants produce either large or small seeds,
this can impose disruptive selection on beak size
Disruptive selection (non-linear)
tiny beaks =
handle tiny
seeds
# of individuals
25
20
big beaks = crack
large seeds
15
10
5
0
0
5
10
15
20
25
# of
individuals
trait
value
Disruptive selection may thus split one generalist species into two
specialist ecotypes that over time, under the right conditions,
may evolve into separate species
Selection-mutation balance
mutation
migration
standing genetic
variation in
a population
selection
(usually reduces
polymorphism)
Multivariate selection
Rather than acting on one trait in isolation, natural selection often
acts on suites of traits that contribute to the overall phenotype
- multivariate meaning multiple traits (variables)
We model multivariate selection using equations that include the
variables themselves (trait values), as well as the correlation
between two variables
50
50
positive
correlation
45
40
35
40
35
30
30
25
25
20
20
15
15
10
10
5
5
0
0
0
5
10
15
trait 1
negative
correlation
45
20
25
30
0
5
10
15
trait 1
20
25
30
Multivariate selection
Example: In the sea slug that my lab studies, finger-like projections
on the back of the slug (cerata) convulse to circulate body fluid,
instead of a beating heart
cerata
Under normal conditions, selection favors a
negative correlation between (a) # of cerata,
and (b) the rate at which cerata beat
50
few, fast-beating
cerata
45
40
35
30
many, slow-beating
cerata
25
20
15
two different ways
to achieve same
basic “heart rate”
most
eggs
10
5
0
0
5
10
15
# of cerata
20
25
30
Multivariate selection
When it rains, slugs with many cerata have
large surface area over which freshwater
rushes into body; they explode
Slugs with fast circulation (high beat rate)
also take on too much water, and explode
Rainfall selects for a
positive correlation
between # of cerata,
and beat rate
50
45
few, slow-beating
cerata confers
high fitness
40
35
30
25
- favors few & slowbeating cerata
20
15
10
5
(no slugs with
many, fastbeating cerata;
all dead)
0
0
5
10
15
# of cerata
20
25
30
Multivariate selection
Marshall & Munroe (2012) studied how competition affected
multi-variate selection on colonies of a marine bryozoan
- bryozoans grow as colonies like a honeycomb, where each
unit is an individual that (a) can reproduce, and (b) will at
some point senesce (stop reproducing; basically die)
- colonies differ in: (a) size of individual units;
(b) offspring size;
(c) how fast units go into senescence
senesced (dead) units
Multivariate selection
Under normal conditions, colonies with
intermediate trait values produced the
most offspring (= had highest fitness)
- medium unit size
- medium offspring size
- medium death rate
= stabilizing
multivariate
selection
Multivariate selection
Strong competition from neighboring colonies
changed the shape of selection on trait correlations
crowding favored a
negative correlation
between offspring size
and senescence rate,
regardless of unit size
= disruptive selection
Correlated selection
Consider: Suppose fish like to bite off cerata, which look like
worms (fish bait). This harms the bitten slugs. Studies suggest
slugs with more cerata get attacked by fish more often.
cerata 1) What kind of selection does fish predation
impose on cerata #, as a trait in isolation?
2) How would you predict cerata # to evolve?
3) Would you expect cerata beat rate to evolve
in response to fish predation?
Why, or why not?