module 1

Ch 22: Evolutionary mechanisms

Evolution

• Descent with modification 

• Viewed as pattern and process 

Pattern: revealed by data from biology, geology, physics, and chemistry (observations about natural world)

Process: mechanisms that produce the observed pattern of change 

Classification of Species

Scala naturae: ladder or scale that life-forms can be arranged on 

Carolus Linnaeus: developed two-part format for naming species and nested classification system (grouping similar species into increasingly general categories)

• Described resemblances among species to pattern in their creation (Darwin argues this later) 

Change over Time

• Darwin drew from fossils (remains of organisms from the past)

Strata: new layers of sediment covers old ones and compresses into superimposed layers of rock 

• Observations made from stratum by Georges Cuvier:

  • The older the stratum, the more dissimilar its fossils to current life-forms 

  • New species appeared when others disappeared (gave idea of evolution)

Lamarck’s Hypothesis of Evolution

• Compared living species with fossil forms, and had two principles from his findings 

Use and disuse: parts of the body used extensively become larger and stronger, while those not used deteriorate 

• Inheritance of acquired characteristics: an organism could pass these modifications to its offspring 

• Darwin rejected this idea

Darwin’s Research 

• Observed plants and animals, describing features that made them well suited to their environments 

Darwin’s Focus on Adaptation

Adaptations: inherited characteristics of organisms that enhance their survival and reproduction in specific environments 

• Based on natural selection

Natural selection: process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits 

Descent with Modification

• Darwin attributed unity of life to the descent of all organisms from an ancestor that lived in the remote past

• Descent with modification led to the rich diversity of life today

• Viewed history of life as a tree (each fork of tree represents most recent common ancestor of the lines of evolution)

  • Can explain large morphological gaps existing between related groups of organisms 

Artificial Selection, Natural Selection, and Adaptation

• Natural selection explains the patterns of evolution and is capable of substantial modifications of species over many hundreds of generations 

Artificial selection: humans have modified other species over generations by selecting and breeding individuals that possess desired traits 

• Brings about dramatic change in a relatively short period of time 

Darwin argues that a similar process occurs in nature off of two observations:

• Members of a population often vary in their inherited traits 

  • Inference: individuals whose inherited traits give them a higher probability of surviving and reproducing in an environment tend to leave more offspring than other individuals  

• All species can produce more offspring than their environment can support 

  • Unequal ability of individuals to survive and reproduce will lead to the accumulation of favourable traits in the population over generations

• Connection between natural selection and the capacity of organisms to overreproduce 

• Organisms heritable traits can influence its performance and how well its offspring cope with environmental changes 

• Natural selection from predators, lack of food, or adverse physical conditions can lead to an increase in proportion of favourable traits in a population

Homology

Homology: similarity resulting from common ancestry 

Homologous structures: represent variations on a structural theme that was present in common ancestor

• Comparing early stages of development in different animal species reveals additional anatomical homologies not visible in adult organisms 

Vestigial structure: feature of an organism that is a historical remnant of a structure that served a function in the organism’s ancestors 

• All forms of life use same genetic code, but molecular homologies go beyond 

• Some homologous genes acquire new function, while some retain their original functions 

• Common for organisms to have genes that have lost their function, even though homologous genes in related species may be fully functional 

Homologies and “Tree Thinking”

Tetrapods: vertebrate group that consists of amphibians, mammals, and reptiles 

Evolutionary trees: hypotheses that summarize our current understanding of patterns of descent 

Convergent Evolution

• Independent evolution of similar features in different lineages 

  • Although they can evolve independently from different ancestors, two mammals adapt to similar environments in similar ways 

Analogous: share similar function, but not common ancestry

The Fossil Record

• Fossil record documents the pattern of evolution

• Indicates that prior to 50-60 million years ago, most mammals were terrestrial 

• Over time, descent with modification produced increasingly large differences among related groups of organisms (resulting in the diversity of life)

Biogeography

• Scientific study of geographic distributions of species 

Plate tectonics: slow movement of Earth’s continents over time 

• Describes why closely related species sometimes live on different continents 

Endemic: found nowhere else in the world 

Ch 23: Evolution of populations

The Smallest Unit of Evolution

Microevolution: evolution on its smallest scale  (change in allele frequencies in a population over generations)

• 3 factors cause allele frequency change: natural selection, genetic drift, gene flow

Genetic variation

• Individuals within all species vary in their phenotypic traits

• Some heritable phenotypic differences occur as either-or (typically determined by a single gene locus, with different alleles producing distinct phenotypes)

• Genetic variation at the whole-gene level is the average percentage of loci that are heterozygous

• Nucleotide variability: genetic variation measured at molecular level of DNA

Formation of New Alleles

• New alleles arise by mutation

• A change in one base in a gene (point mutation) can have significant impact on phenotype 

• Organisms reflect many generations of past selection

• Most new mutations that alter a phenotype are slightly harmful 

• Sometimes, natural selection quickly removes harmful alleles

• In diploid organisms, harmful alleles that are recessive can be hidden from selection 

• Many mutations are not harmful 

• Point mutations in noncoding regions generally result in neutral variation (differences in DNA sequence that do not confer selective advantage or disadvantage)- in introns

• In multicellular organisms, only mutations in cell lines that produce gametes can be passed to offspring 

Altering Gene Number or Position

• Chromosomal changes that delete, disrupt, or rearrange loci are usually harmful, but can be beneficial 

• Source of variation is duplication of genes due to errors in meiosis, slippage during DNA replication, or activities of transposable elements 

Rapid reproduction

• Mutation rates are low in plants and animals 

Sexual reproduction

• Most genetic variation in population results from unique combination of alleles that each individual receives from its parents 

• Shuffles existing alleles and deals them at random to produce individual genotypes 

• 3 mechanisms contribute to shuffling: crossing over, independent assortment of chromosomes, and fertilization

Gene pools and allele frequencies

• Different populations of species can be isolated geographically from one another 

Gene pool: consists of all copies of every type of allele at every locus in all members of the population 

• If only one allele exists for a particular locus, then it is fixed in the gene pool 

Hardy-Weinberg Equilibrium

• Population that is not evolving, allele and genotype frequencies will remain constant from generation to generation 

• RANDOM mating

Applying the Hardy-Weinberg Equation

p^2+2pq+q^2=1 (P^2= dominant homozygous frequency, 2pq= heterozygous frequency, q^2= recessive homozygous frequency)

• Used as test of whether evolution is occurring at specific locus in a population 

• Must assume no new mutations are being introduced into the population and that mates are randomly chosen and ignore effects of survival and reproductive success and assume no effects of genetic drift or gene flow from other populations 

Natural Selection

• Individuals in a population exhibit variations in their heritable traits, and those with traits that are better suited to their environment tend to produce more offspring than those with traits that are not as well suited 

• Selection results in alleles being passed down to next generation in proportions that differ from those in present generation

Adaptive evolution: process in which traits that enhance survival or reproduction tend to increase in frequency over time 

Genetic Drift

• Chance events that cause allele frequencies to fluctuate unpredictably from one generation to the next

• Allele frequencies also affected by chance events during fertilization

Effects: significant in small populations, can cause allele frequencies to change at random, can lead to a loss of genetic variation within populations, can cause harmful alleles to become fixed 

The Founder Effect: few individuals become isolated from a larger population, and smaller group may establish a new population whose gene pool differs from the source population

The Bottleneck Effect: genetic drift that occurs when the size of a population is reduced by natural disaster or human actions

Gene Flow

• Transfer of alleles into or out of a population due to the movement of fertile individuals or their gametes 

• Can affect how well populations are adapted to local environmental conditions

• Can transfer alleles that improve the ability of populations to adapt to local conditions 

Relative Fitness

• In a given environment, certain traits can lead to greater relative fitness (contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals)

• Selection acts more directly on the phenotype than on the genotype (acts on genotype indirectly)

Directional, Disruptive, and Stabilizing Selection 

• Natural selection can alter the frequency distribution of heritable traits in three ways 

• Despite mode of selection, individuals whose heritable phenotypic traits provide higher reproductive success are favoured over traits of other individuals

Directional selection: occurs when conditions favour individuals exhibiting one extreme of a phenotypic range (shifts populations frequency curve for the phenotypic character in one direction or the other)

• Common when populations environment changes or members migrate to other habitat 

Disruptive selection: occurs when conditions favors individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes 

Stabilizing selection: acts against both extreme phenotypes and favours intermediate variants 

• Reduces variation and maintains status quo for particular phenotypic character 

Adaptive Evolution

• Adaptations to environments can arise gradually over time as natural selection increases 

• As the proportion of individuals that have favourable traits increases, the match between a species and its environment improves (adaptive evolution occurs) 

• Physical and biological components of an organism's environment can also change over time 

  • Therefore, a “good match” between an organism and its environment can be moving and changing 

• Environmental conditions can also differ, meaning different alleles will be favoured in different locations (natural selection can cause the populations of a species to differ genetically from one another)

• Genetic drift and gene flow can increase frequencies of alleles, but not consistently 

  • Genetic drift causes frequency of slightly beneficial allele to increase, but can also cause it to decrease 

  • Gene flow can introduce alleles advantageous or disadvantage to environment 

• Natural selection is the ONLY evolutionary mechanism that consistently leads to adaptive evolution

Sexual Selection

• Form of selection where individuals with certain inherited characteristics are more likely than other individuals to obtain mates 

• Can result in sexual dimorphism (difference in secondary sexual characteristics between males and females of the same species- can include size, colour, ornamentation, and behaviour)

Intrasexual selection: selection within same sex (individuals of one sex compete directly for mates of the opposite sex)

Intersexual selection: individuals of one sec are choosy in selecting their mates of the other sex (in many cases, females choice depends on showiness of male)

• Female preferences for certain male characteristics are correlated with good genes

Balancing Selection

• Includes frequency-dependent selection and heterozygote advantage 

Frequency-Dependent Selection: fitness of phenotype depends on how common it is in the population

Heterozygote Advantage: individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes

• Defined in terms of genotype 

• Relationship between genotype and phenotype decides whether heterozygote advantage represents stabilizing or directional selection

Why Natural Selection Cannot Fashion Perfect Organisms

• Selection can act only on existing variations

• Evolution is limited by historical constraints 

• Adaptations are often compromises

• Chance, natural selection, and the environment interact 

Ch 24: Origin of species

The Biological Species Concept

Species: A species is a group of populations whose members:

• Have the potential to interbreed in nature.

• Produce viable, fertile offspring.

• Do NOT produce viable, fertile offspring with members of other such groups.

Key Characteristics: Members are reproductively compatible, at least potentially.
Example:

• A businesswoman from Montreal and a dairy farmer from Mongolia could produce viable, fertile offspring if they met and mated.

• In contrast, humans and chimpanzees remain distinct biological species despite potential territorial overlap due to barriers preventing interbreeding.

Focus: Based on the potential to interbreed rather than physical similarity.
Gene Flow: Transfer of alleles between populations.

• Occurs between different populations of a species.

• Holds the gene pool together, causing genetic similarity within the species.

• A reduction or lack of gene flow can play a key role in the formation of new species.

Reproductive Isolation

• Definition: Reproductive isolation refers to the existence of biological barriers that impede members of two species from interbreeding and prevent the production of viable, fertile offspring

Role in Speciation:

• Essential for the formation of new species

• Blocks gene flow between species

• Limits the formation of hybrids (offspring from interspecific mating)

Effectiveness of Barriers:

• A single barrier may not prevent all gene flow

• A combination of barriers can effectively isolate a species’ gene pool

Types of Reproductive Barriers:

• Obvious Barriers: Example - A fly cannot mate with a frog or a fern

• Less Obvious Barriers: Occur between closely related species

Classification of Reproductive Barriers

Prezygotic Barriers (“Before the Zygote”):

• Function: Prevent fertilization from occurring

Mechanisms:

• Impede mating attempts between different species

• Prevent successful completion of mating if it occurs

• Hinder fertilization even if mating is completed

Postzygotic Barriers (“After the Zygote”):

• Function: Act after the formation of a hybrid zygote to maintain reproductive isolation

Mechanisms:

• Developmental errors reduce the survival of hybrid embryos

• Post-birth issues can result in:

• Infertile hybrids

• Reduced chances of hybrids surviving to reproductive age

Limitations of the Biological Species Concept

Strength of the Concept: Highlights the role of reproductive isolation in speciation

Limitations:

• Fossils: Cannot evaluate reproductive isolation in fossil species

• Asexual Organisms: Not applicable to organisms that reproduce asexually, such as prokaryotes

• Prokaryotes transfer genes among themselves, but this is not part of their reproductive process

Gene Flow Exceptions:

• Species are defined by the absence of gene flow, but some distinct species still exchange genes

• Example: Grizzly bear (Ursus arctos) and Polar bear (Ursus maritimus) produce hybrid offspring called “grolar” or “nanulak” bears

  • Nanulak: Combination of Inuit names for polar bear (nanook) and grizzly bear (aklak)

Natural Selection and Gene Flow:

• Natural selection can maintain species differences even when gene flow occurs

• Need for Alternative Concepts:

• Due to these limitations, alternative species concepts are useful in certain situations

Other Definitions of Species

Contrast with Biological Species Concept: While the biological species concept emphasizes species separateness due to reproductive barriers, other concepts focus on the unity within a species

Morphological Species Concept: Characterizes a species by body shape and other structural features

• Suggests that each species is morphologically distinct

Applicability:

• Can be applied to both asexual and sexual organisms

• Useful even without information on gene flow

Common Usage: Most species are distinguished using this concept in practice

• Disadvantages:

  • Subjective criteria: Researchers may disagree on which structural features define a species

Ecological Species Concept: Defines a species based on its ecological niche—the sum of how species interact with living and nonliving components of their environment

• Example:

• Two species of oak trees may differ in size or drought tolerance but still occasionally interbreed

• Considered separate species because they occupy different ecological niches, despite some gene flow

Applicability:

• Suitable for both asexual and sexual species

Emphasizes: The role of disruptive natural selection as species adapt to different environmental conditions

Diversity of Species Concepts:

• More than 20 species definitions have been proposed

• The usefulness of each concept depends on the situation and research questions

Relevance of the Biological Species Concept:

• Particularly helpful for studying how species originate

• Focuses on the role of reproductive barriers in speciation

Allopatric (“Other Country”) Speciation

Definition: In allopatric speciation, gene flow is interrupted when a population is divided into geographically isolated subpopulations

• Derived from Greek: allos (other) and patra (homeland)

Causes of Geographic Isolation:

• Environmental Changes

• Lake subsidence: Water level drops, creating smaller lakes with separated populations

• River course change: Divides populations of animals that cannot cross

• Colonization: Individuals colonize remote areas, becoming geographically isolated from the parent population

  • Example: Flightless cormorant of the Galápagos Islands likely evolved from an ancestral flying species

The Process of Allopatric Speciation

Impact of Geographic Barriers:

• The effectiveness of a barrier depends on the organism’s mobility:

  • Highly mobile species: Birds, mountain lions, coyotes, windblown pollen, and plant seeds can cross barriers like rivers and canyons

  • Less mobile species: Small rodents may find wide rivers or deep canyons formidable barriers

Genetic Divergence After Isolation:

• Once geographic separation occurs, gene pools diverge due to:

  • Mutations arising independently

  • Natural selection acting differently in distinct environments

  • Genetic drift altering allele frequencies randomly

• Reproductive isolation may evolve as a by-product of genetic divergence

Sympatric (“Same Country”) Speciation

Definition: Speciation occurs in populations that live in the same geographic area

• Derived from Greek: syn (together)

• Key Factors Reducing Gene Flow:

• Polyploidy

• Sexual Selection

• Habitat Differentiation

Polyploidy

Definition: Condition where an organism has extra sets of chromosomes

• Common in: Plants (over 80% of plant species are from polyploid speciation), rare in animals

• Example: Grey tree frog (Hyla versicolor) likely originated via polyploidy

Types of Polyploidy:

1. Autopolyploid: More than two chromosome sets derived from a single species

• Caused by failure of cell division, doubling chromosome number (e.g., from diploid 2n to tetraploid 4n)

• Reproductive Isolation: Tetraploids are fertile with each other but isolated from diploids due to reduced fertility in triploid (3n) offspring

2. Allopolyploid: Results from the hybridization of two species

• Initially sterile hybrids may become fertile through asexual reproduction or chromosomal changes

• New species: Fertile with each other but cannot interbreed with parent species

Habitat Differentiation

Definition: Genetic factors enable a subpopulation to exploit a new habitat or resource, reducing gene flow with the parent population

• Example: Apple Maggot Fly (Rhagoletis pomonella)

• Originally fed on hawthorn; shifted to apple trees about 200 years ago

• Temporal isolation: Apple-feeding flies develop faster due to the quicker ripening of apples

• Genetic divergence: Alleles beneficial for one host plant are harmful for the other, creating prezygotic and postzygotic barriers

Patterns Within Hybrid Zones

Definition: Regions where members of different species meet and mate, producing hybrid offspring

• Hybrid Zones and Environmental Change

Environmental Shifts: Can cause hybrid zones to move or new zones to form

• Example: Northern flying squirrel (Glaucomys sabrinus) and Southern flying squirrel (G. volans)

Climate change (warmer winters) allowed the southern species to expand northward, creating a new hybrid zone

Genetic Variation: Hybrid zones can introduce novel genetic variations that improve adaptability

• Hybridization allows alleles to transfer between species, enhancing survival in changing environments

Hybrid Zones Over Time

Possible Outcomes:

Reinforcement: Strengthening of reproductive barriers

• Hybrids are less fit, so natural selection favors prezygotic barriers

• In sympatric populations, males look different, and females rarely mate with the wrong species

• In allopatric populations, males look similar, leading to more mating mistakes

Fusion: Weakening of reproductive barriers

• Gene flow increases, reducing species differences and potentially merging species

• Stability: Continued formation of hybrid individuals

• Hybrids are consistently produced, even if selected against

The Time Course of Speciation

Sources of Information:

• Fossil record: Reveals patterns of species appearance and extinction

• Morphological and molecular data: Help estimate the time between speciation events

Patterns in the Fossil Record

Punctuated Equilibria: Periods of stasis (little change) interrupted by sudden change

• Species appear suddenly, persist unchanged, then go extinct

Gradual Speciation: Some species change slowly over time without clear breaks

• Fossils can’t always capture rapid changes due to slow sediment accumulation

• Implications:

  • Punctuated patterns: Suggest speciation can occur rapidly (e.g., within 50,000 years)

  • Gradual patterns: Indicate speciation can take millions of years

Speciation Rates

Key Factors:

• No “speciation clock”—timing depends on:

  • Environmental changes

  • Interruptions to gene flow

  • Genetic divergence before gene flow resumes

From Speciation to Macroevolution

Speciation’s Role in Evolution: Small differences (e.g., cichlid color) can accumulate, leading to major evolutionary changes

• Example: The evolution of whales from land-dwelling mammals

Speciation and Extinction:

• As new species emerge, others go extinct, shaping biodiversity over time

• Documented in the fossil record

Ch 25: The History of Life

• Synthesis of Organic Compounds on Early Earth

Formation of Earth: Formed 4.6 billion years ago from a cloud of dust and rocks

• Early Earth experienced intense bombardment by space debris, vaporizing water and preventing the formation of seas and lakes

• Bombardment ended around 4 billion years ago, allowing conditions for life to emerge

Early Atmosphere: Little oxygen, thick with water vapor and volcanic gases:

• Nitrogen, nitrogen oxides, carbon dioxide, methane, ammonia, hydrogen

As Earth cooled:

• Water vapor condensed into oceans

• Hydrogen escaped into space

• Oparin-Haldane Hypothesis (1920s):

• Proposed that Earth’s early atmosphere was a reducing environment (electron-adding)

• Organic compounds could form from simple molecules with energy from lightning and UV radiation

• Early oceans = “primordial soup” rich in organic molecules

Miller-Urey Experiment (1953):

• Simulated early Earth conditions in the lab

• Produced amino acids and other organic compounds

• Later experiments with neutral atmospheres (rich in nitrogen and CO₂) also produced organic molecules

Alternative Hypotheses:

Volcanic Activity:

• Organic compounds may have formed near volcanoes with reducing environments

• 2008 analysis of Miller’s samples showed numerous amino acids formed under volcanic conditions

Deep-Sea Hydrothermal Vents:

• Black smokers: Release superheated water (300–400°C), unstable for organic compounds

• Alkaline vents: Warm (40–90°C), high pH (9–11), potentially suitable for the origin of life

Meteorites:

• Murchison meteorite (4.5 billion years old) contains:

• Over 80 amino acids (equal mix of D and L isomers)

• Lipids, simple sugars, nitrogenous bases (e.g., uracil)

Abiotic Synthesis of Macromolecules

Formation of Macromolecules: Small organic molecules like amino acids and nitrogenous bases are not enough for life

• Life requires macromolecules (proteins, nucleic acids)

Key Findings:

• RNA monomers can form spontaneously from simple precursors

• Polymers of amino acids and RNA nucleotides form when dripped onto hot sand, clay, or rock

• These polymers form without enzymes or ribosomes

• May have acted as weak catalysts for early chemical reactions

Protocells

Definition: Simple, cell-like structures capable of reproduction and metabolism

Formation: Vesicles form spontaneously when lipids are added to water, creating a bilayer like a plasma membrane, Montmorillonite clay speeds up vesicle formation by concentrating organic molecules

Key Properties:

• Self-replication: Vesicles can “reproduce” and grow without content dilution

• Selective permeability: Some vesicles can perform metabolic reactions using external materials

• Vesicles can absorb RNA and other molecules, supporting early biochemical reactions

Self-Replicating RNA

• RNA as the First Genetic Material:

• Likely preceded DNA due to its ability to store information and act as a catalyst (ribozyme activity)

Ribozymes: RNA molecules that catalyze reactions, including self-replication

Molecular Natural Selection:RNA molecules with advantageous shapes replicate faster and more accurately

• Errors during replication can lead to new, more efficient ribozymes

• Suggests an early “RNA world” where RNA molecules both stored genetic info and catalyzed reactions

Modern Experiments:

• In 2013, scientists created vesicles where RNA replication could occur—a key step toward synthetic life

• The Fossil Record

Formation of Fossils: Fossils mainly found in sedimentary rocks formed from layers of sediment called strata

Other fossil types: Amber (fossilized tree sap) and organisms frozen in ice

What the Fossil Record Shows:

• Documents major changes in life forms over time

• Reveals extinct species and how new groups of organisms arose

• Fossil record is incomplete: Many organisms weren’t preserved and some fossils destroyed by geological processes

• Biased toward species that were: Abundant, widespread, and had hard parts (bones, shells)

Notable Discoveries:

• Whale ancestors with hind limbs

• Tiktaalik (discovered in 2006), a transitional fossil linking fish and early land vertebrates

• How Rocks and Fossils Are Dated

Relative Dating: Determining the sequence of fossil layers, like peeling wallpaper to see which layer came first

• Does NOT provide exact ages

Radiometric Dating (Absolute Dating): Based on the decay of radioactive isotopes

• Parent isotope decays to a daughter isotope at a constant rate

• Measured by half-life (time for 50% of the parent isotope to decay)

Key Isotopes:

• Carbon-14: Half-life = 5,730 years, used for fossils up to 75,000 years old

• Uranium-238: Half-life = 4.5 billion years, used for dating ancient rocks

Dating Older Fossils:

• Fossils sandwiched between volcanic rock layers are dated using isotopes trapped in the volcanic layers

The Origin of New Groups of Organisms

Example: The Origin of Mammals

• Mammals are tetrapods (four-limbed vertebrates)

• Unique features that fossilize well:

• Single-bone lower jaw (dentary)

• Three middle ear bones (hammer, anvil, stirrup)

• Differentiated teeth: Incisors, canines, premolars, molars

Fossil Evidence:

• Shows gradual evolution of mammalian traits from earlier tetrapods like cynodonts

• Fossils reveal both direct ancestors and extinct side branches

The First Single-Celled Organisms

Earliest Evidence of Life: 

• Graphite in rocks from 3.95 billion years ago (suggesting biological activity)

• Stromatolites (layered rocks formed by prokaryotes) date back 3.5 billion years

Prokaryotic Dominance: Prokaryotes were the only life forms for over 1.5 billion years

• Transformed Earth’s environment, paving the way for more complex life

Photosynthesis and the Oxygen Revolution

Oxygenic Photosynthesis: First evolved in photosynthetic prokaryotes (like cyanobacteria)

• Released oxygen (O₂) into oceans and atmosphere

Banded Iron Formations: Iron in oceans reacted with O₂ to form iron oxide, creating red sedimentary layers

The Oxygen Revolution (~2.7 billion years ago): O₂ levels rose rapidly, reaching 1-10% of current levels by 2.4 billion years ago

Impact:

• Mass extinction of many anaerobic prokaryotes

• Evolution of cellular respiration in surviving organisms

The First Eukaryotes

Oldest Eukaryotic Fossils: Date back 1.8 billion years

Key Features: Nucleus, mitochondria, endomembrane system, cytoskeleton

Endosymbiosis Theory: Eukaryotes evolved from a host cell engulfing prokaryotic cells that became mitochondria and plastids

Evidence for Endosymbiosis:

• Mitochondria and plastids have:

  • Circular DNA (like bacteria)

  • Bacterial-like ribosomes

  • Double membranes

  • Reproduce by binary fission

The Origin of Multicellularity

Early Multicellular Life: Red algae fossils from 1.2 billion years ago

Ediacaran biota (~600 million years ago): Soft-bodied, large multicellular organisms

Significance:

• Marked the shift from a microbial world to complex life forms

• Set the stage for the Cambrian Explosion

The Cambrian Explosion (~535–525 million years ago)

Rapid Evolution of Animal Life: 

• Sudden appearance of many animal phyla in the fossil record

• Evolution of predators with claws and prey with defensive structures (spines, shells)

Pre-Cambrian Life:

• Mostly soft-bodied organisms with little evidence of predation

• Molecular Evidence: Suggests that animal phyla originated before the Cambrian explosion

The Colonization of Land

First Land Life:

• Cyanobacteria and photosynthetic prokaryotes colonized land over 1 billion years ago

• Plants, fungi, and animals began colonizing land around 500 million years ago

Adaptations for Land:

• Vascular systems in plants

• Waxy coatings to prevent water loss

• Mutualistic relationships between plants and fungi

Animals on Land:

• Arthropods (insects, spiders) were among the first to colonize land (~450 million years ago)

• Tetrapods (four-limbed vertebrates) evolved from lobe-finned fishes (~365 million years ago)

Human Evolution:

• Human lineage diverged from other primates ~6–7 million years ago

• Homo sapiens appeared ~195,000 years ago

Plate Tectonics

Definition: The theory that Earth’s crust is divided into large plates that float on the hot, semi-fluid layer of the mantle

Continental Drift: Movement of continents over time due to shifting tectonic plates

• Supercontinents formed and broke apart at least three times:

• 1 billion, 600 million, and 250 million years ago

• A new supercontinent may form in ~250 million years

Mechanism of Movement: Driven by mantle convection, causing plates to move a few centimeters per year

• Magnetic signals in rocks help track past continental positions

Earth’s Major Plates: North American, Eurasian, Pacific, African, Indo-Australian, South American, Antarctic

Plate Boundaries and Geologic Activity

Divergent Boundaries:

• Plates move away from each other

  • Example: North American and Eurasian plates drifting apart (~2 cm/year)

• Forms mid-ocean ridges and new crust

Transform Boundaries:

• Plates slide past each other

• Causes earthquakes

  • Example: San Andreas Fault in California

Convergent Boundaries:

• Plates collide, leading to:

Subduction: Denser oceanic plate sinks below a continental plate

Mountain formation: When two continental plates collide

• Example: Himalayas formed ~45 million years ago from the collision of the Indian and Eurasian plates

Consequences of Continental Drift

Habitat Changes:

• Alters environments where organisms live

  • Example: Formation of Pangaea (~250 million years ago):

• Deeper ocean basins, lowering sea levels

• Loss of shallow marine habitats

• Interior climate: Cold, dry, harsh conditions

Climate Change:Continents shifting causes climate shifts

• Example: Labrador, Canada moved from the tropics to its current location over 200 million years

• Organisms must adapt, migrate, or face extinction

• Promotes Allopatric Speciation: Geographic isolation occurs as continents drift apart, and each continent becomes an independent evolutionary arena, leading to divergent evolution

Fossil Distribution: Fossils of the same species found on continents now separated by oceans

• Example: Permian freshwater reptile fossils found in both Brazil and Ghana—regions once connected

Modern Biogeography:

• Explains differences in flora and fauna across continents

  • Example: Marsupials dominant in Australia, filling ecological roles similar to placental mammals elsewhere

Mass Extinctions

Definition: A mass extinction occurs when large numbers of species become extinct worldwide due to disruptive global environmental changes

Causes of Extinction:

• Habitat destruction

• Climate change (e.g., ocean temperature shifts)

• Biological factors (e.g., emergence of new species that outcompete others)

• Global environmental disruptions increase extinction rates dramatically

The “Big Five” Mass Extinction Events

• Five major mass extinctions occurred over the past 500 million years

• In each event, 50% or more of marine species became extinct

• Well-documented due to the fossil record of hard-bodied, shallow-sea organisms

1. Permian Mass Extinction (252 million years ago)

• Marks the boundary between the Paleozoic and Mesozoic eras

• Impact:

  • ~96% of marine species went extinct

  • 8 out of 27 insect orders wiped out

  • Occurred over less than 200,000 years

• Causes:

  • Massive volcanic activity in Siberia:

  • Lava flows covered an area half the size of western Europe

• Release of CO₂ led to:

  • Global warming (~6°C increase)

  • Ocean acidification, reducing calcium carbonate for reef-building organisms

  • Ash clouds from coal combustion spread globally, detected in rocks in the Canadian Arctic

  • Nutrient release (e.g., phosphorus) stimulated microbial growth

  • Microbial die-off led to:

  • Oxygen depletion in oceans

  • Growth of anaerobic bacteria, releasing toxic hydrogen sulfide (H₂S) gas

• Overall Effect:

  • A cascade of catastrophic events triggered by volcanic eruptions caused widespread extinctions

2. Cretaceous Mass Extinction (66 million years ago)

• Eliminated:

  • Over 50% of marine species

  • Many families of terrestrial plants and animals

  • All non-avian dinosaurs (birds survived)

• Clues to the Cause:

  • A thin clay layer rich in iridium separates Mesozoic and Cenozoic era sediments

  • Iridium is rare on Earth but common in meteorites, suggesting an asteroid or comet impact

• Evidence:

  • Chicxulub crater (66 million years old) off the Yucatán Peninsula, Mexico

• Impact likely caused:

  • A global debris cloud, blocking sunlight and disrupting climate

  • Volcanic activity worldwide, releasing ash and more CO₂, worsening climate effects

• Overall Effect:

  • The combination of the asteroid impact and volcanic activity led to global environmental collapse and mass extinction

Is a Sixth Mass Extinction Under Way?

Current Extinction Crisis: Human activities (e.g., habitat destruction, climate change) are driving many species to extinction

• Over 1,000 species have gone extinct in the last 400 years

• Extinction rate is 100–1,000 times higher than the background rate in the fossil record

Challenges in Assessment:

• Difficult to track all extinctions, especially in biodiverse regions like tropical rainforests

• Many species may go extinct before discovery

• Comparison to the “Big Five”:

• Current losses haven’t reached the levels of past mass extinctions

• However, projections suggest potential losses of up to 54% of species in the next 100 years

Link to Climate Change:

• Species declines linked to rising temperatures (e.g., polar bears, pine trees)

• Fossil record shows higher extinction rates during warm periods in Earth’s history

Future Outlook:

• Without drastic action, a sixth mass extinction is likely within the next few centuries or millennia

Consequences of Mass Extinctions

Biodiversity Loss:

• Reduces complex ecosystems to simplified forms

• Extinct lineages can never reappear, permanently altering evolution

Recovery Time:

• Takes 5–10 million years for biodiversity to recover

• Permian extinction recovery took ~100 million years

Ecological Shifts:

• Alters community structures, often increasing the proportion of predators

Loss of Advantageous Traits: Innovative lineages can be wiped out before they fully diversify

Opportunities for Adaptive Radiations: Extinctions create ecological vacancies, allowing new species to evolve and diversify

Adaptive Radiations

Definition: Periods of rapid evolutionary change where species diversify to fill new or vacant ecological niches

Triggers:

• Post-Mass Extinctions: Survivors exploit vacant niches

• Evolutionary Innovations: New traits (e.g., seeds, armored bodies) open new ecological opportunities

• Colonization of New Regions: Species face little competition (e.g., Hawaiian Islands)

Worldwide Adaptive Radiations

Mammals:

• Dramatic radiation after the Cretaceous extinction (66 million years ago)

• Mammals evolved from small, nocturnal forms into diverse species occupying former dinosaur niches

Major Radiations in History:

• Photosynthetic prokaryotes (oxygen production)

• Cambrian explosion (rise of predators)

Land colonization: Plants, insects, and tetrapods diversified after adapting to terrestrial life

Regional Adaptive Radiations

Hawaiian Archipelago: Isolated volcanic islands with unique species found nowhere else

Geographic isolation + diverse environments = rapid speciation

• Multiple colonization events followed by adaptive radiation

Effects of Developmental Genes on Evolution

Evo-Devo: Explores how small genetic changes can cause major morphological differences

Changes in Rate and Timing (Heterochrony)

Definition: Evolutionary change in the rate or timing of developmental events

• Example: Human vs. Chimpanzee skulls differ due to changes in growth rates

Paedomorphosis: Retention of juvenile traits in adult form

• Example: Axolotl salamanders retain larval features in adulthood due to genetic changes

Changes in Spatial Pattern

Homeotic Genes: Control the placement and organization of body parts

• Example: Hox genes determine where limbs develop in animals

• Changes in Hox gene expression can lead to new body structures (e.g., crustacean appendages)

Plant Development:

• MADS-box genes control flower formation, leading to diverse floral structures

Origins of Developmental Genes

Ediacaran Fossils (560 million years old): Suggest that genes for complex animals existed 25 million years before the Cambrian explosion

Adaptive Evolution: Driven by natural selection acting on:

• Protein-coding genes

• Gene duplications (creating new genes with novel functions)

• Regulatory changes in gene expression

Changes in Gene Sequence

Gene Duplication: Creates new developmental genes that lead to novel morphological traits

Changes in Gene Regulation

Gene Regulation vs. Gene Sequence:

• Gene regulation affects when, where, and how much a gene is expressed

• Regulatory changes often have fewer harmful side effects than changes in gene sequences

Evolutionary Novelties

Descent with Modification: Complex structures evolve from simpler ancestral forms

• Example: The Eye

  • Evolved in incremental steps:

  • Light-sensitive cells (basic vision in limpets)

  • Complex eyes (evolved independently in mollusks and vertebrates)

  • Evidence of convergent evolution with structural differences (e.g., nerve arrangement in vertebrates vs. mollusks)

Exaptations: Structures that evolved for one function but were later co-opted for another

• Example: Mammalian ear bones:

  • Jawbones in early vertebrates became ear bones (malleus and incus) in mammals

Evolutionary Trends

Definition: Patterns of change in traits over time, often seen in the fossil record

• Evolution is not linear—many extinct lineages show diverse adaptations

Species Selection Model:

• Speciation = Birth of new species

• Extinction = Death of species

• Traits that promote speciation or reduce extinction influence evolutionary trends

• Trends are responses to environmental changes, not driven by an inherent goal or direction

Ch 26: Phylogeny & the tree of life

Binomial Nomenclature

Definition: A two-part scientific naming system for organisms developed by Carolus Linnaeus.

Structure:

• Genus: First part, capitalized (e.g., Homo).

• Specific epithet: Second part, lowercase (e.g., sapiens).

• Format: Both parts are italicized (e.g., Homo sapiens).

Advantages:

• Eliminates confusion from common names (e.g., jellyfish ≠ true fish).

• Universal language used by scientists globally.

• Reflects relationships between organisms (species in the same genus are closely related).

Hierarchical Classification

• System: Organizes species into nested, increasingly inclusive groups:

• Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species

Taxon (plural: taxa): A named group at any level (e.g., Mammalia = class).

• Example (North American Beaver):

  • Domain: Eukarya

  • Kingdom: Animalia

  • Phylum: Chordata

  • Class: Mammalia

  • Order: Rodentia

  • Family: Castoridae

  • Genus: Castor

  • Species: Castor canadensis

Notes:

• Higher levels are not italicized, but capitalized.

• Not always reflective of evolutionary history.

Linking Classification and Phylogeny

Phylogenetic Tree: A diagram representing evolutionary relationships based on common ancestry.

Issues:

• Misclassifications occur if key features are lost or overlooked.

• •The Linnaean system doesn’t always reflect evolutionary paths.

Modern Approach: Some systematists advocate classification based solely on evolutionary relationships.

Visualizing Phylogenetic Relationships

Key Terms:

• Branch Point (Node): Represents a common ancestor.

• Sister Taxa: Groups sharing an immediate common ancestor.

• Basal Taxon: Diverges early, near the root of the tree.

• Rooted Tree: Includes a common ancestor of all taxa.

Important Notes:

• Rotating branches does NOT change relationships.

• Reading from left to right does NOT imply evolutionary sequence.

Morphological and Molecular Homologies

Homology: Similarity due to shared ancestry.

Morphological Homology: Structural similarities (e.g., forelimb bones in mammals).

Molecular Homology: Similar DNA or protein sequences.

Analogy: Similarity due to convergent evolution, not common ancestry (e.g., marsupial vs. eutherian moles).

Distinguishing Homology vs. Analogy:

• More complex, detailed similarities → likely homologous.

• Simple, coincidental similarities → could be analogous.

Evaluating Molecular Homologies

Challenges:

• Insertions/Deletions cause differences in sequence lengths.

Molecular Homoplasies: Coincidental similarities in distantly related species.

Techniques:

• DNA Alignment Tools help compare sequences.

• Statistical Models differentiate true homologies from chance matches.

Cladistics

Definition: A systematics approach classifying organisms into clades based on common ancestry.

Key Concepts:

• Monophyletic Group: Ancestor + all descendants (valid clade).

• Paraphyletic Group: Ancestor + some (but not all) descendants.

• Polyphyletic Group: Distantly related species, excludes common ancestor (invalid).

Shared Ancestral vs. Shared Derived Characters

Shared Ancestral Character: Originated in an ancestor of the taxon (e.g., backbone in mammals).

Shared Derived Character: Unique to a particular clade (e.g., hair in mammals).

Character Loss: Loss of features (e.g., limbs in snakes) can also be a derived character.

Inferring Phylogenies Using Derived Character

Ingroup vs. Outgroup:

• Ingroup: The species under study.

• Outgroup: Related species that diverged earlier, helps determine ancestral traits.

Steps:

1. Identify shared derived characters.

2. Compare with outgroups to determine ancestral vs. derived traits.

3. Build the phylogenetic tree based on evolutionary relationships.

Maximum Parsimony

Definition: The simplest explanation that requires the fewest evolutionary changes is preferred.

Principle: Known as Occam’s Razor—“shave away” unnecessary complexity.

Application:

• In morphology-based trees: Fewer evolutionary events (e.g., trait changes).

• In DNA-based trees: Fewer base substitutions (mutations).

Key Point: Parsimonious trees assume that evolutionary changes are rare events.

Maximum Likelihood

Definition: Identifies the phylogenetic tree that is most likely to have produced the observed data based on probability models of DNA change.

Factors Considered:

• Different rates of mutation for different nucleotides or regions.

• Models that may assume equal substitution rates or more complex patterns.

Comparison to Parsimony:

• Maximum Parsimony: Focuses on simplicity.

• Maximum Likelihood: Focuses on statistical probability of changes over time.

• Tools: Computer algorithms help identify trees that are both parsimonious and statistically likely.

Interpreting Phylogenetic Trees

Phylogenetic Trees = Hypotheses: They represent the best guess based on current data, which may change with new discoveries.

• Patterns of Descent, Not Similarity: Trees show evolutionary relationships, not just physical resemblances.

  • Example: Birds are more closely related to crocodiles than to lizards despite morphological differences.

Tree Modifications: Trees are revised when new data (molecular, morphological) emerge.

Types of Phylogenetic Trees

1. Cladograms

• Depict: Only the branching order (topology).

• Branch Length: Has no meaning—doesn’t represent time or evolutionary change.

• Key Use: Shows sequence of divergence from common ancestors.

2. Phylograms

• Depict: Evolutionary relationships with branch lengths proportional to:

• Genetic change (number of mutations).

• Time (when calibrated with fossils).

• Example: Longer branches indicate more genetic change.

Applying Phylogenies:

• Practical Applications:

  • Forensic Science: Identifying poached animals using DNA phylogenies.

  • Species Identification: Using DNA barcoding (e.g., mitochondrial gene CO1).

  • Evolutionary Predictions: Helps predict ancestral traits using phylogenetic bracketing.

Gene Duplications and Gene Families

Gene Duplication: Increases gene copies, creating potential for new functions.

Gene Families: Groups of related genes from duplication events.

Types of Homologous Genes:

• Orthologous Genes: Homologous due to speciation events (e.g., cytochrome c in humans and dogs).

• Paralogous Genes: Result from gene duplication within a species (e.g., olfactory receptor genes in humans).

Genome Evolution

• Shared Genes: Lineages diverging long ago still share many orthologous genes.

• Gene Count vs. Complexity: More genes ≠ more complexity. Gene versatility matters more (e.g., humans vs. yeast).

Molecular Clocks

Definition: A tool for estimating the timing of evolutionary events based on the assumption that genetic mutations accumulate at a constant rate.

Key Points:

• Orthologous Genes: Mutations = time since divergence.

• Paralogous Genes: Mutations = time since duplication.

Applications:

• Calibrated with Fossil Record: Plot mutations against known divergence times.

  • Example: HIV Evolution traced back to the 1930s using molecular clocks.

Limitations of Molecular Clocks

• Not Always Precise:

• Mutation rates can vary between genes and species.

• Natural selection can affect rates (not all mutations are neutral).

• Clock Speed Differences:

  • Essential genes evolve slowly (mutations are often harmful).

  • Less critical genes evolve faster (mutations are often neutral).

Three-Domain System

Domains:

• Bacteria: Most known prokaryotes.

• Archaea: Prokaryotes in extreme environments.

• Eukarya: Organisms with a nucleus (plants, fungi, animals).

Replaces the Old “Five Kingdom” System: Monera is obsolete due to diversity within prokaryotes.

Horizontal Gene Transfer (HGT)

Definition: Genes transferred between unrelated species.

Mechanisms:

• Plasmids, viruses, endosymbiosis.

Impact on Phylogeny:

• Can cause conflicting evolutionary trees.

• Early life may resemble a web of life rather than a tree.