natural selection

& adaptation
evolution
chapter 3

1
 outline
• environmental change and natural selection
– response to environmental change
– natural selection
– norm of reaction
• case study 1: variation in mouse coat color
• estimating heritability
– a target-gene approach
– alternative paths to phenotype change
– estimating fitness effects
• what is adaptation and what is not?
• case study 2: selection on guppy life-history
– life-history traits
– a selection experiment in the field
• case study 3: selection on swallows by road kill
• case study 4: the Lenski E.coli evolution
experiment
– interpreting change over generations
– responses to selection: repeatability and pace
– antagonistic pleiotropy: selection under trade-
offs
• complex adaptations - how are they possible?
– case study 5: evolution of the eye
– many small steps make big steps
– case study 6: evolution of appendages
• exaptation vs adaptation
– sutures and feathers
• molecular bases of complex adaptations
– gene sharing
– gene duplication
– how opsins evolved
– case study 7: how can a receptor and its ligand
co-evolve?
• constraints on adaptation
– genetic constraints
– trade-offs and physical constraints
– arms-races
– adaptation: step-by-step
2
 can we observe adaptation
within a few years?
• 4-year drought in California à plants
observed to grow faster
• did growth patterns evolve?

3
can we observe adaptation
within a few years?

4
 common garden experiments:
studying phenotypic variation
• grow organisms in the same environment
• à if phenotypic differences observed à must
be genetic
• so, flowering time differences really evolved
• early maturation-related genotype probably
selected by drought
• where did variation come from? new
mutations, or already present?
5
 where did variation come from?
• variation likely already present in the ancestral
population = "standing genetic variation" à
allowed fast selection response

• otherwise need to wait for de novo mutations

– not likely with a limited population (but
could occur in bacteria)

6
what is required for natural selection?
• phenotypic variation
• inheritance of variation (genetic basis)
• differential transmission (fitness)

7
what is natural selection?

8
 what is natural selection?
• change happens at the population level, over
generations
• selection happens at the individual level
• meanwhile, we use abstractions of alleles
being selected, for simplicity

9
 what is natural selection?
• genetic variation arises randomly - may not be
always present for all phenotypes
– no variation à no selection
• trait values & fitness depend on the external
(physical & biological) and internal
environment (genetic background and
epigenetic state) : “norms of reaction”
(phenotypic plasticity)

10
 selection, linkage and pleiotropy
• in real life, multiple traits may be connected,
due to genetic linkage or pleiotropy, and
selected together
• e.g. pigmentation
– although in reductionist biology models, selection
targets a single trait

11
selection, linkage and pleiotropy

12
https://www.nature.com/articles/ng.2007.13
 norm of reaction
• phenotype = genotype + environment + genotype
x environment interaction + random effects

• norm of reaction: differential expression of a

genotype across variable environments =
phenotypic plasticity

• fitness of a genotype will likewise vary across

variable environments
13
norm of reaction

14
norm of reaction

15
case study 1: mouse coat color
variation – what is the basis?

16
case study 1: mouse coat color
variation – what is the basis?

island habitats 6000y old – new phenotype 17

 case study 1: mouse coat color
variation – what is the basis?
• does the difference have genetic basis = is it
heritable?
• if so, which genes involved?
• how many and what type of mutations?
• mutations with small or large effects?
• how much selection = what is the fitness
effect?

18
 is the variation heritable?
• methods for estimating heritability (h2):
• common garden experiments
• parent-offspring correlations
• in humans: mono vs dizygotic twin
comparisons

https://www.nature.com/s
citable/topicpage/estimati
19
ng-trait-heritability-46889
 what are the genes involved?
• methods to determine the genes (mapping)
• linkage mapping
– using F2 crosses (for model organisms)
– using pedigrees
• genome-wide association
– using unrelated individuals and large sample size
• target gene analysis
– using external info from the literature

20
pigmentation pathways

21
 pigmentation pathways
• α-melanocyte-stimulating hormone (α-MSH) –
Mc1R binding à eumelanin (dark)
• Agouti signaling protein (ASP) à
phaeomelanin (light)
• how to evolve light pigmentation?

22
 pigmentation pathways

• at least 2 distinct ways to evolve a light

phenotype 23
 a "target gene" approach
• Mc1r mapped to pigmentation in other
mammals & birds – also in beach mouse?

• sequence the gene in both populations

• study differences
• study allele-phenotype correlations in F2
24
http://www.sciencemag.org/content/313/5783/101.short
 a "target gene" approach
• Mc1r mapped to pigmentation in other
mammals & birds – also in beach mouse?

• sequence the gene in both populations

• study differences
• study allele-phenotype correlations in F2
25
http://www.sciencemag.org/content/313/5783/101.short
a variant correlated with pigmentation
• derived non-synonymous variant in Mc1r
• R65C à changes protein charge
• correlated with pigmentation
• but majority of variation still unexplained

26
http://www.sciencemag.org/content/313/5783/101.short
 when did the variant arise?
• variation in Mc1r
• single mutation
• estimated to have
arisen before
colonization
• selection on
“standing genetic
variation”

27
https://onlinelibrary.wiley.com/doi/full/10.1111/j.1558-5646.2012.01669.x
 an alternative pathway to light
pigmentation
• follow-up study: another F2 linkage
mapping
• identifies derived allele in another gene,
Agouti
• this allele changes expression (non-coding)

28
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050219
an alternative pathway to light
pigmentation

29
http://www.sciencemag.org/content/331/6020/1062.short
 two paths to the phenotype:
a.a. change and expression change
• two loci (and others)
contribute to rapid
evolutionary change
• via 2 main paths:
• 1) protein (a.a.)
sequence change
• 2) expression level
change

30
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0050219
 estimating the fitness effect
• genetic basis of phenotype +
• fitness effect of phenotype ?

31
 estimating the fitness effect
• fitness: differential effect of trait / allele on
the expected reproductive success of an
individual relative to others in its population

• why expected? why reproductive success?

• how to measure relative fitness?

32
 estimating the fitness effect
• field experiments:
– directly, by phenotypic/genotypic analysis of
multiple generations
– indirectly, by studying survival in one generation
• genomics:
– indirectly: estimating selection pressure using
genomic polymorphism data + theoretical pop gen
models describing no selection

33
 field experiments to measure fitness
effects

• fitness effect inferred for color – but any caveats?

34
 field experiments to measure fitness
effects
• this scheme controls for confounding factors, e.g.
behavior or smell

35
 can small fitness differences drive
adaptation?
• assume an allele with only 1% fitness
advantage (s, selection coefficient)
• can selection “see” the difference?

36
 can small fitness differences drive
adaptation?
• 1% fitness advantage
• à beneficial allele freq doubles every 70 gen.
• à from 1 copy, in a population of 10,000,
fixes in <3000 generations

37
 can small fitness differences drive
adaptation?
• remember: this calculation assumes no drift
• in real life:
• a beneficial allele could still be lost when rare
– probability of eventual loss when 1 copy = (1-2s) ~
98% for advantage of 1%
• if recessive, would be lost even easier
– recessive alleles have no observable fitness effect
before becoming common by drift

38
what is adaptation?

39
what is adaptation?

40
 what is adaptation?
• “inherited trait that provides an organism
higher fitness in its abiotic (nonliving) and
biotic (living) environment”
• “risen as a direct result of selection for its
primary function”

41
 what is adaptation?
• increases reproductive potential compared to
the ancestral trait, in a given environment
• also used to refer to the process
– remember: a norm of reaction (plasticity) is also
an adaptation

42
 adaptation vs exaptation?
• strict definition for adaptation: “trait shaped
by natural selection for the same primary
function that makes it beneficial today”

• compare with exaptation: a trait serving a

different function today than in the past
– definition crucial for testing function
– how to test?

43
case study 2: selection on guppy
life history

44
 what are life history traits?
• development
– gestation, weaning
– timing of sexual maturity
– newborn size, adult size
• fecundity
– timing of sexual maturity
– number of times & duration of
reproduction
– litter size, size of offspring
• survival
– rate of senescence
– mean and maximum longevity
45
 K vs r life history strategies
• K: high investment per capita, few number
• r: low investment per capita, high number

46
life-history differences between
upstream vs downstream

47
 can selection by predation explain
guppy life-history differences?

• Trinidad guppies: high

predation vs low
predation environments

• why not both more and

large?
• what is the connection
with predation?
48
 can selection by predation explain
guppy life-history differences?
• hypotheses:
• trade-off: large offspring survive more, but
need more resources à can produce fewer

• large offspring possibly more fit in face of low

(smaller) predators
– can be tested experimentally

49
a selection experiment in the field?

50
a selection experiment in the field?
• transplant 100 male and 100 females from
high-predation à low- predation site,
cordoned off
– “thanks to sperm storage, founding pop size >200”

• longitudinal study: sample at 5 & 12 years =

30-60 generations

51
evolutionary response to predation
• use downstream fish as control
• transplanted fish have larger offspring size
• genetic basis confirmed in “common garden”
experiment à evolutionary response
downstream

transplanted

52
https://www.nature.com/nature/journal/v346/n6282/pdf/346357a0.pdf
evolutionary response to predation
• high predation populations, show increased
shoaling behaviour

53
 case study 3: selection on swallow
wing length by road kill

https://www.cell.com/current-
biology/fulltext/S0960-9822(13)00194-2 54
 natural populations respond to
anthropogenic selection
• «Longer wings have lower wing loading and
do not allow as vertical a take-off as shorter,
more rounded wings»
• what type of experiments could follow?

55
 case study 4:
an ideal experimental evolution setup?
• run evolution for 1000s of generations
• with full control of environment
• across multiple parallel universes
• use time machines to compete ancestors and
descendants
• rerun evolution from any point
• à how does evolution happen? how
predictable is evolution?
56
the Lenski E.coli evolution experiment

57
the Lenski E.coli evolution experiment
• 12 parallel E.coli lines, identical conditions
• 6-7 replications (generations) each day
• every 500 generations à sample stored at
-80°C
• bacteria can be thawed and compared /
competed with ancestors or with descendants

58
the Lenski E.coli evolution experiment
• Ara+/- system
• colors colonies,
but neutral
• useful for
comparing strains
• instead of plating,
today use single
cell sorting

59
 what is expected to happen?
• would the lines evolve new features?
• if yes, would the new features be more fit, or
evolve neutrally?
• would new features be the same or different
features across the 12 lines?
• if the same, using the same or different
mutations?

60
change in cell volume over generations

61
change in fitness over generations

62
interpreting change over generations

• is this evolutionary
change?

• is this change caused

by selection?

• if yes, what is the

cause of selection?
63
E.coli evolution – partly repeatable
• directional + repeated change à must be
selection
• à evolution partly repeatable
• note that changes depend on de novo
mutations
• features allowing better growth in the lab
environment (compared to outside) adaptive
– lab environment different from wild in nutrition,
physical conditions, ecology
64
E.coli evolution – partly repeatable
• why did the lines not change exactly the same
way?
• why did the response slow down?

65
E.coli evolution – partly repeatable
• why did the lines not change exactly the same
way?
• random forces: mutations & drift à limit
repeatability

66
why did the responses slow down?
• slow-down in volume increase: may be due
to trade-offs
• slow-down in fitness increase: simple
mutations used up – further increasing fitness
becomes more difficult in time
– adaptations involving deletions will be simple and
can evolve easily
– adaptations involving new genes will be
complicated and will take long time
67
 a unique adaptation!

• one E.coli population had a population burst

• thanks to a new ability: using citrate
– wildtype E. coli cannot use citrate when O2 present
68
a unique adaptation!

69
 may one adaptation disrupt another?
• thermal adaptation
• E.coli normally lives in the gut at 37C
• but optimal temperature of wild E.coli = 40C
• in the lab: 37C fixed

70
may one adaptation disrupt another?

red:
ancestral
blue:
evolved at
20,000
generations

71
 may one adaptation disrupt another?
• evolved strains better at 37C, but worse at
20C and 42C - why?
• 2 scenarios:
• mutation + drift ("mutation accumulation")
• mutation + selection under trade-offs

72
 antagonistic pleiotropy =
selection under trade-offs
• high mutation strains not worse at 20C / 42C
à drift unlikely
• alternative explanation:
• E.coli got specialized to non-variable 37C lab
environment
• alleles optimised to 37C do worse in other
environments (e.g. cannot respond to
temperature changes) à antagonistic
pleiotropy
73
 antagonistic pleiotropy =
selection under trade-offs

74
 antagonistic pleiotropy =
selection under trade-offs
• antagonistic pleiotropy: an allele that
improves fitness by affecting one phenotype,
but decreases fitness affecting another
phenotype
– e.g. increasing cell wall size can improve
protection (increase fitness in face of predation),
but limit growth rate (increase fitness in the lack
of predation)
– e.g. alleles that increase reproductive potential
may lead to shorter survival, e.g. by promoting
cancer
75
complex adaptations - how are they
possible?

76
https://www.nkcf.org
 complex adaptations - how are they
possible?
• complex adaptations from simple
microevolutionary processes – step by step,
via two mechanisms:
• previous (simpler) stages have similar
function & are beneficial
• previous stages served different function à
exaptation (co-option) for novel use

77
 case study 5: evolution of the eye

the upper panel phylogeny is out of date, the lower one is new 78
https://www.nature.com/articles/s41559-018-0575-6
case study 5: evolution of the eye

79
case study 5: evolution of the eye

80
many small steps make big steps

81
many small steps make big steps

82
 case study 6: evolution of helmets in
treehoppers

83
https://www.nature.com/articles/nature09977
case study 6: evolution of helmets in
treehoppers

84
exaptation vs adaptation

85
 skull sutures in mammals – an
adaptation for birth?
• the cranium has sutures that facilitate birth: a
mammalian adaptation?

86
skull sutures in mammals – an
adaptation for birth?

87
bird feathers – an adaptation for
flight?

88
www.thespruce.com
bird feathers – an adaptation for
flight?

89
 exaptation
• sutures an exaptation for birth
• feathers an exaptation for flight
• both still retain their putative original adaptive
functions (allowing brain growth and
insulation)

90
 exaptation
• large-scale morphological or genetic
structures: rarely appear de novo

• complex phenotypes = "layers of adaptation

& exaptation"

91
 molecular bases of complex
adaptations?
• gene sharing: old genes gain extra use
– causes molecular pleitropy
• gene duplication: new genes with novel use
– neofunctionalization
– specialization

92
gene sharing

93
gene duplication: the main source of
novel genes

94
Zimmer, Tangled Bank 2013
 gene duplication: the main source of
novel genes
• most new genes appear by gene duplication
• rarely, random sequence also gains function
(but exceptional)

95
 gene duplication: the main source of
novel genes
• 1- first mutation: gene duplication
• can happen by: unequal crossing over,
transposon activity, erroneous homologous
repair, retrotransposition
• 2a – subsequent mutations: indels or
substitutions diversify the genes’ functions
• 2b – the duplication event itself may also
create a partial gene copy with new function
directly
96
 gene duplication: the main source of
novel genes
• outcome a: two or more distinct functions
– neofunctionalization
– specialization

• outcome b: one copy becomes a pseudogene

97
 where did opsins come from?

98
http://www.pnas.org/cgi/doi/10.1073/pnas.1204609109
 molecular bases of complex
adaptations?
• gene sharing: old genes gain extra use
– causes molecular pleitropy
• gene duplication: new genes with novel use
– neofunctionalization
– specialization
• new genes from scratch: very rare

• sharing vs duplication: which may better facilitate

adaptation in the long term?

99
case study 7: how can a receptor and
its ligand co-evolve?

100
 the paradoxal evolution of MR and
aldosterone
cortisol
aldosterone

• glucocorticoid receptor (GR) + cortisol:

metabolism, inflammation, and immunity (all
vertebrates)
• mineralocorticoid receptor (MR) + aldosterone:
electrolyte homeostasis (tetrapods)
101
 the paradoxal evolution of MR and
aldosterone
• “If the hormone [aldosterone] is not yet
present, how can selection drive the receptor’s
[MR] affinity for it?
• Conversely, without the receptor, what
selection pressure could guide the evolution of
the ligand?”

102
http://science.sciencemag.org/content/312/5770/97.long
the paradoxal evolution of MR and
aldosterone

103
 the paradoxal evolution of MR and
aldosterone

104
http://science.sciencemag.org/content/312/5770/97.long
could we breed humans to make a
superman?

105
 …or are there constraints on
adaptation?
• possible sources of constraints:
• lack of necessary mutations
• antagonistic pleiotropy: 1 allele à >1
phenotypes with opposite fitness effects
• trade-offs: a phenotype with opposing fitness
effects under different conditions
• gene flow from populations without those
adaptations
106
 can constraints be overcome?
• waiting enough time, these can be partly
overcome, by:
• novel mutations
• mutations that uncouple characters (remove
pleiotropy)
• reproductive isolation preventing gene flow

107
 are perfect phenotypes possible?
• so waiting enough time, should we expect
organisms to reach optimal phenotypes –
“perfect adaptations” in each niche? i.e. can
organisms stop adapting?

108
 are perfect phenotypes possible?
• no, because of:
• ever-changing environment: unceasing
change driven by species interactions
• chemical and physical constraints: some
combinations of adaptations impossible
• Darwinian adaptation's lack of foresight:
some mutation combinations impossible to
evolve

109
 can the environment stop changing?
• no:
• physical environment: seasons, climatic shifts,
geological processes
• biotic environment: pathogens, prey,
predators, etc à change much faster
– we cannot rid ourselves of the cold virus
• co-evolution: evolution in one species affects
evolution of another
• evolutionary “arms race”
110
overcoming physical constraints?
• why don’t they exist?

111
https://askabiologist.asu.edu/explore/prehistoric-insects
 overcoming physical constraints?
• 300m years ago some insects much larger
• possibly related to higher O2 concentrations

112
https://askabiologist.asu.edu/explore/prehistoric-insects
overcoming physical constraints?

113
overcoming physical constraints?

114
 overcoming physical constraints?

• stereoscopic vision needs overlap

• can this constraint be overcome?
115
overcoming physical constraints?

116
adaptation only happens step-by-step
• “evolution lacks foresight” = adaptive
mutations happen and fix one by one
• every intermediate step has to have similar or
higher fitness
• no jumps

117
 getting stuck at local maxima L

https://www.pnas.org/content/112/24/7345 118
 getting stuck at local maxima L
• species may get “trapped” at local maxima in
a fitness landscape, if the intermediate
phenotypes are not adaptive
fitness

phenotype 1 phenotype 2 119

http://www.turingfinance.com/
 getting stuck at local maxima L
• drift can help!
• random genetic changes in small populations:
• à can lower fitness by increasing deleterious
variant frequency
• can also avoid getting stuck at local optima
• à can move the population to a suboptimal
phenotype temporarily, allowing for better
adaptations in later times
• i.e. allow wider search for adaptations

120
 outline
• environmental change and natural selection
– response to environmental change
– natural selection
– norm of reaction
• case study 1: variation in mouse coat color
• estimating heritability
– a target-gene approach
– alternative paths to phenotype change
– estimating fitness effects
• what is adaptation and what is not?
• case study 2: selection on guppy life-history
– life-history traits
– a selection experiment in the field
• case study 3: selection on swallows by road kill
• case study 4: the Lenski E.coli evolution
experiment
– interpreting change over generations
– responses to selection: repeatability and pace
– antagonistic pleiotropy: selection under trade-
offs
• complex adaptations - how are they possible?
– case study 5: evolution of the eye
– many small steps make big steps
– case study 6: evolution of appendages
• exaptation vs adaptation
– sutures and feathers
• molecular bases of complex adaptations
– gene sharing
– gene duplication
– how opsins evolved
– case study 7: how can a receptor and its ligand
co-evolve?
• constraints on adaptation
– genetic constraints
– trade-offs and physical constraints
– arms-races
– adaptation: step-by-step
121