Sexual conflict

Male and female have different interests and goals when it comes to mating and reproduction.
This can lead to competition between males and females over reproduction.
For instance, males may be interested in mating with as many females as possible to increase
chances of passing their genes to the next generation whereas females may be more selective
about males to ensure genetic quality.

Inter locus sexual conflict

Genes enhancing the reproductive success of one will harm the other

Intra locus sexual conflict

Different alleles at the same locus have conflicting effects on male female reproductive success
Ex: if males and females have different mating behaviours controlled by the same gene

Reproductive isolation and IeSc

If a trait that enhances mating success in one population harms female reproduction in another,
it can create a barrier to interbreeding populations.

Adaptation (v) average fitness of a population increases over time

Adaptation (n) average fitness of an individual increases over time

Differences among populations are not always adaptive

Not every trait or use of a trait is an adaptation
Not every adaptation is perfect

Fresh water stickle back

Many experiments determine that the eda allele controlled the production of armour in stickle
back fish
They determined that the eda allele was always present in marine forms but at very low
frequency, thus, armour could still be produced
When stickle backs made their way into fresh water positive selection increased the frequency
of the eda allele resulting in no armour production (production of armour is very costly and
energy could be spent on earlier breeding, higher growth and improved survival)
Did not evolve independently

Evolution of chemical resistance

BT comes from the bacterium that produces toxins that kills insects and nematodes
Can be formulated as sprays and used as insecticides

How do we manage BT resistance

Planting refuges allows for a mixture of BT plants and non BT plants and leads to a mixture of
resistant and non-resistant insects.
Antagonistic pleiotropy
A mutation or gene with beneficial effects for one trait also causes detrimental effects on other
traits.
Can constrain evolution by causing some phenotypes to be unsuccessful even when mutations
may be beneficial
Cost to evolving the trait

Mechanism of resistance
Pink bollworm mutations that confer resistance affect genes for cadherin protein expressed in
larval gut
In resistant larvae BT can no longer bind to it
Gossypol is phenol made by cotton to defend against herbivores
Interferes with larvae growth
Cadherin involved in protecting against gossypol
Resistance to BT makes the worm more vulnerable to cotton defense
But when BT cotton is present the resistant have the advantage

Life history
Aims to understand the diversity of reproductive strategies
The amount of energy an organism can invest is finite and biological processes take time.
Energy and time devoted to one activity are energy and time that cannot be devoted to another

Reproductive strategies
There are several reproductive strategies, but selection should favour individuals that allocate
energy and time with an optimal balance between benefits and costs maximizing lifetime
reproductive success
Different balances are optimal in different environments, environmental variation is the source
of much of life history variation.
Often face an inescapable trade-off in the allocation of energy to different activities crucial to
fitness
Genetic, developmental, and physiological mechanisms allow different individuals to pursue
divergent strategies adaptive under certain circumstances
Natural selection leads to the adjustment of energy allocation that maximizes the totlal lifetime
production of offspring

Why do organisms age and die

Senescence: late life decline in an individual’s fertility and probability of survival (reduced
fitness)

Rate of living theory

Aging= irreparable damage to cells and tissues, errors in transcription, translation, and
replication, accumulation of poisonous metabolic by products
Organisms selected to resist or repair cells tissue damage to the max extent that is possible
Lack the genetic diversity that would enable them to evolve more effective repair mechanisms
than they already have

Predictions:
1. Age is correlated with metabolic rate: organisms that live long should have slow
metabolic rate and all organisms should expend the same amount of energy per gram
per lifetime.
Results: wide variation of energy expenditure among mammals between and within
orders. Does not support that aging needs to be associated with metabolic rate
2. Species should not evolve longer life spans whether subjected to artificial or natural
selection: an experiment conducted to select for the longevity of fruit flies revealed that
they were able to artificially shift life span of flies significantly
Can be consistent with the first prediction if long lived populations have evolved slower
metabolic rate

Rate of living theory persists

Intrinsic limits based on cumulative effects on molecular mechanisms of cell division
Telomeres: tandem repeat sequences found at the ends of eukaryotic chromosomes prevent
ends of chromosomes from being mistaken for strand breaks by repair machinery
If telomere gets shorter= aging
P53: transcription factor that put the cell into senescence or apoptosis
Trade-off between cancer risk and aging
Elevated levels of P53 make molecular mechanisms more sensitive to small damages and
triggers apoptosis rather than repair; organisms with this die faster but have lower instance of
cancer

The evolutionary theory of aging

Aging caused by the failure of repair mechanisms leading to gradual decay and collapse

Mutation accumulation hypothesis

Mutations causing premature cell death are weakly selected against
Few organisms live long enough to experience the ill effects of late acting deleterious mutations
Fatal mutations in early life strongly selected against

Antagonistic pleiotropy hypothesis of aging

Mutations that cause benefits in early life and costs in late life can be advantageous on balance

Ecological mortality and the evolution of aging

Prediction: Populations with lower rates of ecological mortality (predation, disease, accidents)
will evolve delayed senescence
Results: Island opossums (lower ecological mortality rates) have lower rates of physiological
aging)
Late acting deleterious mutations
Lower ecological mortality means that a higher fraction of zygotes will live long enough to
experience deleterious effects
Mutations with pleiotropic effects
Lower ecological mortality means that a higher fraction of zygotes will live long enough to
experience both early life benefits and late life costs

How many offspring should an individual have?

Lacks hypothesis of the evolution of clutch size in birds: selection favours clutch size that
produces the most surviving offspring
Theory is not supported because lack assumes no trade-off between parents reproductive
efforts in one year and its survival of performance in future years

Life histories in a broader context

Natural selection for a trait should reduce the genetic variation for the trait
Life history traits should show less genetic variation and lower heritability than other kinds of
traits

Evolutionary forces that maintain variation

Mutation, heterozygote advantage, frequency dependent selection, and genotype by
environment interactions.

Behavioural studies
Proximate studies= focus on how behaviour is elicited (psychology neuroscience)
Ultimate studies= focus on why behaviours have evolved as adaptations

Genes influence behaviours

Behavioural differences can be caused by genetic differences

Four kinds of behaviour

Mutual benefit +  +
Selfishness +  -
Altruism -  +
Spite -  -

Social conditions that determine behavioural strategies

Positive frequency dependent selection: majority advantage

Negative frequency dependent selection: minority advantage promotes diversity

Frequencies may exist where all phenotypes have the same fitness
Example:

Altruism
There is always cost to social behaviour
Decreases the fitness of the individual possessing the trait (donor= cost) and increases the
fitness of one or more individuals (recipient=benefit)

Kin selection
Direct fitness: an organisms own reproductive success
Indirect fitness: reproductive success of genetic relatives facilitated by an individual’s actions
Inclusive fitness: direct and indirect
Kin selection: selection arising from the indirect benefits of helping relatives

Hamilton’s rule
B= benefit to recipient (fitness of helped individual) – (fitness of unhelped individual)
C= cost to helper (fitness of unhelped individual) – (fitness of helper)
R= relatedness of recipient to helper
Altruism evolves when Br>C = Br- C > 0

Calculation relatedness

Descendent kin:
Offspring 0.5
Grandchildren 0.25
Great-grandchildren 0.125
No descendent kin:
Full sibs 0.5
Half sibs, nephews, nieces 0.25
Cousins 0.125

The green beard effect

Describes the phenomenon by which individuals with a particular genetic trait recognize and
favour the others with the same trait even if they are unrelated.

Example: slime moulds

When a mould amoeba aggregate to make fruiting bodies the cells that form the stalk are
sacrificing themselves on behalf of cells that form spores.
In an experiment they knock out a locus responsible for adhesion protein
Without this protein you cheat the system because those with the protein automatically
become the stalk
In soil the cells with adhesion were able to exclude cells without adhesion proteins (green
beard effect work together to collectively survive)

Eusociality in insects
Social organisations that consist of sterile workers that labour on behalf of reproductive
individuals
Sterile workers that cooperate in the care of the young

How did eusociality evolve (Haploploidy)

Females develop from fertilized eggs and are diploid
Males develop from unfertilized eggs and are haploid

Relatedness:
Sisters or workers relatedness to each other: 0.75
Sister to brother relatedness: 0.25
Parents are equally related to offspring: 0.5
High relatedness between sisters promotes evolution of altruism among sisters and hence the
evolution of eusociality.

Species distribution/ range limits

All species have limited distributions in time and space
Occupy very different geographic ranges/ regions
Restricted to certain geographic areas

Idealized geographic range

Under optimal conditions fitness is highest (R>=1)
R<1 outside of the geographic range and reproduction drops below self-replacement

Populations at range limit

- Smaller
- Lower fitness and population growth
- Subject to more geographic variation
- Further apart from one another (affect gene flow and drift)
- Extinction
- Low diversity
- Genetically distinct
- Adapted to extreme conditions
Edge populations may not be best adapted for range expansion
Adaptation might not be necessary for successful range expansion
Constraints on adaptation remain a major problem in evolutionary biology

Biological species concept

Species are a group of potentially interbreeding populations that are reproductively isolated
from other groups

Difficulty in recognizing species

Can be difficult to tell apart
Different morphology, song pattern, distribution
Ranges may not overlap but two groups still may be able to interbreed which makes it hard to
apply the biological species concept

Phylogenetic species concept

Smallest possible group descending from a common ancestor and recognizable by unique
derived traits; focuses on phylogenetic history.

General lineage species concept species are metapopulations (group of spatially separated
populations of the same species that interact at some level) that exchange alleles frequently
enough to comprise the same gene pool
Species described in terms of genetic differences among populations
Speciation
One cohesive population splits into two or more reproductively isolated populations
Requires the disruption of gene flow and evolution of reproductively isolating mechanisms

Prezygotic barriers before fertilization

Pre-mating
Different breeding times or places
Different behaviours so meet but don’t mate

Post-mating
Copulation occurs but gametes are not transferred
Gametes are transferred but eggs are not fertilized; Could be a result of gametic incompatibility

Postzygotic barriers

Extrinsic
Ecological inviability (hybrids have a lower chance of survival; intermediate phenotypes are less
fit)
Behavioural sterility

Intrinsic
Hybrid inviability
Hybrid sterility (Horse x Donkey= Mule)

Allopatric speciation

Allopatry: populations are not overlapping (geographic barriers to gene flow)

Geographic isolation
Spatial restriction of gene flow not just physical distance

Sympatric speciation

Sympatry: populations in the same geographic area but remain distinct

No geographic restriction to gene flow
Requires non-random mating based on genetic or phenotypic factors

Parapatric speciation
Geographic barrier only partially seperates populations
Some gene flow is possible
Requires non-random mating based on genetic or phenotypic factors
Speciation requires strong sexual selection
Hybridization
If populations have diverged during a period when groups have lived apart, then any hybrid
offspring that are produced should have markedly reduced fitness relative to individuals in each
parental population

Intrinsic barrier to hybridization

Postzygotic reproductive barriers could be due to genetic incompatibility
Postzygotic isolation is often partial with one reciprocal cross producing viable offspring and the
other producing sterile offspring
These incompatibilities result of chromosomal differences or epistatic interactions among genes

Bateson-Dobzhansky-Muller incompatibilities: Populations accumulate allelic differences at two

or more loci, that cause gamete incompatibilities when combined in hybrids.

Populations become fixed for an allele at two or more loci

Relies on negative interactions among genes (hybridization of parent alleles interact negatively)

Hybridization and gene flow between species

Even when two populations are considered a separate species there is some gene flow between
them,
When species do not interbreed, and gene flow occurs there are 3 possible outcomes:
1. Incompatibility selection against hybrids
2. Extrinsic inviability
3. Hybrids favoured due to novel traits (hybrid zones in transitional habitats)

Reinforcement (prezygotic isolation)

If hybrids have reduced fitness compared to parents, then selection should favour traits that
minimize the production of hybrids

Hybrids may do better than their parents in changing environment

Polyploid speciation and hybridization

Autopolyploidy: duplication of the chromosome of a single species (non-disjunction during
meiosis)
Allopolyploidy: duplication of a combination of chromosomes from different species
Two species hybridize and a duplication event produces offspring with double the number of
chromosomes. The new species is now reproductively isolated from either parent and its
effectively a new species

Speciation by sexual selection

In lapala crickets, as species arrived on a new island they rapidly radiated into several new
species
Speciation involved divergence in courtship song: species differ in male son and female
preferences

Speed of speciation
Barrier to gene flow develops
Slow accumulation of genetic differences through mutation, drift, and natural selection
Genetic divergence leads to reproductive isolating mechanisms (RIMs) as a by product
Perhaps secondary contact, with some level of hybridization possible

Species pairs with greater genetic distance have greater reproductive isolation.

Adaptive radiations
Evolution of ecological and phenotypic diversity within a rapidly multiplying lineage
Differentiation of a single ancestor into an array of species that inhabit a variety of
environments and that differ in traits used to exploit those environments

Horizontal gene transfer in E.coli

Makes classification difficult
Instead of being neatly divided by species barriers the genomes of microbes have been mixed
together by horizontal gene transfer
Challenges how we think about species and species relationships
Serious implications for how we understand bacterial evolution.

Coevolution
 1) Exert selective pressure on each other
2) Evolve in response to each other
Coevolution outcomes depend on intensity of selection, genetic drift and gene flow among
populations
One important feature in coevolution is that selective environments is constantly changing

Why does coevolution occur

positive or negative interactions that affect the interacting partners differently

When does coevolution occur

Predator prey
Parasite host
Mutualism
Competition

Variation can be maintained when traits have other costs

Coevolutionary arms race

Arms race: coevolving species constantly must improve to meet each new adaptation with a
better adaptation of their own
Interacting antagonistically and exerting reciprocal directional selection
Escalation: coadaptation’s become increasingly powerful, yet species are not any better
adapted because this selective landscape is constantly changing
Like the red queen hypothesis: running as fast as possible just to stay in the same place

TTX resistance in snakes

Blocks the skeletal muscle sodium channel
Increased resistance evolved in different lineages in common garter snakes

Geographic mosaic theory

Hotspot: selection strong on both species
Coldspot: selection weak on one or both species
Whether a region is a hot or cold spot can depend on species abundance, amount of gene flow,
presence of predator or prey, environmental conditions
Interactions vary in direction or intensity in different populations
Variation is maintained by frequency dependent selection

Mullerian mimicry
Due to convergent evolution of unrelated organisms, where both benefit by learned avoidance
Batesian mimicry
Harmless organisms copy warning pattern of toxic species
Deriving protection from predators
Human population structure is not race
Genetic differences among populations are relatively small and much of the variation is shared
among populations
There are no well-defined discrete populations
Race is not a biological category
Race is an important sociological variable, as it captures how society treats people and groups
of people

Key events in hominin evolution

Split from apes about 8mya
Diversification in the past 1-5 million years
Emerged during drastic climate change
Bipedal locomotion, changes in teeth and jaw and cognition allowed to adapt to new and more
open environments.

Australopithecus sediba: sister to homo

Has a mix of both ancestral and derived traits
Early species of homo were fully committed to walking on ground

Environmental change during hominin evolution

- Temp drop
- Africa received less rainfall
- Drier wood and grasslands expanded
- Seasonality of rain and droughts
- Environment more unpredictable

Diet of the early hominins changed

A shift to seeds and nuts and away from tough fruits and plant matter

Early evolution of hominins

Bipedalism and upright posture
Shifts in climate and emergence of open grasslands and wood lands played a big role in
bipedalism

Emergence of homo
Early members of homo had lost tree climbing adaptations
Hominins such as homo erectus had long legs and other traits efficient for walking and hunting
H.naledi appears to have split from the rest of the homo clade and evolved similar traits to
modern human independently

Homo born to run

Many traits enhance the ability to run long distances:
Stabilization, thermoregulation, respiration, energetics and shock absorption
Endurance hypothesis: to hunt or scavenge in Africa’s savanna habitat
Expanded out of Africa about 2.1 mya
Fossils of homo found in asia show variations in morphology suggesting the expansion of
different lineages of homo from Africa
Expansion to the Americas via land bridges about 15 000 years ago or much earlier

Shift in diet facilitated change in brain size

Meatier diet
Narrow rib cage and small molars suggest they ate more meat
Hypothesis: dietary shift may have been critical to evolving larger brains requiring huge
amounts of energy

Increased cognition evidence of tools and art

Recent homo sapiens

Emerged 600 000 – 800 000 years ago
- H.heidelbergensis
- H.neanderthalensis
- Denisovans
- H.sapiens

Neanderthals evolved in Europe and asia

- 300-40 kya
- May have evolved from h.heidelgernesis or close relative
- Adapted to the harsh, ice age climate
- Large brains
- Neandrethals had broad shoulders and hips and muscular build
- Artifacts revealed sophisticated behaviour

Fossils of denisovans date to 50 000 years ago

DNA analysis suggests enough differences to consider denisovans to be a distinct lineage
Presence of small amounts of both Denisovan and neanderthal DNA in humans indicated
hybridization

Emergence of distinct homo sapien species (200kya)

- Likely evolved from h.heidelbergensis in Africa
- Taller and narrower
- Smaller face, teeth, jaws
- Chin
- Large brain
- Worldwide expansion
- Accelerating change in tools
- Art
- Language
Genomics reveal interbreeding between Neandrethals, denisovans, and homo sapiens
These groups represent lineages descending from a common ancestor
There was subsequently interbreeding between lineages
Neandrethal DNA: up to 2.6% of the genome
Denisovan DNA: up to 5% of the genome

Evolution of hominin brains

- Drastic evolution over the past 4 million years
- Ecological social cultural factors are driving forces
- About 2mya hominin brains began to increase in size and growth accelerated 1 million
years ago.

Language is at the core of human nature

Each of the 6000 languages is the product of culture and history
Syntax arrangement of words and phrases to form well-structured sentences is a commonality
between all languages
Adaptation shaped by natural selection; FOXP2 involved in language has been overturned
because we now have access to more sequence data and DNA from archaic humans and
Neanderthals

4 mechanisms of evolution:
 1. Variability
2. Heritability
3. Reproductive success
4. Variation in survival and reproduction is non-random with respect to phenotype

Microevolution:
Small scale evolutionary changes occurring within a population over a short period of time
(changes in gene frequency or developmental traits)
Evolutionary mechanisms responsible for change

Macroevolution:
Large scale evolutionary changes that focus on the evolutionary relationships of organisms

Model of special creation:

1. Species do not change
2. Variation is limited
3. Species were created independently
4. Earth and species are young

Descent with modification:

1. Species change
2. Speciation
3. Life can arise from earlier forms
4. Species derived from a common ancestor
5. Earth is old

Gene flow
Exchange of genes between populations
Isolation leads to evolution

Variation
Mutations are a source of variation

Inheritance
Original hypothesis called blending inheritance, thought that favourable variants would be
diluted into existing traits

Law of segregation (alleles segregate equally) and law of independent assortment (genes assort
independently)
New variant can drive changes in populations they are not diluted away
4 postulates of modern synthesis:
1. Variation from mutation, segregation, and independent assortment
2. Individuals pass on alleles
3. In every generation some individuals are more fit than others
4. Highest fitness= alleles that adapt organism to the environment

Creationism
Tries to disprove the theory of evolution
Adaptations must result from the actions of a conscious entity

Artificial selection:
Domestication, selection for favourable traits
Traits selected for often deleterious in the wild

Evolution by natural selection:

If all four postulates hold true then population inevitably changes
Change in allele frequencies between generations
Traits that are conducive to survival and reproduction will become more and more frequent

Important clarifications about natural selection:

1. Population changes
2. Selection acts on phenotype but evolution= change in allele frequencies
3. Not future oriented
4. Not progressive
5. Does not act for the good of the species
6. Does not lead to perfection
7. Selection acts on existing traits, new traits can evolve through mutation and
recombination

Evolutionary grouping:

Monophyletic: includes ancestor and all descendants

Paraphyletic: ancestor but not all descendants
Polyphyletic: two convergent descendants but no ancestor

Parsimony:
Choosing the hypothesis that requires the fewest evolutionary changes

Homoplasy:
Independent origin of similar traits

Shared trait:
Trait that two lineages have in common

Shared derived trait:

Trait shared by a group of organisms and their common ancestor but is not present in more
distant ancestors.

Phenotype= Genotype +Environment + GXE (interaction)

Frequencies
30 GG
60 Gg
10 gg

Phenotype:
Green= 90/100 = 0.9
Brown= 10/100= 0.1

Genotype:
GG 0.3
Gg 0.6
Gg 0.1

Allele
G 0.3+0.3 = 0.6
g 0.3+ 0.1 = 0.4

Predicting the next generation

A (p) = 0.6
a (q) = 0.4

AA= 0.36 p^2

Aa=0.24 pq
Aa=0.24 pq
aa=0.16 q^2

p^2+2pq+q^2

Most mutations are mildly deleterious

Mutation rate
Mutation rate is low but genome is large
Mutations rates become larger as organism get larger
Hardy Weinberg equilibrium:

p^2+2pq+q^2= 1

p+q= 1

populations in hardy Weinberg do not have changing allele frequencies

random mating yields predictable equilibrium frequencies
a single generation of random mating restores hardy Weinberg

Hardy Weinberg assumptions

1. No selection
2. No mutations
3. No migration
4. No chance events (population is infinitely large)
5. Random mating

Implications of hardy Weinberg

Rare alleles are primarily found in heterozygotes
Mutations are rare and almost always occur in heterozygous form
Heterozygosity maximized when allele frequencies are intermediate

Primary uses of hardy Weinberg:

1. Compute genotype frequency from generation to generation
2. Serves as a test for evolution, observed vs expected (if they differ by 0.05 or more we
call them different)
3. Forensic analysis

Chance events (finite populations)

In a population that is finite we will not get allele frequencies in their exact proportions

Genetic drift
- Allele frequencies shift
- Alleles are lost more rapidly in small populations
- Changes are less predictable in small populations

Rare alleles are more likely to be lost in a population bottle neck

One allele will eventually drift the fixation while the other is lost
Probability that it will be fixed or lost is proportional to its frequency in the population
Frequency of heterozygosity declines

Non-random mating (inbreeding)

Inbreeding: selfing, mating with genetic relatives
Can cause a variety of problems due to pairing of deleterious recessive alleles in homozygous
state.

Disassortative mating: genotypes different from each other may mate more often than
expected

Assortative mating: genotypes similar to each other may mate more often than expected

Increases number of homozygotes than expected under HW

Frequency of heterozygotes is halved in every generation
Causes genotypic frequencies to change

Inbreeding coefficient
Probability that to alleles are identical by descent
Using pedigree and multiplying chances of receiving the allele in every generation

Calculating relatedness (F)

F= look at all the alleles and repeat the path for each allele
Add probability of each of these alleles

Quantifying the amount of inbreeding

F= 1- Ho/Hexp (frequency of heterozygotes if all mating were random)

F= 0 there is HWE within populations Hexp=Hobs

F=1 all individuals in populations are homozygous (either allele)
F<0.5 in highly inbred populations or selfing species

Inbreeding
- Causes individuals to contain alleles that are identical by descent from a common
ancestor
- Causes a loss of heterozygosity
- Causes uniformity
- Causes inbreeding depression
- More likely chance of combining deleterious alleles

Can we predict the long-term effects of selection?

If directional selection is maintained, a favourable allele will increase in frequency.
Change is fastest when the selection is strong and allele frequencies are similar

Additive relationship
Allele yield twice the phenotypic effect when two copies are present

Dominant relationship
Dominant allele masks the presence of recessive heterozygote

Selection is more powerful in larger populations because drift is weaker

Directional selection
One of the two alleles has higher fitness
Allele will increase in frequency in the population
Rate and final frequency depend on the selection coefficient (s, selection strength on a
genotype) and dominance (h, what happens to the heterozygote).

h=0 A1 is dominant
h=1 A2 is dominant
h=0.5 codominance

any value of h between 0.1-0.9 (except 0.5) means that alleles are partially additive

Find selection strength of the least fit homozygote

hs= 1-fitness of heterozygote

h=previous answer/s

most fit will have a relative fitness of 1

Heterozygote advantage
Has the highest fitness
Both alleles are maintained
Natural selection can maintain deleterious mutations
Promotes genetic diversity
Population is fixed at an intermediate point (stable equilibrium)

Heterozygote disadvantage
Heterozygote has lowest fitness
Unstable equilibrium
One allele is fixed one is lost

Negative frequency dependent selection:

Allele becomes less fit as it becomes more common
Both alleles are maintained
Factors driving allele frequencies back and forth
Something must drive a switch
Fitness is greatest when phenotype is rare
Positive frequency dependent selection:
Leads to unstable polymorphism
(Maintaining both alleles is unstable)
Fitness of a genotype increases with its frequency
Unstable equilibrium at p=q
p>q A goes to fixation
p<q a goes to fixation

Assortative mating
Like mates with like

Population subdivision:
No subdivision Fst=0
Extreme subdivision (no migration, no gene flow) Fst=1
Some subdivision (some migration, some gene flow) 0<Fst<1

Measuring genetic differentiation (Fst= variation in allele frequencies among populations):

Differ in allele frequencies
When two adjacent populations are genetically differentiated, we know that gene flow has not
homogenized them

Fst= (Ht-Hs)/Ht

Hs= average heterozygosity in the subpopulations

Ht= total expected heterozygosity is subpopulations were homogenized
qmean=0.5 pmean=0.5 2pqmean=0.5

Population 1:
p= 1 fixed
q=0 lost

Population 2:
p=0
q=1

Hs= 0

Fst= 1-0/0.5= 1

Genetic linkage:
Genes on the same chromosome are said to be linked
Further apart are less linked
On separate chromosomes not physically linked= genetic equilibrium

Recombination:
Loci further apart they are more likely to recombine
When loci are close together recombination almost never occurs (inherited together)

Linkage disequilibrium:
Relationship between alleles at different loci
When D>0
Knowing the allele at one locus enables you to predict what the allele at the other locus likely is

DA1B1 (extent of linkage disequilibrium) = PA1B1 (observed) – PA1 X B1 (expected frequency of

A1B1 individuals if in linkage disequilibrium)

D= 0 fully recombining
D>0 means excess of A1B1 and A2B2
D<0 means excess of A1B2 and A2B2

PA1= A PA2=a PB1=B PB2=b

Allele frequencies= expected values

Chromosome frequencies (from Punnett square) = observed values

What eliminates linkage disequilibrium

- recombination
- Crossing over

What causes linkage disequilibrium

- Physical linkage
- Natural selection favouring AB or ab combos
- Gene flow where AABB arrive in aabb populations
- Assortative mating

Expected frequency for unlinked loci

More recombination, inherited separately thus have equal frequencies

Expected frequency for linked loci

No recombination, inherited together where A1 goes B1 goes
50% A1B1 and 50% A2B2
QTL analysis uses experimental cross to create linkage disequilibrium then uses markers
throughout the genome to find the regions where there is a statistical association between
phenotype of interest and molecular markers

QTL of flower colour

Each region of a chromosome contributes genes that may or may not affect the trait of interest
By recombining chromosomes one can find regions that contribute to phenotype

Advantages of sex:
1. Combining beneficial mutations
2. Generation of novel genotypes (recombination)
3. Faster evolution (more diversity more natural selection)
4. Clearance of deleterious mutations

Disadvantages:
1. Two-fold cost (not all progeny can produce offspring)
2. Search cost
3. Reduced relatedness
4. Risk of transmitting infection

The two-fold cost

Cost of producing males
Asexual female has twice the fitness and should be selected and increase over time

Genetic cost of meiosis (reduced relatedness)

Only half of parents’ alleles are passed to the offspring
Asexual females have twice the relatedness btw parent and offspring

The cost of finding mates

Exacerbated by low population density
Time spent looking for mate could be spent foraging

Infection
Increase transmission of pathogens and infections
Exposure to predators

Combining beneficial mutations

Can be combine across lineages

Novel genotypes
Reduces linkage disequilibrium, allowing for independent trait evolution
Crossing over= unique gamete combinations
Sex allows for faster evolution
Genetically diverse progeny allows natural selection to act on advantageous traits
Red queen hypothesis

Sex can remove deleterious mutations (Mullers ratchet)

Deleterious recombination helps the evolution / removal of deleterious and accumulation of
beneficial mutations
Muller ratchet refers to accumulation of deleterious mutations in asexual lineages
Deleterious mutations can become fixed in asexual populations and purged in sexual
populations

Sex is common
Few eukaryotes are purely asexual
Asexual species evolve due to huge short term benefits but often go extinct because short-term
is countered by long term advantages of sex

Correlation btw sex and parasite infection in sexual and asexual snails
Snail infected by trematode
H1: parasitism selects for sex
H2: asexuality provides reproductive assurance under low density

Thus, an evolutionary arms race between snails and trematodes selects in favor of sex in the
snails, then sexual snails should be more common

Polygenic traits
Influences by many genetic loci and environment
Discrete phenotype= maintain distinct phenotype
Continuous phenotype= trait displays a range of expression
Meristic= recorded counting whole numbers

Quantitative genetics
Study of genetic mechanisms of polygenic traits
Traits that vary widely about their mean have bigger variance

Heritability
H^2 = genetic variance/ phenotypic variance
Proportion of phenotypic variance due to genotypic differences among individuals

Broad sense heritability

H^2= VG/VP= VG/VG+VE
Measured in a particular population at a particular place and time
When there is a lot of environmental variances there is lower heritability

“Common garden” to measure heritability

Put replicates of a genotype in the same and different environments
If the replicates of a genotype look identical all variation is due to genetic differences.
If replicates of a genotype look different, the variance is due to the environment

Twins
Monozygotic: whole genome
Dizygotic: half genome
High heritability: monozygotic resemble more strongly than dizygotic
Low heritability: monozygotic resemble no more strongly than dizygotic

Estimating heritability with relatives

Resemblance btw relatives: parent offspring regression
If slope of regression= 0 then trait is not heritable
If slope of regression = 0.5 the trait is somewhat heritable
If slop of regression=1 then the trait is highly heritable

Narrow sense heritability

h^2= VA (additive variance)/ (VA+VP+VI (VG) +VE)=VP

VA= additive variation

VD= dominance variation
VI= epistatic variation

Slope of parent offspring regression = narrow sense heritability

Phenotypic variance attributed to additive genetic variance

What is h^2

1. Can be reliably passed on

2. Cannot reliably passed on dominance effects because phenotype depends on allele at a
locus on another chromosome
3. Cannot reliably pass on interaction (epistatic) effects because phenotype depends on
the allele at a locus on another chromosome and recombination and independent
assortment during meiosis break up associations btw alleles at different loci
4. Cannot reliably pass on environment effects because phenotype depends on
environment of offspring

Epistatic gene interactions

Two or more genes interact to affect a trait
Two loci influence coat colour in old field mice, and they interact epistatically
Predicting these effects is hard because phenotype is affected by genotypes at multiple loci

Low heritability could be due to high VP or low VA

High heritability could be due to low VP or high VA

Natural selection
Within generation process phenotypic variation and fitness differences
(not all members of parental generation contribute equally)
Between generation process phenotypic selection is coupled with inheritance to produce
genetic response

Directional selection
Changes the population mean and reduces variation

Stabilizing selection
Intermediate trait is favoured
Reduces variation, does not change mean

Disruptive selection
Extremes are favoured
Increases variance, does not change population mean value

Breeders’ equation
R (response to selection, amount of evolutionary change in a population)= h^2 X S

Measuring directional selection

Difference between the mean of the whole population and the mean of selected parents
Within generation measurement

h^2= R/S
relative change in mean phenotype from one generation to the next equals the proportion of
total phenotypic variation associated with additive effects

when all populations are under the same selective pressures the greatest evolutionary
response= the highest heritability

High heritability results in higher change

h^2= 0
R= 0XS=0
No response

0<h^2<1
Some response

h^2=1
R=S
strongest response

S= XS-XP
R=X’-XP

We can predict how populations evolve if we have S and R

OR we can measure R and know h^2, and calculate (S)

Phenotypic plasticity
Single genotype produces different genotype depending on the environment

Evolution of plastic traits

Evolution can act on plasticity itself
Genotypes that are most plastic could be favoured if the environment is frequently changing

Polyphenisms
Simple genetic polymorphisms can sometimes respond to their environment, and produce
multiple discrete phenotypes
Often due to a threshold sensitivity to the environment

Norm of reaction
Phenotypes produced by a single genotype exposed to different environmental conditions

No genetic variation within an environment (all individuals have a similar phenotype within an
environment) and all genotypes show the same plasticity lines are parallel (overlapping)

Genetic variation within an environment all genotypes show the same plasticity (lines parallel
not over lapping) VG and VE

Genetic variation within environment and genetic variation in plasticity VGXVE slopes are
crossing

VGXVE>0 plastic traits can evolve

Homolog= same gene in different lineages

Ortholog= homologous genes separated by speciation event (lineages diverge through time)
Paralogs=homologous genes resulting from duplication events

Coalescence
Looks at where the lineage splits
Looking at how many generations this took
Coalescent process
Takes longer in larger populations because drift is weaker
Takes longer when purifying selection is strong or little selection
Positive selection can accelerate the rise in frequency of a beneficial allele leading to shorter
coalescence time
Coalescence time varies in different genes

Gene and species trees do not always match

Alternate alleles can persist in populations for long periods of time
Such alleles may be passed down in ways that do not reflect actual branching history of a
species
Incomplete lineage sorting results in gene tree that differ from true phylogenies
Researchers use many genes when constructing phylogenies
Incomplete lineage sorting occurs when an allelic variant persists through a speciation event

Effective population size

Census size (N) =/ effective size (Ne)
Census N= number of individuals in a population
Ne= # of individuals in an ideal population (every individual reproduces) in which the rate of
genetic drift would be the same as it is in the actual population

Ne is usually smaller than N due to:

-biased sex ratios
- non-random mating
-fluctuations in population size
-selection

Drift events means decreased variation thus unequal contribution

Never make assumptions from the census but from the effective size
When Ne is smaller coalescence is faster and slower when Ne is larger

In a population that is expanding the rate of coalescence slows and more events occur at the
base of the tree

Genomics
Study of the structure and function of the genome
Mapping genes and DNA sequencing and unites molecular biology, evolutionary genetics, and
computational biology

Variation in genome size

Bacterial genome varies mainly depending on # of genes
Eukaryotic genomes vary due to non-coding DNA
As more genomes are sequences our understanding of genome evolution is changing
Positive selection
Selecting to increase the frequency of the beneficial allele

Negative selection
Selecting to decrease the frequency of the allele
Deleterious or harmful and has low fitness
Long coalescence time

Many mutations are neutral

Probability of fixation for novel mutations depends on effective population size and strength of
selection

Molecular clock
Most mutations will yield nucleotide substitutions equivalent to the rate of mutation we know
the rate of mutation and can use the # of bp substitutions to estimate the time since two
groups shared an ancestor
Deviations from the molecular clock can indicate mutations under selection

Methods to detect selection at the genomic level

Increased differentiation between populations in genomic regions under selection
Extended linkage disequilibrium around the beneficial allele and decrease in genetic variation
around the selected site

Mutations in the third position are synonymous

Mutations in the second and first are non-synonymous

#NS subs/ #NS sites vs #S subs/ #S sites

dN/dS= 1 neutral
dN/dS>1 advantageous substitution
dN/dS<1 deleterious substitution

Fst outlier
Detects loci with allele frequencies that re more different than expected between populations
These loci are likely to be in regions of the genome experiencing strong selection

Outcomes of gene duplication:

Neofunctionalization: second copy takes on new function

Sub functionalization: two copies split function. Both accumulate deleterious mutations but
together maintain function

Genes conservation: both copies with same function

Non functionalization: second copy becomes non functional

Complex adaptations and novel traits

- Suits of co-expressed traits that together experience selection for a common function
Multiple components must be expressed together for trait to function
- Regulatory networks are often involved in complex adaptations
- Novel traits can arise when existing genes are expressed in a new developmental
context
- Duplicated genes accumulate mutations rapidly

Parhtogenesis
Organism develops from unfertilized egg

Hermaphrodism
Organism possesses both male and female parts or change sex at the same point in their lives

Haloploidy
Haploid males develop from unfertilized eggs, diploid female from fertilized egg

Environmental
Early developmental environment determines the sex of the individual

Anisogamy
Females invest few large gametes
Males invest many small gametes

Sexual selection
Fitness measured relative to the same sex
Sexual selection can produce costly traits that compromise survival
Reproductive success depends on mating success

Sexual dimorphism
Male and female look difference

Intrasexual selection
Within sex interactions (male-male competition)

Intersexual selection
Between sex interactions (female choice of males)

Batemans principle
Female is the limiting factor
Intense sexual selection of males
Female choice direct benefits
Increase reproductive output
Increased nutrition
Provisioning
Paternal care

Female choice indirect benefits

Benefit effects genetic quality of offspring
Showy ornaments often serve as indicators of high quality males

Good genes process

Genetically superior males create fitter offspring

Arbitrary choice
Mating between males with exaggerated traits and females with preference for trait can lead to
genetic correlation between genes and preference
Meaning offspring may be choosy for specific traits

Arbitrary choice leading to maladaptive traits

When trait and preference are genetically correlated, trait can evolve beyond genetic
quality...can decrease male fitness
The only benefit to female choice in this case is that her sons inherit the most attractive trait