01-23-2015 Lecture 1

Read Tattersall article

Science
- Evolution
- Genetics
What is Science?
- Approach to gaining knowledge; QUESTION-driven; EVIDENCE-based
- Apprx understanding of natural world
Neil Degrasse Tyson astrophysicist
Properties of Science
- Evidence, data
- CONSTANTLY updating
- Not authoritative; ideas adopted based on evidence, not who proposed
them
- Objective (Chimpanzee birth)
- Not a public vote
Common misconceptions are based on anecdotes
- Bulls see red; become enraged; Truth is they dont care
- Humans have an attraction to red
- Myth that we only use 10% of our brain
- Science is the business of theories
o Theories: gravity, evolution, plate tectonics, germ, cell, heliocentric
Testable ideas are called hypotheses
- Constructed based on overarching theories
- If they dont add up, there is something about the theory we dont
understand
- When they consistently dont add up, theory is modified
**Correlation V. CausationMECHANISM
- Test hypotheses in part my looking at cause and effect
- Pirates and global warming (arent related, but there is correlation)
Pre-Darwinian
- Chain of being, Aristotle, no such thing as extinction, 6000 yr. old earth,
geological changes bc of catastrophe, immune species
Summary
Science is evidence based and willing to be wrong. No matter who proposes ideas,
unless there is evidence that supports a theory it cannot be taken seriously. Science
is constantly updating (ie. Germ theory was only a 21 st century thing where
surgeons starts washing their hands). Even if the majority believe something, it
might not be true.

01-26-2015 Lecture 2
Pre-Darwinism Scientific Revolution
Russell Wallace ALMOST came up with natural selection
Carl Linnaeus
- Swedish taxonomist
- Genus, species naming system
George Louis Leclere
- Transformist; believed species werent always on earth, they evolved
- Suggested earth was 75,000 years old
Mary Anning
- British paleontologist
- Challenged that emxtinction never happened
- Discovered plesiosaur and other dinosaurs
- Age of reptiles
George Cuvier
- Fossils can be grouped with modern organisms; related
- Work assured that extinction existed
- Catastrophe theory
James Hutton & Charles Lyell
- UNIFORMITARIANISM: laws of nature are constant across time and space
- Deep time (time beyond which we conceive)
- Earth was much older than 75,000 years
Lamarck
- Giraffe Stretching neck
- Except reproduction
Thomas Malthus
- Fertility or population size limited by resources
- Population increases at a faster rate than resources
Charles Darwin & Wallace (Indonesia) came up with same natural selection idea at
the same time
Darwins Argument
1. Natural populations (elephants)
2. Despite potential exponential growth, population relatively small
3. Many individuals do not leave many offspring (they die or dont reproduce)
4. Those best suited to the environment leave offspring (some elephants
survive and reproduce and have the traits best suited for environment)
5. Heredity: Offspring like their strong traited parents; fit
6. Reproduction of the fittest over deep time; build individuals that are well
adapted

Evidence

Existence and pattern of fossil record

Homology; same structural evidence but different features (bat, human,
cat, horse bone structure)
Vestigial Organs; whale vestigial tiny bones that were evolved from four
legged mammals
Developmental similarities (fetus similar beginnings)
Ernst Phylogony (?) tail
Universal genetic code; structurally the same across all living code
Analogy with plants and animal breeding
o Artificial selection vs. humans do selecting, not nature
Direct Observation; finches
o Beaks on Daphne Major
o Drought period, seed size and hardness changed (large hard seeds)
o Lamarckinism; that they grew a bigger beak, which is not the case
o Reproduction of big beaked finches
o When the small seeds came back, high mortality with large beaked
birds so they die
o Traits must justify their cost; adaptation
o Pesticide resistance and antibiotic resistance
Massive shift of thinking; no great chain of being (plant insect, animal,
then us)
Every living thing is equally evolved and well-adapted to environment

Misconceptions
- Not goal directed; selection imparts an advantage to individuals in a
particular environment
- Individuals develop, environments evolve
- Evolution = natural selection
Summary:
Natural populations could grow exponentially, however populations are relatively
stable. Many individuals therefore do not leave that many offspring. The ones with
the most advantageous characteristics will leave the most offspring, and the
offspring will have those traits. Over generations, natural selection builds individuals
that are well adapted to environment.

01-30-2015 Lecture 3
Recap Misconceptions
- Heritable Variation + Differential reproduction
- Some species are more evolved
- NS is goal directed
- NS is random
- Scientists fight over evolution
o Not true: they fight over ie. graduation vs. punctuated
- Evolution is over
- NS favors what is good for species
Gene-Level Selection
- Genes replicate, NS benefits anything that helps genes get themselves to
next generation
- Bodies are successful because of genes
Adaptations are built of existing variation
- Variation comes from mutation (which is random)
- Most mutations will be harmful, but rarely one might be more
advantageous
- Adaptation is slow; governed by time and strength of the selection
pressure
- Any trait that gives a reproductive advantage will spread, even if the
advantage is small
- layered adaptations; half an eye over time
- Complex and integrated, all features work together for a reproductive
process
- Specialized; favoring better traits (ie. Organs)
- Costly adaptations; fish with no eyes; when theres no benefit, NS calls
them out (eyeless fish did better because they saved energy)
Complex
-

Adaptations
Bat sonar
Plug up their ears when they scream
Sea turtle adaptation out of date

02-04-2015 Lecture 4
Darwins Critics
- Green frog DILUTED out the next generation
- Will go back to being yellow; Blending
- More adapted should become numerous but blending model suggests
being diluted out
Mendels Breakthrough
- Peas easy because only 2 variants (green and yellow), Shape, wrinkle and
smooth, height short or tall
- F1 generation (the offspring) were always yellow
- Yellow and Green
Explanation for Mendel
- The hereditary factors are particulate, do not blend
- Adults have a double dose of these factors
- Only half are passed on to the offspring (by chance)
Hereditary Factors = Genes
Double dose = diploid
- Diploid describes a state where organisms have two copies of each gene
Adults pass half = haploid
- Gametes mean sex cells (sperm or egg)
- Haploid gametes have only one egg
Alleles
- Genes can come in different variations
- Dominant vs. recessive
- Genotype = homozygous dominant or recessive, heterozygous
- Phenotype (physical appearance)
Chromosomes
- Genes on chromosomes; locus, place where alleles are found
- Homologous chromosomes
- Homozygous locus VS. Heterozygous
- 23 pairs of chromosomes = 46 chromosomes total
- Prokaryote haploid ?
- Eukaryote diploid except gametes
- Somatic cells: components of body tissue (ie. Skin cells, muscle cells
- Meiosis: diploid cells become haploid gametes
- Mitosis: Diploid parent cells make copy of themselves

02-06-2015 Lecture 5

Quiz
1.
Egg and sperm cells are haploid meaning:
Chromosomes are not in pairs, but contains only one set of 23
2.
Mendel studied pea plants because:
Pea plants breed true and have only two variants for difference traits
3.
Alleles are recessive when:
They are only expressed in the phenotype homozygous condition
4.
The locus:
Is a place where the alleles are found, like an address, and matches up in
homologous chromosome pairs
Meiosis V. Mitosis Basic Occurrence
- Meiosis is where sex cells are produced
- Recombination: before haploid gametes are made, chromosomes must
mix up
o Chromosomes become damaged and cross over each other
o Crossing over leaves to offspring having a combination of maternal
and paternal genotype
o Major engine for creation of new trait combinations
Molecular Genetics
- Chromosome is tightly coiled strand of DNA
- Sugar-phosphate backbone
- Bases: adenine, thymine, cytosine, guanine
- Base pairing rule is key to exact replication
- Mutations = change in the bases
- Protein Syntheses
o DNA -> mRNA -> tRNA -> Protein
o mRNA has Uracil instead of Thymine
o Start and stop Codons
Modern Synthesis Criticism
- Normal Distribution and despite this we have continuous variation
- Natural selection: gradual accumulation of small changes overtime
- If beak depth were controlled by different placed alleles
o Would solve the blending problem
- NS depletes variation: Because the alleles best suited usually stay
- Stabilizing selection for birth weights (too small, too big, will die)
Facultative Adaptations
- Sun tanning ability: input from environment = uvb rays (sun); output =
tanning
- Facultative behavior: soapberry bugs mate guarding
02-11-2015 Lecture 6
Speciation and Classification

Microevolution vs. Macroevolution (Speciation)

- Macro = longer time scales and production of new species
- Micro= below species level, shorter time scale
- Variation
Species
- Biblical: diff species have no ancestors
- Real biological concepts
- Ernst Mayr
o Allopatrics speciation
o Interbreeding natural population which are reproductively isolated
o Fully functioning (mule, lyger, sterile offspring, cant pass on genes)
- Alopatrics Speciation
o Founder effect (ie. Lizard island)
o Flies in the other range example, different selection pressures
o If divergence isnt great, 2 populations can breed again
o AS need complete barrier to gene flow
Physical (anything that separates)
Behavioral
Temporal
o Divergent selective pressures
- Genetic Drift
- Small portion of population not perfect representation
- Occur with population bottlenecks
- Parapatrics Speciation
o Salamander example Ring species
o PS needs:
Wide species range
Divergent selective pressures across range
o Produces alongside
- Sympatry vs. Parapatry vs. Allopatry
- Diversifying selection
- Sympatric speciation
Length of Speciation
Gradualism vs. Punctuated Equilibrium
- Adapted radiation lemurs of Madagascar
Taxonomy
- Categorize different organisms
- Domain, kingdom, phylum, class, order, family, genus, species

02-13-2015 Lecture 7
Review Terms
Taxonomy, systematics, phylogeny, cladistics
Cladogram = Phylogeny How to Construct

1. Descent/relatedness (cladistics) DNA (not available for most extinct

species),
2. Similarities of traits
- Traits like lactation
- Locomotion
- Egg-laying
Function of adaptations = COMPARATIVE METHOD
- Convergence
o Two distantly related species adaptations converge to a common
solution
Ie. Eye-less fish and eyeless shrimp in caves
Analogy (vs. Homology)
o Is a problem for cladistics because its is similar traits for selection
pressures not ancestry
o We want patterns of descent/relatedness
- Divergence
o Two closely related species diverge from one another
Ie. Fish that have eyes vs. fish that dont
- Derived Vs. Primitive traits
Primates
- Reasoning by homology; we share a common ancestor, primates
- Postcranium (opposable thumbs, nailes instead of claws, friction,
fingerprints, clavicles), cranium (olfaction, forward facing eyes, less
prognathism, large brain size relative to body, teeth), life history (live long
lives, reproduce late, single offspring),
- Arboreal 3-d environments, grasping
- Visual Predation

02-17-2015 Lecture 8
Primate Ecology
Ecology the inter-relationships of animals, plants, and their environments; activity
patterns, diet, predation

When are Primates Active?

- Nocturnals: active at night; many prosimians, owl monkeys
- Diturnal
- Cathemeral
- Crepuscular (adaptive radiation, filling niches)
Primate Diets
- Morphology: body size and dentition (teeth)
- Frugivores, folivores, insectivores, gumnivores
- Dentition: incisors, canines, premolars, molars
o High cusps, low cusps

02-18-2015 Lecture 9
Theory of Sexual Selection
-

Peacock tail problem: Structures and behaviors that have no clear baring
on survival or usefulness
Sexual reproduction
- Costly; meiosis only half of our genes passed (as opposed to asexual
reproduction)

Red Queen Hypothesis: Sexual reproduction helps organisms evade fastbreeding (and therefore, fast evolving) parasites
Parasitism increases when asexual reproduction increases
Other potential answers:
o DNA repair during recombination
o Clearance of deleterious (harmful) mutations
o Spread an ad
Sexual Selection (Darwins solution to Peacock problem)
o More mates and better mates
o Get genes to next generation
Sexual dimorphism (why is it almost always males that we see
conspicuous characteristics)
Sex differences and reproductive rate
o Males are faster and producing
Cost of feeding for females
Males give sperm; Female give egg, gestation, lactation, other costs

Primates
-

Dentition, dental formula 2.1.2.3

1 quadrant; 2 incisors, 1 canine, 2 premolars, 3 molars
Note top and bottom can be different
Teeth have evolved as mechanisms that allow animals to maximize energy
intake
Primate teeth (mammal teeth) are heterodont a varied pattern of different
shaped teeth
Insectivore: tarsier; foliovore: howler monkey; frugivore talapoin monkey
(guenon)
Bunodont (apes) vs. Bilophodont (OWM) molars
Generalized mammals
Limbs & Locomotion
o Tendency toward upright posture
o Flexible, generalized limb structure
o Prehensile Hands
Retention of 5 digits on the hands and feet
Opposable thumb and big toe
Nails instead of claws
Tactile pads with enhanced sensory innervation
Diet and Teeth
o Generalized dentition
o Lack of dietary specialization (omnivory)
Senses & Brain
o Enhanced vision
Color vision
Depth perception
Maturation, learning, behavior
o More efficient means of fetal nourishment, longer gestation, reduced
number of offspring (single births), delayed maturation low life history

Greater life expectancy

Strepshirines
-

Lemurs, lorises, galagos

Characteristics
o Tooth comb
o Rhinarium
o Smaller brain
o No post-orbital septum; but has post-orbital bar sometimes

Haplorhines
-

Lack tapetum lucidum (no red-eye)

Lack tooth comb
Have a post-orbital

Platyrhines
-

Are haplorrhine primates

Prehensile tails
Dental formula 2.1.3.3.
Noses are flat with side facing nostrils

02-20-2015 Lecture 10
Sex differences in reproductive rate
- Males have a faster potential reproductive rate because male reproductive
parts are --Sexual Selection
- Men limited by their access to fertile female
- Ways to increase female access

Compete directly, complete for status, Compete for territory where

females live
Polgyny
o

Mating systems in apes

- Male gorillas have:
o Much larger body size, larger canines (In order to compete for the
territories)
- In order to compete for sole sexual access
- Gibbons no sexual dimorphism
Dominance Hierarchies
- Emerge from competitive encounters between individuals
- Female philopatric species: females stay, males disperse and hierarchy
remains stable until a new male enters
- Male philopatric species: male stay, female disperse; up and coming
challenges alpha
- Trade-off living in a social group
- Dominancy hierarchies
- Hierarchies exist to reduce the costs of competition for feeding sites and
mating access
- opportunity costs
- Male dominance = conception opportunity (mating opportunities)
- Infanticide (during the takeover of a group from a new male)
-

02-23-2015 Lecture 11
Primates are social Benefits
- Solitary, Monogamy, Polyandry, etc.
- Humans are extremely social
- Being social = more eyes to see predators
- Less chance of being singled out by predators (herd animals, schools of fish)
- More to attack

Mates are easier to find

More individuals to look for food and defend food

When to be Social = When benefits outweighs the costs

Social animals are those that either
- Reply on food that is hard to find but easy to share
- Rely on active (detection, defense) anti-predator strategies (vs. passive being
small)
- Live in close proximity and live cooperatively (ie. Grooming, alliances, alarm
calls and predator defense)
- These actions are costlywhy do them
- Altruism: taking a cost to benefit another individual
Difficult to explain: if a predator is out there and you call, then you are at
extra risk
Types
-

of Cooperative behavior
Altruistic, Mutualism, Spiteful, Selfish
Altruism: How does this help the genes pass on to next generation
Kin selection: WD Hamilton genes have 2 routes to next generation
o Direct: Producing more offspring my meeting challenges of the
environment
o Indirect: altruistically helping others with same gene
Kin Selection Formal model total advantage must take into account costs,
benefits, and the probability the same gene is in the other individual
Rb>c
o R is the coefficient of relatedness
o B
o C
Example of Hamiltons Rule
o A and B siblings example
o Cost to A to let B know of predator: 3 fitness unites
o Benefit to B: 7 fitness unites
o R=(0.5)b=(7)> c=(3)
Inclusive fitness
Hamiltons rule also accounts for conflict
Reciprocal Altruism
o Bats give food to those that have helped them in the past

Cooperation & Strategies

- Cheaters must be discriminated against
- Tit-for-tat strategies
o Always cooperate the first turn
o Do what the other player did in the previous turn
- Always defect, always cooperate, grim trigger are other strategies
-

02-25-2015 Lecture 12
1. Life cycle is punctuated by the maturational and reproductive events, including
Age at weaning (cessation of breast feeding)
Age at sexual maturation
How fast to grow
When to stop growing
Age at first birth
How long to wait between birth (interbirth interval)
How many offspring to have
When to die, and how rapidly to age

Strategies
- Allometry: study of different traits scale with body size
o Ie. Larger the body size, longer the lifespan, age in first reproduction
later, fertility (less fertility, fewer offspring cat versus human)
- Mortality
- Costs and benefits of going slow (gains from growing?)
o Benefits; harvest resources faster, more energy for reproduction,
better defense against mortality assaults, for males it helps contest in
competition
o Costs; costly time and energy, more energy to maintain, takes
time/energy away from reproduction (which is the ultimate goal from
an evolutionary perspective
Mammals Growth Stages
- Infancy (ends with weaning) and adulthood
- Juvenile period extended learning
Dominancy Hypothesis
- Stay small and avoid aggression from older, more dominant members of the
group
Organisms have demands on their time and energy; maintenance, growth,
reproduction

MIDTERM PRACTICE
1. Adaptive evolution of a trait (such as shape of bird beak):
b. depends on some variants being more successful than other
-

Natural selection cannot occur without variation

Vast majority of mutations are not beneficial

2. A broad genetic definition of evolution is:

e. the sum total of forces on gene frequency in a population

Survival is important but reproduction is necessary

Evolution = importance of reproduction
Natural selection favors genes that get them to the next generation

3. Natural Selection favors certain genes. What is the most general specification of
the kind of genes that selection will favor?
d. Alleles that, by any mechanism, are better at getting into the next generation
that their alternative alleles
4. Adaptations
a. are built from mistakes
-

Mutations are the mistakes

Doesnt ALWAYS benefit survival; should mention reproduction

5. Which of the following would allow you to determine the exact genetic code of a
gene?
b. the sequence of nucleotides on the individual mRNA
-

Not amino acids because redundancy

Sugar and phosphate is always the case; stays the same

6. Adaptations ultimately serve__.

b. reproduction
-

Not organism but genes

7. ___and ____ show evidence of convergence

d. sharks and whales
-

Distantly Related species, similar adaptations

Divergent whales and cows

8. Strong sexual dimorphism is associated with:

a. polygyny
Strong competition one male, many females
- Know all the connections between all
9. F; asexual reproducers can evolve
10. T;