Biology Chapters 13-15

Galápagos Islands observations

• The Galápagos Islands are volcanic, ~900 km off South America.

• Darwin observed unique animals:

  • Blue-footed boobies

  • Giant tortoises (called galápagos in Spanish)

  • Marine iguanas

  • Many species of finches

• Finches had different beak shapes, adapted to different foods:

  • Seeds

  • Cactus flowers

  • Insects

• Some finches even eat parasites off tortoises.

• These observations helped Darwin think about adaptation and evolution.

Early ideas about species

• The ancient Greeks believed life could change over time.

• Aristotle believed species were perfect and unchanging.

• Judeo-Christian beliefs supported the idea that:

  • God created species

  • Earth was only ~6,000 years old

• Fossils showed organisms different from living species → suggested a change over time.

• Lamarck’s idea (early evolution theory)

  • Proposed that organisms change during life and pass traits to offspring.

  • Example: giraffes stretched necks → longer necks in offspring.

  • This idea is wrong (acquired traits are not inherited).

  • But Lamarck helped introduce the idea that species evolve.

Darwin’s voyage on the HMS Beagle

• Born in 1809, loved nature.

• Studied medicine → quit → studied to become clergy.

• At age 22, I joined the HMS Beagle voyage (1831).

• Collected plants, animals, and fossils around the world.

• Noticed:

  • Fossils similar to living species in the same region

  • Different environments → different adaptations

  • Galápagos species similar to South American species

• Influence of Charles Lyell

  • Lyell’s geology showed that Earth changes slowly over time.

  • Earth must be very old.

  • This helped Darwin realize evolution could take millions of years.

Darwin’s theory of evolution

• Published On the Origin of Species (1859).

• Proposed:

  • Species change over time

  • All species share ancestors

  • Called this descent with modification

• Artificial selection

  • Humans breed organisms for traits.

  • Example:

    • Dog breeds

    • Crop plants

  • Shows big changes can happen over generations.

• Natural selection

  • Key ideas:

    • Organisms produce more offspring than survive.

    • Individuals vary.

    • Some traits help survival.

    • Those with helpful traits reproduce more.

  • Result:

    • Helpful traits become common.

    • Populations change over time.

  • Important points:

    • Populations evolve, not individuals.

    • Only heritable traits evolve.

    • Evolution has no goal.

    • Adaptations depend on the environment.

Examples of natural selection

• Finches in Galápagos:

  • Dry years → larger beaks survive

  • Wet years → smaller beaks survive

• Insects & pesticides:

  • Some insects resistant

  • Survivors reproduce → resistance spreads

• Natural selection:

  • Does not create traits

  • Selects traits already present

Fossil evidence

• Fossils = remains of past organisms.

• Types:

  • Bones/shells

  • Casts and molds

  • Footprints (trace fossils)

  • Preserved in amber, ice, and bogs

• The fossil record shows:

  • Layers of rock = timeline

  • Older fossils deeper

  • Shows a gradual change over time

• Examples:

  • Early humans (Homo erectus)

  • Whale evolution from land mammals

  • Mammals from reptile ancestors

• Oldest fossils

  • ~3.5 billion years old (prokaryotes)

Biogeography (location of species)

• Species resemble nearby species.

• Galápagos animals similar to those in South America.

• Australia → marsupials evolved separately.

• Conclusion:

  • Species evolved from local ancestors.

Comparative anatomy (body structures)

• Homologous structures

  • Same structure, different function.

  • Example:

    • Human arm

    • Cat leg

    • Whale flipper

    • Bat wing

  • Shows common ancestor.

• Embryology

  • Embryos of vertebrates share features:

    • Tails

    • Pharyngeal pouches

  • Shows shared ancestry.

• Vestigial structures

  • Leftover parts from ancestors:

    • Whale pelvis bones

    • Blind cave fish eyes

Molecular evidence

• DNA similarities show relationships.

  • Similar DNA → closer ancestor

  • Different DNA → distant ancestor

• All life:

  • Uses DNA

  • Uses the same genetic code

• → Suggests all life has a common origin.

Evolutionary trees

• Show relationships between species.

• Branch point = common ancestor.

• Example traits:

  • Tetrapod limbs

  • Amnion

  • Feathers

• Trees are based on:

  • Fossils

  • Anatomy

  • DNA

Key ideas to remember

• Evolution = change in populations over time

• Natural selection = main mechanism

• Evidence comes from:

  • Fossils

  • Anatomy

  • DNA

  • Geography

  • Observations of selection

• All life shares a common ancestor

Evolution at the Population Level

• Evolution Does NOT Happen to Individuals

  • Common misconception:

    • Individuals do not evolve during their lifetime.

    • Natural selection acts on individuals, but evolution occurs in populations.

  • Example:

    • Some insects survive pesticides because they carry resistant alleles.

    • Those insects reproduce more.

    • Over generations, the population becomes more resistant.

Populations and Gene Pools

• Population

  • A population =

  • A group of individuals of the same species living in the same area that interbreed.

  • Characteristics:

    • Populations may be somewhat isolated.

    • Individuals usually mate with nearby members.

    • Members of the same population are genetically more similar.

Gene Pool

• The gene pool =

  • All the genes and alleles in a population.

• Example:

  • In an insect population:

    • One allele gives pesticide resistance

    • Another allele does not

• If pesticides are used:

  • Resistant allele increases

  • Non-resistant allele decreases

Microevolution

• Microevolution =

  • A change in allele frequencies in a population over generations.

• Example:

  • Increase in pesticide-resistant insects.

Genetic Variation (Required for Evolution)

• Evolution needs variation between individuals.

• Example differences:

  • Appearance

  • Behavior

  • Physiology

  • DNA sequences

• Example species with variation:

  • Lady beetles

  • Garter snakes

Phenotype vs Genotype

• Phenotype

  • Observable traits

  • Influenced by genes AND environment

• Genotype

  • Genetic makeup

  • Inherited

• Important:

  • Only genetic variation can be passed to offspring.

• Example:

  • Building muscle from exercise cannot be inherited.

Types of Genetic Traits

• Polygenic Traits

  • Controlled by many genes.

  • Result:

    • Continuous variation.

  • Example:

    • Human height

Single-Gene Traits

• Controlled by one gene.

• Example:

  • Pea flower color

  • Human blood type

Sources of Genetic Variation

• 1. Mutation

  • Mutation = change in DNA sequence.

  • Important points:

    • Ultimate source of new alleles

    • Only mutations in gametes can be inherited

• Most mutations:

  • Harmful or neutral

• Rarely:

  • Beneficial (increase survival)

• Example:

  • DDT-resistant flies

2. Gene Duplication

• Sometimes genes are copied during meiosis.

• Effects:

  • Extra gene copies accumulate mutations

  • Can evolve new functions

• Example:

  • Mammals have many olfactory receptor genes for smell.

3. Sexual Reproduction

• Major source of variation.

• Three mechanisms:

  • Crossing Over

    • Chromosomes exchange genes during meiosis.

  • Independent Assortment

    • Chromosomes separate randomly into gametes.

  • Random Fertilization

    • Any sperm can fertilize any egg.

• Result:

  • Every offspring has a unique combination of alleles.

Hardy–Weinberg Principle

• Scientists use the Hardy–Weinberg principle to test if evolution is occurring.

• Idea:

  • If no evolution occurs, allele frequencies stay constant.

• This state is called the Hardy–Weinberg equilibrium.

Example (Blue-Footed Boobies)

• Allele frequencies:

  • p = 0.8

  • q = 0.2

• Genotypes:

  • WW = p² = 0.64

  • Ww = 2pq = 0.32

  • ww = q² = 0.04

• If no evolutionary forces occur:

  • These frequencies stay the same each generation.

Conditions for Hardy–Weinberg Equilibrium

• A population must meet 5 conditions:

  • Very large population

  • No migration (no individuals moving in/out)

  • No mutations

  • Random mating

  • No natural selection

• Reality:

  • Real populations rarely meet all conditions

  • So evolution usually occurs.

Factors That Cause Evolution

• If Hardy–Weinberg conditions are broken, evolution happens.

• Main factors:

  • Small population size

  • Migration (gene flow)

  • Mutation

  • Nonrandom mating

  • Natural selection

Key Takeaways

• Evolution occurs in populations, not individuals.

• Evolution = change in allele frequencies.

• Genetic variation comes from:

  • Mutations

  • Gene duplication

  • Sexual reproduction

• Hardy–Weinberg equilibrium describes populations not evolving.

• Breaking its conditions leads to microevolution.

Causes of Microevolution

• Microevolution = change in allele frequencies in a population.

• Hardy–Weinberg equilibrium stays constant only if 5 conditions are met.

  • If they are broken → evolution occurs.

• Main causes of evolutionary change:

  • Natural selection

  • Genetic drift

  • Gene flow

• Mutation and nonrandom mating matter, but usually less.

Mutation

• Creates new alleles.

• Happens randomly.

• Rare in sexually reproducing organisms.

• Alone → usually small effect on allele frequencies.

Nonrandom mating

• Individuals choose mates based on traits.

• Changes genotype frequencies.

• Usually does NOT change allele frequencies by itself.

Natural Selection

• Condition broken:

  • All individuals must reproduce equally (never true in nature).

• Reality:

  • Individuals vary.

  • Some survive better.

  • Some reproduce more.

• Example:

  • Webbed-foot birds swim better → survive more → allele increases.

• Result:

  • Allele frequency changes.

  • Population evolves.

• Natural selection leads to adaptive evolution

  • = better fit to the environment.

Genetic Drift

• Genetic drift =

  • Random change in allele frequencies due to chance.

• More likely when the population is small.

• Example idea:

  • Flip a coin 10 times → uneven result possible.

  • Flip a coin 1000 times → closer to 50/50.

• Same with genes:

  • Small populations change more by chance.

• Effects:

  • Alleles can disappear.

  • Alleles can become common randomly.

Bottleneck Effect

• Bottleneck = drastic population reduction.

• Causes:

  • Fire

  • Flood

  • Earthquake

  • Hunting

  • Habitat loss

• Result:

  • Survivors have different allele frequencies.

  • Less genetic variation.

• Example:

  • Greater prairie chickens

    • The population dropped to <50

    • Lost 30% of alleles

    • Low egg hatch rate

• Human-caused bottlenecks:

  • Florida panther

  • African cheetah

• Even if the population grows again:

  • Variation stays low.

Founder Effect

• Founder effect = a small group starts a new population.

• Small group ≠ original gene pool.

• Result:

  • Different allele frequencies.

  • Some traits become common.

• Example:

  • Tristan da Cunha island

    • 15 founders

    • One carried a blindness allele

    • Much higher frequency later.

Gene Flow

• Gene flow = movement of alleles between populations.

• Happens when:

  • Individuals move

  • Gametes move (pollen)

• Effects:

  • Adds new alleles

  • Removes alleles

  • Makes populations more similar.

• Example:

  • Prairie chickens

    • New birds added

    • Genetic diversity increased

    • Hatch rate improved.

Natural Selection = Chance + Sorting

• Chance:

  • Mutation

  • Recombination

• Sorting:

  • The environment favors some traits.

• Only natural selection consistently produces:

  • Adaptive evolution

Relative Fitness

• Fitness = reproductive success.

• Not strength.

• Not survival alone.

• Fitness =

  • Number of offspring that survive and reproduce.

• Traits that increase fitness:

  • Better camouflage

  • Better mating success

  • Better food gathering

• Example:

  • Moths hidden from predators → more offspring.

Types of Natural Selection

• Use the mouse fur color example.

• Population starts with:

  • Light

  • Medium

  • Dark

• Bell curve distribution.

1. Stabilizing Selection

• Favors middle traits.

• Removes extremes.

• Result:

  • Less variation.

• Example:

  • Human birth weight

    • Too small → risk

    • Too large → risk

    • Medium survives best.

2. Directional Selection

• Favors one extreme.

• Population shifts.

• Example:

  • Dark fur better after fire

  • Larger beaks during drought

  • Pesticide resistance

  • Antibiotic resistance

• Common when:

  • Environment changes

  • Species move to a new area.

3. Disruptive Selection

• Favors both extremes.

• Middle selected against.

• Result:

  • Two phenotypes.

• Example:

  • Finches:

    • Big beaks eat hard seeds

    • Small beaks eat soft seeds

    • Medium bad at both

• Can lead to new species.

Sexual Selection

• Sexual selection = traits that help get mates.

• Not always good for survival.

• Example:

  • Peacock tail

  • Bright feathers

  • Lion mane

• Two types:

  • Intrasexual selection

    • Same sex compete.

    • Example:

      • Male vs male fights.

  • Intersexual selection

    • Mate choice.

    • Usually:

      • Females choose males.

    • Traits females prefer:

      • Bright color

      • Long call

      • Strong display

    • Good genes hypothesis:

      • Preferred traits show health.

    • Example:

      • Gray tree frogs

      • Long calls → healthier offspring.

Antibiotic Resistance

• Example of directional selection.

• Antibiotics kill most bacteria.

• Some have mutations → survive.

• Survivors reproduce.

• Result:

  • Resistant bacteria spread.

• Human causes:

  • Overuse of antibiotics

  • Using antibiotics for viruses

  • Not finishing medicine

  • Antibiotics in livestock

• Example:

  • MRSA bacteria

• Evolution makes treatment harder.

Why Variation Does NOT Disappear

• Natural selection removes bad traits…

• But variation stays.

• Reasons:

Diploidy

• Two alleles per gene.

• Recessive alleles can hide in heterozygotes.

• So, selection cannot remove them easily.

Balancing Selection

• Keeps multiple alleles.

• Heterozygote advantage

  • Heterozygotes survive best.

  • Example:

    • Sickle-cell allele

      • AA → malaria risk

      • SS → sickle-cell disease

      • AS → protected

    • Both alleles stay.

Frequency-dependent selection

• A rare phenotype has an advantage.

• Example:

  • Scale-eating fish

    • Left-mouth vs right-mouth

• If one type is common:

  • Prey defend against it.

• Rare type survives better.

• Result:

  • Frequencies stay balanced.

Imperfect Organisms

• Evolution does not make perfect organisms.

• Reasons:

  • Works with existing traits

  • Limited by history

  • Environment changes

  • Trade-offs exist

• Natural selection makes:

  • Better than before, not perfect.

Key Points

• Evolution caused by:

  • Natural selection

  • Genetic drift

  • Gene flow

• Small populations change faster.

• Selection can be:

  • Stabilizing

  • Directional

  • Disruptive

• Sexual selection affects mating traits.

• Variation maintained by:

  • Diploidy

  • Balancing selection

  • Mutation

Evolution of Populations 

• Key Vocabulary

  • Population

    • A group of individuals of the same species living in the same area

  • Gene Pool

    • All the genes (alleles) in a population

  • What produces variation?

    • Mutations (random DNA changes)

    • Sexual reproduction (crossing over, independent assortment, fertilization)

Hardy-Weinberg Principle

• Definition:

  • A population will NOT evolve if certain conditions are met

  • It’s a baseline to compare real populations to

• Equation:

  • p² + 2pq + q² = 1

    • p = dominant allele frequency

    • q = recessive allele frequency

    • p + q = 1

Five Assumptions (SUPER IMPORTANT)

• A population must have ALL of these to stay in equilibrium:

  • No mutations

  • Random mating

  • No natural selection

  • Extremely large population (no genetic drift)

  • No gene flow (no immigration/emigration)

• If ANY of these are broken → evolution occurs

Mechanisms of Evolution

• Natural Selection

  • Individuals with helpful traits survive & reproduce more

• Genetic Drift

  • Random changes in allele frequencies (strong in small populations)

• Gene Flow

  • Movement of genes between populations (migration)

• Founder Effect

  • A small group starts a new population → less genetic diversity

Types of Natural Selection

• Stabilizing Selection

  • Favors average traits

  • Reduces variation

  • Example: average birth weight

• Directional Selection

  • Favors one extreme

  • Shifts population

  • Example: darker moths during pollution

• Disruptive Selection

  • Favors both extremes

  • Can lead to speciation

Sexual Selection

• Traits increase mating success (not survival)

• Sexual Dimorphism

  • Males & females look different

  • Example: peacocks

Antibiotic Resistance

• How it happens:

  • Some bacteria randomly have resistance

  • Antibiotics kill non-resistant bacteria

  • Resistant ones survive & reproduce

• Why it’s a problem:

  • Infections become harder (or impossible) to treat

Balancing Selection

• Keeps multiple alleles in a population

• Frequency-Dependent Selection

  • Fitness depends on how common a trait is

  • Rare traits often have an advantage

Charles Darwin & Evolution

• Charles Darwin

  • Traveled to the Galápagos Islands

  • Studied finches → noticed variation

• Evolution

  • Change in allele frequencies over time

• Fossils

  • Preserved remains of ancient organisms

• On the Origin of Species

  • Introduced natural selection

Steps of Natural Selection

• Variation exists

• Overproduction of offspring

• Competition

• Survival of the fittest

• Traits passed on

Natural vs Artificial Selection

• Natural Selection

  • The environment selects traits

• Artificial Selection

  • Humans select traits

  • Example: dog breeding

Evidence of Evolution

• Fossils

  • Show changes over time

• Biogeography

  • Species distribution (islands = unique species)

• Comparative Anatomy

  • Homologous structures → common ancestry

• Molecular Biology

  • DNA similarities

• Evolutionary Trees

  • Show relationships between species

Observing Evolution Today

• Antibiotic-resistant bacteria

• Pesticide-resistant insects

• Changes in finch beaks

Quick Summary

• Evolution = change in allele frequencies

• Variation is required

• Hardy-Weinberg = “no evolution” model

• Natural selection is NOT random (but mutations are)

• Multiple types of selection shape populations

Species & Speciation

• Defining Species

• Biological Species Concept

  • Species = organisms that can interbreed and produce fertile offspring

• Other Concepts

  • Morphological: based on physical traits

  • Ecological: based on niche

  • Phylogenetic: based on evolutionary history

Speciation

• Formation of new species

Hybrids

• Offspring of two species

• Often:

  • Infertile (ex, mule)

  • Less viable

Reproductive Isolation

• Prezygotic Barriers (before fertilization)

  • Habitat Isolation (different locations)

  • Temporal Isolation (different times)

  • Behavioral Isolation (different mating behaviors)

  • Mechanical Isolation (incompatible structures)

  • Gametic Isolation (sperm/egg can’t fuse)

Postzygotic Barriers (after fertilization)

• Reduced viability (offspring weak)

• Reduced fertility (offspring sterile)

• Hybrid breakdown (offspring weak over generations)

Types of Speciation

• Allopatric Speciation

  • Geographic separation

• Sympatric Speciation

  • Same area, but reproductive isolation

• Polyploidy

  • Extra chromosome sets (common in plants)

  • Can instantly create new species

Adaptive Radiation (again)

• One species → many quickly

• Key to biodiversity

Hybrid Zones

• Regions where different species interbreed

Punctuated Equilibria

• Evolution happens in quick bursts

• Followed by long periods of little change

Darwin & Early Ideas of Evolution

• Charles Darwin studied the Galápagos Islands

• Noticed:

  • Islands were geologically young

  • Full of unique species (ex, flightless cormorant)

• Realization:

  • Species are new and changing over time

• Called the origin of new species the “mystery of mysteries.”

Microevolution vs. Speciation

• Microevolution

  • Small changes in a population’s gene pool over generations

  • Leads to adaptation

• Speciation

  • Formation of new species

  • Increases biodiversity

• Without speciation, Earth would only have one evolving species, not millions

Big Picture of Evolution

• Life started ~3.5 billion years ago

• One ancestral species → split → more splits → millions of species

• Explains:

  • Unity of life → shared ancestry

  • Diversity of life → branching evolution

What is a Species?

• Hard to define because:

  • Some species look very different but are the same (humans)

  • Some look similar but are different (meadowlarks)

Biological Species Concept

• A species = organisms that:

  • Can interbreed in nature

  • Produce fertile offspring

• Key idea: reproductive compatibility

Reproductive Isolation

• Prevents gene flow between species

Hybrids

• Offspring of two species

• Example:

  • Grizzly bear + polar bear → “grolar bear”

• Often:

  • Rare

  • Less fit or sterile

Limits of the Biological Species Concept

• Doesn’t work well for:

  • Fossils (can’t test breeding)

  • Asexual organisms (no mating)

Other Species Concepts

• 1. Morphological Species Concept

  • Based on physical traits

  • Pros:

    • Works for fossils & asexual species

  • Cons:

    • Subjective

2. Ecological Species Concept

• Based on the ecological niche (role in the environment)

• Example:

  • Same-looking fish but different diets/habitats

3. Phylogenetic Species Concept

• Based on evolutionary history

• Species = the smallest group with a common ancestor

Reproductive Barriers

• Two types:

Prezygotic Barriers (BEFORE fertilization)

• Prevent mating or fertilization

• Types:

  • Habitat isolation

    • Same area, different habitats

  • Temporal isolation

    • Breed at different times

  • Behavioral isolation

    • Different mating behaviors/signals

  • Mechanical isolation

    • Body parts don’t fit

  • Gametic isolation

    • Sperm & egg can’t fuse

Postzygotic Barriers (AFTER fertilization)

• Hybrids form, but have problems

• Types:

  • Reduced hybrid viability

    • Offspring don’t survive

  • Reduced hybrid fertility

    • Offspring sterile (ex, mule)

  • Hybrid breakdown

    • Next generation weak or sterile

Key Takeaways

• Evolution = change + branching

• Speciation = source of biodiversity

• Species are defined mainly by their ability to reproduce

• Reproductive isolation keeps species separate

• Multiple definitions exist because nature is messy and complex

How New Species Form (Speciation Basics)

• Speciation often begins with population separation

• Once isolated:

  • Gene pools evolve independently

  • No gene flow between populations

• Changes happen via:

  • Natural selection

  • Genetic drift

  • Mutation

Allopatric Speciation (Geographic Separation)

• Definition: New species form due to physical barriers

• Barrier examples:

  • Mountains

  • Rivers/canyons (ex, Grand Canyon squirrels)

  • Oceans/continents splitting

• Key idea:

  • Isolation → different environments → different adaptations → reproductive barriers

Evidence for Allopatric Speciation

• Snapping shrimp split by the Isthmus of Panama

  • Closely related pairs on opposite sides

• Shows:

  • Geographic separation → speciation

How Isolation Leads to New Species

• Different environments cause:

  • Different food sources

  • Different predators

  • Different pollinators

• Leads to:

  • Trait changes

  • Eventually reproductive barriers

Lab Evidence (Diane Dodd Experiment)

• Flies raised on:

  • Starch vs. maltose

• Result:

  • Preferred mating with the same diet group

• Shows:

  • Prezygotic barrier forming

  • Speciation can begin quickly

Pollinator Isolation Example

• Monkey flowers:

  • Pink → bees

  • Red → hummingbirds

• Changing flower color → changed pollinators

• Result:

  • Reproductive isolation

Sympatric Speciation (Same Location)

• New species form without geographic separation

• Happens through:

  • Polyploidy

  • Habitat differentiation

  • Sexual selection

Polyploidy (Common in Plants)

• Organisms have extra chromosome sets

• Key outcomes:

  • Tetraploid (4n) can form from diploid (2n)

  • Cannot reproduce with parent species → instant speciation

• Hybrid Polyploidy:

  • Two species hybridize → sterile

  • Chromosomes double → fertile new species

Sympatric Speciation in Animals

• Less common

• Happens via:

  • Different habitats

  • Mate preferences

• Example:

  • African cichlid fish

    • Different diets

    • Female choice based on color

Polyploidy in Agriculture

• Many crops are polyploid:

  • Wheat

  • Bananas

  • Potatoes

  • Cotton

• Example:

  • Bread wheat evolved through hybridization + chromosome doubling

Adaptive Radiation

• One species → many species adapted to different niches

• Happens in:

  • Isolated areas (like islands)

Darwin’s Finches (Classic Example)

• Charles Darwin studied them in the Galápagos

• 14 species evolved from one ancestor

• Differences:

  • Beak size/shape

  • Diet

  • Habitat

Real-Time Evolution (Grants Study)

• Studied finches for decades

• Found:

  • Drought → larger beaks survive

  • Competition → smaller beaks favored

• Shows:

  • Evolution can happen quickly

Hybrid Zones

• Areas where species meet and interbreed

• Possible outcomes:

1. Reinforcement

• Hybrids are weak → selection favors stronger reproductive barriers

• Example:

  • Flycatcher birds evolve more distinct appearances

2. Fusion

• Barriers are weak → species merge back into one

• Example:

  • Cichlid fish (due to pollution affecting mate choice)

• 3. Stability

• Hybrids continue, but species remain distinct

• Example:

  • Some finch populations

Patterns in the Fossil Record

• 1. Punctuated Equilibrium

  • Long periods of little change

  • Short bursts of rapid speciation

2. Gradualism

• Slow, steady evolution over time

Time Scale of Speciation

• Can take:

  • 4,000 to 40 million years

• Average: ~6.5 million years

Big Picture Takeaways

• Speciation often starts with isolation

• Can happen:

  • With barriers (allopatric)

  • Without barriers (sympatric)

• Evolution is:

  • Sometimes fast

  • Usually very slow

• Leads to:

  • Biodiversity + major evolutionary changes

Evolution & History of Life 

• Abiotic Synthesis of Organic Molecules

  • Early Earth conditions allowed organic molecules to form from inorganic substances.

  • Supported by the Miller-Urey Experiment

  • Key idea: life’s building blocks can form naturally without life already existing

Macroevolution

• Large-scale evolutionary changes over long time periods

• Includes:

  • Origin of new species

  • Mass extinctions

  • Evolution of major groups

Major Events in the History of Life

• First Cells

  • ~3.5 billion years ago

  • Prokaryotic (simple, no nucleus)

• Oxygen Revolution

  • Photosynthetic bacteria released oxygen

  • Led to the extinction of anaerobic organisms + new life forms

• Colonization of Land

  • Plants first (~500 mya), then animals

  • Required adaptations like:

    • Preventing water loss

    • Structural support

Radiometric Dating

• Uses radioactive decay to determine the age of fossils/rocks

• Based on the half-life of isotopes

Geologic Record

• The fossil record shows life’s history in rock layers

• Older layers = deeper

Geologic Time Scale (Know Order)

• Eons → Eras (focus here):

  • Precambrian

  • Paleozoic

  • Mesozoic

  • Cenozoic

Plate Tectonics & Continental Movement

• Plate Tectonics

  • Earth’s crust is divided into moving plates

• Continental Drift

  • Continents move over time

• Pangaea

  • All continents were once joined together

  • Broke apart → modern continents

Mass Extinctions

• Sudden loss of many species

• Example: Cretaceous–Paleogene extinction event

• Often followed by adaptive radiation

Adaptive Radiation

• Rapid evolution of many species from a common ancestor

• Happens after:

  • Mass extinctions

  • New environments

Phylogeny & Tree of Life 

• Phylogeny

  • Evolutionary history of a species/group

  • Represented with phylogenetic trees

Convergent Evolution

• Unrelated species evolve similar traits

• Due to similar environments (NOT common ancestry)

Taxonomy

• Naming and classifying organisms

• Hierarchy (DKPCOFGS)

  • Domain

  • Kingdom

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

Clades

• A group of organisms with a common ancestor

• Includes all descendants

Traits

• Shared ancestral character = trait from a distant ancestor

• Shared derived character = trait unique to a group

Cladograms (How to Build)

• Use shared derived traits

• Steps:

  • List organisms

  • Identify traits

  • Arrange from least → most derived

• Closer branches = more closely related

Origin of the Universe & Earth

• Universe Basics

  • Earth is one of 8 planets orbiting the Sun

  • The Sun is one of billions of stars in the Milky Way galaxy

  • The Milky Way is one of the trillions of galaxies in the universe

  • Closest star to the Sun: ~40 trillion km away

• Big Bang Theory

  • The universe began 12–14 billion years ago

  • All matter was once condensed into one mass

  • A massive explosion (Big Bang) caused the expansion

  • The universe has been expanding ever since

Formation of Earth

• Earth formed ~4.6 billion years ago

• Originated from a swirling cloud of dust and gas

• Particles collided and stuck together → formed larger bodies

• Gravity pulled in more material → formed planets

• Early Earth Conditions

  • Very hot and molten due to:

    • Meteor impacts

    • Gravitational compression

  • Earth is separated into layers by density

    • Dense materials → core

    • Lighter materials → crust

Early Atmosphere & Oceans

• Early atmosphere contained:

  • Water vapor

  • Carbon dioxide

  • Nitrogen

  • Methane

  • Ammonia

  • Hydrogen

  • Hydrogen sulfide

• No oxygen (O₂) initially

• As Earth cooled:

  • Water vapor condensed → oceans formed

• Environment Differences

  • Much more:

    • Lightning

    • Volcanic activity

    • UV radiation

When Did Life Begin?

• Oldest fossils: ~3.5 billion years old

• Example: stromatolites

  • Layered rocks formed by photosynthetic prokaryotes

• Life may have started even earlier (~3.9 billion years ago)

Spontaneous Generation vs. Reality

• Old belief: life comes from nonliving matter

• Disproved by Louis Pasteur (1862)

  • Life comes from preexisting life

How Did Life Arise? (4 Stages Overview)

• Scientists propose life formed through:

  • Abiotic synthesis of organic molecules

  • Formation of polymers (chains of molecules)

  • Formation of protocells (membrane-bound structures)

  • Self-replicating molecules (RNA)

Stage 1: Abiotic Synthesis (Miller-Urey Experiment)

• Key Scientists

  • Stanley Miller (1953)

  • Based on ideas from:

    • A. I. Oparin

    • J. B. S. Haldane

• Experiment Setup

  • Simulated early Earth with:

    • Water vapor

    • Hydrogen gas

    • Methane

    • Ammonia

  • Added electric sparks (lightning)

• Results

  • Produced:

    • Amino acids

    • Organic molecules (building blocks of life)

• Key Idea

  • Organic molecules can form without life

Other Sources of Organic Molecules

• Volcanic environments

• Hydrothermal vents (deep ocean)

• Meteorites

  • Example: meteorite (1969, Australia)

  • Contained:

    • Amino acids

    • Lipids

    • Sugars

    • Nitrogen bases

Stage 2: Formation of Polymers

• Monomers (small molecules) → polymers (chains)

• Can happen without enzymes:

  • Heat + concentration → bonding

• Possible early Earth scenario:

  • Waves splash molecules onto hot rocks

  • Chains form → washed back into the ocean

Stage 3: Protocells

• Lipids in water → form vesicles (membrane bubbles)

• Properties:

  • Can grow and divide

  • Create an internal environment

• Clay may have helped:

  • Concentrates molecules

  • Speeds up reactions

Stage 4: Self-Replicating RNA (RNA World)

• Key Idea

  • RNA may have been:

    • Genetic material

    • Catalyst (like enzymes)

• Evidence

  • RNA can:

    • Self-assemble

    • Copy itself (with errors → mutations)

  • Some RNA acts as enzymes → called ribozymes

• “RNA World” Hypothesis

  • Early life used RNA for:

    • Information storage

    • Chemical reactions

From RNA to DNA

• Over time:

  • DNA replaced RNA as genetic storage (more stable)

• Protocells evolved into true cells

• Natural selection began shaping life

Big Picture Summary

• Universe formed → Earth formed → conditions allowed chemistry

• Simple molecules → complex molecules → protocells → RNA

• RNA → DNA → first true cells → evolution of life

Macroevolution Overview

• Macroevolution = large-scale patterns of evolutionary change over long time periods

• Studies the history of life on Earth from origin → present

Geologic Time Scale

• Eons of Earth’s History

  • Archaean + Proterozoic

    • Together = ~4 billion years

    • Early life forms develop

  • Phanerozoic

    • Last ~500 million years

    • Most visible life (plants, animals)

Origin of Prokaryotes

• Oldest fossils (~3.5 billion years): stromatolites

• Early life = prokaryotes only for ~1.5 billion years

• Oxygen Revolution

  • Photosynthetic prokaryotes released oxygen (O₂)

  • Timeline:

    • ~2.7 billion years ago → O₂ appears in atmosphere

    • ~2.2 billion years ago → rapid increase (oxygen revolution)

• Effects

  • Many anaerobic organisms → extinct

  • Some survived in oxygen-free environments

  • Others evolved cellular respiration → used O₂ for energy

Origin of Eukaryotes

• First eukaryotic fossils: ~2.1 billion years ago

• Formed by endosymbiosis:

  • Smaller prokaryotes lived inside larger cells

• Key Developments

  • Diversity of single-celled eukaryotes

  • Multicellular ancestors: ~1.5 billion years ago

  • First multicellular fossils: ~1.2 billion years ago (algae)

Cambrian Explosion

• Occurred ~535–525 million years ago

• Rapid increase in animal diversity

• Many major animal groups appear

Colonization of Land

• Early life on land:

  • Photosynthetic prokaryotes (>1 billion years ago)

• Major Land Colonization (~500 million years ago)

  • Plants + fungi moved onto land together (mutualism)

  • Animals followed:

    • Arthropods (insects, spiders)

    • Tetrapods (4-limbed vertebrates)

• Humans

  • Human lineage split: 6–7 million years ago

  • Modern humans: ~195,000 years ago

  • On a 1-hour Earth timeline → humans appear in the last 0.2 seconds

Dating Fossils (Radiometric Dating)

• Key Idea

  • Based on the decay of radioactive isotopes

• Important Terms

  • Half-life = time for 50% of the isotope to decay

• Example: Carbon-14

  • Half-life: 5,730 years

  • Used for fossils up to ~75,000 years old

• Other Isotopes

  • Potassium-40

    • Half-life: 1.3 billion years

    • Used for very old rocks

• Relative Dating

  • Fossil age estimated using:

    • Rock layers above and below

Fossil Record

• Fossil record = sequence of fossils in rock layers

• Shows evolutionary history over time

• Helps build the geologic record

Eras of the Phanerozoic Eon

• 1. Paleozoic Era (“ancient life”)

  • Life was mostly aquatic at first

  • By ~400 million years ago:

    • Plants & animals established on land

2. Mesozoic Era (“middle life”)

• Age of reptiles (dinosaurs)

• First:

  • Mammals

  • Flowering plants

• Ends with mass extinction

  • Dinosaurs die out (except birds)

3. Cenozoic Era (“recent life”)

• Begins ~65 million years ago

• Rapid evolution of:

  • Mammals

  • Birds

  • Insects

  • Flowering plants

• Includes modern life forms

Mass Extinctions

• Mark boundaries between eras

• Many species disappear → survivors diversify

• Smaller extinctions mark period boundaries

Big Picture Summary

• Life started simple → prokaryotes → eukaryotes → multicellular life

• Oxygen changed Earth dramatically

• Life moved from water → land

• Major events (like extinctions) reshaped evolution

• Humans are a very recent addition

Factors Shaping Macroevolution

• The fossil record shows major evolutionary changes, influenced by:

  • Plate tectonics

  • Mass extinctions

  • Adaptive radiations

Plate Tectonics & Continental Drift

• Structure of Earth

  • Crust = outer layer (tectonic plates)

  • Mantle = hot, flowing layer beneath

  • Core:

    • Outer = liquid

    • Inner = solid

• Plate Tectonics

  • Earth’s crust is broken into moving plates

  • Plates “float” on the mantle

• Types of Plate Movement

  • Move apart → new crust forms

  • Slide past → earthquakes

  • Collide → mountains + volcanoes

• Continental Drift

  • Continents slowly move over time

  • Example: North America & Europe → ~2 cm/year apart

Supercontinents

• Continents have merged 3 times into supercontinents

• Most recent: Pangaea (~250 million years ago)

• Effects of Pangaea

  • Lower sea levels → loss of shallow marine habitats

  • The interior became cold & dry

  • Many species went extinct

  • Survivors adapted → new opportunities

Breakup of Pangaea

• Split into:

  • Laurasia (north)

  • Gondwana (south)

• Continents became isolated

  • → organisms evolved separately

• Example Effects

  • Australia → isolated → marsupials dominate

  • India colliding with Asia → formed the Himalayas (still growing)

Biogeography Evidence

• Marsupials

  • Originated in Asia → spread → isolated in Australia

  • Evolved to fill many ecological roles

• Lungfish

  • Fossils found worldwide → existed before continents split

  • Now only in:

    • Africa

    • South America

    • Australia

Plate Movement Dangers

• Earthquakes

  • Caused by plates sticking → sudden release

  • Example:

    • 1906 San Francisco

    • 1989 Loma Prieta

    • 2010 Haiti

• Tsunamis

  • Caused by underwater earthquakes

  • Example: 2004 Indian Ocean tsunami

• Volcanoes

  • Release:

    • Lava

    • Ash

    • Gases

  • Can cause local & global damage

  • Example: Mt. Vesuvius (Pompeii)

Extinction

• Causes

  • Habitat destruction

  • Climate change

  • New predators/competition

  • Most species that have ever lived are now extinct

Mass Extinctions

• 5 major events in the last 500 million years

• Each wiped out ≥50% of species

Major Examples

• 1. Permian Extinction (~251 MYA)

  • ~96% of marine life died

  • Possible causes:

    • Massive volcanic eruptions

    • Global warming (~6°C increase)

    • Ocean oxygen loss

    • Toxic gases

2. Cretaceous Extinction (~65 MYA)

• Killed:

  • Dinosaurs (except birds)

  • Many marine species

• Evidence

  • Iridium layer (from asteroid)

  • Chicxulub crater (Mexico)

• Effects

  • A dust cloud blocked the sunlight

  • Climate collapse

  • Massive die-off

After Mass Extinctions

• Recovery

  • Takes 5–10 million years (or longer)

  • Example: Permian recovery → ~100 million years

• Key Idea

  • Extinctions are random

  • Can remove even successful species

Possible 6th Mass Extinction

• Caused by human activity:

  • Habitat destruction

  • Climate change

• Extinction rate:

  • 100–1000× normal

• Not yet as severe as past events—but rising

Adaptive Radiation

• Definition

  • Rapid evolution of many species from a common ancestor

• When It Happens

  • After:

    • Mass extinctions

    • New habitats

    • New adaptations

• Example

  • Mammals after dinosaur extinction:

    • Became larger

    • More diverse

    • Filled empty niches

Evo-Devo (Evolution + Development)

• Studies how genes control body form

• Small genetic changes → big physical differences

Changes in Timing (Heterochrony)

• Example: Axolotl

  • Adults keep juvenile traits (gills)

• Humans vs. Chimps

  • Humans:

    • Slower jaw growth

    • Larger brain

    • More “childlike” skull

Changes in Spatial Pattern

• Homeotic Genes

  • Control body structure (e.g., limbs)

• Example: Snakes

  • Lost limbs due to gene expression changes

Gene Changes

• Gene Duplication

  • Extra gene copies → new functions

  • Helped evolve:

    • Backbone

    • Jaws

    • Limbs

Gene Regulation

• Changes in when/where genes turn on

• Example: Stickleback Fish

  • Ocean fish → spines present

  • Lake fish → spines absent

  • Same gene, different expression

Evolution of Complex Structures

• Gradual Refinement

  • Complex traits evolve step-by-step

• Example: Eyes

  • Simple light-sensitive cells → complex eyes

  • Each stage had a function

Exaptations

• Definition

  • Trait evolves for one purpose → used for another

• Example: Feathers

  • Originally:

    • Insulation/display

  • Later:

    • Flight

• Other Example

  • Penguin wings → used for swimming

Evolutionary Trends (Horses)

• Early horses:

  • Small

  • Multiple toes

• Modern horses:

  • Large

  • One toe

  • Grazing teeth

• Important Idea

  • Evolution is branching, not linear

  • No “goal” in evolution

Species Selection

• Species that:

  • Survive longer

  • Produce more new species

  • → shape long-term trends

Big Picture Summary

• Earth’s movement reshapes habitats → drives evolution

• Mass extinctions reset life → open niches

• Adaptive radiation fills those niches

• Small genetic changes → major differences

• Evolution is:

  • Not goal-directed

  • Driven by environment + chance

Phylogeny & Classification

• Phylogeny

  • Phylogeny = evolutionary history of a species or group

  • Based on:

    • Fossil record

    • Morphology (structure)

    • Molecular data (DNA)

• Fossil Record Limits

  • Incomplete because:

    • Not all organisms fossilize

    • Fossils can be destroyed

    • Many haven’t been discovered

Homology vs. Analogy

• Homologous Structures

  • Similar due to common ancestry

  • May have different functions

  • Example:

    • Whale flipper vs. bat wing → same bone structure

• Analogous Structures

  • Similar due to convergent evolution

  • NOT from the common ancestor

  • Example:

    • Australian mole (marsupial) vs. North American mole (placental)

Convergent Evolution

• Unrelated species evolve similar traits

• Caused by:

  • Similar environments

  • Similar selective pressures

Systematics & Taxonomy

• Systematics

  • Study of:

    • Classification

    • Evolutionary relationships

• Taxonomy (developed by Carolus Linnaeus)

  • Naming & classifying organisms

Binomial Nomenclature

• Two-part scientific name:

  • Genus (capitalized)

  • Species (lowercase)

• Example:

  • Sciurus carolinensis

Classification Hierarchy

• From smallest → largest:

  • Species

  • Genus

  • Family

  • Order

  • Class

  • Phylum

  • Kingdom

  • Domain

• Key Term

  • Taxon = any classification group

Phylogenetic Trees

• Show evolutionary relationships

• Branching diagrams

• Each branch point (node) = common ancestor

• Important

  • Show pattern of descent, NOT exact time (usually)

Cladistics

• Clades

  • Group = ancestor + ALL descendants

  • Called monophyletic

• Key Idea

  • Group organisms by common ancestry

Shared Characters

• Shared Ancestral Character

  • Trait from a distant ancestor

  • Example: backbone in mammals

• Shared Derived Character

  • New trait unique to a group

  • Example: hair in mammals

• Used to define clades

Ingroup vs. Outgroup

• Ingroup = group being studied

• Outgroup = related group used for comparison

• Helps identify derived traits

Parsimony

• Choose the simplest explanation

• The tree with the fewest evolutionary changes is preferred

Trees Are Hypotheses

• Based on current evidence

• Can change with new data

• Example Insight

  • Birds are actually part of the reptile clade

Molecular Systematics

• Uses DNA/protein comparisons to determine relationships

• Key Idea

  • More similar DNA → more closely related

Genome Evidence

• Many genes are shared across species

• Examples:

  • Humans & mice → ~99% homologous genes

  • Humans & yeast → ~50%

• Strong evidence for common ancestry

Molecular Clocks

• Definition

  • Use DNA mutation rates to estimate divergence time

• How It Works

  • More differences in DNA → more time since split

• Limitations

  • Mutation rates can vary

Example: HIV

• The molecular clock is used to trace the origin

• HIV-1 likely spread to humans in the 1930s

Gene Evolution

• Gene Duplication

  • Creates extra gene copies

  • Allows new functions to evolve

Domains of Life

• 3-Domain System

  • Bacteria

  • Archaea

  • Eukarya

• Key Insight

  • Archaea are closer to eukaryotes than bacteria

Horizontal Gene Transfer

• Genes move between species (not just parent → offspring)

• Methods:

  • Viruses

  • Plasmids

• Impact

  • Early evolution may look like a network, not a tree

Tree vs. Ring of Life

• Traditional view: tree

• New idea: ring/network

  • Due to gene mixing early in evolution

Big Picture Summary

• Phylogeny = evolutionary history

• Classification reflects evolutionary relationships

• Homology = shared ancestry; analogy = similar function

• Cladistics groups organisms into clades

• DNA evidence strengthens evolutionary trees

• The evolution of life may be more complex than a simple tree