Evolution Study Guide Exam 1

Chapter 1

Lineage: a chain of ancestors and their descendants

Natural selection: mechanism that can lead to evolution
Convergent evolution: independent origin of similar traits in separate lineages
Ex: Flippers of whales vs flippers of fish
Synapomorphies: derived form of a trait shared by a group of related species
Ex: Dorudon atrox has mammalian middle ear enclosed in a hollow shell
(ectotympanic), in which the inner wall (involucrum) forms a thick lip made of
bone
Pakicetus: whale that lived on land
Skull very similar to that of Dorudon, but lived in very shallow water
Ambulocetus: walking whale
Rodhocetus: short legs resembled seal
Concluded that cetaceans were most closely related to artiodactyls (hippos in
particular)
Another synapomorphy discovered is pulley-shape of astragalus bone
Phylogeny: visual representation of evolutionary history
Seawater has oxygen with 10 neutrons while freshwater has 8 neutrons
Allows us to track down transition of land -> water in cetaceans
Two lineages of extant whales:
Toothed whales: produce high-pitched sounds with blowholes to locate prey
Baleen whales: lost teeth and evolved huge, stiff pleats to filter prey from
water
Grew baleen while still having teeth, teeth eventually left through
mutation
Big brains of dolphins allow them to communicate, form alliances, etc.
1.2 Viruses: The Deadly Escape Artists
Hemagglutinin: studs on viruses that latch onto proteins of host cell
Mutation: change to genomic sequence of an organism
Reassortment: ability of viruses to swap genes
Molecular clock: method used to estimate time in which viruses diverge

Chapter 2

2.1 Nature Before Darwin

Carl Linnaeus: organized all living things into taxa
Taxa: group of organisms (species, order, etc.)
Nicolaus Steno: discovered existence of fossils; Earth was filled with changes, and
layers of organisms recorded that change
2.2 Evolution Before Darwin
Buffon: everything was formed by laws of physics; everything is made of atoms
A species organic particles would change according to habitat changes
Essentially proposed that populations changed over time
Paleontology: study of prehistoric life
Cuvier: proposed phenomenon of extinction

James Hutton: small changes to Earths geography can produce vast changes over
time
William Smith: discovered relationship between rock layers and eras
Lamarck
1. Simple to complex
2. Organisms can adapt to their environment
3. Acquired traits can be passed onto offspring (wrong!)
2.3 The Unofficial Naturalist
Charles Lyell: argued that changes to landscapes was by a series of small changes,
not by big catastrophes
Known as uniformitarianism
Darwinian logic
1. Fact 1: populations can grow exponentially
2. Fact 2: populations normally display stability
3. Fact 3: resources must be limited
Organisms must struggle for existence
This struggle is not equal as certain traits are more beneficial -> natural
selection
Homology: traits that are similar because they are inherited from a common
ancestor
Thomas Malthus: populations expand much faster than resources; only those that
produce useful work can survive
2.4 Darwin in the Twenty-First Century
Sexual selection: individuals of one sex compete for individuals of other sex

Chapter 3

3.1 The Ancient Earth

William Thomson Kelvin: made false argument against age of Earth based on
temperature of Earth
Scientists used radioactive clocks
Radioactive atoms decayed into other elements at a precise rate
3.2 A Vast Museum
Most organisms do not fossilize
Fossil record is incomplete and stages of evolution are missing
Lagerstatten: fossil deposits preserving soft tissue
Burgess Shale: a Lagerstatten in Canada that preserved many fossils from the
Cambrian period
Hallucigenia: spikey worm
Melanosomes: pigment-loaded cells found in both living birds and fossilized feathers
Anchiornis: feathered dinosaur most closely related to birds; had similar
melanosomes
Crest of hadrosaurs produced sounds that matched frequency of sound that they
could hear
Used to make species-specific sounds
Coal: dead plants transformed under tremendous heat and pressure
Biomarkers: individual molecules from ancient organisms

Okenane was found on 1.64 byo rock

Okenane is formed from okenone, which is produced only by purple sulfur
bacteria
Purple sulfur bacteria only exists now in extreme environments, indicating
toxicity of ocean in the past
C4 plants have higher levels of C-12, while C 3 plants have higher levels of C-13
Allows us to figure out the diet of extinct species
3.3 Lifes Earliest Marks
Stromatolites: layered structures formed by the mineralization of bacteria
3.4 The Rise of Life
Three domains: Bacteria, Archaea, Eukarya
Oxygen levels rose with the emergence of cyanobacteria
Euryarchaeota: only known group of organism to produce methane
3.5 Life Gets Big
Animals are closely related to fungi, but each gained multicellularity independently
Unicellular organisms can form biofilms and work together
3.6 The Dawn of the Animal Kingdom
Sponge: earliest appearance of animals in fossil record
Ediacaran fauna: weird Precambrian fossils found ~500 myo
Chordates: phylum including vertebrates
1. Notochord
2. Hollow nerve chord
3. Pharyngeal slits
4. Post-anal tail in embryo
Trilobites: extinct marine arthropods of the Cambrian period
3.7 Climbing Ashore
Prokaryotes: earliest hints of terrestrial life
First plant fossils were mosses and liverworts
Mutualistic relationship between plants and fungi helped transition from water to
land
3.8 Recent Arrivals
Teleosts: includes almost all species of fish
Synapsids: evolved into mammals
Carboniferous period: expansion of plants and trees
Grass is one of the most widespread forms of flowering plants today, but did not
evolve long ago
Sahelanthropus: one of the oldest hominin fossils

Chapter 4

Tiktaalik roseae was the fossil found in the Arctic Circle which explains transition
from water to land
4.1 Tree Thinking

Phylogeny: hypothesis about the relationships among species represented as a

tree
Tips: terminal ends of an evolutionary tree (can be twisted around with other
tips)
Branches: lineages evolving through time between successive speciation
events
Node: point where a lineage splits
Internal nodes: nodes representing ancestral species that have gone extinct
Clade: includes an organism and all its descendants
Cladogram: phylogeny that only shows the relationship between species
4.2 Phylogeny and Taxonomy
Monophyletic: aka clade, can be snipped off the tree with a single cut
Ex: Mammals are a monophyletic group
4.3 Reconstructing Phylogenies
Characters: heritable aspects that can be compared across taxa
Taxon: group of organism (order, species, etc.)
Cannot simply add shared character states to form taxa
Only shared derived characters work
Ex: Production of milk evolved in the immediate common ancestor of
mammals, but are absent from relatives such as birds and iguanas
Synapomorphy: shared derived character state
Cladistics: synapomorphy-based approach to phylogeny
Homoplasy: convergent evolution (not shared derived character)
Convergent evolution: lineages that independently evolve the same trait
Ex: birds, bats, beetles
Evolutionary reversal: derived character state evolves into ancestral one
Ex: reptile -> snake
Outgroup: a group of organisms that is outside of the monophyletic group, but is
closely related to that group
Hennig method: labeling characters with 0 and 1s to reconstruct phylogeny; does
not account for homoplasy
4.4 Fossils, Phylogeny, and the Timing of Evolution
Fossils tell us the minimum age of species, but not their maximum age
Ex: fossil found to have lived 50 million years ago, but could have existed
50.1 or 501 million years old
Coelocanth and lungfishes (aquatic vertebrate species) thought to be closest living
relatives of tetrapods
Tiktaalik: transition between lobe-fin fish and tetrapods
Missing link: scientists do not search for missing links because organisms that
share synapomorphies often evolve their own unique characteristics; hence,
discoveries of species always have their own branch and are not considered
the direct ancestor (node) of any modern organism
Acanthostega evolved digits after Tiktaalik
Synapsids: tetrapods considered to be the ancestral relatives of mammals
3 living branches of mammals:
Monotremes: produce milk through loose glands (rather than nipple),
lay eggs

Ex: platypus, echidna

Therian: the other 2 branches
Marsupials: bear live young, young crawls into pouch after birth
Ex: kangaroo
Eutherian: develop placenta to feed embryos in uterus
Ex: humans
Evolution of mammalian traits
Transformation of jaw led to change in ear which eventually made it possible
to pick up vibrations
Dentary (frontmost bone of jaw) became bigger as bones in back shrank
Exaptations: trait that changes function over course of evolution
Archaeopteryx: fossil that had bird skeleton and feather, but also had other traits
absent in birds
Theropods: group of dinosaurs that birds evolved from
Melanosomes: cellular structures that allowed scientist to reconstruct colors
on theropods
Feathers were probably used for recognition or to attract mates prior to
flight
Features of early hominins
1. Smaller canine teeth than apes
2. Foramen magnum (hole in skull where spinal cord exits) was oriented
downwards instead of backwards
3. Had a ball on top of thigh bone -> adaptation for bearing weight of upper
body
Ardipithecus ramidus: large portion of this fossil was found and reconstructed
Short toes with big opposable toe, could walk better than earlier hominins but
lacked adaptations to climb trees
Australopithecus: had even more human features
Mainly open woodlands at the time, so walking>climbing
Homo erectus: flatter face and slender arms/legs
Homo heidelbergensis may have given rise to Neanderthals and possibly to Homo
sapiens

Chapter 5

5.1 Evolutions Molecules: Proteins, DNA, and RNA

Proteins
Amino acids are the building blocks
Sequence of AA determines proteins function
DNA
Nucleotides are the building blocks
Nucleobase: the other end of a nucleotide that stores information necessary
to build proteins
Adenine, Cytosine, Guanine, Thymine
Mutations: errors during copying of DNA
RNA and the Regulation
Transcription
Translation: happens inside ribosome
Codon
Gene Expression

Transcription factors: bind to regulatory region of DNA

Hormones: binds to surface of cells and triggers signals that eventually reach
DNA
Alternative splicing: cut out different sets of exons to produce different
proteins
rRNA: form core of ribosome, stick new amino acids to end of growing protein
MicroRNA: silence genes by binding to mRNA molecules
Pseudogenes: genes that can no longer make functional molecules
Mobile genetic elements: parasite-like genes that replicate themselves and
take up a lot of space in the genome
Mutations
Point Mutation: single base change
Insertion
Deletion
Duplication: a segment of DNA is copied
Inversion: segment of DNA is flipped and reinserted backwards
Chromosome fusion: two chromosomes join together as one
Aneuploidy: chromosomes are duplicated or lost
Cis-acting elements: stretches of DNA near a gene that influences its
expression
Trans-acting elements: stretches of DNA that are far away from the gene that
it influences
Somatic mutations: mutations to the body; not passed down to offspring
Germ-line mutations: mutations that affect sperm/egg and are passed down
to offspring
Heredity
Allele: version of a gene
Meiosis: sexual form of reproduction that occurs only in eukaryotes
Genetic recombination: pairs of chromosomes cross over during meiosis and
exchange segments of DNA
Genetic polymorphism: simultaneous occurrence of two or more phenotypes;
responsible for certain diseases
Polygenic trait: trait for which several phenotypes can arise from a single
genotype
Quantitative trait: phenotypes that vary among individuals over a given
range
Morphogen: signaling molecule that flows between cells to alter expression of
genes
Phenotypic plasticity: changes in phenotype that are impacted by the
environment

Chapter 17

17.1 An Origin among the Apes

Apes branched off of Old World monkeys during Miocene period
Miocene apes eventually went extinct in Europe and Asia; humans evolved
from African apes
Hominins: fossil apes closer to humans than other apes
Sahelanthropus: oldest fossil found
Hominids: great apes including humans, chimpanzees, and bonobos

17.2 Walking into a New Kind of Life

End of Miocene period -> temperature dropped, less rainfall, more unpredictable
weather
All great apes except humans live in thick forests (most apes probably could
not adapt and died)
C-12:C-13 ratio in plants and soil allow scientists to know terrain of the past
Trees began to retreat = more open land
Favored bipedalism
Foramen magnum points downwards instead of backwards
Orronin: hominin fossil with angle of joint between femur and pelvis
supports upright torso
Ardipethecus ramidus: same pelvis orientation as humans, flat toes for walking
upright, but still had opposable toes for climbing trees (could not climb
as well as chimpanzees though)
Possible benefits of walking upright:
Travel farther to find more food
Expose less skin to sunlight
Compared to chimpanzees, hominins had smaller incisors and canines, and their
molars were bigger
Shift from fruits and plants to seed, nuts, and other foods that required
crushing force
Ex: Paranthropus
Australopithecus africanus was more flexible and seemed to eat a variety of
food
Gona: site where the first hominin tools were found
Oldowan, used to carve out meat and break bones for protein
Australopiths: bipedal apes
Austrolopithecus sediba: australopith-like arms with short hands, australopith-like
ankle bones, tiny brain
Homo: genus of humans, completely lost ability to climb and could run to find food
Acheulean technology: more advanced tools shaped like hand axes used by early
Homo
17.3 Out of Africa, the First Time
Many Homo fossils out of Africa are similar to Homo sapiens except for a few
Homo georgicus: found in Republic of Georgia, very short and small braincase
Homo floresiensis: found on Indonesian Island, stood just 1 meter tall and had
small skull
Some believe they are diverged from either Homo sapiens or Homo
erectus
Some believe the first hominins to leave Africa might not have looked
human
17.4 Parallel Humans
Levallois tools: even more advanced tools with broad, flat shape made by Homo
heidelbergensis
Legs became stubbier, chest grew wider, and muscles grew -> evolved into Homo
neanderthalensis
Brain size same as ours

Colored their shells and made advanced tools

Homo sapiens evolved in Africa, while Neanderthals evolved in Europe and Asia
17.5 New Discoveries from Ancient Genes
Neanderthal genes more similar to Europeans and Asians than Africans
Suggests that some interbreeding occurred to form hybrids
Denisovans: another species of hominin that could have diverged from
Neanderthals
17.6 Evolving a Human Brain
Earlier ancestors depended more on smell than on vision
Old World monkeys and apes depended on sight to judge when a fruit was ready to
be picked
Duplication of the gene opsin helped give better vision of red and orange
leaves with high nutritional content
Sight allowed primates to recognize and communicate with facial expressions
Social evolution drove the expansion of our brain
Children did no better than apes on physical tests, but did significantly better
on social tests
Glucose being displaced from muscle to the brain as a mutation might have caused
brain expansion
FOXP2: gene responsible for speaking
Defect in FOXP2 lead to less activity in Brocas area
Regions of brain are connected by a bundle of nerve fibers called the arcuate
fasciculus
If damaged, the ability to speak is damaged too
17.7 Bottlenecks in the Origin of Modern Humans
Genetic drift spread populations with uneven allele distributions
Only small percentage of humans left Africa
Ancestors of non-Africans had had unusually high number of alleles, causing
some diseases
Ex: myotonic dystrophy, muscles slowly waste away due to gene
repetition
Bottleneck: population size is reduced for at least one generation
Founder Effect: new colony is started by a few members of the original population
17.8 Recent Natural Selection
Tibetians had 2 mutations in gene EPAS1 that allowed them to sense oxygen levels
Natural selection allowed them to live in higher altitudes
Andean peoples were also able to live in high altitudes through mutations of EGLN1
Case of convergent evolution
Milk tolerance in adults was heavily favored after cattle domestication in agriculture
People in Europe and Middle East who eat more plants share the PRLP2 gene
People with similar diets share more genes
Woman with low cholesterol = more children
Amygdala: part of the brain responsible for fear
Some fears are instinctive when our ancestors were threatened by them
Ex: snakes

Oxytocin: released by hypothalamus in mammals; induces motherly instincts and

causes mammary glands to begin producing milk
Romantic love must have evolved when affectionate interactions began to elicit
signaling through the oxytocin-vasopressin pathway (vasopressin: another
similar hormone to oxytocin)
Male meadow voles do not bond with female, but prairie voles do
Prairie voles have higher vasopressin expression
Meadow voles can be injected with vasopressin to increase bonding between
couples
Homo economicus
Model that suggests humans are rational and will make as much as possible
with minimal loss
On the contrary, people care less about gains and more about losing
less

Chapter 18

18.1 How Diseases are Born

Cytomegalovirus strains differ in that each only affects a particular species
Strains evolve very closely with the evolutionary tree
Ex: human strain evolved from chimpanzee strain
SARS originated in China and was spread around the world through flight
passengers
Most related to pathogen coronavirus
Found that virus came from humans eating civets, and that civets got it from
Chinese bats
Viruses can jump across genus, but they grow very slowly and require constant
exposure to adapt
Vaccines are strains of viruses mixed with monkey cells that affect monkeys but not
humans
2 reasons why pathogens evolve so quickly in humans:
1. They reproduce extremely fast
2. Lack repair enzymes to fix errors in replication
18.2 The Evolution of Virulence
Virulence: the ability of a pathogen to cause disease
Pathogen strains may appear dangerous in one host, but inflict no harm in others
Ex: SARS affects humans, but produces no symptoms in mice
Competing factors in natural selection of viruses
1. Highly virulent pathogens wins within host, but may kill host too fast
before transmission
2. Moderately virulent pathogens that are weaker win across host, because
host can travel around more and have more time to transmit to others
Ebola is extremely infectious to humans, but because it kills its host extremely
quickly, it is localized and unable to spread to other populations quick enough
Flu virus is composed of only 8 short strands of RNA
Each segment is independently replicated, then reassembled
When two different flu viruses affect the same cell, their strands may
sometimes get mixed together and produce a new combination of genes
This is known as Viral Reassortment

1918 Flu was extremely virulent

Was still able to travel around easily because it transferred between soldiers
and was brought to the warfront in other countries
18.3 Molded by Parasites
Coevolution between diseases and hosts
Diseases adapt to hosts, hosts adapt to diseases
Sickle-cell anemia is caused by inheriting 2 copies of HbS
If a person only has 1 copy, he/she is much less prone to malaria
Tuberculosis-resistant polymorphism was denser in populations that urbanized
earlier
Ex: Turkey urbanized 8000 years ago (99% resistant), nomads urbanized 20 th
century (71%)
18.4 Evolutions Drug War
Frog skin contains peptides to burst pathogens -> pathogens make protein to cut up
peptide -> peptides evolve to become stiffer
Antibiotics may sometimes drive the evolution of pathogens instead of eradicating
them
Resistance: ability of pathogen to survive exposure to antibiotics
Patients that do not complete antibiotics cycle produce resistant bacteria that
replicate
18.5 Human Variation and Medicine
Founders effect in Pingelap (Pacific Island)
Typhoon in 1775 reduced population to 20 people, 1 person being colorblind
Population today is 5% colorblind
Amish population only interbreeds with each other, and suffers from high rates of
extra fingers and dwarfism
People respond to drugs differently
Warfarin stops blood clots for certain patients, but causes lethal uncontrolled
bleeding in others
Old age is a natural phenomenon in animals
Eventual mutation to p53 gene (stops cancer cells)