College Board AP® Your notes

Biology
Evolution
Contents
Evidence for Evolution
Phylogeny
Speciation
Extinction
Origins of Life on Earth

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 Evidence for Evolution
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Evidence for evolution

The theory of evolution by natural selection is now widely accepted by the scientific
community due to its being supported by a great deal of evidence

Data that provides evidence for evolution

Geological evidence examines fossil distribution and rock strata to trace organism
changes over time
Geographical evidence links organism distribution to shared ancestry
E.g. finches in the Galápagos Islands and honeycreepers in the Hawaiian Islands
demonstrate adaptive radiation

The Hawaiian honeycreepers show continuous variation across their geographical range,
suggesting that they diverged gradually from a common ancestor

Physical evidence includes fossils and homologous structures

E.g. transitional fossils like Archaeopteryx, a bird-like dinosaur fossil which provides
a bridge between dinosaurs and current-day birds
Biochemical evidence uses DNA and protein sequence comparisons
E.g. cytochrome c sequence similarities across species indicate common ancestry
Mathematical models calculate divergence times and genetic similarity

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 E.g. molecular clocks measure mutation rates in genes to estimate divergence
The greater the number of differences there are between nucleotide Your notes
sequences, the longer ago the common ancestor of both species existed
Evidence of changes in organisms over time
Fossil dating methods
The age of fossils can be determined using radioactive isotopes to date the fossils or by
studying the age of the layers where the fossils are found
E.g. naturally occurring carbon-14 in an organism decays at a known rate, based on
the half-life of the carbon 14 isotope
Scientists measure the level of carbon-14 in fossilized organisms to estimate how
long ago that organism died
Geographical data considers the physical location of species and fossil distribution
which allows scientists to establish where common ancestors link different species
together
A combination of fossil dating and geographical data can be used to build timelines of
evolution

Morphological homologies
Homologous structures are similar structures which have different functionalities
despite common ancestry
E.g. the pentadactyl limb shows structural similarity as well as adaptation
Vestigial structures, e.g. pelvic bones in whales and wings in flightless bird, suggest
evolutionary leftovers from common ancestors

The bone structure of the pentadactyl limb of a human, whale, bird, frog, and
alligator; they all have the same basic layout despite having evolved for different
functions

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Molecular and cellular evidence
Similarities in DNA nucleotide sequences, e.g. Hox genes, and protein amino acid Your notes
sequences, [Link], show evolutionary relationships between different
species
Higher sequence similarity indicates a closer relationship between species and a more
recent divergence from a common ancestor

The results of DNA and protein sequencing enable evolutionary trees to be built that show
the evolutionary relationships between species

Conserved processes
Similarities in cellular processes e.g. DNA replication, cellular respiration, and
protein synthesis highlight shared ancestry
Structural evidence
Common uses of structural cell components suggest evolutionary links
Ribosomes in all cells perform protein synthesis
Shared genetic codes and membrane structures (e.g. phospholipid bilayers)
indicate a common origin

Evidence for common ancestry

Eukaryotic ancestry
Structural evidence indicates common ancestry of all eukaryotes:

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 Membrane-bound organelles (e.g., nucleus, mitochondria, chloroplasts) indicate a
shared origin in eukaryotic organisms
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Linear chromosomes in eukaryotes contrast with circular DNA in prokaryotes
The presence of introns in eukaryotic genes supports a common eukaryotic lineage
E.g., endosymbiotic theory explains how mitochondria and chloroplasts
originated from prokaryotes
Continuing evolution
Life continues to evolve indefinitely driven by changing environments
There are many observations in the modern day which demonstrate this continual
evolution, e.g.:
genomic changes
Mutations and genetic drift drive divergence over time where greater
differences between organisms indicate a more distant common ancestor
fossil records
Evidence from fossils shows continuous change in traits over time
resistance development
Mutations are acquired which provide a survival advantage, demonstrating
natural selection in action.
Evolution of antibiotic-resistant bacteria like MRSA demonstrates natural
selection in action
Plants and animals evolve resistance to pesticides, e.g. DDT, or herbicides
Cancer cells show an increasing resistance to chemotherapy drugs
emerging pathogens
Seasonal flu variations evolve every year through mutations which alter antigens
and cause current vaccinations to become ineffective
Diseases like COVID-19 show rapid evolution of pathogens due to
environmental pressures

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 Phylogeny
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Phylogenetic trees and cladograms

Phylogenetic trees and cladograms are types of diagrams that show evolutionary
relationships among groups of organisms or lineages
Both diagrams represent hypotheses about evolutionary relationships based on
shared characteristics
These relationships are not finalised but are continuously revised as more evidence
arises over time

Constructing phylogenetic trees and cladograms

Information that is considered during the construction of a cladogram or phylogenetic
tree includes:
shared characteristics
Traits present in more than one lineage indicate a shared evolutionary history
shared derived characteristics
Homologous traits within a specific lineage indicate common ancestry
These are shown in a group called a clade which is set apart from other
organisms in the cladogram
common ancestry
Nodes on the cladogram represent common ancestors
A more recent common ancestor indicates that two species are more
closely related
The root of the cladogram represents the common ancestor of all members of
the tree
The out-group represents the lineage that is least closely related to the other
organisms in the diagram

Cladograms
Cladograms show the relationships between organisms based on shared derived
characteristics (synapomorphies)
They are primarily concerned with branching patterns, not time or genetic distance

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 Your notes

A cladogram like this one contains no numbers or time scale, so it does not show the
number of base or amino acid changes that have occurred , or how much time has passed
between nodes

Interpreting cladograms
The cladogram above can be interpreted as follows:
1. the node representing the common ancestor of all vertebrates
2. five nodes need to be traced back to here to link placental mammals with
coelacanths, indicating a more distant relationship
3. three clades are directly linked to one common ancestor, indicating that this
cladogram was built without enough data to determine which of these three clades
are more closely related
4. only one node needs to be traced back to here link crocodilians and birds, so they
are more closely related to each other than to any other clade
5. the node representing the common ancestor of all mammals
6. note that the reptiles are not a true clade, as they do not include the birds, with
which they share a common ancestor

Phylogenetic trees

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 Phylogenetic trees show evolutionary relationships along with the evolutionary time or
genetic divergence between organisms
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These timescales are calibrated using the fossil record or molecular clocks

The molecular clock

Molecular data about DNA and protein sequences can be used to determine an
evolutionary timescale
Differences in sequence data arise from DNA mutations, which occur at a fairly
constant rate
The number of differences between sets of sequence data provides information on
how closely related two species are
The more differences there are between the sequences, the longer ago the
species diverged
Molecular comparisons, e.g. after DNA sequencing, are typically more accurate and
reliable than morphological traits for constructing phylogenetic trees and
cladograms
Morphological traits may also occur as a result of convergent evolution rather
than as a result of any evolutionary link, e.g. the independent evolution of wings
in unrelated animals such as bats, birds and insects

A phylogenetic tree includes a timescale that shows the evolutionary distance between
different species based on morphological or molecular changes over time

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 Speciation
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The mechanism of speciation

A species, according to the biological species concept, is defined as:
a group capable of interbreeding and exchanging genetic information to produce viable,
fertile offspring
Speciation refers to the evolution of a new species
Speciation occurs as follows:
1. restriction of gene flow between groups of organisms
2. the separate groups then evolve differently under different selection pressures
3. over time the genetic differences between the two groups mean they are no longer
able to interbreed to produce fertile offspring
The populations are said to be reproductively isolated and are no longer
considered to be the same species

The rate of speciation and evolution

The rate of evolution and speciation is influenced by ecological factors:

Gradualism
Gradualism is the name given to speciation that occurs gradually through the
accumulation of small changes over time
The fossil record shows evidence of slow, long-term evolutionary changes aligned with
geological cycles
Charles Darwin supported gradualism, citing vestigial structures as evidence of
evolutionary remnants from ancestral species
E.g. the human appendix or wings of flightless birds

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 The iconic image of evolution implies gradualism as humans and chimpanzees both
evolved from a common ancestor via intermediate species
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Punctuated equilibrium
In punctuated equilibrium, speciation can occur abruptly, characterized by long periods
of stability followed by short bursts of rapid evolution
This may occur after sudden environmental changes, e.g. through events like volcanic
eruptions or meteor strikes
Some evidence for punctuated equilibrium has come from the fossil record which shows
breaks with no intermediate species, challenging the idea of gradualism

Divergent evolution
Speciation can occur more rapidly if new habitats become available through adaptive
radiation
Several groups of organisms evolve adaptations that allow them to occupy
different ecological niches
Different selection pressures result in the accumulation of genetic differences
leading to speciation
E.g. Darwin's Finches

Types of speciation
Speciation introduces diversity to life forms

Allopatric speciation
Allopatric speciation occurs due to geographical isolation
A population is split into two or more groups by natural barriers, e.g. mountains pr
rivers, or man-made barriers, e.g. roads
There is no gene flow between populations
Selection pressures and genetic drift cause changes in allele frequencies and
phenotypes, leading to divergence
Over time populations become physiologically, behaviorally, and morphologically
distinct, forming new species

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 Your notes

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 The natural geographical barrier of a mountain range can lead to allopatric
speciation in trees Your notes
Allopatric speciation examples
Hawaiian Drosophila: two distinct species of fruit fly, of the genus Drosophila, have
emerged by allopatric speciation on different islands of the Hawaiian archipelago
Ancestral Drosophila colonized the islands, then as new islands formed the
populations were physically isolated
This isolation prevented gene flow between populations on different islands
Over time selection pressures, e.g. differences in climate, food sources, and
habitats, and genetic drift caused the populations to diverge
These evolutionary changes led to the development of distinct traits in each
population
Drosophila silvestris now inhabits Hawai’i Island and Drosophila planitibia
inhabits the island of Maui
Caribbean Anolis: one colonizing species has diverged into around 150 distinct species
via geographical isolation across the islands of the Caribbean
An ancestral Anolis species colonized different islands in the region
Physical separation by water created isolated populations on each island,
preventing gene flow
Each island presented unique environmental conditions and selection pressures
Over time genetic drift and natural selection led to the evolution of populations
with distinct traits

Sympatric speciation
Sympatric speciation takes place with no geographical barrier
Populations in the same location diverge into distinct groups with no gene flow
between them
Mechanisms for separation include:
ecological separation, where populations are separated because they live in
different environments within the same area
E.g. soil pH can differ greatly in different areas, having a major effect on plant
growth and flowering
behavioral separation, where populations are separated because they have
different behaviors
E.g. differences in feeding, communication or social behavior

Sympatric speciation example

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 Apple maggot Rhagoletis
The apple maggot fly (Rhagoletis pomonella) originally laid eggs on hawthorn fruits Your notes
A new niche was introduced with some flies laying eggs on apples
This gave two ecological niches within the same geographical area: hawthorn and
apple
Flies developed a preference for either hawthorn or apple, which influenced mating
behavior since mating occurs near the host fruit
Over time genetic isolation arose due to the lack of gene flow between flies using
different fruits
Overtime, this led to the evolution of two distinct populations despite no
geographical barrier

Maintaining reproductive isolation

Reproductive isolation occurs when species are unable to interbreed to produce fertile
offspring; this indicates that speciation has taken place
Reproductive isolation can be maintained by mechanisms that prevent gene flow
These barriers may occur at different stages in the reproductive life cycle, either
before or after zygote formation

Pre-zygotic barriers
Barriers that prevent fertilization or zygote formation are described as pre-zygotic
Examples of pre-zygotic barriers include:
habitat isolation; organisms in different locations cannot interact to mate
temporal isolation; mating is prevented by differences in activity periods or
breeding seasons
behavioral isolation; mating occurs only with compatible behaviors, e.g. specific
mating calls or dances
mechanical isolation; incompatible reproductive organs block gamete exchange
gametic isolation; gametes cannot fuse, preventing zygote formation

Post-zygotic barriers
Barriers that prevent the zygote from developing into a viable or fertile adult are
described as post-zygotic
Examples of post zygotic barriers include:
reduced hybrid viability; offspring fail to survive to reproductive age, restricting
allele mixing to one generation
reduced hybrid fertility; hybrids are sterile, preventing further reproduction

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hybrid breakdown; hybrids may initially be viable and fertile, but their descendants
weaken and disappear over generations
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 Extinction
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Extinction: causes & effects

Extinction is when a species comes to an end or dies out
Extinction can be a natural, biological process that happens on planet Earth and studies
of fossils and ancient DNA have shown that millions of species have gone extinct in the
past
Mass extinction events have also occurred in the past where a very large number of
species went extinct at one time
The rate of extinction during these periods was very high
Past mass extinctions were likely caused by major and sudden shifts in the
environment such as an Ice Age or an asteroid hitting the Earth
Scientists have been studying the current rates of extinction in recent years and many
believe that the Earth is undergoing a current mass extinction with humans being the
main cause

Causes of extinction
Climate change
Burning fossil fuels increases CO₂ levels, causing the greenhouse effect
This leads to rising temperatures, sea levels, ocean acidity, and melting ice caps
Habitat loss forces species like polar bears to travel further for food, threatening
survival
Competition
Limited resources (food, water, habitat, mates) drive competition within and
between species
Species unable to compete effectively face population decline
E.g., wild dogs in North America declined due to competition with Asian cats
Introduction of non-native species
Human introduction of species disrupts ecosystems
Non-native species often outcompete natives due to lack of predators
E.g. gray squirrels introduced to the UK displaced red squirrels through
competition and disease (squirrel pox)
Hunting by humans
Historically essential but now largely recreational or commercial
Rare species are often targeted, accelerating population decline

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 Overhunting can reduce numbers beyond recovery, leading to extinction
Habitat destruction
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The leading cause of extinction due to deforestation, pollution, and land
conversion
Loss of habitat forces species to relocate or compete for limited space
If no viable habitat remains, species cannot survive and go extinct
Effects of extinction
Extinction, which reduces the number of species, can be thought of as an opposing
force to speciation
The level of biodiversity in an ecosystem can be monitored by the rates of speciation
and extinction
Extinction liberates niches that can then be occupied by different species, some of
which are newly speciated

Genetic diversity & extinction

Impact of genetic diversity on populations
Genetic diversity is the variety of alleles within a species or population
Maintaining genetic diversity is crucial for the long-term survival and adaptability of
populations in changing environments
If environmental changes occur, different selection pressures act on the population
Under new selection pressures, alleles that were beneficial in one environment may
become harmful
This will alter the fitness of individuals, influencing survival and reproduction rates
Populations with high genetic diversity are more likely to include individuals with
traits that help them adapt and withstand new selective pressures
Populations with low genetic diversity are more vulnerable to changes
There is an increase in the risk of decline or extinction, as fewer individuals
possess adaptive traits

Examples of genetic variety

California condors
The California condor is the largest North American landbird
Declined in the 20th century due to DDT use, poaching, and lead poisoning
Low population numbers caused low genetic diversity, reducing resilience to
environmental challenges

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 Your notes

CC BY-SA 2.0 Don Graham, via Wikimedia Commons

Black-footed ferrets
The black-footed ferret (Mustela nigripes) is a critically endangered predator
Its diet primarily consists of prairie dogs, which have been exterminated as agricultural
pests in parts of the USA and Canada
Loss of prairie dog habitats has reduced the ferret's main food source
The species' low genetic diversity makes it vulnerable to environmental changes,
further threatening its survival

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 Your notes

USFWS Mountain-Prairie, Public domain, via Wikimedia Commons

Prairie chickens
The prairie chicken (Tympanuchus cupido), also called a boomer for its mating call, is
highly endangered in North America
Its habitat, tall grass prairie, has been largely lost to agriculture in the 20th and 21st
centuries

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 CC BY 2.0 Ron Knight, via Wikimedia Commons

Potato blight Your notes

Potato blight is a disease caused by the protoctist Phytophthora infestans, which
shares some fungal characteristics
It spreads via spores, initially causing dark brown marks on leaves that quickly spread
The pathogen destroys potato and tomato crops, rendering them inedible
The Irish Potato Famine in the mid-19th century, caused by potato blight, killed ~1 million
people and spurred emigration to North America
This highlights the importance of maintaining genetic diversity in crop plants to prevent
similar agricultural disasters

I.Sáček, CC0, via Wikimedia Commons

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 Origins of Life on Earth
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Evidence for the origins of life on Earth

These hypotheses provide scientific explanations for how life may have originated on
Earth

Geological evidence
Earth formed around 4.6 billion years ago (bya) and remained too hostile for life until
3.9 bya
Earliest fossil evidence of life dates to 3.5 bya, suggesting a plausible time range for
life's origin

Organic molecules
Organic monomers, e.g. amino acids and nucleotides, formed from inorganic
molecules
These monomers joined to form polymers capable of replication, and storing and
transferring information
The Oparin-Haldane hypothesis suggests that life arose from inorganic precursors
under early Earth conditions
The Miller-Urey experiment simulated primitive Earth, showing that organic
molecules could form from inorganic compounds
The extra-terrestrial origin hypothesis states that organic molecules may have
arrived via meteorites, such as the Maribo meteorite, which contained early organic
matter

RNA world hypothesis

This hypothesis proposes that RNA was the first genetic material
RNA can store genetic information and catalyze chemical reactions, meaning that it
could have enabled early life processes
Modern ribosomes and self-replicating RNA support this theory

LUCA (Last Universal Common Ancestor)

Fossil and genetic evidence suggest LUCA may have lived in hydrothermal vents, using
chemosynthesis for energy
Likely characteristics of LUCA:
anaerobic; it survived without oxygen
hydrogen was the energy source
CO₂ was converted into glucose

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survived in extreme heat (thermophilic)

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