College 1

Why versus What? Tinbergen’s 4 questions

- What is it for?
- How did it develop during the lifetime of the individual?
- How did it evolve over the history of the species?
- How does it work?
- current: mechanism (causation) / adaptive value (function)
- historical: ontogeny (development) / phylogeny (evolution)

Practical applications of evolutionary biology

Fisheries biology:
- genetic consequences of selective harvesting
- bigger fish get caught more and fish who are more reproductive
- natural mortality vs. fishing mortality (selection gradient)
→ maturation at smaller size / lower age
- genetic consequences of
→ managing evolving fish stocks: evolutionary impact assessment is a framework for
quantifying the effects of harvest-induced evolution on the utility generated by fish
stocks

Bottleneck​: extreme reduction in population size (massive inbreeding results in less genetic
diversity)

Conservation biology:
- identification of evolutionarily significant units (ESUs)
- avoidance of inbreeding depression in captivity
- avoiding the loss of adaptive variation (adaptive rescue)
- identification of minimal population size for viability
- predicting the response to global change

Human health
- evolution of pathogens and antibiotic resistance
- understanding gene function through comparative study
- tracing the origin and spread of infectious diseases
- detection of nucleotide changes responsible for genetic disorders from gene
genealogies
- long-term consequences of medical intervention

- Pharmaceutical industry:
- drug design by in vitro or in vivo evolution
- targeted searches for natural products: bio prospecting
- evolution of antibiotic resistance
 - Agriculture:
- crop & livestock improvement by selective breeding
- evolution of pesticide resistance
- transgenic organisms: advantages and risks

Primary goals of evolutionary biology:

- to document evolutionary history: how has life changed through time?
- to understand the mechanisms that drive biological change through time
- to apply this knowledge to understand the genetic underpinnings of biological
diversity, and to solve practical problems in the life sciences

What is evolution
- descent with modification
- changes in the properties of populations that transcend the lifetime of a single
individual
- changes in allele frequencies over time
- key ingredients:
- change that is heritable across generations
- a property of populations, not individuals
All evolving systems have the following properties:
- populations​: groups of entities
- variation​: membres of the population differ from one another with respect to some
characteristic
- hereditary similarity​: offspring resemble parents

Historical background
Aristotle (384-322 BC): believed that all living organisms could be arranged in a ‘scale of
nature’ or Great Chain of Being. The ladder of life consists of graduation from inanimate
material through plants, through lower animals and humans to other spiritual being

Before Darwin (and other early developers)

- orthodoxy: species fixed, designed by God
- variation = imperfection
- earth is young, Ussher’s chronology: calculated how old the world was
→ but evolutionary thinking began

Carolus Linnaeus​: established the modern system of taxonomy in an attempt to discover

order in the diversity of life (for the greater glory of god)
- grouping based on similarity
- hierarchical relationships of organisms
Jean-Baptiste Lamarck: first theory of evolution:
- organism continually arise by spontaneous generation
- ‘nervous fluid’ acts to move each species up the ‘great chain of being’, no extinction
just continuous change
- organisms develop adaptations to changing environment through the use and disuse
of organs
- acquired characteristics are inherited
→ problems with Lamarck’s ideas:
- there is no evidence of spontaneous generation and plenty of extinction
- there is no evidence of an innate drive toward complexity

Emerging field of geology lead to a new concept of the age of the Earth
- the history of the earth extends back through vast time periods
- the processes at work today are the same as those that have been operating
throughout the entire history of Earth
- these concepts became known as ​uniformitarianism

Darwin’s four theories of evolution

- evolution has occurred
- the primary cause of evolutionary change is natural selection
- elements of natural selection
- competition​: more individuals are born than survive
- variation​: vary in traits directly related to their ability to survive and reproduce
- heritability​: advantageous traits are passed onto offspring
- iteration
- splitting of single species into two or more species has occurred
- evolutionary change is gradual (not always true can be really fast)
evolution = in response to differences in survival and reproduction → mutations are random

evolution by natural selection:​ a necessary outcome of differential survival and

reproduction provided the characteristics that caused those differences are heritable
- a mechanism, as mechanical as any physical law
- acts on individuals, but only populations evolve
- opportunistic, not goal seeking – backward-looking, not anticipatory
- not the only mechanism of evolution.

principles of homology and common descent

- evolution can be viewed as a series of bifurcations in a phylogenetic tree - all life can
be traced back to a common ancestor
- groups of species that share a common ancestor derive attributes from that ancestor
- once related lineages are reproductively isolated, evolution can lead to modifications
of the basic plan
- nevertheless, future evolutionary paths are constrained by past history
Evidence for evolution: homology of the vertebrate limb
- comparative anatomy shows that the same skeletal elements appear in very different
species.this phenomenon only makes sense as a process of descent with
modification
- s imilarity between species that is not functionally necessary

Major lines of evidence for evolution:

- the fossil record
- direct observation of evolutionary change through time
- homology and common descent

Why dangerous?
- static → dynamic view of nature
- creationism = implausible
- natural selection has no goal, no consistent direction
- evolution is not progress

Evolution generally accepted but:

- viewed as progressive (towards a goal)
- natural selection rejected
→ no theory of heredity (how characteristics passed on)

The Modern Synthesis

Mendelian genetics rediscovered in 1920s By 30s/40s widely accepted :
- acquired characters not inherited
- Continuous variation explained by Mendelian genetics (Fisher)
- Theoretical works show natural selection can work with what is available in nature,
nothing else required Speciation only requires natural selection. not macromutation
/acquired characters

Tenets of modern synthesis

- populations have variation from random, not adaptively directed, mutation &
recombination
- populations evolve through changes in gene frequency by drift, gene flow and natural
selection
- change is gradual because because most genetic variants have slight effects on
phenotype
- Diversification (​speciation​) is due to gradual reproductive isolation among
populations
- Over time, changes give rise to new taxa

Modern evolutionary biology, two principal goals:

- inferring history of evolution
- elucidating the mechanisms (what is the drive, how does diversity arise?)
- modern evolutionary theory: provide explanation for patterns of life in space & time &
the processes by which these patterns arose
College 2

Natural selection
- in nature most organisms struggle to survive
- there is large variation in ‘form’: fittest individuals that have traits that lend them to be
most fit to the environment they live in, shall increase in frequency in the population
genetic theory of natural selection:
- When traits are determined by Mendelian genes, and genotypes differ in fitness
- Natural selection will increase the frequency of the fittest genotype in a given
environment, changing allele frequencies.

Darwinian fitness (W)

- the relative contribution of a particular individual to the next generation (absolute
fitness vs. relative fitness)
fitness takes into account both survival an reproductive success
natural selection is context dependent, depends on an interaction between an organism and
its environment → most fit genotype will vary over time

What are the 3 preconditions for natural selection

- variation
- heritability
- differential reproductive success

Postulate 1: Variation, at 2 levels

- variation within the population
- variation between populations

Postulate 2: Heritability is important:

- reflects the proportion of variation in a trait that has a genetic basis
- necessary for a trait to respond to selection with a change in the average trait value
in the population
→ Only if offspring resemble their parents will the distribution of traits in the next generation
reflect the traits of the most successful individuals in the parental generation. How can you
test whether variation in a trait is heritable? --observation or manipulation?
- heritable = variation that can be passed from parents to offspring

Postulate 3: More offspring are produced than (can) survive

- The individuals that survive & reproduce the most are those with variations that best
suit their environment.

Postulate 4: Survival and reproduction are nonrandom.

- The individuals that survive & reproduce the most are those with variations that best
suit their environment. larger flowers received more bee visits
- caged some about-to-flower Skypilots with bumblebees
- measured flower size when Skypilots bloomed and later collected their seeds
more bee visits led to higher seed production
 - planted seedlings back out in the original parental habitat
- six years later she counted the number of surviving offspring produced by
each of the parent plants She used the number of surviving 6 year old
offspring as her measure of fitness
- larger flowers received more bee visits → more bee visits led to higher seed
production
- larger flowers received more bee visits + more bee visits led to higher
seed production → plants with larger flowers should have higher
fitness

This process, natural selection on individuals, results in changes in the proportion of the
population with certain variations.
Quantitative genetics allows us to measure the degree to which variation in a trait is is
heritable (and therefore can respond to selection), we can also measure the strength of
selection. Combining heritability and strength of selection allows us to predict evolutionary
change in response to selection

Need to make sure that the environment is not causing some of the variation because
“environment runs in families too.”
- Account for possible environmental causes of similarity between parent and offspring.
- Take young offspring and assign them randomly to parents to be raised (cross
fostering approach)
- In plants, randomly plant seeds in a given field

Requirements for evolution: selection

h^2 can be estimated by using the breeder’s equation R = h^2 x S, h^2 = R / S

S = mean of ‘new’ population - mean of initial population
Forms of selection
- directional selection: changes the population’s mean
- population endures extended cold weather
- food source dies
- swallows die → who’s left / why?
- body fat stores helped carry them through thin times (body size class
undergoes a shift in the mean)
- stabilizing selection: reduces variation, no change in the mean
- exp. very small and very large babies are more likely to die, leaving a
narrower distribution of birthweight
- disruptive selection: Increases variation No change in mean
Directional Stabilizing Disruptive

Analysis of adaptation
- adaptation: ​feature that, because it increases fitness, has been shaped by NS
- When analyzing adaptation we need to remember:
- not all features of a population are adaptive
- not all adaptations are perfect
- We also need to:
- show that a trait has been shaped by natural selection
- determine the agent of selection
- Ways to identify an adaptation
- complexity​: complex structures are usually adaptive e.g. ampullae of
Lorenzini
- engineering​: does the trait fit efficient model predicted by engineering
(appearance of design)?
- e.g. Fish shapes
- Fits aerodynamic prediction
- Form fits function
- e.g. larger bodies of birds and mammals in colder environments
(Bergmann's rule) and shorter ears/legs (Allen’s rule) → both act to
reduce the rate of body heat loss by decreasing the ratio of surface
area to body mass
- convergence​: correlational evidence: convergent evolution
 - Preconditions for natural selection
- there is variation between individuals
- there is heritability across generations
- there is differential survival/reproduction P
→ study of adaptation is largely the study of these preconditions

Stephen Jay Gould and Richard C. Lewontin: everything can be explained as “consistent
with evolutionary theory”; therefore all things are presented as evidence for natural selection

Adaptationist program: pitfalls

- the character is the result of historical constraints
- the character is a byproduct of something else
- the character is not the product of natural selection (e.g.: drift)
- physical constraints
- vestigial traits (no longer functional)
→ questions less the idea that there are adaptations than the idea that everything
qualifies as one

Adaptive traits can evolve from preexisting features

The study of adaptation proceeds in three conceptual stages:

- Identify the phenotypic variation associated with a trait. (i.e.: does it vary and can it
respond to selection?)
- Develop a hypothesis of the traits function.
- Test the hypothesis predictions.
→ A good hypothesis will predict the features of the trait exactly, and the predictions
will be testable.

Four main methods are available to test an adaptive hypothesis:

- Observational studies:​ examine if traits are associated with a given postulated
function/advantage (such as reduced predation).
- Conduct experiment,​ especially if trait can be manipulated experimentally. For
example, paint out the wing stripes of a butterfly species. If the butterflies with their
stripes painted out survived equally well as control butterflies, the wing-stripes are
therefore probably not adaptations to increase survival.
- Experimental evolution​: conduct laboratory studies of selection.
- Comparative method​: examining similar traits in related/unrelated species. Look for
parallelism/convergence in character states.
College 3

1. observational studies​: examine if traits are associated with a given postulated

function / advantage
- mark / recapture
- can involve natural experiments, such as responses to natural disasters
natural introductions to islands etc.
- form some of the most compelling examples of adaptation
- advantages​:
- can study interesting features of species in the wild
- can use strong inference to test adaptive hypothesis under natural
conditions
- problems​:
- are often correlative and lack clear links with causality
2. manipulative studies​: manipulate; environment, phenotype, physiology and
genotype
- study for tail length in sexual selection
3. experimental evolution​: conduct laboratory studies of selection
- artificial selection is breeding for a specific phenotype
- experimental evolution allows examination of evolutionary processes under
defined and reproducible conditions over many generations
- ideal features​:
- ease of laboratory propagation
- rapid generation time
- ease of genetic manipulation
- extensive genomic and genetic information
- is evolution repeatable?
- can be done with microbial evolution studies
- experimental conditions:
- daily serial transfer
- single genotype
- single source
- 12 replicate cultures
→ estimating microbial fitness during pairwise competition assays:
phenotypic parallalism (evolution = the same)
- key variables that influence probability
- population size (N)
- mutation rate
- recombination
- parasite
 -
questions addressed by experimental evolution:
- what factors promote or constrain adaptation?
- what is the advantage of recombination? h
- how do competitors coexist?
- how does virulence evolve?
- how does cooperation (or cheating) evolve?
- how does speciation begin?
- what is the role of predators/parasites on adaptation?
→ many methods to determine if a trait is adaptive , not all provide causal
evidence and not all are suitable for all species
4. comparative method

College 4

Does adaptation lead to perfection?

From an evolutionary perspective an extremely fit organism would:
- live a very long time
- produce many offspring frequently
- reproduce asexually
From an ecological perspective an extremely successful organism would:
- outcompete its neighbours
- colonize distant patches
- utilize all available resources
- resist predators and stress
→ organisms deal with physical constraints and tradeoffs

What are tradeoffs

- a​ trade off​ occurs when improvement in performance (e.g.,
fitness) under one set of circumstances comes with a loss in
performance in another set of circumstances.
- the inability to have the “best of all worlds” in every world is at the
heart of a tradeoff.
- the existence of a tradeoff leads to ranking reversals and may
produce specialists and generalists or different functional types.

Coexistence between multiple species is possible when there are tradeoffs:

- in efficiency using different resources:
- Tilman (1976) showed that two species demonstrating a tradeoff between
growth under limiting phosphate and limiting silicate could coexist under
certain concentrations of both nutrients
- between tolerance to stress and competitive ability:
- Connell (1961) found that two species of barnacles demonstrating a tradeoff
between stress tolerance and competitive ability were able to coexist in the
rocky intertidal
 - between resistance to predators and competitive ability:
- Bohannan & Lenski (1997) showed that two strains of E. coli (T4 resistant and
T4 sensitive) could coexist due to a resistance/competitive trade off

→ experimental example: study on adaptive radiation in a heterogeneous environment

- Paul Rainey and Michael Travision: used bacterium Pseudomonas fluorescens
- Information on the microbe:
- colonizes plant surfaces and soil particles
- produces a green fluorescent pigment
- it is a obligate aerobe
- it is motile by means of multiple flagella
- Authors placed a single ancestral strain of this bacterium into two different types on
environments:
- unshaken microcosm (in which gradients of O2 could develop)
- shaken microcosm (in which such gradients were destroyed, heterogeneous)
- By following the pattern of diversification between treatments, authors studied the
effect of structure and gradients on the origin of variants

→ When a single genotype is placed into an unshaken microcosm, several different colony
morphs evolve, among them:
- smooth morph (SM; like the ancestor)
- wrinkly spreader (WS)
- fuzzy spreader (FS)
Each morph is associated with a particular physical location within the tube:
- SM throughout the broth
- WS at the air-broth interface
- FS at the bottom of the tube
The same morphs reliably appear across experimental replicates and the sequence of
appearance was also maintained. This radiation occurred over the course of 7 days and
diversity continued to remain high for as much as a month later

The role of trade offs

- Rainey & Travisano placed the bacteria producing Morph A Morph B two different
colony morphologies in a tube together in 1:100 ratio
- by measuring the density of both morphs at the beginning and end of a growth cycle,
the authors could calculate relative fitness:
- With one exception (FS invading a population of WS), every morph could
increase when rare
- The WS produces an extracellular cellulosic polymer allowing large numbers
of this type to form a biofilm at the air-broth interface. Such production is
costly and in competition for well-oxygenated broth, the WS is selected
against by the SM that avoids the cost.
→ ​Thus, we have a competition/cooperation tradeoff!

functional interference​: characteristics good for one function are bad for another
limits on adaptation:
- constraints: factors that slow or prevent the evolution of an ideal trait, can be:
- physical, developmental, allocation constraints
- structural constraints
- genetic constraints
- functional constraints
- trade-offs: byproduct effects of one trait on another

Trade-offs in life history evolution

what is a Life history?
- period from fertilization (in sexual reproducers) through death – includes
embryogenesis, birth, larval/juvenile period, sexual maturation, breeding and rearing
of offspring
Differences in natural selection over the life cycle → a trait’s effect on fitness may change
during the life cycle

Trade-offs in life histories

→ productive success (lifetime vs. single season)
→ offspring size vs. number (parent-offspring conflicts)
- tradeoff between offspring size and the number that can be produced:
- few large offspring
- many intermediate-sized offspring
- hundreds / millions of tiny offspring
What is the ideal compromise between offspring size and the number produced?
two assumptions:
- tradeoff between offspring size and the number produced (good experimental
evidence)
- individual offspring will have a better chance of survival if they are large
Natural selection on parental fitness often favors offspring smaller than the size favored by
selection on offspring fitness → may lead to conflict of interest between parents and
offspring

Lack's Hypothesis:
Natural selection will favor the clutch size that produces (birds) the most surviving offspring
- Explicit assumptions of Lack's hypothesis:
- Offspring within a clutch are all the same size (identical energy investment)
- Probability of individual offspring’s survival decreases with increasing clutch
size
→ supported by experiments in which researchers added eggs to nests
College 5

Sexual dimorphism​: differences between the sexes (color, size, weapons etc.)
→ ​Sexual selection​:
- special form of selection that accounts for many elaborated traits and behaviors in
organisms
- arises from differences in the ability to find / mate with members of the opposite sex
- occurs when access to one or the other sex is limiting, (example: when there is
competition for mates or offspring)

→ sexual selection is ​non-random variance in reproductive success

two forms of sexual selection:
- intrasexual selection​: direct competition for mates between members of the same
sex, usually male-male competition.
- intersexual selection​: differences in attractiveness to the opposite sex, usually
non-random mate choice by females.

→ sexual selection is directly related to the ​relative investment in offspring production

- the sex that invests more in offspring production has fewer reproductive
opportunities, as a result they:
- should be more discriminating (choosier)
- become a limiting resource for the opposite sex
- anisogamy (dissimilar gametes)
- females: sex that produces few, well-provisioned gametes (eggs)
- males: sex that produces many, ‘cheap’ gametes (sperm)
→ asymmetric nature of sexual selection often leads to dramatic sexual dimorphism in
characters directly related to male-male competition and/or female choice
- reproductive success is more variable in males than in females
- some males never reproduce, some may sire up to x number of offspring
Intrasexual selection
- sperm competition​ (postcopulatory competition):
- when females mate with more than one male, competition for fertilizations
does not end with securing a mating event
- adaptations for sperm competition include:
- mate guarding (the last male to mate often fertilizes most eggs)
- more elaborate mating structures increase sperm production
Intersexual selection
- female preference​: some traits e.g. tail length in widowbirds are more attractive
- reasons for female choice or preference:
- Direct benefits:
- females may benefit from increased nutrition, provisioning, or paternal care
that increases their reproductive output or the quality of their offspring.
 - Indirect benefits:
- Good Genes Hypothesis​: genetically superior mates produce fitter offspring.
The trait is an indicator of fitness.
- Sexy Son Hypothesis​: females that mate with preferred fathers produce
sons that will have high mating success. The sexually selected trait is not an
indicator of fitness

An alternative to the Good Genes Hypothesis:

- Assortative mating within a population between males with the most exaggerated trait
and females with the strongest preference can lead to a genetic correlation between
trait genes and preference genes. The female preference genes will hitchhike onto
the successful male genes.
- When the trait and the preference are genetically correlated, then the trait can evolve
way beyond the point where it indicates overall genetic quality.
- Runaway of the male trait can proceed to a point of exaggeration where it actually
decreases male fitness.
- The runaway process leads to a situation where the only benefit to female choice is
that her sons inherit the most attractive state of the trait. This is in direct contrast to
the Good Genes Hypothesis and has been referred to as the ​Sexy-son Hypothesis

Alternative hypothesis for the origin of female preference: ​sensory bias

- pre existing preferences for certain traits may be hardwired in females and lead to the
development of exaggerated traits in males

Why sexual reproduction:

- What factors favor the evolution and maintenance of sexual reproduction?
- Is there an advantage or cost to asexual reproduction?
Asexual Sexual
- Benefits​: - Benefits​:
- no need to mate - genetic variation
- simpler - Drawbacks:
- faster - need a mate
- energetically less costly - more complex
- Drawback: - slower
- no genetic variation - energetically costly
- risk of disease / predation
- injury
Why sex evolved
- proofreading
- originated in asexual bacteria
- repair damaged DNA via template replacement
- sex filters out deleterious mutations
Evolutionary costs
- sex is expensive at proximate & ultimate scale
- production of males in sexual populations has ecological cost
- female produces offspring
- sons do not result in as many offspring → cost when female is investing so
much in reproduction
- sexual females half as related to offspring compared to asexual females
- i.e. sexual reproduction yields half of the reproductive fitness as asexual
reproduction
→ possible advantages of sex
- Muller’s ratchet
- an asexual genome cannot produce offspring better than itself, except by rare
back mutation
- the ratchet advances when the best class leaves no offspring, or if all of its
offspring have acquired new deleterious mutations
- a mutational meltdown begins when the mutation load is so great that the
populations is unable to replace itself
- increased variation (Fisher-Muller hypothesis)
- sex may facilitate response to environmental change by generating new gene
combinations allowing populations to track a dynamic environment
- this is because adaptive favorable mutations can be combined horizontally
through a population
- red queen
- a related hypothesis attributes environmental heterogeneity to species
interactions
- for example, sex would be favored in host parasite interactions because it
generates diverse progeny, some of which may have novel resistance
genotypes and be able to withstand parasite attack or disease

Advantages to asexuality
- avoids the two-fold cost of producing males
- no need to locate mates, an advantage at low density
- maintains coadapted gene complexes, an advantage in stable environments

Disadvantages to asexuality
- deleterious mutation accumulation (Muller's Ratchet) in small populations
- time delay in acquiring optimal multilocus genotypes in changing environments
- slow rate of evolution allows sexually reproducing antagonists (parasites,
competitors, and predators) to get the upper hand

College 6

Evolution​: change in allele frequencies within a population

Population​: group of organisms that share a gene pool (same species, same location, able
to share genes through mating)
Population genetics​: study of genetic structure of populations (allele frequencies /
genotype frequencies)

Alleles, genotypes, phenotypes

- 2 alleles (R and r)
- 1 locus (“flower color”)
- 3 genotypes (rr, Rr, RR)
- 3 phenotypes (white, pink, red)
→ calculate genotype / allele frequencies
- 200 white (rr) Genotype frequency Allele frequency
- 500 pink (Rr) - 200/1000 = 0.2 rr - 900/2000 = 0.45 r
- 300 red (RR) - 500/1000 = 0.5 Rr - 1100/2000 = 0.55
- total = 1000 - 300/1000 = 0.3 RR R

What frequencies can tell us:

Frequencies of all alleles at a locus must add to 1.0
Individual allele frequency must be between 0 and 1.0
- Frequency of allele = 0:
- Allele is lost Frequency of allele = 1.0:
- Allele is fixed 0 < frequency < 1.0: Locus is ​polymorphic
→ polymorphism: more than one allele at a locus

Genotype frequencies Allele frequencies

0.25 GG → G 0.25 [0.25 + (0.4/2)] = 0.45 G 360/800 = 0.45 G
0.40 Gg → G 0.2, g 0.2 [0.35 + (0.4/2)] = 0.55 g 440/800 = 0.55 g
0.35 gg → g 0.35

How do we get genotype and allele information:

- observe phenotypes
- DNA sequencing (use SNPs, single nucleotide polymorphism)
Hypothesis 1: little variation Why?:
- Mutations are good or bad (not neutral)
- Selection should rapidly fix ‘good’ / more fit alleles
- Selection should remove ‘bad’ / less fit
Hypothesis 2: lots of variation
- most mutations are neutral selectionist theory
- variation in selection maintains different alleles in population
- heterozygote advantage
- fluctuating selection (selection varies in time or space)
- frequency-dependent selection (rare allele is advantageous)
→ By knowing the basic expectation, we can realize when these conditions do not occur
Null Model for Population Genetics: Hardy-Weinberg principle
- what are the equilibrium conditions ?
- no changes to allele or genotype frequencies
- expectations for Hardy-Weinberg:
- random mating
- large population size
- no mutation
- no migration
- no selection
→ changes in allele frequencies may occur (i.e. Evolution!)

Is a population is at equilibrium for a given locus?

- If at equilibrium: H-W assumptions are fulfilled:
- p & q don’t change between generations
- p2 + 2pq + q2 = 1
→​ ​If not at equilibrium : At least one of the assumptions is violated We cannot predict
the genotypes from the allele freqs

What can change population genetic structure?

- mutation​: spontaneous change in DNA (creates new alleles, ultimate source of all
genetic variation)
- migration​: individuals move into population (introduces new alleles, gene flow)
- natural selection​: certain genotypes produce more offspring (differences in survival
or reproduction, leads to adaptation)
- genetic drift​: genetic change by chance alone (sampling error)
- non-random mating​: mating combines alleles into genotypes (non-random mating
→ non-random allele combinations)

Selection
- non-random survival or reproductive success of different phenotypes
- differential reproductive success of different phenotypes (encoded by different
genotypes)
- if genotypes differ in average fitness, then some genotypes will contribute more
alleles to future generations
→ with random mating diversity is still preserved in the heterozygote

Balancing selection:
- frequency-dependent selection The fitness of a trait changes depending on its
frequency
- heterogeneous environment: variable environmental conditions through time or
space select for different alleles
College 7

When Hardy-Weinberg assumptions are violated:

- no selection
- large population size
- random mating
- no mutation
- no migration

Large populations size → all populations are finite

- most are actually smaller than 100 individuals
→ therefore, the assumption of “large population size” is commonly violated

Each generation is a random sample of the previous generation:

- sampling will always incur some error
- generation t → generation t + 1
- with limited sampling: fixed allele / allele lost, with bigger samples fixating will be
harder
- when populations are small, random sampling error will cause allele frequencies to
change randomly
- in finite populations, evolution occurs due to sampling error

Sampling error is random, can genetic drift have predictable effects?

- genetic drift for one population is unpredictable: average allele frequency among all
populations does not change
- Genetic drift behaviors
- expected change in allele frequency due to drift is 0 Freq(A) will not go up or
down on average
- drift decreases genetic variance in a population, eventually a single allele will
become fixed
- drift increases genetic variance between populations, eventually populations
fix different alleles
- among populations, the average allele frequency does not change
- Can we predict which allele will fix?​: no not in specific populations, however we
can predict the probabilities that each individual allele will fix
- the probability of an allele fixating depends on its initial frequency
- probability of allele A fixing in any population is equal to the initial freq(A) prior
to drift
- The influence of genetic drift on allele frequencies is directly related to the size of a
population → real populations do not keep a constant size
- census size is not always equal to the effective population size, Ne
- fluctuating population size: periodic catastrophes, boom / bust
dynamics
- bias in male/female sex ratios
Natural processes that can magnify drift
- founder effect​: a small group leaves a large population and starts a new population
- allele frequencies may differ due to sampling error → lower genetic diversity
- bottleneck effect​: large population shrinks to a small number of individuals, which
reproduce to repopulate
- allele frequencies may differ due to sampling error

Consequences of founder and bottleneck effect

- significant change of allele frequencies
- isolated populations can diverge → speciation
- can fix mildly deleterious alleles
- changes will be non-adaptive

Migration​: movement of alleles between populations (through mating)

- movement of individuals will result in evolution only if it results in gene flow
- must move and reproduce in new population

Mutation:
- mutation rates are low < 1/10,000 per generation per allele
- loss-of-function mutations are much more common than back mutations that restore
function
- through mutation rate allele frequencies can change (takes a long time)
- mutation-selection balance removal by selection offsets recurrent mutations
- more mutations per generation → higher frequency of mutant allel at equilibrium
- stronger selection against mutant allele → lower frequency of mutant allele at
equilibrium

Only natural selection can cause adaptation!

Genetic drift
- each population has a unique trajectory
- drift has greater influence in small populations
- drift can cause large changes in allele frequencies over time
- over time, alleles can be lost

College 8

Coevolution​: reciprocal evolution of species in response to each other, differs from other
types of evolution in two ways:
- coevolution involves mutual responses in the two species
- predator species evolves to be faster allowing it to catch more, results in
greater selection on speed in the prey
- coevolution promotes diversity of adaptations
- evolution often converges on the same solution for the same problems
- coevolution involves specific, unique response to specific challenges
Species A evolves and adaptation in response to species B <--> Species B evolves in
response to the adaptation of species A

What is coevolution?
Two (or more) species:
- exert selective pressures on each other, and
- evolve in response to each other
→ because each species is evolving in response to the other, one important feature of
coevolution is that the selective environment is constantly changing

When does coevolution occur?

- selective pressure will be strongest when there is a close ecological relationship
- close ecological relationship = usually specialist rather than generalist
- important ecological relationships that give rise to coevolution:
- predator & prey (+ / -)
- parasites & host (+ / -)
- mutualists (+ /+)
- competitors (- / -)
→ evidence of parallel evolution between taxa is required for coevolution
examples:
- Aphid - Buchnera symbiosis (co-speciation)
- Fig - wasp mutualism (twist: parasitic wasp)
- Plant - herbivore coevolution (plants produce toxic chemicals, herbivores have
evolved to detoxify these chemicals)

Coevolution in host-parasite systems

- hosts and parasites change evolutionarily in response to each other
- resistance: the ability of the host to combat the parasite
- virulence: the ability of the parasite to harm the host

Life-Dinner Principle
- predator is hunting for its dinner: if it fails in an encounter with a prey, it loses only a
meal and the effect on predator fitness is relatively small
- prey is running for its life: if it fails in an encounter with a predator, it loses its life and
the effect on prey fitness is very large
→ natural selection on the prey species to evolve defenses is stronger than natural
selection on the predator species to evolve hunting ability
→ arms-race coevolution is typically asymmetrical (selection by predator on prey is
strong, selection by prey on predator is weak)
- the intensity of coevolution depends upon the reciprocity of the fitness effects of
predator on prey and prey on predator.
- life-dinner principle suggests a lack of reciprocity of fitness effects, and thus the
intensity of coevolution resulting from the arms race is weak.
→ however, when prey are dangerous or toxic, then dinner for the predator means a
risk of death
→ this reciprocity of the fitness effects means a strong arms race
Coevolution between competitors
- greater divergence in morphology in sympatry than in allopatry, is ​character
displacement
- region of allopatry (species A) - region of sympatry (overlap species) - region of
allopatry (species B)

College 9

Social interactions and social evolution

- social interaction has two players
- actor: carries out a directed act towards another individual
- recipient: enjoys (or not) the effects of this act
→ cooperation is universal

Definitions of cooperation
- investment of resources in a common interest shared by other group members (Greg
Velicer)
- cooperation by definition involves an interaction between individuals that benefits the
recipient but not necessarily the donor (Joel Sachs)
- a behavior is cooperative if it provides a benefit to another individual and it has
evolved at least partially because of this benefit (Stu)

Potential benefits of sociality Potential costs of sociality

- pooled resources / shared - shared resources
defenses - parasitism
- division of labor - cheaters
- increase indirect fitness (by helping
relatives reproduce)

Shared defenses
- dilution​ ​effect​: prey group together in large numbers to overwhelm the feeding
capacity of the predator
- selfish​ ​herd​: prey found on the inside of a clump will tend to survive, those on the
outside are eten
→ prey constantly moving towards middle of a group in school or flock

Altruism​ → is exploitable, individuals who aren’t cooperative can free-load on the altruistic
behaviours of others without paying the costs of the cooperative trait
- cooperation usually a balance of costs and benefits
- would be even better to exploit without being exploited

Example: model organism for diversity & cooperation

- Pseudomonas fluorescens: soil dwelling microbe associated with plants
- WS is costly morph relative to SM
- WS is susceptible to invasion by defectors
- assuming SM types are cheats; have a negative effect on WS
Hamilton’s rule
- an altruist improves the fitness of a recipient at a fitness cost to itself
- between any two individuals a coefficient of relatedness r can be computed
- this coefficient is basically the probability that the recipient has the same allele as te
donor (by descent)
The ultimate criterion which determines whether [a gene wills pread is not whether the
behaviour is to a benefit of the behaver but whether it is to the benefit of the gene
Hamilton’s rule: b / c > 1 / r (b > c)
- r = relatedness
- b = benefit
- c = cost

Example: kin selected behaviours

- belding’s ground squirrels: social rodent living in subalpine meadows
- when they see hawks, they whistle.. this results in captures 2% of the time by the
hawk
- if they don't whistle. this results in captures 28% of time
- if they spot a mmal hey trill, trill results in 8% captures of the time, not trilling results
in 4% captures of the time
→ whistling is selfish, trills are altruistic
- females are more likely to trill with relatives in earshot (more related to kin)

Reciprocity
- generally refers to cooperation among unrelated individuals
- individual expects a favor in return (of their favor)
- costs of an altruistic act to the donor need to be smaller than the benefit to the
recipient, who in turn will help the donor in the future
- problem: how do you know that the recipient will actually reciprocate?
→ time delay between reciprocal acts allows cheaters to gain benefits and
never return the favour

The evolution of reciprocity

- donors must be able to recognise cheaters and refuse to feed individual who have
not reciprocated
- sufficient pairwise interactions and high probability for a given individual to be a
donor as well as a recipient
- the cost of donating a given amount of aid to the donor must be lower than the
benefit to the recipient

Example: kin selected behaviours

- suicide and sterility in social insects
- potentially cooperative traits / interactions in bacteria: social development, quorum
sensing, biofilms and antibiotic production or secretion of public goods
Cooperation in social amoeba, ​life cycle can be broken down in 3 stages:
- aggregation​: when cells starve they come together
- migration​: the collection of cells move as a ‘slug’
- culmination​: fruiting body is formed in which non-reproducing cells form a stal to
hold up reproductive spores
→ stalk cells are altruist: sacrificing future reproduction to help disperse the spores in
their collection
cheats can be prevented if:
- even mixing occurs within slug (no tendency to cheat)
- or non-relatives are recognized and excluded (non-kin)
→ cheating exists (experiment)
- even mixing does not occur within slugs
- non-relatives appear not to be excluded
→ ​does not happen as much in nature

Cooperation is ubiquitous and is susceptible to exploitation

- kin selection helps explain cooperation among related individuals
- hamilton’s rule formulizes this b/c > 1/r