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Selection in Nature
I.
Ecological Interactions
A. Resources
- Darwin’s Finches
Selection in Nature
I.
Ecological Interactions
A. Resources
- Darwin’s Finches
Selection in Nature
I.
Ecological Interactions
A. Resources
- Darwin’s Finches
- Quantitative Traits like these -- affected by many genes -- have a higher
probability of including a pleiotrophic gene – a gene that affects more than one trait.
So, we might expect complex, quantitative traits (and their response to selection) to be
CORRELATED to other traits.
BUT: if selection is acting on both traits in different ways, neither will be “optimized”.
Adaptations will be a compromise, depending on the relative strengths of the selective
pressures, the relative values of the adaptive traits, and their heritabilities (ease with
which they can respond to selection).
Consider the Grant’s work on medium ground finches during the drought of ‘76-’77.
Birds with deep and narrow beaks had the greatest fitness.
Consider the Grant’s work on medium ground finches during the drought of ‘76-’77.
Birds with deep and narrow beaks had the greatest fitness. But beak depth and
beak width are POSITIVELY CORRELATED (probably developmentally).
Consider the Grant’s work on medium ground finches during the drought of ‘76-’77.
Birds with deep and narrow beaks had the greatest fitness. But beak depth and
beak width are POSITIVELY CORRELATED (probably developmentally).
So, although
selection should
have pushed the
pop along the
blue line, it went
along the green
line.
Selection in Nature
I.
Ecological Interactions
B. Competitors – “Character Displacement”
- Darwin’s Finches
(on Daphne Major)
Selection in Nature
I.
Ecological Interactions
B. Competitors
- Darwin’s Finches
Competition in sympatry leads to
resource partitioning and
selection for the most efficient
morphology to use this subset of
resources… the morphological
change is “character
displacement”
Selection in Nature
I.
Ecological Interactions
B. Competitors
- Anolis (Stuart and Cambell)
(islands off east coast of FLA)
Niche partitioning….
Selection in Nature
I.
Ecological Interactions
B. Competitors
15 years later…patterns
persisted and morphological
adaptation (character
displacement) had occurred
- Anolis (Stuart and Cambell)
(islands off east coast of FLA)
Sig.
Selection in Nature
I.
Ecological Interactions
C. Predators
- Peromyscus polionotus
(Hoekstra)
Levels of predation
on clay models
Selection in Nature
I.
Ecological Interactions
C. Predators
- Peromyscus polionotus
(Hoekstra)
Selection in Nature
I.
Ecological Interactions
C. Predators
- Scarlet kingsnake
(Harper and Pfennig)
Stickebacks colonizing
predator-free lakes lose
their armor.
Selection in Nature
I.
Ecological Interactions
C. Predators
- Scarlet kingsnake
(Harper and Pfennig)
Predators only learn to
avoid mimics if they
experience the dangerous
model.
Selection in Nature
I.
Ecological Interactions
C. Predators
- Goldenrod gall fly
(Abrahamson)
Selection in Nature
I.
Ecological Interactions
C. Predators
- Goldenrod gall fly
(Abrahamson)
Mean gall sizes induced by flies
from different families.
Selection in Nature
I.
Ecological Interactions
C. Predators
- Goldenrod gall fly
(Abrahamson)
Stabilizing selection for
intermediate gall size, which
is a heritable trait in both
plants and flies.
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Domesticated Species
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Domesticated Species
Aurochs
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Domesticated Species
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Domesticated Species
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Domesticated Species
Nagasawa et al. 2015.
•Fig. 1 Comparisons of behavior and
urinary oxytocin change among long
gaze dogs (LG, n = 8, black bars and
circles), short gaze dogs (SG, n = 22,
white bars and circles), and wolves
(wolf, n = 11, gray bars and square).(A)
Behavior during the first 5-min
interaction. (B) and (D) Changes of
urinary oxytocin concentrations after a
30-min interaction. Urinary oxytocin
concentrations in owners (B) and dogs
or wolves (D) collected before and after
a 30-min interaction are shown. (C) and
(E) Comparisons of the change ratio of
urinary oxytocin among LG, SG, and
wolf for owners (C) and dogs or wolves
(E). The results of (A), (B), and (D) are
expressed as mean ± SE. (C) and (E)
reflect median ± quartile. ***P < 0.001,
**P < 0.01, *P < 0.05.
Fig. 2 Comparisons of behavior and urinary
oxytocin between oxytocin and saline
treatment conditions.(A) to (C) The effects of
oxytocin administration on dog behaviors.
Panels show the mean duration of dogs’ gaze
at participants (A), touching participants (B),
and time spent in the proximity of less than 1
m from each participant (C). Black and white
bars indicate, respectively, oxytocin- and
saline treatment conditions. OW, owner; UP,
unfamiliar person. (D) to (G) Change in
urinary oxytocin concentrations after a 30-min
interaction after oxytocin or saline
administration. Urinary oxytocin
concentrations of owners (D) and dogs (F)
before and after a 30-min interaction are
shown for oxytocin and saline groups. The
change ratio of urinary oxytocin in owners (E)
and dogs (G) is compared between male and
female dogs. ***P < 0.001, **P < 0.01, *P <
0.05. The results of (A) to (D) and (F) are
expressed as mean ± SE. (E) and (G) reflect
median ± quartile.
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Domesticated Species
‘selective sweep’ fixes adaptive alleles, but brings other
linked alleles along for the ride – increasing homozygosity
Selection in Nature
I.
Ecological Interactions
D. Humans as Selective Pressures
- Hunted/fished Species
Shackle et al, 2009.
(a) Mean length (cm) and (b) mean
mass (kg) for fish functional groups
from 1970 to 2008. Linear
regression equations of body size
through time are shown. Dots are
annual values and lines show 3year running averages. Grey lines
denote the direct measure of
growth ((a) length and (b) mass at
age 6 as weighted by species
biomass within a functional group).
Selection for smaller fish that
breed at a younger age. The
problem is that small young fish
produce fewer eggs.
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
Why do flying fish return to water?
Gravity… and they are fish.
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
Why do larger animals have
proportionally larger legs?
(mass scales as the cube of length; cross-sectional area of leg, which supports
the body mass, scales as the square of length. Proportional growth leads to
legs to weak to support the mass.) Conforming to physics is not an adaptation.
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
Lack of genetic variation and/or maladaptive valleys:
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
Small
leaves
Water Availability
Sunny
dry
desert:
Photosynthetic Potential
B. Contradictory Selective Pressures
Leaf Size
Shady
wet
jungle:
large
leaves
Photosynthetic Potential
Small
leaves
Or
none!
Water Availability
Sunny
dry
desert:
Leaf Size
Shady
wet
jungle:
large
leaves
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
B. Contradictory Selective Pressures
Survival (growth and metabolism) or reproduction?
Many small offspring or a few large ones?
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
B. Contradictory Selective Pressures
C. Antagonistic pleiotropy
A gene has an adaptive effect for one trait or in one
environment, but a deleterious effect on another trait or in another
environment.
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
A. Physical / Evolutionary Constraints
B. Contradictory Selective Pressures
C. Antagonistic pleiotropy
D. Implication
Not all structures are adaptations!
D. Implication
Not all structures are adaptations!
“The spandrels of San Marco and the Panglossian paradigm: A
critique of the adaptationist programme”” – S. J. Gould and R. C.
Lewontin (1979)
D. Implication
Not all structures are adaptations!
“The spandrels of San Marco and the Panglossian paradigm: A
critique of the adaptationist programme”” – S. J. Gould and R. C.
Lewontin (1979)
“Things can not be other than they are…
everything is made for their best purpose.”
Dr. Pangloss, “Candide” (Voltaire)
Selection in Nature
I.
Ecological Interactions
II. Constraints on Selection
III. Back to the Neutral Theory!
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
- Rates should vary in different codon positions. Variation at the
third position should be higher, because these are usually silent mutations.
Mutations at the second position change amino acids, and these changes are
deleterious. PATTERN CONFIRMED.
- Rates should vary in coding and non-coding regions. Variation in
Introns should occur more rapidly than variation in exons, since introns are
not transcribed and are also invisible to selection. PATTERN CONFIRMED
- Rates should vary in functional and non-functional regions of
proteins. PATTERN CONFIRMED
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
2. Rates of replacement (substitution of one fixed allele by another
that reaches fixation) should be constant over geologic time.
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
2. Rates of replacement (substitution of one fixed allele by another
that reaches fixation) should be constant over geologic time.
- If changes are random and mutations occur at a given rate, then
replacement should "tick" along like a clock.
- Selection should speed rates when a new adaptive combination
occurs, like in obviously adaptive morphological trait. Then inhibit further
change unless it is adaptive or neutral - PATTERNS CONFIRMED (usually).
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
2. Rates of replacement (substitution of one fixed allele by another
that reaches fixation) should be constant over geologic time.
3. Rates of morphological change should be independent of the rate
of molecular change.
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
2. Rates of replacement (substitution of one fixed allele by another
that reaches fixation) should be constant over geologic time.
3. Rates of morphological change should be independent of the rate
of molecular change.
- "Living Fossils" show extreme genetic change and variation, yet
have remained morphologically unchanged for millennia. And, their rate of
genetic change in this morphologically constant species is the same as in
hominids, which have changed dramatically in morphology over a short
period. PATTERN CONFIRMED
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
2. Rates of replacement (substitution of one fixed allele by another
that reaches fixation) should be constant over geologic time.
3. Rates of morphological change should be independent of the rate
of molecular change.
4. A truly neutral clock should tick off mutations at a constant rate.
But should this ticking occur per unit time, or per generation?
III. Back to The Neutral Theory
A. Neutral Variation
- change in protein that does not affect fitness
- ‘silent’ or ‘synonymous’ mutations are the prototype
B. Predictions and Results
1. Rates of molecular evolution should vary in functional and nonfunctional regions
2. Rates of replacement (substitution of one fixed allele by another
that reaches fixation) should be constant over geologic time.
3. Rates of morphological change should be independent of the rate
of molecular change.
4. A truly neutral clock should tick off mutations at a constant rate.
But should this ticking occur per unit time, or per generation?
- Mutations occur during DNA replication of the DNA, so a truly
neutral clock should tick at a rate dependent on the generation time of the
organism. Species with rapid generation times should accumulate mutations
at a faster rate than long-lived species with slower generation times.
- This is true of non-coding DNA... but not true for proteins. Proteins
accumulate mutations in absolute time, not generational time. THIS IS
INCONSISTENT WITH THE NEUTRAL MODEL
III. Back to The Neutral Theory
A. Neutral Variation
B. Predictions and Results
C. Ohta’s “Nearly Neutral” Model
III. Back to The Neutral Theory
A. Neutral Variation
B. Predictions and Results
C. Ohta’s “Nearly Neutral” Model
- Included weak selection against slightly
deleterious alleles. if s < 1/2Ne, then alleles are
essentially neutral and become fixed as drift
would predict.
- In small populations, drift predominates
unless selection is fairly strong (in a
population of Ne = 5, drift will predominate
unless s > 0.1).
- In large populations, selection predominates,
even if it is fairly weak (if Ne = 10,000, then
selection will predominate if s > 0.00005).
SO.
Sub. Rate
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
OBS.
EXP.
Short
GEN TIME
Long
SO.
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
- So, something must be 'slowing down' this rate of substitution in
species with short gen. times. What's slowing it down is their large
populations size, such that the effects of drift, alone, are reduced.
Sub. Rate
LARGE
POP. SIZE
OBS.
EXP.
Short
GEN TIME
Long
SO.
- We observe a constant AA substitution rate across species, even
though we would expect that species with shorter generation times should
have FASTER rates of substitution.
- So, something must be 'slowing down' this rate of substitution in
species with short gen. times. What's slowing it down is their large
populations size, such that the effects of drift, alone, are reduced.
- Likewise, species with long generation times have small
populations, and substitution by drift and fixation is more rapid than
expected based on generation time, alone.
Sub. Rate
SMALL POP.
SIZE
OBS.
EXP.
Short
GEN TIME
Long
SO.
- The constant rate of AA substitution across species is due to the
balance between the effects of generation time and population size.
Sub. Rate
SMALL POP.
SIZE
OBS.
EXP.
Short
GEN TIME
Long
III. Back to The Neutral Theory
A. Neutral Variation
B. Predictions and Results
C. Ohta’s “Nearly Neutral” Model
D. New Developments
…. Some ‘synonymous’ substitutions are NOT neutral!
- ‘synonymous’ mutations in exons may slow the rate of protein
synthesis and cell growth.
Patrick Goymer (2007) 'Genetic variation: Synonymous mutations break
their silence', Nature Reviews Genetics 8, 92 (February 2007).
Chamary, J. V. & Parmley, J. L. & Hurst, L. D. 'Hearing silence: non-neutral
evolution at synonymous sites in mammals'. Nature Rev. Genet. 7, 98-108
(2006).
Grzegorz Kudla et al (2009,Science 10 April 2009).
Chamary and Hurst (2009) 'The price of silent mutations', Scientific
American, June 2009, pp34-41. It appears that bases in protein coding
exons can be also intron splicing recognition sites, and that a synonymous
mutation can prevent intron splicing, resulting in mutated proteins