Midterm
Historical Development of Evolutionary Theory
Early Philosophical Views on Species
• Aristotle (384-322 BCE): Greek philosopher who believed that species were fixed (unchanging)
• Scala Naturae: A scale of increasing complexity of species developed in classical thought
Classification Systems
Linnaean Classification System (1707-1778)
• Carolus Linnaeus: Developed a hierarchical classification system that groups similar species into increasingly inclusive categories
• Used binomial nomenclature format for naming species
• Linnaean hierarchy: D. K. P. C. O. F. G. S (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species)
Cladistic Classification System
• Evolutionary system based on evolutionary relationships
• Represents descent with modification
Geological Influences on Evolutionary Thought
James Hutton (1726-1797)
• Proposed that Earth's geologic features could be explained by gradual mechanisms
• Foundational to understanding Earth's age and geological processes
Georges Cuvier (1769-1832)
• Paleontology: Developed the study of fossils
• Key observations:
• Older strata contain fossils less similar to current organisms than more recent strata
• From layer to layer: new species appear while others disappear
• Important perspective: Opposed the idea of evolution but inferred that extinctions are common occurrences
• Speculated that boundaries between strata represented sudden catastrophic events that destroyed species, followed by repopulation from other areas
Charles Lyell (1797-1875)
• Incorporated Hutton's approach into a comprehensive geological theory
• Key principle: The same geological processes operating today have operated in the past at the same rate
• "The same processes that are happening now happened in the past"
• Known as the Father of Modern Geology
• Introduced Uniformitarianism: Present is the key to the past
Catastrophism vs. Uniformitarianism
• Catastrophism: Sudden catastrophic events that changed Earth periodically over time
• Uniformitarianism: The same processes that are happening now happened in the past (gradual, continuous change)
Jean-Baptiste de Lamark (1744-1829)
Lamark's Hypothesis
• Compared living species with fossil forms and identified what appeared to be several lines of descent
• Each line represented a chronological series of older to younger fossils leading to a living species
• Believed evolution occurred because organisms have an innate drive to become more complex
Lamark's Two Principles
Use and Disuse
• Parts of the body that are used extensively become larger and stronger
• Parts not used deteriorate Inheritance of Acquired Characteristics
The Evolution of Populations (Chapter 23)
Foundations of Evolution
• Genetic Variation: Differences among individuals in the composition of their genes or other DNA sequences
• Essential requirement: Evolution cannot occur without genetic variation
• Hardy-Weinberg equation: Tool used to test whether a population is evolving
• Evolution definition: Change in allele frequencies in a population over generations
Mechanisms that Alter Allele Frequencies
There are three main mechanisms that cause changes in allele frequency in populations:
Natural Selection
• The only mechanism that consistently improves the degree to which organisms are adapted to their environment
• The only mechanism that causes adaptive evolution
• Actively removes harmful alleles from populations
Genetic Drift
• Changes in allele frequency caused by chance events
• Does not consistently improve adaptation
Gene Flow
• Transfer of alleles between populations
• Alters allele frequencies but does not necessarily improve adaptation
Microevolution
• Definition: Change in allele frequencies within a population over generations
• Result of the three mechanisms acting on genetic variation
Types of Natural Selection
• Disruptive Selection: Favors extreme phenotypes
• Stabilizing Selection: Favors average phenotypes
• Frequency-Dependent Selection: Fitness depends on allele frequency in the population
• Heterozygote Advantage: Heterozygotes have higher fitness than homozygotes
• Sexual Selection: Selection based on traits related to reproduction
• Balancing Selection: Maintains multiple alleles in a population
Genetic Variation: Types and Quantification
Heritable Phenotypic Variation Patterns
Either/Or Basis (Discrete Variation)
• Determined by a single gene locus with different alleles
• Produces distinct, separate phenotypes
• Example: Mendel's pea plant flowers (purple or white flowers)
Continuous Variation (Gradational)
• Varies along a continuum
• Influenced by two or more genes affecting a single phenotypic character
• Produces range of phenotypes rather than distinct categories
Gene Variability
• Measurement: Quantified as the average percentage of loci that are heterozygous
• Indicates genetic diversity within a population
Nucleotide Variability
• Definition: Genetic variation measured at the molecular level
• Key characteristic: Hardly results in phenotypic variation
• Occurs primarily in introns (noncoding segments of DNA)
• Introns lie between exons (regions retained in mRNA)
• Introns affect RNA processing but often don't alter phenotype
• Demonstrates that not all genetic variation produces observable differences
Sources of Genetic Variation
Three primary sources generate new genetic diversity:
1. Mutation: Creates new alleles
2. Gene Duplication: Increases number of genes available for variation
3. Sexual Reproduction: Shuffles existing alleles through recombination and independent assortment
Harmful Alleles and Adaptation
Recessive Alleles in Diploid Organisms
• Harmful recessive alleles can be hidden in heterozygous individuals
• Can persist for generations through propagation in heterozygotes
• Natural selection cannot efficiently remove them when rare because they remain concealed
Heterozygous Protection
• Definition: Harmful effects of alleles are masked by more favorable dominant alleles
• Allows harmful recessive alleles to remain in populations at low frequencies
• Demonstrates how genetic load is maintained in diploid organisms
Speciation: The Origin of New Species
Fundamental Concepts
What is Speciation?
• Speciation: The process by which one species splits into new species, producing tremendous diversity of life
• Species origin: New species originate from existing species through genetic divergence and reproductive isolation
• Forms a conceptual bridge between microevolution (changes in allele frequencies within a population) and macroevolution (broader patterns of evolutionary change above the species level)
The Biological Species Concept
• "A species is a group of populations whose members have the potential to interbreed in nature, produce viable fertile offspring, and do not produce viable fertile offspring with members of other such groups"
• This is the primary definition used in this chapter and essential for understanding speciation
• Gene flow: Movement of genes between populations that holds species together genetically
• Physical similarity is not always a reliable indicator of genetic relatedness or species membership
Evolution is Non-Linear
• Evolution branches in many different directions
• Environmental factors and selective pressures constantly change, creating a "moving goal post"
• Processes that work well in an environment are reinforced; those that don't work are eliminated
• As external factors change, selective pressures acting on species also change
Genetic Divergence and Reproductive Isolation
• When populations have gene flow, genes are shared and passed along
• Reproductive barrier: A biological barrier preventing gene flow between populations
• When reproductive barriers prevent interbreeding, populations can begin to diverge genetically
• Reproductive isolation and absence of interbreeding are the first steps toward speciation
Reproductive Barriers
Overview
• Reproductive isolation: Results when biological barriers impede members of two species from interbreeding and producing viable fertile offspring
• Barriers limit formation of hybrids: offspring resulting from interspecific mating (mating between two different species)
• Barriers classified as pre-zygotic (before zygote formation) or post-zygotic (after zygote formation)
• The distinction depends on whether a zygote is actually formed
Pre-Zygotic Barriers
Block fertilization by preventing species from attempting to mate, preventing successful completion of mating, or preventing fertilization if mating does occur.
Habitat Isolation
• Two species in different habitats within the same geographic area encounter each other rarely or never
• Example: Apple maggot flies isolated from blueberry maggot flies because they feed and lay eggs on different fruits
Temporal Isolation
• Species breed at different times: different times of day, different seasons, or different years
• Organisms cannot reproduce if they are not breeding simultaneously
• Example: Western and eastern spotted skunks have habitat overlap but breed at different times of year
Behavioral Isolation
• Species have unique courtship rituals or mating behaviors that effectively prevent mating with other species
• Example: Blue-footed booby has complex, unique mating displays that are not recognized by other similar species
• Requires correct and complete performance of mating behavior for female choice and successful reproduction
Mechanical Isolation
• If mating is attempted, morphological differences prevent successful completion
• Example: Snails in genus Bradybania have genital openings that do not align at the shell because shell spirals in opposite directions
• Physical incompatibility prevents reproduction even when organisms meet
Gametic Isolation
• Sperm of one species cannot fertilize eggs of another species
• Surface proteins on sperm and eggs from different species bind poorly to each other
• Example: Sea urchin species have surface proteins on sperm and eggs that prevent binding and zygote formation
• Prevents fertilization even if mating occurs
Post-Zygotic Barriers
Prevent a hybrid zygote from developing into a viable fertile adult through one of three mechanisms:
Reduced Hybrid Viability
• Genes from different parent species interact in ways that impair hybrid development or survival
• Example: Salamander hybrids do not fully complete development or metamorphosis if they hybridize
• Hybrids cannot complete their life cycle in the environment
Reduced Hybrid Fertility
• Meiosis fails to produce normal gametes, resulting in sterility
• Parent species have chromosomes of different numbers or structures
• Example: Mule (offspring of male donkey and female horse) is robust and healthy but sterile and cannot reproduce
• Successful reproduction between species produces offspring that cannot reproduce themselves
Hybrid Breakdown
• First generation hybrids are fertile but offspring in next generation are feeble or sterile
• Example: Hybrid fruits or crops—if you plant seeds from a hybrid fruit, resulting plant lacks the vigor of the hybrid parent
• Common in cultivated rice, corn, and other agricultural crops
• Hybrid strain has strength and disease resistance, but these traits do not pass to subsequent generations
Alternative Species Concepts
Limitations of the Biological Species Concept
• Cannot be applied to fossils: No way to observe mating behavior of extinct organisms or assess reproductive compatibility
• Cannot be applied to asexual organisms: No sexual reproduction or genetic mixing; includes all prokaryotes
• Emphasizes separateness and reproductive barriers rather than unity within species
• Gene flow occurs between morphologically and ecologically distinct species in some cases
Example of Gene Flow Between Distinct Species
• Grizzly bears and polar bears: Very distinct species that occasionally mate and produce "growler bears"
• Likely increasing with climate change as polar bear habitat warms and overlaps with brown bear range
• Raises question: Could this hybridization avenue lead to a new species?
Morphological Species Concept
• Distinguishes species by structural features
• Applicable to sexual and asexual species
• Can be used for extinct species through examination of fossil evidence and physical characteristics
• Based on morphological or physical appearances
Ecological Species Concept
• Defines species by its ecological niche: the sum of interactions with living and nonliving parts of the environment
• Applicable to sexual and asexual species
• Emphasizes the role of disruptive selection in maintaining species
Allopatric Speciation
Definition and Mechanism
• Allopatric: Roughly translates to "other country"
• Speciation occurs when populations are geographically isolated, preventing gene flow
• Gene flow is interrupted when populations are divided into geographically isolated subpopulations
• Can occur without geographic change when individuals colonize remote areas (island biogeography)
How Geographic Isolation Works
• Water bodies that become disconnected may develop unique species of fish over time
• Flying species or aquatic species commonly become stranded on islands
• Can occur with land animals on islands, but most common in flying species
• Geographic barriers effect: Depends on organisms' ability to move around
• Canyon creates barrier for small rodents but not for birds or coyotes
Genetic Mechanisms of Divergence
• Genes of isolated populations may diverge through mutation, natural selection, or genetic drift
• Reproductive isolation: May arise as a byproduct of genetic divergence
• Isolated populations accumulate genetic differences over time
• Example: Mosquito fish isolated populations became reproductively isolated as a result of selection under different predation levels
• With predators: body shape enables rapid bursts of speed
• Without predators: body shape favored for long, steady swimming
Evidence for Allopatric Speciation
Laboratory Evidence
• Reproductive barriers develop between isolated laboratory populations subjected to different environmental conditions
• Model organisms: Drosophila (fruit flies) commonly used because they have short generational cycles, easy to raise, very small, quick generational turnaround
• Can observe many generations quickly and push populations in different directions
• Example experiment: Feed fruit fly populations different diets (starch vs. maltose medium) over 40 generations
• Mates adapt to same diet
• After 40 generations, different populations can digest different food sources
• Can change outcomes by changing selective pressures
• Ethanol experiments: Isolated populations develop different capacities to digest alcohol
• Different selective pressures cause natural selection to drive genetic change
Natural Examples
• Sister species of snapping shrimp (genus Alpheus): Diverged 3-9 million years ago as populations were isolated by isthmus of Panama
• Different species now exist on either side of the isthmus
• Hawaiian islands: Have unique plants found only on individual islands
• Island chains: Great places to observe speciation—Galápagos and Hawaiian islands show isolation from mainland and between islands
• General pattern: Highly subdivided regions usually have more species than those with fewer barriers
• Geographic distance: Reproductive isolation between populations generally increases with geographic distance
Important Note on Physical vs. Biological Barriers
• Physical separation due to geographic isolation prevents interbreeding but is not a biological barrier to reproduction
• If geographically isolated populations are brought back together, it's possible they could still be physically capable of reproducing (unless other barriers have evolved)
Sympatric Speciation
Definition and Occurrence
• Sympatric: "Same country"—speciation occurs in populations living in the same geographic area
• Much less common than allopatric speciation
• Gene flow reduced by factors such as polyploidy, different sexual selection pressures, or habitat differentiation
Polyploidy
Overview
• Polyploidy: Accidents during cell division cause presence of extra chromosomes
• Can form new species within a single generation
• Primarily seen in plants, rarely in animals (not the typical mutation model seen in X-Men)
Auto-polyploidy
• More than two sets of chromosomes all derived from a single species
• Comes from mitotic errors
• Can result in production of tetraploid ($4n$) cell from diploid ($2n$) cell
• Fertile offspring: $4n$ can be produced through self-fertilization or mating among tetraploids
• Triploid mating: Mating between tetraploid and diploid produces triploid offspring ($3n$) with reduced fertility due to chromosome misalignments in gametes
Allo-polyploidy
• More than two sets of chromosomes derived from different species
• Chromosomes from different species do not pair during meiosis, resulting in hybrid sterility
• Sterile hybrids: Cannot reproduce sexually
• Asexual reproduction: Serial hybrids can reproduce asexually
• Chromosome doubling: Allo-polyploids form if chromosome number doubles in subsequent generations
• Diploid cells from species A and B combine to form sterile hybrid with $N = 5$ (3 + 2)
• Mitotic or meiotic errors in hybrid plant cell double chromosome numbers
• Results in viable fertile allopolyploid with $2N = 10$ (sum of diploid numbers of both parents)
Allopolyploid Characteristics
• Successfully interbreed with each other but not with either parent species
• Diploid number of new allopolyploid species equals sum of diploid numbers in both parents
• At least five new species have originated by polyploidy since 1850
• Example: Two allopolyploid species have evolved from diploid parent species from genus Tragopogon
Agricultural Importance
• Many important crops are polyploids: oats, cotton, potatoes, tobacco, wheat
• New polyploid agricultural species produced using chemicals to induce errors in cell division
• Used to exaggerate desired characteristics: fruit production, disease resistance, etc.
Sexual Selection
• Different mate preferences or sexual selections drive reproductive isolation
• Female choice and male competition cause sexual selection and sympatric speciation
• Example: Cichlids in Lake Victoria—sexual selection based on color
• When fish put under monochromatic light, females could not distinguish between different species with distinct coloration
• Sexual selection changed based on visual perception ability
• This weakened reproductive barriers
Habitat/Resource Exploitation
• Speciation results from exploitation of new habitats or resources
• Example: Apple maggot flies in North America
• Evolved after switching hosts from hawthorns to apples (closely related plants)
• Maggot flies mate on their host plant, creating habitat isolation between groups using different hosts
• Temporal isolation: Apple-feeding flies develop faster than hawthorn-feeding flies
• Alleles: Those benefiting flies using one host plant differ from those using the other, causing post-zygotic isolation
• Multiple mechanisms contribute to true speciation and habitat differentiation
Hybrid Zones
Definition and Formation
• Hybrid zone: Region where members of different species mate and produce hybrid offspring
• Hybrids result from mating between species with incomplete reproductive barriers
• Form along narrow bands where habitats overlap
• Example: Fire-belly toads (genus Bombina) interbreed along narrow hybrid zone where two species overlap
Three Possible Outcomes
Reinforcement
• Definition: Strong selection for pre-zygotic barriers, driving species further apart
• Occurs when hybrids are less fit than parent species
• Strong selection against hybrid production
• Reinforcement stronger for sympatric than allopatric populations
Fusion
• Species come back together into single species
• Occurs when hybrids are as fit as (or more fit than) parent species
• Weak reproductive barriers: Can be overcome by substantial gene flow
• Reproduction barriers weaken and two parent species merge
• Example: Lake Victoria cichlids—pollution has made it difficult for females to differentiate males by color
• Weakened reproductive barriers lead to fusion occurring
• Turbid water variant may become single fused species
Stability
• Separate lineages maintained alongside hybrid lineage in middle
• Extensive gene flow from outside hybrid zone can overwhelm selection for increased reproductive isolation within zone
• Example: Fire-belly toads maintain separate species with stable hybrid population in middle
Speciation Rates and Patterns in the Fossil Record
Open Questions
• How long does it take for new species to form? No single static answer exists
• Rate depends on intrinsic factors specific to each species and individual organisms
• Change likely depends greatly on the species involved and unique circumstances
Speciation Rates from Fossil Record
• Can observe broader patterns in fossil record
• Relies heavily on morphological understanding of species
• Molecular data also used to determine time intervals between speciation events in particular groups
Fossil Record Patterns
Punctuated Equilibrium
• Definition: Describes periods of apparent stasis (no change) punctuated by sudden change
• Sudden events that produce rapid change in speciation
• Sometimes dramatic loss of genetic diversity
• Example: Major extinction events bottleneck genetics followed by rapid speciation
• "The model that we use to describe this is called punctuated equilibrium. So punctuated equilibrium describes these periods of apparent stasis punctuated by sudden change"
Gradual Change Model
• Some species show gradual change over time rather than punctuated pattern
• Gentle, slow separation from common ancestor into two separate lineages over long period
• Slow and steady change observed in some lineages
Both Patterns Observed
• Fossil record shows evidence for both punctuated equilibrium and gradual change
• Both models happening simultaneously in different lineages
• No one-size-fits-all answer to speciation timescale
• Depends on unique circumstances surrounding species, population, and sometimes subpopulation
Key Biological Processes
Gene Flow and Speciation
• Gene flow shares genes between populations
• Reproductive barriers interrupt gene flow
• Without gene flow, populations diverge genetically
• Absence of gene flow allows accumulation of genetic differences
Natural Selection and Speciation
• Different selective pressures in isolated populations drive genetic divergence
• Selective pressures change with environmental conditions
• Directional selection can accumulate different alleles in isolated populations
• Disruptive selection emphasized in ecological species concept
Genetic Drift
• Random genetic changes in isolated populations
• One of three mechanisms (along with mutation and natural selection) driving divergence
• More pronounced in small populations
Meiosis and Reproductive Barriers
• Zygote formation: Result of sexual reproduction fertilization between male and female sex cells from genetically different organisms
• Gamete production via meiosis can fail in hybrids
• Chromosome alignment problems in hybrids with different chromosome numbers
• Mitotic errors can cause polyploidy
Summary and Context
Darwin's Work
• Very interested in process of speciation
• Process by which one species splits into new species
• Speciation explains tremendous diversity AND unity of life—everything shares common ancestor but diverse mechanisms produce different life forms
Chapter Scope
• Focuses on defining species and speciation
• Examines genetic mechanisms enabling speciation
• Discusses processes through which new species originate from existing species
• Explores role of adaptation and environmental influence
Chapter 25: The History of Life
Overview of the Lecture
• Examines very large chunks of geological time and how life on Earth has changed over time
• Focuses on processes like fossil formation and understanding how organisms adapted to environmental changes
• Example explored: How aquatic species like the psilosaurus ended up in desert environments (Sahara was once ocean)
Processes Causing Life to Change Over Time
• Internal geological changes within the Earth
• Environmental and climate shifts at Earth's surface
• External impacts: meteorite and asteroid strikes causing mass extinctions
• Tracking evolutionary processes through animal lineages across time
• Past organisms were often very different from modern species
Definition of Key Concepts
• Macroevolution: The broader pattern of evolution above the species level, evidenced primarily through the fossil record
Origin of Life
Chemical and Physical Conditions on Early Earth
• Earth formed approximately 4.6 billion years ago
Phylogeny & Systematics Fundamentals
Core Definitions
• Phylogeny: The evolutionary history of a species or group of related species
• Systematics: A discipline focused on classifying organisms and determining their evolutionary relationships
• Purpose: Organization system to classify organisms based on common ancestry and evolutionary history, identifying ancestry patterns, convergence, and divergence of different groups
Key Concepts
• Phylogenies help organize living things based on common ancestors, where adaptations appear, and individual taxa of organisms represented on phylogenetic trees
• Example: Glass lizards are legless lizards (not snakes), representing a secondary loss of limbs through evolutionary processes—raising questions about how organisms evolve into seemingly different forms despite shared ancestry
Binomial Nomenclature & Taxonomic Classification
Two-Part Naming System
• Binomial nomenclature: Two-part naming system attributed to Carolus Linnaeus
• Two key features that remain meaningful today:
1. Two-part naming system (genus and specific epithet)
2. Hierarchical classification of organisms in nested hierarchy
• First letter of genus is capitalized; entire species name is italicized or underlined
• Example: Panthera leo (lion), Panthera pardus (leopard)
Hierarchical Classification Levels
Linnaeus introduced a system for grouping species in increasingly inclusive groups, from broadest to most specific:
• Domain (broadest inclusivity)
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species (most specific—one organism type)
"Did King Philip come over from good Spain?" — Mnemonic device: Did (Domain), King (Kingdom), Philip (Phylum), Come (Class), Over (Order), From (Family), Good (Genus), Spain (Species)
Nested Hierarchy Example
Classification of the Lion (Panthera leo):
• Domain: Eukarya
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Carnivora
• Family: Felidae
• Genus: Panthera
• Species: leo By species level, there is only one Panthera leo, but many species within genus Panthera, many genera in family Felidae, many families in order Carnivora, etc.
Historical Evolution of Classification
• Two kingdoms: Historically, all species classified as plants or animals
• Five kingdoms: By 1960
• Three domains: Recently adopted—Bacteria, Archaea, and Eukaryota
Phylogenetic Trees & Tree Interpretation
Definition & Purpose
• A phylogenetic tree is a branching diagram representing the evolutionary history of a group of organisms
• Represents a hypothesis about evolutionary relationships—not necessarily absolutely accurate, but the most accurate hypothesis of evolutionary relationship available at that point
• Shows patterns of descent, not phenotypic similarity
Key Structural Elements
Branch Points & Divergence
• Each branch point represents the divergence of two evolutionary lineages from a common ancestor
• Evolutionary lineage: A sequence of ancestral organisms leading to a particular descendant taxa
Sister Taxa
• Groups that share a common ancestor that is not shared by any other group
• Example: Chimps and humans are sister taxa; they share an ancestor not shared by other organisms
Rooted Trees
• Include a branch representing the most recent common ancestor of all taxa in the tree
• Allow determination of which taxa are ancestral to which
Basal Taxon
• A lineage that diverges from all other members of the group early in the history of that group
Important Principle
• Should NOT be assumed that a taxon evolved from the taxon next to it in the tree diagram
Characteristics & Homology
Homology vs. Analogy
• Homology: Similarity due to shared ancestry—organisms with similar morphology or DNA sequences are likely more closely related
• Analogy: Similarity due to convergent evolution—unrelated species can evolve superficial similarities through convergent evolution in similar natural conditions/environments
• Example: Australian mole and African golden mole are very similar but not closely related; similarities result from adaptation to similar lifestyles and habitats
Types of Characteristics
Shared Ancestral Characteristics
• A character that originated in an ancestor of the taxon
• Present in broader taxonomic groups
Shared Derived Characteristics
• An evolutionary novelty unique to a particular clade
• Often the core for building cladograms
• Can include loss of features as well as new features
• Example: Loss of limbs in snakes and glass lizards is a shared derived characteristic
• Example: Loss of limbs in whales
Relative Nature of Characteristics
• Whether a character is ancestral or derived depends on what part of the phylogenetic tree is being examined
• Example: Having a backbone is ancestral within vertebrate clade but derived when distinguishing vertebrates from other animals
• Can define both what unites a clade and separates it from other groups
Group Classification in Cladistics
Three Types of Groups
Monophyletic Groups (Clades)
• Group consisting of an ancestor and all of its descendants
• Only groups that include a common ancestor and all descendants are named in modern systematic classification
• "A clade is a group of species that includes an ancestral species and all of its descendants. Clades can be nested within larger clades."
• These are the desired groupings when building cladograms
Paraphyletic Groups
• Consist of an ancestor species and some, but not all, of the descendants
• Unlike polyphyletic groups, the common ancestor to all members is part of the group
• Often initial classifications before full understanding of evolutionary history
Polyphyletic Groups
• Include distantly related species but not their most recent common ancestor
• Essentially a catch-all grouping that may not have a distinct clear common ancestor
• When new evidence indicates a group is polyphyletic, members are typically reclassified
In-groups & Out-groups
• In-group: The group of species being studied
• Out-group: A species or group closely related to but not part of the in-group
• Each in-group species is compared with out-groups to differentiate between shared derived and shared ancestral characteristics
• Characters shared by out-group and in-group are assumed to be ancestral
Character Table Example
Vertebrate classification using characteristics:
• Vertebral column (backbone): All except lancelets
• Jaws: All except lampreys and lancelets
• Forelimbs: All except fish
• Amnion: All except frogs
• Hair: Strictly mammalian, excludes all others
"In each one of those groups, we're using a specific characteristic to separate them out and differentiate them from other groupings of organisms."
Methods for Building Phylogenies
Data Sources
• Morphological data: Physical structure of fossil evidence or extant (living) species
• Molecular data: DNA sequences, genes, biochemistry, and other molecular lines of evidence
• Modern systematics rely increasingly on molecular evidence to supplement or revise morphological classifications
Analytical Principles
Maximum Parsimony
• Assumes the most likely tree is the one requiring the fewest evolutionary events
• Based on principle that simplest explanation is probably most accurate
• For DNA-based phylogenies, most parsimonious tree has fewest base changes
Maximum Likelihood
• Identifies the tree most likely to have produced a given set of DNA data
• Based on probability rules about how DNA changes over time
• Example: May assume all nucleotide substitutions are equally likely
Phylogenetic Bracketing
• Method to predict that features shared by two closely related groups will be present in their ancestor and all descendants
• Used to make predictions about extinct organisms (e.g., dinosaurs)
• Example: Birds and crocodiles both have four-chambered hearts, songs for mating, nest building, and brooding behavior
Phylogeny & Systematics Fundamentals
Core Definitions
• Phylogeny: The evolutionary history of a species or group of related species
• Systematics: A discipline focused on classifying organisms and determining their evolutionary relationships
• Purpose: Organization system to classify organisms based on common ancestry and evolutionary history, identifying ancestry patterns, convergence, and divergence of different groups
Key Concepts
• Phylogenies help organize living things based on common ancestors, where adaptations appear, and individual taxa of organisms represented on phylogenetic trees
• Example: Glass lizards are legless lizards (not snakes), representing a secondary loss of limbs through evolutionary processes—raising questions about how organisms evolve into seemingly different forms despite shared ancestry
Binomial Nomenclature & Taxonomic Classification
Two-Part Naming System
• Binomial nomenclature: Two-part naming system attributed to Carolus Linnaeus
• Two key features that remain meaningful today:
1. Two-part naming system (genus and specific epithet)
2. Hierarchical classification of organisms in nested hierarchy
• First letter of genus is capitalized; entire species name is italicized or underlined
• Example: Panthera leo (lion), Panthera pardus (leopard)
Hierarchical Classification Levels
Linnaeus introduced a system for grouping species in increasingly inclusive groups, from broadest to most specific:
• Domain (broadest inclusivity)
• Kingdom
• Phylum
• Class
• Order
• Family
• Genus
• Species (most specific—one organism type)
"Did King Philip come over from good Spain?" — Mnemonic device: Did (Domain), King (Kingdom), Philip (Phylum), Come (Class), Over (Order), From (Family), Good (Genus), Spain (Species)
Nested Hierarchy Example
Classification of the Lion (Panthera leo):
• Domain: Eukarya
• Kingdom: Animalia
• Phylum: Chordata
• Class: Mammalia
• Order: Carnivora
• Family: Felidae
• Genus: Panthera
• Species: leo By species level, there is only one Panthera leo, but many species within genus Panthera, many genera in family Felidae, many families in order Carnivora, etc.
Historical Evolution of Classification
• Two kingdoms: Historically, all species classified as plants or animals
• Five kingdoms: By 1960
• Three domains: Recently adopted—Bacteria, Archaea, and Eukaryota
Phylogenetic Trees & Tree Interpretation
Definition & Purpose
• A phylogenetic tree is a branching diagram representing the evolutionary history of a group of organisms
• Represents a hypothesis about evolutionary relationships—not necessarily absolutely accurate, but the most accurate hypothesis of evolutionary relationship available at that point
• Shows patterns of descent, not phenotypic similarity
Key Structural Elements
Branch Points & Divergence
• Each branch point represents the divergence of two evolutionary lineages from a common ancestor
• Evolutionary lineage: A sequence of ancestral organisms leading to a particular descendant taxa
Sister Taxa
• Groups that share a common ancestor that is not shared by any other group
• Example: Chimps and humans are sister taxa; they share an ancestor not shared by other organisms
Rooted Trees
• Include a branch representing the most recent common ancestor of all taxa in the tree
• Allow determination of which taxa are ancestral to which
Basal Taxon
• A lineage that diverges from all other members of the group early in the history of that group
Important Principle
• Should NOT be assumed that a taxon evolved from the taxon next to it in the tree diagram
Characteristics & Homology
Homology vs. Analogy
• Homology: Similarity due to shared ancestry—organisms with similar morphology or DNA sequences are likely more closely related
• Analogy: Similarity due to convergent evolution—unrelated species can evolve superficial similarities through convergent evolution in similar natural conditions/environments
• Example: Australian mole and African golden mole are very similar but not closely related; similarities result from adaptation to similar lifestyles and habitats
Types of Characteristics
Shared Ancestral Characteristics
• A character that originated in an ancestor of the taxon
• Present in broader taxonomic groups
Shared Derived Characteristics
• An evolutionary novelty unique to a particular clade
• Often the core for building cladograms
• Can include loss of features as well as new features
• Example: Loss of limbs in snakes and glass lizards is a shared derived characteristic
• Example: Loss of limbs in whales
Relative Nature of Characteristics
• Whether a character is ancestral or derived depends on what part of the phylogenetic tree is being examined
• Example: Having a backbone is ancestral within vertebrate clade but derived when distinguishing vertebrates from other animals
• Can define both what unites a clade and separates it from other groups
Group Classification in Cladistics
Three Types of Groups
Monophyletic Groups (Clades)
• Group consisting of an ancestor and all of its descendants
• Only groups that include a common ancestor and all descendants are named in modern systematic classification
• "A clade is a group of species that includes an ancestral species and all of its descendants. Clades can be nested within larger clades."
• These are the desired groupings when building cladograms
Paraphyletic Groups
• Consist of an ancestor species and some, but not all, of the descendants
• Unlike polyphyletic groups, the common ancestor to all members is part of the group
• Often initial classifications before full understanding of evolutionary history
Polyphyletic Groups
• Include distantly related species but not their most recent common ancestor
• Essentially a catch-all grouping that may not have a distinct clear common ancestor
• When new evidence indicates a group is polyphyletic, members are typically reclassified
In-groups & Out-groups
• In-group: The group of species being studied
• Out-group: A species or group closely related to but not part of the in-group
• Each in-group species is compared with out-groups to differentiate between shared derived and shared ancestral characteristics
• Characters shared by out-group and in-group are assumed to be ancestral
Character Table Example
Vertebrate classification using characteristics:
• Vertebral column (backbone): All except lancelets
• Jaws: All except lampreys and lancelets
• Forelimbs: All except fish
• Amnion: All except frogs
• Hair: Strictly mammalian, excludes all others
"In each one of those groups, we're using a specific characteristic to separate them out and differentiate them from other groupings of organisms."
Methods for Building Phylogenies
Data Sources
• Morphological data: Physical structure of fossil evidence or extant (living) species
• Molecular data: DNA sequences, genes, biochemistry, and other molecular lines of evidence
• Modern systematics rely increasingly on molecular evidence to supplement or revise morphological classifications
Analytical Principles
Maximum Parsimony
• Assumes the most likely tree is the one requiring the fewest evolutionary events
• Based on principle that simplest explanation is probably most accurate
• For DNA-based phylogenies, most parsimonious tree has fewest base changes
Maximum Likelihood
• Identifies the tree most likely to have produced a given set of DNA data
• Based on probability rules about how DNA changes over time
• Example: May assume all nucleotide substitutions are equally likely
Phylogenetic Bracketing
• Method to predict that features shared by two closely related groups will be present in their ancestor and all descendants
• Used to make predictions about extinct organisms (e.g., dinosaurs)
• Example: Birds and crocodiles both have four-chambered hearts, songs for mating, nest building, and brooding behavior
Prokaryotes: Overview and Characteristics
Definition and Distribution
• Single-celled organisms comprising domains bacteria and archaea
• Adapted to diverse environments; found almost everywhere on Earth
• Most abundant organisms on planet by huge margin
• First organisms to inhabit Earth (3.5 billion years ago)
• Most unicellular, though some species form colonies
• Size: 0.5-5 micrometers (compared to eukaryotic cells: 10-100 micrometers)
• Shapes: spheres, rods, and spirals (classification basis)
Cell Structure
Cell Walls
• Help maintain shape and protect cells; prevent bursting in hypotonic environments
• Eukaryotic cell walls: made of cellulose or chitin
• Bacterial cell walls: contain peptidoglycan (unique characteristic)
• Peptidoglycan: network of sugar polymers cross-linked by polypeptides
• Archaeal cell walls: contain variety of polysaccharides and proteins; NO peptidoglycan
Gram Staining Classification
• Gram-positive bacteria:
• Simpler walls with large amount of peptidoglycan
• Thick peptidoglycan section
• Stain readily adheres
• Gram-negative bacteria:
• Less peptidoglycan overall
• Outer membrane, peptidoglycan layer, and plasma membrane (more complex structure)
• Stain doesn't adhere as well
Capsules
• Sticky layer of polysaccharides or proteins surrounding cell wall
• Example use: bacteria causing tonsillitis adhere to tonsil cells via capsule
Endospores
• Metabolically inactive forms produced when water and nutrients are lacking
• Cell copies chromosomes and surrounds with multi-layered protective structure
• Can withstand extreme conditions and remain viable for very long periods
• Bacteria enter dormancy state until conditions improve
• Once conditions favorable, bacteria exit endospore and resume metabolic processes
Surface Appendages
• Fimbria: hair-like appendages
• Allow sticking to substrate or other individuals
• Look like fuzz or hairs on cell wall
• Used to create colonies and stick together
• Pili: longer than fimbria
• Function to pull cells together
• Enable exchange of DNA
• Used primarily for bacterial modes of reproduction
Motility
Taxes
• Definition: Movement towards or away from stimulus
• Chemotaxis: movement toward/away from chemical stimulus
• Positive chemotaxis: movement toward chemical
• Negative chemotaxis: movement away from chemical
Flagella
• Most common structures for prokaryotic movement
• Look like little tails used to swim
• May be scattered over entire surface or concentrated at cell ends
• Structure: filament, hook, and motor (situated in plasma membrane)
• Use: twist and spin to enable swimming
• Note: Prokaryotic and eukaryotic flagella differ in structure, propulsion mechanism, and molecular composition
Internal Organization
• Lack complex compartmentalization (unlike eukaryotic cells with organelles)
• Some prokaryotes have specialized membranes for metabolic function
• Usually infoldings of outer cellular membrane
• Aerobic prokaryotes: respiratory membrane
• Photosynthetic prokaryotes: thylakoid membrane
Endosymbiosis Theory
• Eukaryotic cells hypothesized to have originated from serial endosymbiosis
• Mitochondria origin: likely from respiratory/aerobic prokaryote engulfed by another cell; respiratory membrane developed into mitochondrial organelle
• Chloroplasts: similarly derived from engulfed photosynthetic prokaryotes with thylakoid membrane structure similar to chloroplast components
DNA and Genetics
• Prokaryotes:
• Less DNA and produce fewer proteins than eukaryotes
• One circular chromosome (housed in nucleoid region with no membrane)
• May possess plasmids: smaller rings of independently replicating DNA
• Eukaryotes:
• Multiple linear chromosomes housed in nucleus
Prokaryote Reproduction and Genetic Diversity
Binary Fission
• Splitting in two; asexual reproduction
• Can divide every 1-3 hours under optimal conditions
Key Characteristics Contributing to Success
1. Very small size
2. Reproduce by binary fission (no sexual reproduction required)
3. Short generational times
These three characteristics result in high genetic diversity in prokaryote populations due to rapid reproduction, high mutation rates, and capacity for genetic recombination
Genetic Recombination
• Combining of DNA from two sources
• Contributes to prokaryote diversity
• Three mechanisms: transformation, transduction, conjugation
Horizontal Gene Transfer
• Movement of genes between individual prokaryotes of different species
Protist Classification and Definition
Overview
• Informal grouping of microorganisms that don't fit cleanly into other categories
• Classified into three types: plant-like, animal-like, and fungi-like
• Originally designated as Kingdom Protista but no longer considered a kingdom
• Individual protists are more closely related to plants, fungi, or animals than to other protists collectively
• "protists are kind of interesting in that they're kind of an informal grouping that lumps together a bunch of different things that aren't quite anything else"
Evolutionary Significance
• Demonstrate progression from prokaryotic single-celled organisms through eukaryotic multicellular organisms
• Show colonial phase in between this developmental chain
• Illustrate mechanisms of evolutionary transition between cellular complexity levels
• "we can kind of see the progression through protists of sort of the prokaryotic single-celled organisms into the eukaryotic multicellular organisms"
Eukaryotic Cell Characteristics
Fundamental Features
• Contain nuclei and other membrane-bound organelles
• More complex than prokaryotic cells
• Organelles isolate and compartmentalize functions
Membrane-Bound Organelles
• Mitochondria
• Chloroplasts
• Golgi apparatus
• Other specialized structures
Cytoskeleton
• Well-developed in protists
• Enables asymmetrical cell shapes
• Allows cells to change shape and move
• Critical for creating asymmetry and motility
Protist Cellular Complexity
• Among most complex single cells of any organism
• Most are unicellular; some are colonial or multicellular
• Each unicellular protist performs all functions of living organism
• Exhibit more structural and functional diversity than any other eukaryotic group
• Some possess organelles not found in most eukaryotic cells
Specialized Organelles
• Oscilloid: eye-like organelle in dinoflagellates used for light sensing; provides rudimentary light detection rather than complex vision
Nutritional Modes
• Photosynthetic (autotrophic): use $CO_2$ and light energy to produce ATP
• Heterotrophic: consume organic matter as carbon source
• Mixotrophic: combine photosynthetic and heterotrophic feeding mechanisms
• Some switch between autotrophic and heterotrophic modes depending on environmental conditions
Endosymbiosis and Evolution
Endosymbiosis Concept
• Relationship where one organism lives inside another organism's cells
• Process involves phagocytosis (engulfing another cell)
• Engulfed cell remains rather than being digested
• Develops into mutualistic relationship over time
Origin of Mitochondria and Plastids
• Mitochondria evolution gave rise to eukaryotes
• Plastids arose when heterotrophic eukaryotes engulfed photosynthetic cyanobacteria
• Process occurred multiple times in evolutionary history
Primary and Secondary Endosymbiosis
• Primary endosymbiosis: heterotrophic eukaryotes engulfed cyanobacteria → development of plastids
• Secondary endosymbiosis: heterotrophic eukaryotes ingested red and green algae (which already contained plastids)
• Occurred multiple times creating different protist lineages
Key Products of Secondary Endosymbiosis
• Red algae and green algae evolved from plastic-bearing ancestors (common ancestor)
• Red algae subsequently ingested by heterotropic eukaryotes
• Green algae subsequently ingested by heterotropic eukaryotes
• Example: chloroarchaeophytes likely evolved when heterotrophic eukaryotes engulfed green algae
Nucleomorph
• Vestigial nucleus remaining from engulfed cell
• Remnant of formerly functional nucleus now without function
• Evidence of evolutionary history preserved in modern cells
• "The engulfed cell can the vestigio nucleus, and it's called the nucleomorph"
Vestigial Structures
• Remnants of previously functional structures no longer serving purpose
• Examples in humans: tail bones (coccyx), appendix, ear muscles
• Examples in protists: nucleomorph in chloroplasts
• Provide evidence of evolutionary relationships and ancient functions
• "it's the remnants of what was previously a functional structure but doesn't really have any function now"
Four Supergroups of Eukaryotes
Excavata
General Characteristics
• Characterized by distinctive cytoskeleton
• Some members possess excavated feeding grooves on one side of body
• Contains three monophyletic groups: diplomonads, parabacilids, euglenozoans
Diplomonads
• Lack plastids
• Possess reduced mitochondria called mitosomes
• Mitosomes lack electron transport chains
• Anaerobic respiration generates much less ATP than aerobic respiration
• Possess two equal-sized nuclei
• Multiple flagella for locomotion
• Many are parasitic organisms
• Example: Giardia intestinalis — causes severe gastrointestinal illness
Parabacilids
• Reduced mitochondria called hydrogenosomes
• Generate energy anaerobically (without oxygen)
• Release hydrogen gas as byproduct of anaerobic metabolism
Euglenozoans
• Function as top predators in microhabitats and microorganisms
• Include photosynthetic autotrophs, mixotrophs, and parasites
• Main distinguishing feature: spiral or crystalline rod inside each flagellum
• Composed of two groups: kinetoplastids and euglenids
Kinetoplastids
• Single mitochondrion containing organized mass of DNA called kinetoplast
• Free-living species consume prokaryotes in freshwater, marine, and moist terrestrial ecosystems
• Some parasitize animals, plants, and other protists
• Genus Trypanosoma causes sleeping sickness in humans
• Approximately 10,000 people infected annually
• Possess undulating membrane enabling movement through blood cells
Euglenids
• One or two flagella emerge from pocket at one end of cell
• Relatively large: 5 micrometers across, 2-3 times that in length
• Many are mixotrophs switching between autotrophic and heterotrophic modes based on environmental conditions
• Contain chloroplasts used for photosynthesis
• Possess rudimentary eye spot (stigma) enabling light/dark perception
• Have nucleus and plasma membrane
• Readily visible in pond water as actively swimming organisms
• "really neat critters...they're going to have often a rudimentary eye spot that lets them sort of perceive the world sort of in lights and darks"
SAR Group
General Characteristics
• Highly diverse
• Defined by DNA similarities rather than physical characteristics
• Composed of stromatopiles, alveolates, and rhizarians
Stromatopiles
Overview
• Include some of most important photosynthetic organisms on Earth
• Most possess hairy flagellum paired with smooth flagellum
• Three important groups: diatoms, oomycetes, brown algae
Diatoms
• Unicellular algae with unique features
• Glass-like wall composed of silicon dioxide ($SiO_2$)
• Silicon wall withstands enormous pressures protecting organism