ONLY READ FROM TEXTBOOK WHAT IS

IN THE TEXTBOOK!
(starting form lecture 13) Chapter 27 (To November 11)
->(outline p 544-545)
Phylogeny: evolutionary history of a group of organisms
-. Tree shows ancestor-descendant relationships among populations or species
-> Built from data (DNA, traits) to depict evolutionary hypothesis (its a
evidence based guess)
-Monophyletic group (clade): Ancestor and all of its descendants
Adaptive Radiation: Pattern in history with instances of rapid diversification in species/forms
Associated with new ecological opportunities and/or new trait
Phylogeny and fossil record used to study history of life (ex time of divrgnce)
Mass Extinction (+constant background extinction)
In a phylogenetic tree:
Taxa: The smallest group at the end of the phylo tree. Probably same thing as tips
Tips: Things at the end of the phylogenetic trees
Nodes: Where two branches meet
Branches: Any line on the tree (length=/=relative time, unless specified. Aka cladogram)
Sister Groups: two things that are closely related: the two adjacent groups branching off
from the most recent node (the node is used as reference)
Estimating phylo trees
Genetic: (DNA, Amino acids, enzymes, chromosomes)
Morphological: (internal or external size and shape
Behavioural, ecological: (Sociality, habitat preferenes)

Ways to build trees:

-Phenetic: distance approach. Based on similarity %
-> If DNA: Percent DNA sequence divergence
-> If morphology, using multidimensional statistic: ei length of arm,
width of skull
Problem: Assume: If youre similar, you evolved once, you MUST have a
common ancestry
->Distance matrices can also summarize variation between clades
-> Generally not used to build actual phylogenies
-Cladistic approach: based on shared derived characters (synapomorphies)
-> modified from an ancestral trait (given common descent)
-> Maximum parisimony: Minimize number of changes on tree
-> Fewest evolutionary steps
-> For DNA: Check for derived sequence changes. Ex: AAC and AGA are
derived from AAA. Then the two are descendant of the
AAA
Probabilistic approach:
-

Also based on synapomorphies

Maximum likelihood and Bayesian approaches use a model of

evolutionary transitions.

Provides statistical likelihood of the correctness of the phylogeny.

Calculates probability using a data matrix.

In practices, multiple methods are used (combined)

Homology: when traits are similar due to common descent

Homoplasy: When traits are similar for different reason.
Convergent Evolution (Aka ecological convergence)
Question: In which treeing method is homoplasy the greatest problem in ?
Phonetic, NOT cladistics. It actually cant be cladistics since homoplasy
species cant be used at all in this method. Cladistics only takes homology
based species.
Convergent evolution: Occurs when nat sel favors similar solutions to the same problems, but
not because of common ancestry. (common cause of homoplasy)///oct 15
Lecture 14:
Clarification:

-> Phenetic: Criterion of similarity (morphological or genetic distance)

Cladistic: Criterion of synamorphies (derived traits or genetic traits). Also
maximum parsimony
Probabilistic: Statistical analysis based on data. likeliest tree is the correct
answer:

Phylogeny and Tree of Life: While traits can converge, so can DNA.
Convergence example: Fish that moved onto land and gained limbs.
Remember that convergence isnt always homoplasy (but I think it
mostly is)
Living Fossils
Living specimen of species that were thought to have gone extinct.

Case Study: Whale Evolution

Instead of the traditional cladograms, which are based off morphological data, using a
DNA sequencing showed that whales had a close relationship with hippos. (morphological data

would not reveal this). However, cladogram from DNA data would then turn the tree into its nonparsimonious form.
SINE( short interspersed nuclear elements) show that whales and hippos share several
SINE genes that are absent in other artiodactyl groups, which shows that theyre slowly evolving
(conservatively)

(this is known as the whippo hypothesis). In addition, homoplasy is rare in

SINEs, which further supports that whales are hippos had a more recent ancestor.

Conclusion: New phylogeny is less parsimonious, but is most parsimonious overall due to
SINEs
Further proofs: Transitional forms during whale evolution
Tools for Studying History: The Fossil Record
Only direct evidence about ancient organisms morphology.
Provide minimum ages for groups. In other words, a group must be at least
as old as the oldest fossil of that group
Only form under ideal conditions.
(skipping how fossils are formed)
Cast Fossils: When remains decompose, and leaves a cast
Permineralized Fossils: when remains rot extremely slowly and dissolved minerals
infiltrate interior of cells and harden into stone.

Limitations of the fossil record:

Habitat Bias: Organisms living in areas with more sediment deposits are more likely to
fossilize more than others.
Taxanomic Bias: Some organisms have hard parts (ie stronger bones), and decay slower,
leaving more fossil evidence.

Temporal Bias: More recent fossils are more common and ancient fossils.
Abundance Bias: abundant organisms are widespread and long lived, leaving more
evidence
(conclusion: For the above reasons, not all organism have been fossilized, or
fossilized as much as they should have been, leading to error, or bias in observation.)
Despite the bias and incompletion, fossils are the only direct evidence to see
extinct life.

Time Trees: Phylogenies + Fossils

- Phylogenies show evolutionary relationships and relative age of divergence
- Fossils provide information to convert relative age to absolute age (in years)
-Minimum age of clade: clade must be at least as old as the oldest
fossil found.
- Crown Group: common ancestory of living species + all decendents
- Stem Group: includes extinct species on branch leading to the crown group
(Both groups show what category a fossil belongs in. Uses Cladistic analysis using
morphology. Crown: fossil belongs in a living clade, and Stem: Fossil belongs outside
the living clade)
Lecture 15:
Molecular Clock: A graph with time on the x axis, and a %divergence for a trait on
Y axis (I think the trait is molecular trait, like DNA). This can replace
fossils in the making of a timetree.
Time Tree: Time-scaled phylogenetic tree calibrated to absolute time. Can be used to
reconstruct the timescale of evolutionary history to include tempo and mode
of change (timing, speed, and model of evolution)

 A timetree answers: When was the time of divergence? How fast is it?
Driven by what (compare time of divergence to
environmental conditions at the time)?
- Ex: Penguin evolution. By using a timetree for penguins, it can be concluded that
they diverged 11-16 mya, which overlaps with the sharp decline in Antarctic
temperatures that began apprx 12mya (suggests relationship between the 2)

Adaptive Radiation: Instances of rapid diversification of species in a lineage due to

ecological diversification (changes in the environment. For example,
creation of new food, or a barrier)
Triggered by ecological opportunity or morphological innovation
Usually includes high species diversity and great ecological divergences
- In a single lineage, its the differentiation of a single ancestor into an array of species
that inhabit a variety of environments and differ in traits used to exploit those
environments.

symptoms of adaptive radiation: Common ancestry, rapid speciation,

phenotype-environment correlation, and divergence of traits and their utility.
May result in something like this:

(thats due to the rapid divergence)

(true phylogeny still shows a bit of difference in the time of speciation)
(estimated phylogeny shows all speciations as happening at one single time)
Trigger of adaptive radiation is ecological opportunity, or the availability
of new resources.

(lots of examples in lecture notes, but not sure if imp.)

Uncertain Conclusion: Adaptive Radiation doesnt only happen on islands, but physical
isolation seems to play a big role in it
Lecture 16:
-(A lot of talking about rats moving, and about how it supports dispersal speciation.
After rats migrate by water, by reaching a new ecosystem, they experienced adaptive radiation.)
-Ecological limits constraining the radiation:
-> given enough time, the ecological resources that lead to radiation becomes
limiting, expected to lead to slowed down rates of diversification

Adaptive Radiations Summary:

Islands: Galapagos finches, Hawaiian (honeycreepers, silverswords, lobeliads), Malagasy
vangids, and Caribbean anolis lizards.
Lakes: Cichlids of African Great Lakes
Continents: South American caviomorph rodents.
Timeline of Life:
Four

Eons:

Precambrian

supereon

(Hadean,

Archaean,

and

Proterozoic

Eon),

Phanerozoic (paleozoic, Mesozoic, and Cenozoic Era) lectures notes say know these
Precambrian: Formation of Earth to appearance of most animal groups (4.6b-542mya)
During this supereon, liquid water formed, then origin of life, first
eukaryotic fossils, first photosynthetic eukaryotes, diversification of multicell

organisms, then first bilaterally symmetric animals (in this order)

Phanerozoic Eon: Many animal groups appear in Paleozoic era. Mass extinction at the
end of Paleozoic era. Then, diversification of unicellular organisms
into multicellular is called the Cambrian Explosion. Then is the
Mesozoic era aka age of reptiles (first dino, first mammals, first bird).
This era ends with the mass extinction of dinosaurs, only birds survive.
Then is the Cenozoic era, aka age of mammals (first primates, first
apes, and then, the Homo sapiens.
Background Extinctions: When certain populations are reduced to zero non-randomly
by normal environmental change, disease, or competition
Mass Extinctions: when a sudden, abnormal and temporary change in the environment
Currently is the 6th Mass Extinction: 1000-10000x the rate of bkground extinction.

Lecture 17:
Dating Fossils: Radiometric methods: Potassium -> Argon dating. Since argon is absent from lava,
any detection of argon is the decay of potassium into argon. (absolute dating)

(Relative dating: extinction dates, magnetic reversal)

Index fossils: define certain geologic periods. Used for biostratigraphy, or
correlation of rock strata according to the fossils contained in them (find age
by rock contents. If it has a fossil of a really old organism, rock must be old)
Primates, monkeys, apes
Primates: Order.
Monkeys and Apes: Part of a suborder of primates.

Are humans apes or monkeys? Were both.

Early Primates Evolution: after Pangaea breakup, there was a revolution in the plan lineage, and
flowers evolved, creating new niches. Primate were among the first
that evolved to fill these niches
Seed-Producers: Most have endosperm within seed, and most also produce fruit that contain the
seeds. (angiosperm definition: Seed-producing plants
Seeds are an innovation that evolved in the ancestor of gymnosperm and
angiosperm plants (both are seed-producing plants). Before this all plants
used spores, but seeds have much more stored food resource.

Gymnospems: Produce ovules that lack a cover (naked seed)

Angiosperms: Produce ovules that are covered by the ovary (covered seeds). Seed can also have
a fruit coat around the seed coat.
Angiosperms replaced conifers(gymnosperms) as the dominant trees. They
have more mutualistic interactions with animals than conifers did.
Early Primate Evolution: Favored traits:
-Binocular vision
-Grasping hands and feet
-Nails on fingers and toes
> May have evolved together or sequentially to enhance ability to predate arboreal insects,
forage on fruit or nectar, and facilitate locomotion.
What is a primate?
-Adaptations for climbing and other forms of locomotion
-Most have opposable thumbs and prehensile tails. Also grasping hands

-Increased reliance on having two eyes. 3-color vision in some species

-Relatively large brains, short snouts
-Nails on toes and fingers (instead of claws), which may be related to small branch foraging
New World Monkeys: monkeys that reached South America by the late Oligocene (~25mya)
flat nosed primates.
Oligocene Primates: Primates similar to modern forms. Prosimians (wet nosed) and anthropoids
(flat nosed and downward nosed) adaptively radiated due to cooler
Temperature in the Oligocene period
Miocene Primates: Initial warm climates, resulted in diversification of apes (hominoids) @Miocene
Apes: Differ from monkeys in dental and skeletal traits, brain size, and life history patterns.
They dont have sitting pads like old and new world monkeys, and therefore dont tend
to sit on tops of branches. (sitting pads=ischial callosities)

(Lecture 18)

Hominoids/Apes: Apes have relatively long arms, short legs, long fingers, short stiff lumbar. They
also lack tails (but some old world monkeys have reduced tails)
Gibbons: lesser apes only in Southeast Asia. 18 species. Lesser Apes refer to being smaller and
having less sexual dimorphism than all of the great apes. (difference among lesser
apes that is not sex-related do not fall under this)
The Congo River: Impassable barrier between bonobos and other apes (bonobos left, chipanzees
on the right side of the banks) (gorillas also live on the right)
Hominoid developments occurred in the following events:
Moved from: Africa->Southeast Asia -> Africa -> World

The Origins of Violence: In evolutionary context:

->Think about Social Organizations: group size, distribution of sexes and ages
-Monogamy: Pair bonding
-Polygyny: 1 male with more than 1 male (polygamy)
-Polyandry: females with more than 1 male (polygamy)
-Promiscuity: Both male and female have more than 1 partner.

Gibbons: Mostly live in monogamy.

Orangutans: Live solitary (male live separately to females). Promiscuity: Males access to females,
Sometime forced coppulations
Gorillas: Live in polygyny, and live in harems. Sometimes, when a new male dominates a harem,
the male may decide to kill off the old males offspring.
Chimpanzees: Multi-male and female groups dominated by males. Lives in promiscuity, and
males use strength to dominate and raid other groups
Bonobos: Multi-male and female groups, but not as hierarchical. Elder females are central to the
group. Highly Promiscuous.
Gombe Chimpanzee war: war between two communities of chimpanzees in Gombe Nation park.
6 males and 2 females killed by a group-> retaliating group won, but
accidently invaded a 3rd group -> 3rd group made the winner group
retreat.
Peaceful Bonobos: Bonobos perform every position and variation one can imagine (Kama Sutra,
sexual reference). Sociosexual behavior in that theres copulation between
males and females NOT during her fertile period. Range of partners, such
as homosexual, old-young, old-old, young-young, and range of activities.
Chimpanzees resolve sexual issues with power. Bonobos resolve power issues with sex.

 Expression of goodwill, greeting, bonding, tension relief, and reconciliation.

Sex is a widely applied social lubricant that keeps them amiable.
Hypothesis: Chimpanz and gorillas are both right bank, so they compete for resources, and
forced to be territorial, which influences their social structure. Bonobos on the left bank lack
competition from other primates and can be peaceful

Humans: Possible major changes since transition into agriculture. Shows there was a recent shift
from polygyny to monogamy (by comparison of mitochondrial DNA (female) and Ychromosome DNA (male) which shows increase in diversity since the Neolithic transition to
agriculture.
How are they different from apes?: Bipedalism, teeth(less canine), slow development, large brain
relative to body size.
Miocene and Pliocene Primates: global cooling led to decreased rainfall, and tropical rainforests
shrank in size. Dry woodland and grassland habitat expanded.
Hominin Fossil Record: All found in Africa(!!) Major burst of diversity 2-4 mya
Chimp-Human split: Genetic data suggest that most recent common ancestory (MRCA) of chimps
and humans lived about 5-7 mya.
Hominin development: Sahelanthropus: Foramen magnum (hole in skull for spinal cord)
Orrorin: thick enamel, long femoral neck (leg bone), suggesting bipedalism
Aridipithecus: Generalized diet, shorter arms, upright posture
In general : small molars, thin enamel, canines still larger than humans,
large brow ridge, small braincase compared to modern humans
Derived features: Forward foramen magnum(bipedalism), small canine
teeth, changes in the femur and pelvis, flattening of the
face, diversification of hominin lineage.

Australopithecus: Small bipeds with small teeth

Paranthropus: Small bipeds with big teeth, prob ate plants

Kenyanthropus: small teeth and a flat face
Early Homo: Much larger brain and smaller jaw muscles. Signs of tool use.
Bipedalism: The morphology of pelvis is affected
-

Alignment of femur and tibia

No evidence that bipedalism is any more efficient than quadrapedal

Theories on bipedalism: Walking on two legs keep them cooler (temperature wise)
-

Arms free to carry objects

Makes sense in context of tool use

Response to increased dependence of offspring (hold with hand as

opposed to carrying on back

Predisposition (as in, it was meant to be this way) due to

suspensory locomotion

Adaptations for suspensory locomotion (hanging on trees, etc):

-

Short trunk and legs

Long arms and fingers

Fingernails over claws

Inward closing hook-like fingers

Opposable thumbs

More mobile shoulder, wrists, and other joints

Loss of tails

Why do so few primates have this now?

The ones that have bipedalism have suspensory locomotive ancestry, which
leads to the thought that suspensory locomotion is a pre-adaptation for
bipedalism.

Dr Bolker: Lecture 1: October 22: Evolution of modern humans

To answer: what separates humans from hominins? from chimps?
Hominins: ancestor of humans in the branch that includes chimps
What are the genetics of these differences? How do we know?
Evolutionary history of humans and hominins?
Are Homo sapiens really that special biologically?
Morphology of Homo Sapiens relative to other hominins:
Large, round skull, high forehead
Small face and teeth protruding chin
Protruding chin
Less robust skeleton (gracile)
Long limbs
-lots of possibilities, but not known for certain
Adaptationism: Talking about all biological features as though they are meant to do something.
AVOID ADAPTATIONISM (Just-So Stories)
Example: Protein called microcephalin
Having a homozygous mutation for microcephalin makes you microcephalic, which is a
smaller brain. Theres evidence of this being positive selection. Mutations dont correlate
with cognitive ability)
Neanderthal vs Human: Which is not a difference between Neanderthal vs humans?
a) Nean has stronger brow ridge(x)
b) H. sapiens has higher forehead(x)
c)

H, Sapienss nose is larger(x)

d) H. Sapiens has larger brain (o)

e) Neanderthal has occipital bun (x)

Truth: Homo sapiens have longer lifespan, better health, and smaller brains
Behavior: -Cant only look at DNA. For simple behavior like walking, language, we can look
at morphological evidence, but more complex behaviors like tools and arts are
extended phenotypes that require archaeological evidence. Behavior and extended
phenotype cannot be determined just by genetic information, but can be expected.
Gene has brain smart enough to make structures -> then this organism may
have made structures of some sort
(Bolker Lecture 2 October 24)
Genetic Evidence:
Human-Chimp Differences:
-

Very small differences, like finding needles in haystacks

-1% sequence divergence overall
-5% allowing for insertions/deletions
-70% of genes differ (difference at anywhere in the sequence of
genes)
->what genes differ?
-> are they changing due to selection?
->What are they doing (effects of difference)
-genes refer to sequences that will be translated into proteins

Synonymous vs nonsynonymous mutations:

Synonymous: a replacement that results in the same amino acid (silent mutation)
Nonsynonymous: Nonsense-> leads to STOP codon, missense -> change leads to diff amino a.
^ this should show us why only measuring differences in nucleotides doesnt matter
as much
dN/dS = ratio of nonsynonymous to synonymous changes in a population.

Problem: Its possible to change an organism a whole lot by messing with regulatory region, and
not the coding region.
Regulatory errors: Hard to find. To find important regulatory changes is to: look for highly
accelerated regions (HAR1), we look for number of copies of the same gene
produced at a time, (Gene number variation or copy-number variation)
(ends up creating accelerated regions because more copies= more production
at once. This requires very good genomic data.), or RNA analysis, which
requires live tissues
Human-Neanderthal Differences: Much harder to do. They had smaller divergence, DNA
Evidence is hard to find, and no live Neanderthals to get tissue
from.

(Recently,

we

got

high

quality

genome

for

Neanderthals.
Human prehistory via genetics: Evolutionary history
H Sapiens in Africa around same time/place as Neanderthals and Denisovans
in Africa apprx 200 KYA.
Evidence for gene flow between the 3 after the split
Signatures of bottlenecks: results in: low variation, and low effective population size. This was
demonstrated when a small population left Africa and found new
settlement.
Which of the following is the least likely alternative explanation for lower levels of genetic
variation in non-African populations?
A) Stronger stabilizing selection
B) Weaker diversifying selection
C) Smaller population sizes
D) Lower mutation rates (o)
E) Stronger assortative mating (similar geno/phenotypes reproduce)
(prof agreed in the end that all are reasonable, but mutation rates would not have
changed much just because the population moved away from Africa, and does not

vary much between the same species)

Inference from trees: Mitochondrial DNA and Y-chromosome are non-recombinant DNA that will
not

change for descendants except by mutation. (haplotype=non-

recombinant. (mitochondrial eve= ancestor of all living humans (all humans

have mitochondria, and Y-chromosome Adam=ancestor of all males Ychromosome. But eve was not mated to adam, as the names suggest). Use
this to infer where and when the most recent ancestor was, aka coalescent
theory: tracing all alleles of a gene shared by all members of a
population to a single ancestral copy.
Non-consistent gene trees: Where trees look like a gene jumped from the genome of one
species to another species. (probably result of hybrids: ei Neanderthals
breeding with a homo sapiens.
Intergression: gene flow by repeated backcrossing of a hybrid with one of its parent species.

Genetic data indicate that modern humans and Neanderthals:

a) Are more closely related to each other than either is to Denisovan hominins (o?)
b) Never interbred
c) Interbred in Africa
d) Interbred in Europe
e) Both interbred with archaic hominins (hominins that were ANCESTOR to the 3
hominins were used to)
//OCT 24 49:00
Summary till now: Morphological diff between humans, chumps, Neanderthals, behavioral
evidence, genetic evidence (ditto (wtf?). Also gives information about population history)
Lecture 3: October 28
Human population genetics:
Questions to answer: What maintains deleterious alleles against natural selection? What creates
and maintains genetic diversity? What maintains geographic variation? What are the implications

of variation?
Know the Hardy-Weinberg Violations
Of the 5, 3 are more important for human population genetics: mutation,
drift, and selection (nr mating and migration less considered in bolker)
Evidence for history and function of genes:
Gene-trait associations (allele A is found in people with trait B)
Mechanistic arguments (allele A makes a protein that does C)
Gene-environment associations (allele A is found in environment D)
Geographic variation in diversity (allele A is more variable at place E)
Haplotype pattern (allele A is found in a selected region)

Mendelian traits:

Equation: Mutation (m) selection balance (s)

S=(1-survivors)
(balancing selection :number of process by which multiple alleles are maintained in the gene
pool of a population. Heterozygous advantage is an example because it maintains dominant and
recessive together)
Dominant= m/s
Recessive = sqrt(m/s)
Deleterious alleles: Alleles that give low average ftness, which depends on epistasis (gene to
gene interaction) and environment (gene to environment interaction) ex
phenylketonuria (overdominant selection : where the phenotype of a
heterozygous lies outside the phenotypical range of both homozygous
parents, like sickle cell anemia)
Purifying selection: aka negative selection. When the hybrid is selected against (stabilizing

selection.)

as opposed to deleterious genes, they are genes that

deviate from preexisting.

Achondroplasia: Mutation in FGFR3. Normally has a negative regulatory effect on bone
growth. A dominant trait, homozygous dominant is fatal. Fastest known
mutation rate.
Genetic Drift: Founder effects or bottlenecks.
Hay-Sachs Disease: lethal abnormality, but has heterozygote advantage. Found in jews,
French Canadians, Cajuns, . Is a recessive allele.
Sickle-cell: Overdominance gives malaria resistance (homozygous is bad though). Its
consistent with malaria distribution, and is evidence for positive selection.
Balanced polymorphism: situation in which two versions of a gene are maintained in a
population because heterozygous gives an advantage than either
homozygous.
All cases of overdominance depends on genetic makeup of the population
Chance of mating with carrier is higher if allele is more common
Easier to calculate at the level of alleles

Iclicker: Suppose mass immigration into a malaria area lowers the frequency of
sickle-cell allele. Which is expected?
a) SC homozygosity up, SC fitness down
b) SC homozygosity down, SC fitness up (o) Im pretty sure now. When homozygosity goes
down, fitness of SC increases (rarity causes more heterozygote advantage)
c) SC homozygosity up, SC fitness up

(could be this, too)

d) SC homozygosity down, SC fitness up

//October 28th.

Lecture 4 October 29
Selective sweeps: Suppose a highly advantageous mutation. Then individuals carrying that will

be highly fit, the allele rapidly taking over the population. Then other genes
located near that mutation are likely to tag along. Then deleterious alleles that
are adjacent may be carried along with it (hitchhiking the haplotype). Over time,
genes eventually narrow down to leave only the haplotype (or close to it). This
only works when theres non-recombinant (haplotype) gene to hitchhike onto.
If we see a quick decline in chromosome pattern, we can assume selective
sweep. Also, the narrower the regions around the haplotype, the longer the
selective sweep has been in place.

Other malaria-protective variation

-

Hemoglobin variants

Enzyme variants

Duffy antigens

Cystic Fibrosis:
Lethal lung disease -> mucus buildup, homozygous recessive.
Mutated cftr gene, changes chloride metabolism. Protection from Cholera?
Pleiotropy: Multiple (seemingly-unrelated phenotypic) effects from one gene.
Summary: Variation in Mendenlian traits: -simple inheritance (recc/dom, autosomal/x/y-linked)
-Estimate how something happened (what led to what?)
- Balancing selection, G x E
Selection in changing environments: -Selection pressures change, and gene frequencies are
going to change. We have better healthcare, and even
gene therapy, which allows people with deleterious
genes to survive longer, hence allowing genes that would

otherwise have not survived to be passed on. (healthcare

removes pressure against some diseases and lets it live)

Example 2: obesity/diabetes: thrifty phenotype. Were adapted for low

calorie diet, and in rich environments, our
metabolism cant take it.
-Genome-wide association study: examination of common genetic
variants in individuals to see if any variant is associated with a trait. On
the graph, bars above the line is considered something to observe, and
statistically significant. However, this only explains 1.45% of variation, and
may not take into account G x E copy-number variation. This graph is
grouped by regions, and it may be hard to narrow if some regions have
more than a single group of people (like Canada, with lots of immigrants)
Cultural and Genetic Evolution:
Humans modify their environment (extended phenotype: niche construction)
Agriculture lead to malaria which lead to sickle-cell.
Cultural evolution: heritable behaviors that are passes on to offspring.
Horizontal Transmission is possible only for cultural evo: It is possible to
teach someone whos not your offspring.
Rules of inheritance? Phylogenies of idea/language can be used for culture
Lactase persistence: Usually lactase would be stopped after weaning age. However, as can be
seen in fossils, as culture changed such that humans drank milk, lead to

lactose persistence.

Lactase persistence dynamics: Is G x E. Dairying culture improves fitness of lactase persistence

estimated strength of selection is 0.05-0.15
Continuously varying traits: Quantitative variation: Partition variation: half siblings: 25% related
Full Sibs: 50% related
Dizygotic twins: 50% +fetal environment
Monozygotic twins: 100% related

GWAS: Genome Wide Association Study:

180 genes affecting height
small effects each (max 4mm per trait)
only explain 10%/80% of variation
Body Size: Genetic variation vs phenotypic plasticity (ability of organism to change phenotype in
response to the environment)
November 4th :
Alcoholism: High variety of response, and usually messes people up.
Environmental Components: Availability of alcohol, family members who make the
social environment an alcohol dependent one.
Some specific genes that matter: ALDH2 and ADH1B (alcohol metabolizing genes).
Flushing response and hangover with the lack of ^. May be protection from alcohol
because this makes people stay away from alcohol.
Human Skin Color: Darwin: sexual selection- like skincolor may mate with skin color (unlikely)
-

Prevent photolysis of folate (UVA/UVB), and allow UVB synthesis of

Vitamin D (because UV map of the map shows skin color trend). Its
probably not skin cancer prevention because most people mate
before getting skin cancer, so doesnt affect reproductive fitness. UV
argument isnt complete either, because without some UV , its not
possible to synthesis vitamin D
What about race: variation does exist. Its easy to overstate importance of biomarkers associated
with race. Easy to confound economic/social with genetic variation, and trying
to relate genes with health may lead to ignoring sociological, economic, and
other environmental factors.
-

BiDil: Candidate drug for heart attack, but it was shown to be a not
very effective drug. Then, someone looked at the data and noticed
that the drug had a strong effect on people of African descent.
Then, they tested it on only black people and found that the trials
went very well so stopped the tests early and marketed it.

Learning evolution: Rats CAN learn from arbitrary cues and stimuli, but are better at learning
about the edibility of food.
Environment

of

evolutionary

adaptation:

organisms

are

adapted

to

their

ancestors

environments (our hunter gatherer lifestyle, restricted diet, food sharing, small groups)
Skepticism: How do we determine how much of behavior is genetically determined? (romance
books show how men/women should act to have best chance in the Darwinian(
survive to reproduce) game
Genetics of Inbreeding: deleterious alleles are rare. Risk of deleterious phenotype increased by
inbreeding.
Human Inbreeding: Spanish Habsburgs. Inbreeding at distance more than parent child or brother
-sister. 3-5 lethal equivalents in average human genomes

November 5
Inbreeding Avoidance (non-humans)
-

Self-incompatibility system in plants

Sex-specific dispersal (male offspring to one side, female to other)

Not breeding with your own offspring: age-dependent+ sex-specific

dispersal.

^ Inbreeding aversions (avoidances)

Inbreeding Avoidance (humans)

-

Westermarck effect: childhood closeness stifles (lessens) desire

kibbutzes^ example: All children in a community are grown up in a

group, and children tend not to get married within the group they
were raised in.

Olfactory(smell)/HLA cues: Smelling out HLA and instinctively

knowing to stay away.

Non-human culture: Social Learning: (transmission of behavior from one to another)

Possible explanations for Social Learning:
-

Social

facilitation(local

enhancement):

offspring

environment that facilitates learning

-

Observational learning: Information transmission

Teaching: Teachers behavior changes

Tool use in non-humans: Use of objects-otters, monkeys can do it too.

Use of tools (modified objects) is unique to humans
Learning and cultural variation in non-humans:
-

Different behaviors in different populations

Vocalization: songbirds, cetaceans etc

stay

in

an

Chimps: termite fishing learned by daughters

Tai Forest vs Gombe ant-fishing: fuctional difference?

I suck at bio

Iclicker:
What distinguishes teaching from other forms of social learning?
a) The individual being copied changes its behavior (o) I love cock
b) Learning takes place because the recipient stays in an appropriate environment
c) It is the only form of social learning that allows cumulative cultural evolution
d) It allows vertical as well as horizontal transmission
e) It allows more than one individual to learn at a time

Cultural Evolution:
-theres vertical AND horizontal transmission
-allows faster, but potentially misguided, evolution
-meme: An idea/behavior that spreads from person to person within a culture. Selfish meme
have better chance of spreading
-Gene only spreads every generation: culture can spread many times faster.
- For diseases, vertical transmission is much less lethal because its in the diseases best
Interest to keep the mother alive to pass it on to the offspring.
Cumulative cultural evolution: allows extreme adaptation to novel environments.

Why dont cheaters win in evolutionary setting?

Self-interest: action benefits group AND self (Or, selfish herd group behavior
into individual advantage
Kin selection: Belding ground squirrels make alarm calls- females, at most
time. These females are most likely to call when relatives are nearby.
Reciprocal altruism

 Group selection

Nov 7:
Reciprocal Altruism: Prisoners delimma. The rational solution is to defect.
Im only helping you because youre gonna help me
later
-Tit for tat strategy: cooperate at first, defect if opponent cheats, but
try cooperating again.
Sex asymmetries: Start with anisogamy (form of reproduction involving the
fusion of two dissimilar gametes. Females are choosy
because they expend more energy than males in
producing offspring. (also why polygyny is more
common than polyandry)
Polyandry: Co-husbands are often related
Mate-guarding
Reproductive assurance
Iclicker: which of the following would probably be the most effective way to determine how
much of the difference in mate preference is genetic?
a) Twin/relatedness study (o)
b) Scan the genome for selective sweeps
c) Genome-wide association study
d) McDonald-Kreitman test (dN/dS) ratio
e) Look for biochemical differences in candidate genes

November 11: