Module Topics:

I. How Evolution Works

A. Why/how are we similar to our parents?
B. Why/how are we similar to other species?
C. How did human traits evolve?
II. Primates
A. Where do humans fit on the tree of life?
B. What human traits simply reflect primate heritage?
C. What about humans is unique?
III. Our extinct hominin ancestors
A. When did human traits evolve?
B. What conditions led to human evolution?
C. What was the diet of our early ancestors?
D. What were their cognitive abilities?
IV. Modern Humans
A. Is there a biological basis to race?
B. Behavior
C. Culture

Expectations:
1) 1 in-class quiz at the end of each Module
2) Weekly in-person labs
3) 1 journal entry per week (Canvas) (can ask for feedback)

Four Major Areas of Anthropology:

I. Sociocultural
A. Comparative study of ways in which people live
B. Largely descriptive
C. Social and political organization, subsistence patterns, religion
D. Behavior is due to cultural factors, not biological
II. Linguistics
A. Study of human languages
B. Concerned with understanding the nature of each language
C. Trace languages across time and space
III. Archaeology
A. Study of material culture - Objects that are left behind
B. Understand the behavior of the people who left those objects behind
IV. Evolutionary
A. Goal: unravel human evolutionary history
B. Used to be called “physical anthropology”
C. Now a huge interdisciplinary field

The Scientific Method

Step 1: Observation and description of a puzzling phenomenon
-Generate a QUESTION
Step 2: Formulate a HYPOTHESIS that explains the phenomenon
- A proposed explanation
- What is the underlying mechanism
Step 3: Generate TESTABLE PREDICTIONS that stem from this hypothesis
- What you expect to observe if the hypothesis is true
Step 4: Test the predictions with OBSERVATION & EXPERIMENTS

Video-
Puzzling:
- Sharing? Stealing? (Why do they share food?)
Explanation/Hypothesis:
-Communal behavior - Giving a little bit to others so that you do not need to fight
them off as much - Gilby 2006
- Proximity, age, hierarchy, maybe they all worked together? Trading for various
things?

Hypothesis: Trade meat for grooming or other services

You expect to see the members of a group to exchange hunted food for grooming or
other services.

A hypothesis must be FALSIFIABLE

“Chimpanzees only eat fruit” vs. “A giant gorilla lives in the woods near Portland.”

Both could be proven to be false

“Theory”: a hypothesis that has received overwhelming support through repeated

studies
Occam’s Razor
- When two hypotheses have the same predictions and available data cannot
distinguish between them, the most likely is that it is the most simple solution.

Module 1- Evolution—-------------------------------------------------
1/12/23 - Natural Selection

Notes from: What is Evolution by Natural Selection?

-Individuals are different in the ways they reproduce
-Species changing
-Traits that species have allowing them to persist across generations

Two Observations:

● Animals and plants are extremely well suited to their environments

● Many of these traits are extremely complex (sensitive hearing- allows them to
see)

Biological Complexity

The Eye

● Eyes are adaptive to the environment they live in

● Shape of a fish’s eye is different because of the way light works under water

Intelligent design
The argument:

● Some structures far too complex to have arisen by chance

● Remove one element, it doesn’t work properly (gear on a clock)
● Therefore, must have been ‘designed’ by a creator
● Prevailing view in the 1800s, recent resurgence

Darwin’s theory of adaptation

Charles Darwin (1809-1882)

● Medicine, then religion
● Talented, enthusiastic, naturalist
 ● 1831: 5 year voyage on HMS Beagle
● South America and Galapagos islands
● Ideas about changes in organisms through time

Darwin's Observations
● Fossils: plants and animals can change over time
● Flora and fauna of South America showed similarities and differences to those
species of the Galapagos Islands
(Especially finches)

Galapagos finches
● 13 species of finches (on different islands) that were similar in plumage,
but different in size and the shape of their beak.
● Darwin hypothesized that one mainland species had given rise to 13
different species.
● On mainland, only one species of finch

Selected breeding of domesticated animals

● Pigeons
● Offspring resemble their parents
● Agriculture: selective breeding can lead to more desirable traits
● Artificial selection

Thomas Malthus
● The Principle of Population (1798)
● Population could grow exponentially if resources unlimited
● But, resources are limited->competition

Putting it together
● Struggle for existence->competition
● Favorable variations would tend to be preserved and unfavorable ones to be
destroyed

Alfred Russell Wallace (1823-1913)

● British naturalist and explorer
● 1848 Amazon expedition
● 1854 SE Asia expedition
● Same ideas as Darwin

The Origins of Species (1859)

Darwin’s 3 Postulates

1. There is a ‘struggle for existence’

-Any given population has the potential to expand indefinitely but the ability of the
surrounding environment to support that population has a limit
(Competition for food, resources, space)

2. Variation

-Organisms within populations vary and this variation affects the ability of
individuals to survive and reproduce

3. Inheritance of variation

-Individual variation is transmitted from parents to offspring

Natural Selection
● Some inherited variants increase the chances of surviving the struggle to access
resources and reproduce

The Environment is Key

● The value of these variants is dependent on the environmental context

Natural Selection in Action

● Galapagos Islands, Ecuador
● Darwin's finches

Different species had different beak shapes, which were associated with diet
● Thick beaks- large, hard seeds
● Thin beaks- small, soft seeds

Peter and Rosemary Grant’s 30 year field study (graduated from Princeton)

One Species: Medium ground finch (Geospiza fortis) (only studied this specie)
● Morphological measurements
● Behavior
● Genetics
● Ecology
-Took blood samples to determine mother, father, and offsprings
-Recorded what they ate
-Did it every year so they could track measurements

Postulate 1: The struggle for existence

-Annual rainfall can vary considerably

-Rainfall has major effects on vegetation
-Severe drought 1976-77
-Fewer seeds
-Small seeds quickly eaten, leaving only large, hard seeds
-Many birds died: 1,200 reduced to 180

Postulate 2: Variation in fitness

-Beak depth varied considerably
-Small-beaked birds have trouble with large, hard seeds
(within same species)

-Beak depth varied considerably

- Small-beaked birds have trouble with large, hard seeds
- Small-beaked birds more likely to die in drought

Postulate 3: Variation passed on

Characteristics of population change over time

- Large beaks more likely to survive
- Large beaks had large beaked offspring
- Mean beak size increased in population.

So if droughts are common why don’t all birds have large beaks?

Natural selection can produce change or maintain stabiity

● Small beaked birds can’t process hard seeds

● Large beaked birds have higher juvenile mortality
● Selection favors intermediate beak size
● At equilibrium, selection will maintain stasis (no change)
(Large beak takes more energy higher death rates)
“For the good of the species” (thumbs down)

Individual Selection

● Selection operates on an individual level

Example:
- Primate females usually have one offspring at a time
-Low-fecundity females better for species because fewer animals to deplete resources
(True, but not why trait evolved)
(But high fecundity favored even at species’ expense)
(Fecundity= # of offspring)

-Assume heritable individual variation in litter size

(Litter: how much offspring is produced at one sitting)

-Natural selection is a gradual step by step process

-Positive changes remain negative ones disappear

Selection for Intermediate Steps

● Intermediate forms can be adaptive

● Living mollusks show step in eye evolution
● Evolution is tinkerer, not an engineer

Convergent evolution

● Marsupial wolf (Australia) resembled North American wolves, yet more closely
related to kangaroos
● Flight evolved separately in several different animal groups

Rates of Evolutionary Change

● How long will it take for the medium ground finch to resemble the large ground
finch?
-2000 years

Darwin’s Difficulties Explaining Variation

● Is there blending inheritance?

 ● How is variation maintained if natural selection eliminates it?
● Where do novel forms come from if they are not already present in the original
population?

Carcinization- nature MUST return to crab

1/17/23 Mendelian Genetics Notes (Continued)

Gardeners and Farmers

Blended Characteristics

● Casual observations of traits such as fur color or body size led to the idea of
blended characteristics
● The results of a cross between a basset hound and a poodle

Blending can’t be the mechanism

- Blending would remove any variation in populations
- Eventually everything would look the same.

Gregor Mendel (1822-1884)

● Augustinian monk
● At university Mendel learned about atoms and molecules
● Wondered if “particles” could govern heredity
● Experiments with plant hybrids (1865)
● First to trace characteristics of successive generations of living things

Peas
● 7 different traits/characteristics where each has two possibilities (128
combinations of these traits)

Advantage of Experimenting on Pea Plants:

● Self-pollinating
● Male and Female structures

Step One:
● Mendel bred 14 strains of pure-breeding plants
 ● When self-fertilized they all produced offspring that looked just like the adults

Anatomy:
● Anther and Filament make up the Stamen
● The sigma is where the pollen goes to fertilize the plant

Plant 1: removed Anthers

Plant 2: collect pollen (Brushed them on to plant 1)

Step 2:
Mendel made monohybrid crosses
-these are matings between plants that differed only in one trait

Example: crossed green seed (pea) and yellow seed plants (Parental of P gnerations)

● Not blending inheritance

● Mendel conducted yellow was dominant

Step 3:
● Mating between siblings
● ¼ of all plants produced green seeds and ¾ yellow seeds
● 3:1 Yellow: Green

Dominant Trait (yellow) trait masked the disappearing trait (green) 75% of time

Principle of Segregation
● Different expressions of a trait are controlled by discrete units that occur in
pairs
● Separation of the pair (segregation) during reproduction
● Offspring inherit one unit from each parent
● During fertilization the pairs reunite to determine the expression of the trait in
offspring

Mendel didn’t know this but

-the particles of units controlling a trait were really alleles of genes at a particular
locus

GENE -Segment of DNA that directs the production of a protein with a certain
function ( determines seed color)
ALLELE- version of a gene that directs the production of a form of the protein that
produces a specific trait (yellow)

Locus = Page - the physical locations of a recipe in a cookbook (e.g. pancake always on
pg. 9)
(each organism has 2 cookbooks)

Dominant and Recessive

Dominant- a trait that is governed by an allele that is expressed regardless of the

other allele at the same locus

Recessive- a trait that is not expressed if there is a dominant allele at the same locus.
There must be two alleles of the same recessive trait to express that trait

Dominant allele: CAPITAL LETTER

Recessive allele: lower letter

Homozygous: two of the same alleles present at a locus (YY, yy)

Heterozygous: two different alleles present at a locus (Yy)

Genotype: the specific genetic makeup of a trait (YY, Yy, yy)

Phenotype: The physical expression of the genes or what we see (green or yellow
seeds)

Punnett Square of Mating Matrix (different ways alleles can be combined)

Independent assortment

Mendel: Different traits inherited independently

(tall plants didn’t always have yellow seeds)
Now: Alleles for different traits )not at the same locus) are sorted separately in each
cross

Genes controlling different traits are inherited independently of each other

Mendelian Inheritance in Humans

● Mendelian traits are controlled by alleles at one locus (monogenic)
● >9600 mendelian traits in humans
○ Most are invisible (biochemical)
○ Some examples
■ Ear wax (wet vs dry)
■ Blood type
■ Dimples
■ Albinism
● Co-dominance
○ Blood type: Single locus
○ 3 alleles (A, B, o) determine which antigens are present on blood cells
■ o is recessive to both A & B
■ A & B are co-dominant (both are expressed)

Common Misconceptions about Mendelian Genetics

● Recessive alleles are completely hidden (not always)
● Dominant alleles are more common (if so you would have webbed feet)

Non-Mendelian Inheritance
● Polygenic Inheritance
○ Multiple genes for one trait
○ Includes more traits of the skeleton
○ Traits are continuous, rather than discrete
● Pleiotropy
○ One gene influences one trait
● Genotype ≄ Phenotype
-strong environmental effects

Eye and skin color

- Melanin production influenced by 3-6 loci, each of which have at least 2 alleles

Environmental Influence
● Most mendelian traits will not be influenced by environment
● Many polygenic traits are influenced by the environment
1/19 Notes

Life is a self replicating chemical process involving protein synthesis

Proteins

Structural – muscle and bone

Antibody – bind to foreign elements, protection
Enzyme – carry out chemical reactions, metabolism (brings them together)
Messenger – coordinate biological processes among
cells and organs; hormones
Transport – bind and carry molecules throughout
body; e.g. hemoglobin

20 Amino Acids that are joined together in long chains to form protein (infinite
combinations)

Mitochondrion: where energy is created (provides energy for cellular processes)

Nucleus: contains DNA

DNA: Deoxyribonucleic acid

-is made up of billion nucleotides (sugar Molecule, phosphate molecule, one of four
bases GTCA)

G-C , A-T

Human genome= 3.5 Billion nucleotides in every cell

Rosalind Franklin, Ph.D.

● Produced X-ray diffraction images of DNA, which led to discovery of its double
helix structure by James Watson & Francis Crick
● Died in 1958
● Watson & Crick received Nobel prize in 1962

DNA Functions

1) Protein synthesis
 ● Codes for traits→ Variation
2) Replication
● Growth & maintenance
● Reproduction
● Inheritance (key parts of Darwin’s theory)

Protein: sequence of 20 different amino acids

Each codon (set of 3 bases) is associated with a specific amino acid

Genetic Code

DNA
-double stranded
-Deoxyribose Sugar
-Thymine

RNA
-single stranded
-Ribose Sugar
-Uracil

Each amino acid can have multiple codes to generate it

Two Types of RNA

Messenger RNA
● mRNA
● Creates mirror image of DNA bases and moves the message to the ribosome
Transfer RNA
● tRNA
● Links amino acids together to form a protein in the ribosome

Transcription- transcribing message in DNA

Translation- the message in the mRNA is transferred

When replication starts to occur uncoiled DNA molecules start to coil up become thick
chunks called chromosomes
Chromosome- one long strand of DnA that has been compressed down to a visible
chunk

Human Karyotype
1-22 chromosomes are called ‘autosomes’
1 set of chromosomes is xy female vs male

Organization of a Chromosome
-organized as a series of genes
-genes interspersed with Non-coding DNA

Genes for particular traits are always found on the same locus on the same
chromosome

Cell Division and DNA Replication

● The unique pairing of A with T and G with C (for DNA) implements protein
synthesis
● This same property of DNA also makes possible DNA replication, cell division,
growth, maintenance, and reproduction

Gene
- A sequence of DNA that codes for a specific protein with specific functions(s)
- A gene is found in the same location on a specific chromosome
- A unit or particle of inheritance.

What is an allele?
● An allele is an alternative form of a gene with potential effects on protein
structure and function
● Remember a gene is just a sequence of DNA bases that codes for a specific
protein
● This variation in protein structure and function is the variation that natural
selection works with

Example:

● The gene for pea color is always found at the same location on a chromosome.
This gene is found in two forms:
Allele 1: Yellow
Allele 2: Green
Somatic Cells
● Diploid = 2 copies of each chromosome
● Humans: 23 pairs of chromosomes, 46 total

Gametes
● Haploid = 1 copy of each chromosome
● Humans: 23 chromosomes, not paired

Mitosis- somatic cell division in which a single cell divides into two identical daughter
cells

Meiosis- cell division that leads to the formation of gametes (sperm and ova)

Homologous chromosomes- are the same size and contain DNA that codes for the
same traits (eye color) but can contain different alleles, one from mom and one from
dad

Sister chromatids- are exact replicas resulting from duplication

Mitosis – Somatic Cell Production

Somatic cell division for growth or

healing

1: Diploid cell with 46 (23 pairs of

homologous) chromosomes

2: Each chromosome replicates,

forming sister chromatids

3: Sister chromatids separate

4: Cell divides resulting in identical

diploid cells with 46 chromosomes

Meiosis – Gamete Production

● Production of sex cells for reproduction
● Characterized by 2 divisions

START: 1 diploid cell with 46

chromosomes (22 pairs of
homologous autosomes and 1 pair of
sex chromosomes)

END: 4 haploid cells with 23

chromosomes (22 autosomes and 1
sex chromosome)

DIPLOID cells contain pairs of homologous

chromosomes

HAPLOID cells contain only one copy of a

chromosome

● Egg = haploid =23 chromosomes

● Sperm = haploid = 23 chromosomes
● THEY UNITE!
● A single cell results that is diploid = 46 chromosomes

Haploid Cells = 1 copy of each

chromosome

Diploid Cells = 2 copies of each

chromosome

1 one from father

1 from mother

1/24 Notes

The Modern Synthesis

-a synthesis of Mendel’s and Darwin/Wallace’s views was not achieved until the mid-
1930s (hence “modern”

-Evolution is a two stage process

1. The production and redistribution of variation via meiosis mutation
2. Natural selection acts on this variation
Problem: Natural selection hinges on gradual accumulation of small changes. Seems
incompatible with Mendelian genetics

One gene- two alleles- 3 phenotypes

Two genes- each with two allele with equal frequency- 5 phenotypes

-Three genes- each with two alleles of equal frequency

-Bell-curve distribution emerges
-But still some gaps

-Beak growth affected by environmental variation

(how well the bird nourished)

-And almost certainly more than 3 genes involved

-Many many genes or alleles passed down in the same way

-400 gene regions affect human height (consider variation in diet!)

Mutations
-Changes in an individual’s DNA sequence
-Out of 3.5 Billion nucleotides in the human genome, each individual has (only) 58
new mutations that differ from their parents
-Occur in mitosis and meiosis
-cells or DnA being replicated offers an opportunity for a mutation to occur

Redundancy
-Each codon only codes for one amino acid, but an amino acid can be coded for by
more than one codon

(Alanine= CGA, CGG, CGT, CGC,CGA= ONLY alanine)

-Safety net to protect against mutation resulting in a different amino acid

Genetic Variation
-Mutation are the Only source of new alleles
-Therefore, evolution is only possible because of mistakes made with replicating DNA
-occur in mitosis as well
Point mutations
- A change in one base

EX)
Original sequence:
TAACTGCAGGT

Point mutation:
TAACCGCAGGT

A point mutation: Sickle cell anemia

Insertion Mutation
- 1 base is inserted (add base)

EX)

Original sequence:
TAACTGCAGGT

Insertion: (causes a frameshift)

TAACCTGCAGGT

An insertion mutation: Crohn's Disease

Deletion mutation
- 1 base is deleted (causes frameshift)

A deletion mutation: Cystic fibrosis

Inversion Mutation
- A portion of DNA is flipped (base pairs flipped around) (affects two different
codons)

Effects of Mutation (Bad-> Good

-non-viable zygote Bad
-protein non-functional
-reduced protein function ↓
-neutral effect
-protein has improved function Good
-protein has new function

Improved Function
-May lead to an increase in fitness
- Sickle Cell anemia and malaria
- Heterozygous individuals have increased immunity to malaria

Improved Function
-May lead to an increase in fitness
-Adult lactase expression

Take Home Messages

-Mutations are rare
-Mutation can increase or decrease fitness (most have neutral effects)
-Mutation are the only source of new alleles
-Mutations provide the variation with natural selection and other forces of evolution
work

Microevolution (evolution on a small scale)

-Changes in the frequencies of alleles within a population

Population
- A community of individuals of the same species that are able to mate (and
reproduce)

Gene Pool
- All of the alleles in a population

Allele Frequencies
- The proportion of one specific allele compared to the total number of alleles in
a population

Genotype Frequencies
-The proportion of a population that possess a particular genotype

How do allele frequencies change from one generation to the next

-Natural Selection
A mutation: Brown beetles
(birds prefer to eat green beetles)

If this continues after many generations of beetle reproduction we won't see anymore
green beetles.

How do allele frequencies change from one generation to the next?

Gene flow: the movement of alleles among populations through interbreeding

Gene Flow 1
- If random gene flow, allele frequency in each adjacent population will converge

Gene Flow 2
- One way movement from a large population to a small one

Gene Flow 3
- Each group receives migrants only from neighboring populations

Clines- resulting from gene flow with neighbors

Limits to gene flow

-social ‘rules’ or preferences

Genetic Drift
-Random changes in a allele frequency over time
-Genetic drift can cause populations to randomly lose genetic variation
(small populations)

Genetic drift Founder effect

-random chance that this group leaves

Examples of the Founder Effect in Humans

-Mennonite Community

Genetic Drift-Bottleneck
-random sampling of survivors
-population growth-> different allele frequencies in post tornado popualtion

Random Change vs Selection

-Mutations, gene flow, and genetic drift are random
-natural selection promotes specific alleles above others
-differences in reproductive success lead to adaptive shifts in the population
-Always relative to the environment

Evolutionary forces
-Mutation: source of new alleles

Gene flow: Transmission of alleles among populations

Genetic drift: random change in alleles frequencies

Selection:
Natural selection
Sexual selection

1/26

Species
● Group that has similar traits and can reproduce
● Variation within populations

-Helps interpret the variation we observe in fossil record

Before Darwin

Typological Species Concept

● A species defined by its fixed, unchanging properties"Species are as many as
were created in the beginning by the Infinite.” (Linnaeus, 1758)

Populations, variation and reproduction

● Populations of organisms vary, yet there is a limit to this variation.

● In sexually reproducing animals and plants, these packages of variation usually
correspond to reproductive boundaries.
● Populations of organisms vary, yet there is a limit to this variation.
 ● In sexually reproducing animals and plants, these packages of variation usually
correspond to reproductive boundaries.
● Gaps in behavioral and morphological variation are helpful for identifying
species, but ultimately it is the reproductive boundaries that
● matter.

The Biological Species Concept

● A species is a group of interbreeding organisms.
● Connected through gene flow
● Reproductively isolated from other species

Reproductive isolation

Pre-mating
● Failure to mate
● Physical, temporal, ecological, behavioral,
mechanical factors

Post-mating
● Gametic incompatibility (no fertilization)
● Zygotic mortality (embryo doesn’t form)
● Hybrid inviability (fetus or neonate dies)
● Hybrid sterility (offspring survive, but can’t reproduce)

● Almost half of all “species” are not reproductively isolated.

● Some species have little or no gene flow among populations.

The Ecological Species Concept

● Reproductive isolation
not necessary
● Natural selection keeps species distinct from one another.

Most agree that reproductive isolation is the essential factor

Speciation: the process by which new species arise from existing ones.
Allopatric Speciation:
• Geographic isolation
• Combination of reproductive isolation and natural selection

Speciation by geographic isolation of small, peripheral populations

(=peripatric speciation)

a population becomes isolated on periphery of range, often in a marginal

habitat, leading to rapid evolutionary change and reproductive isolation
(“founder effect”)

Parapatric Speciation:
• Partial genetic isolation
• Populations mostly separate due to habitat, but some areas of interbreeding
• Speciation occurs if hybrids have lower fitness

Sympatric Speciation:
- No geographic separation
- Different morphs (or behavior) that are equally successful.
Ex: Lake Malawi
cichlid fish
● >1000 species
● Lake only 40,000 y
● 2 million y old

Adaptive Radiations (completely new habitat opens up, there are no plants or animals
there, it gets colonize by one species)
● Ecological niche – The way an organism “makes a living” – More niches leads
to more species (where it eats, shelters, how it finds mates, does it have
predators)
● Adaptive radiation – Rapid diversification fills niches.

1/31 - Phylogenies

Species → Genus → Family → Order → Class → Phylum → Kingdom

Phylogeny
• Depicts relationships between species
• Reflects branching of species from common ancestors tree-like in form
• Reconstructs pattern of events leading to the diversity of life

• Phylogenies are inferred by identifying

heritable features (characters) that are
shared among species.

Species with more traits in common are more

closely related

- Morphological (skeletal, soft tissue)

– Chromosomal (number, structure)
– Molecular (nucleotide & amino acid sequences)
– Behavioral (courtship, dietary, locomotor)

We need to determine WHY traits are similar

• Shared characters that result from inheritance through common ancestry are called
homologies.
Similar characters that are NOT due to common ancestry (i.e., that evolved
independently) are called homoplasies.

Convergence: due to similar environmental pressures,

natural selection produced similar adaptations in species
from different evolutionary lineages

Homoplasy: the Panda’s thumb

Convergence: due to similar environmental pressures, natural selection produced

similar adaptations in species from different evolutionary lineages
Species that are more similar are assumed to be more closely related.

If we used homoplasies to compare, we would get the wrong answer

Two Types of Traits

Ancestral (old) characters—present in

more distant common ancestor(s) of
the group

Derived (new) characters—evolved in

the most recent common ancestor of
the group

How to identify ancestral characteristics:

- May be visible early in development

- Compare with fossils
- Compare with ‘out-groups’
Outgroup —closely related group outside
the study group

-shared derived characters

-ex: mammary glands in mammals

Why Reconstruct Phylogenies?

1) Explain when certain adaptations

evolved
Example: Knuckle-walking (some do and some don’t)

2) Deduce the function of behavior or

morphology using the Comparative
Method

3) Taxonomy (grouping and naming)

Taxonomy: Names
• Names based on degree of
relatedness
– Example: genus Pan(chimpanzees and bonobos)
– Family: Pongidae
– Superfamily: Hominoidea
– Order: Primates
– Class: Mammalia