Bio Module 4

• Phylogenies: __________________________

• Systematics: A discipline that __________________________

  • ____________ are a tool used in systematics

• Phylogenies can scale depending on what type of system we’re looking at

  • ____________ is the largest phylogeny

• Phylogenies: the branching evolutionary history of organisms

• Systematics: A discipline that reconstructs phylogenies and classifies organisms based on those relationships

  • Phylogenies are a tool used in systematics

• Phylogenies can scale depending on what type of system we’re looking at

  • Tree of life is the largest phylogeny

What a Phylogenetic Tree Represents

• Main point is showing patterns of __________

• Branches: ____________________

• Nodes: ____________________

• Tips/Leaves: _____________________________________

  • Never ancestors of other tips

What a Phylogenetic Tree Represents

• Main point is showing patterns of relatedness 

• Branches: populations through time

• Nodes: Hypothetical common ancestor 

• Tips/Leaves: Living (current line) or extinct (finished species)

  • Never ancestors of other tips

• Polytomy: __________________________________

  • Also represented by a _________ _________

• _________ _________: Each other's closest relative, like A & B

• Misconceptions: nothing present descends from _________ _________

  • Ex. We didn’t evolve from chimps. Humans and chimps both evolved from an ancient common ancestor

• Species closer together on the tree are not necessarily more _________, it depends on how far back the _________ _________ is 

  • Nodes can be flipped around and show the same thing

• They’re _________, not facts 

• Polytomy: either two diverged at the same time, or representing that we don’t know specifically where/how they diverged

  • Also represented by a dotted line

• Sister taxa: Each other's closest relative, like A & B

• Misconceptions: nothing present descends from present lineages

  • Ex. We didn’t evolve from chimps. Humans and chimps both evolved from an ancient common ancestor

• Species closer together on the tree are not necessarily more related, it depends on how far back the ancestor node is 

  • Nodes can be flipped around and show the same thing

• They’re hypotheses, not facts 

Characters and Traits, Data Matrices

• Heritable characters

  • ______________

  • ______________

  • ______________

  • ______________

• Traits: Specific states of a character

  • (Character/Trait) = eye color

  • (Character/Trait) = green eyes 

Characters and Traits, Data Matrices

• Heritable characters (BMBD)

  • Morphological

  • Molecular

  • Behavioral

  • Developmental 

• Traits: Specific states of a character

  • Character = eye color

  • Trait = green eyes 

Ancestral vs. Derived Traits, Synapomorphies

• Apomorphy: _______________________

• Plesiomorphy: _______________________

• Autapomorphy: _______________________

• Synapomorphy: _______________________

• Homoplasy: _______________________

Which is most important and used to identify monophyletic groups? _____________

Ancestral vs. Derived Traits, Synapomorphies

• Apomorphy: Derived trait 

• Plesiomorphy: Ancestral trait inherited from earlier ancestors 

• Autapomorphy: Derived trait unique to a single lineage 

• Synapomorphy: Shared derived trait 

• Homoplasy: Similarity not due to shared ancestry 

Which is most important and used to identify monophyletic groups? Synapomorphy

Monophyletic vs Non-Monophyletic Groups

• Paraphyletic group: __________________________

• Polyphyletic groups: __________________________

• Monophyletic groups: __________________________

  • Can scale (all three boxes are monophyletic) 

Monophyletic vs Non-Monophyletic Groups

• Paraphyletic group: Ancestor and some of its descendants (???) 

• Polyphyletic groups: Based on similar characteristics but not ancestry

• Monophyletic groups: Common ancestor and all of its descendants (Clade) 

  • Can scale (all three boxes are monophyletic) 

Homology vs Homoplasy

• Homology: Similarity (due/not due) to common ancestry 

• Homoplasy: Similarity (due/not due) to common ancestry 

  • Common dolphin & Ichthyosaur 

Convergent Evolution

• Example of (homoplasy/homology)

• Bat, bird, and insect wings evolved wings (together/independently)

Homology vs Homoplasy

• Homology: Similarity due to common ancestry 

• Homoplasy: Similarity not due to common ancestry 

  • Common dolphin & Ichthyosaur 

Convergent Evolution

• Example of homoplasy

• Bat, bird, and insect wings evolved wings independently 

Parsimony

• Method used to reconstruct evolutionary trees by selecting the hypothesis requiring the __________ __________ __________

• Better trees have fewer steps because we assume evolution takes __________ __________ __________

  • Not foolproof strategy

Parsimony

• Method used to reconstruct evolutionary trees by selecting the hypothesis requiring the fewest evolutionary changes

• Better trees have fewer steps because we assume evolution takes the fewest steps 

  • Not foolproof strategy

Taxonomy of Living Things: (Dear King Phillip Came Over For Good Soup) 

• _________ → _________ → _________ → _________ → _________ → _________ → _________ → _________

• Species name is: [_________] [_________]

  • Ex. Homo Sapiens 

Taxonomy of Living Things: (Dear King Phillip Came Over For Good Soup) 

• Domains → Kingdoms → Phylum → Class → Order → Family → Genus → Species

• Species name is: [Genus] [Species]

  • Ex. Homo Sapiens 

• Eukaryotes = ________

• Prokaryotes = ________ + ________

  • ________ are much simpler, have very similar cells, no nucleus, and circular dna 

• Estimated that there are 3 x 10^30 individual cells 

  • ________ dominate in numbers, but most are undescribed and relatively unstudied 

• Oldest known fossils are ________, and they were the only ones on the planet for a long time 

• Eukaryotes = Eukaryota

• Prokaryotes = Bacteria + Archaea 

  • Prokaryotes are much simpler, have very similar cells, no nucleus, and circular dna 

• Estimated that there are 3 x 10^30 individual cells 

  • Prokaryotes dominate in numbers, but most are undescribed and relatively unstudied 

• Oldest known fossils are bacteria, and they were the only ones on the planet for a long time 

Bacteria vs Archaea: Fundamental Differences

• Shared features:

  • (Unicellular/Multicellular)

  • (Prokaryotic/Eukaryotic)

  • Generally (small/large) and morphologically (simple/complex)

• (Bacteria/Archaea) have peptidoglycan in their cell wall, while (Bacteria/Archaea) don't, which makes targeting them with drugs challenging 

Bacteria vs Archaea: Fundamental Differences

• Shared features:

  • Unicellular

  • Prokaryotic 

  • Generally small and morphologically simple 

• Bacteria have peptidoglycan in their cell wall, while archaea don't, which makes targeting them with drugs challenging 

Studying Prokaryotes 

• Culture method: __________________________

  • Strengths: __________________________

  • Limitations: __________________________

• Culture-Independent: __________________________

  • Allows us to discover new lineages

  • “Metagenetics” 

  • Tells us about community composition & functional potential

Studying Prokaryotes 

• Culture method: Controlled conditions in a lab to grow microbes

  • Strengths: Allows for direct observations & experimental control

  • Limitations: Less than 1% of prokaryotes can be cultured in a lab, and need unknown or very specific conditions 

• Culture-Independent: Extract & Sequence DNA from something like soil. 

  • Allows us to discover new lineages

  • “Metagenetics” 

  • Tells us about community composition & functional potential

Phylogeny of Bacteria and Archaea

• (#)S rRNA: Prokaryotes

• (#)S rRNA: Eukaryotes 

Morphological Diversity in Bacteria 

• ________ varies

• ________ varies

• ________ varies 

Phylogeny of Bacteria and Archaea

• 16S rRNA: Prokaryotes

• 18S rRNA: Eukaryotes 

Morphological Diversity in Bacteria 

• Size varies

• Shape varies

• Motility varies 

Genetic Variation via Lateral Gene Transfer

• Hard to fight prokaryotes because of the amount and ______ of ______

• Prokaryotes have no ______, ______, or whole ______ ______

  • Transformation: ______________________________

  • Transduction: _______________________________

• Evolutionary consequence: _______________________________

Genetic Variation via Lateral Gene Transfer

• Hard to fight prokaryotes because of the amount and spread of variation 

• Prokaryotes have no meiosis, gametes, or whole genome recombination 

  • Transformation: Taking up loose DNA from the environment 

  • Transduction: Viruses move DNA from cell to cell 

• Evolutionary consequence: Rapid acquisition of novel traits and antibiotic resistance can spread horizontally 

Cell Wall Structure and Gram Staining

• Gram Staining: ___________________________

  • Gram-Positive: Cells appear ________, and have a thick layer of _________ lining the cell wall

  • Gram-Negative: Cells appear _________ and don’t have this thick layer 

Cell Wall Structure and Gram Staining

• Gram Staining: Staining cells so they become visible 

  • Gram-Positive: Cells appear purple, and have a thick layer of peptidoglycan lining the cell wall

  • Gram-Negative: Cells appear pink and don’t have this thick layer 

Ecological and Global Impacts of Microbes

• Lead to alterations of the ________, ________, and ________

• ___________: Transformed earth

  • First to perform oxygenic photosynthesis 

• Can learn a lot about early life 

Ecological and Global Impacts of Microbes

• Lead to alterations of the oceans, atmosphere, and sediments

• Cyanobacteria: Transformed earth

  • First to perform oxygenic photosynthesis 

• Can learn a lot about early life 

• Prokaryotes: ________ ________

• Eukaryotes: ___________

  • Range from ________ ________ organisms to ________ ________ organisms

• Share: Nuclear ________, Mitochondria, Cytoskeleton, Mitosis & ________

• Morphological and cellular innovations

  • Much more diversity in forms

• Prokaryotes: bacteria and archaea

• Eukaryotes: Eukaryota

  • Range from single celled organisms to complex multicellular organisms

• Share: Nuclear envelope, Mitochondria, Cytoskeleton, Mitosis & Meiosis

• Morphological and cellular innovations

  • Much more diversity in forms

What are “Protists”?

• A unique group of organisms because of the way it is classified

  • Has a common ancestor but not all of its descendants are protists → it is __________

  • General group of organisms, doesn’t have __________ __________ to unify the entire group of organisms

  • No defining __________ unique to the protists

• The idea of protists is useful in discussing early evolution of __________

  • More about practical convenience

What are “Protists”?

• A unique group of organisms because of the way it is classified

  • Has a common ancestor but not all of its descendants are protists → it is paraphyletic

  • General group of organisms, doesn’t have shared traits to unify the entire group of organisms

  • No defining synapomorphies unique to the protists

• The idea of protists is useful in discussing early evolution of eukaryotes

  • More about practical convenience

Why Biologists Study Protists

• _________ importance similar to bacteria and archaea

  • Ex. malaria

• Ecological importance

  • Dominant primary producers in _________ ecosystems

  • Form base of _________ food webs

  • Control nutrient cycling and energy flow

• Evolutionary Importance

  • Provide insight into different processes

    • Origin of _________

    • Origin of _________

    • Early _________ diversification

Why Biologists Study Protists

• Medical importance similar to bacteria and archaea

  • Ex. malaria

• Ecological importance

  • Dominant primary producers in aquatic ecosystems

  • Form base of aquatic food webs

  • Control nutrient cycling and energy flow

• Evolutionary Importance

  • Provide insight into different processes

    • Origin of multicellularity

    • Origin of organelles

    • Early eukaryotic diversification

• Extremely high population densities of ________ in the water

  • Can dominate biomass in surface waters

• Photosynthetic protists (________) fix approximately 50% of Earth’s ________

• Energy flows from the protists to the ________ to the ________ ________

• Can lead to harmful ________ ________ → involves dinoflagellates

  • Depletes oxygen

  • Deters predators

  • Big ecological and social impact

• Extremely high population densities of protists in the water

  • Can dominate biomass in surface waters

• Photosynthetic protists (phytoplankton) fix approximately 50% of Earth’s CO₂

• Energy flows from the protists to the consumers to the top predators

• Can lead to harmful algae blooms → involves dinoflagellates

  • Depletes oxygen

  • Deters predators

  • Big ecological and social impact

Studying Protist Diversity: Morphology

• Didn’t get full picture until ________ ________

• Morphological synapomorphies: ________ structure, coverings, _______ grooves

• As protists, not ________, but certain groups WITHIN the protists are monophyletic

• ________ ________ data used to define phylogeny of the protists → huge step, but still doesn’t give the full picture

• ________ ________: Using environmental DNA and sampling directly, not all can be cultured

Studying Protist Diversity: Morphology

• Didn’t get full picture until electron microscopy

• Morphological synapomorphies: Flagella structure, Cell coverings, Feeding grooves

• As protists, not monophyletic, but certain groups WITHIN the protists are monophyletic

• DNA sequencing data used to define phylogeny of the protists → huge step, but still doesn’t give the full picture

• Direct sequencing: Using environmental DNA and sampling directly, not all can be cultured

• Origin of the mitochondria (endosymbiosis)

  • Leading theory: ______________________________

• Evidence:

  • ______________

  • ______________

  • ______________

  • ______________

• Enabled efficient _______ ________

• Supported increased cell _______ and _______

• Origin of the mitochondria (endosymbiosis)

  • Leading theory: ______________________________

• Evidence:

  • Size and structure

  • Circular DNA

  • Bacteria-like ribosomes

  • Double membranes

• Enabled efficient aerobic metabolism

• Supported increased cell size and complexity

Origin of the Nuclear Envelope

• Also thought to have evolved from an ancestor of the ____________

• Infoldings of plasma membrane surround the chromosomes → eukaryotic cell arises → forming nuclear envelope and endoplasmic reticulum

• Led to separation of ____________ and ____________

• Enabled ____________ processing & regulations

Origin of the Nuclear Envelope

• Also thought to have evolved from an ancestor of the eukaryotes

• Infoldings of plasma membrane surround the chromosomes → eukaryotic cell arises → forming nuclear envelope and endoplasmic reticulum

• Led to separation of transcription and translation

• Enabled RNA processing & regulations

3 Main Protist Feeding Strategies:

1. Ingestive feeding (aka _________): Cells engulf food particles (______________________________)

2. Absorptive feeding: ___________________________________

3. Photosynthesis

Some species will combine multiple strategies for feeding → allows them to ____________________ (Feeding innovations leads to ____________)

3 Main Protist Feeding Strategies:

1. Ingestive feeding (aka phagocytosis): Cells engulf food particles (Pulls solid objects in and then breaks them down)

2. Absorptive feeding: Cell absorbs dissolved nutrients directly through the membrane

3. Photosynthesis

Some species will combine multiple strategies for feeding → allows them to diversify food resources they’re using (Feeding innovations leads to diversification)

Movement and Locomotion

• _________ motion

• Flagella and _________

  • Feature of _________ evolution

• Moving is important because they need to

  • _________ _________

  • _________ _________

  • _________ __ _________

Movement and Locomotion

• Amoeboid motion

• Flagella and cilia

  • Feature of convergent evolution

• Moving is important because they need to

  • Locate food

  • Avoid predators

  • Position for photosynthesis

• Protists can be __________ or __________

• Multicellularity evolved __________ __________ in the eukaryotes

• Common in some groups (e.g. algae, fungi, animals)

• Multicellularity allowed us to reach ______________

• Earlier stages

  • Cells would __________ __________ after division

  • Selection then favors __________ → could lead to the first origin of multicellular organisms

• In addition to multicellularity, there’s other evidence of convergent evolution (___________________) in the eukaryotes

  • E.g. photosynthesis

  • E.g. parasitism

• Protists can be unicellular or multicellular

• Multicellularity evolved multiple times in the eukaryotes

• Common in some groups (e.g. algae, fungi, animals)

• Multicellularity allowed us to reach more complex forms

• Earlier stages

  • Cells would stick together after division

  • Selection then favors cooperation → could lead to the first origin of multicellular organisms

• In addition to multicellularity, there’s other evidence of convergent evolution (developing similar traits individually) in the eukaryotes

  • E.g. photosynthesis

  • E.g. parasitism

• For most of earth’s history life was _________

• Challenges associated with land

  • _________ (Drying out) 

  • ___ _________

  • Lack of _________ _________

    • Water provides buoyancy and less effect of _________

  • _________ without water 

• _________ were the first organisms to successfully colonize land 

• For most of earth’s history life was aquatic 

• Challenges associated with land

  • Desiccation (Drying out) 

  • UV Radiation

  • Lack of structural support 

    • Water provides buoyancy and less effect of gravity 

  • Reproduction without water 

• Plants were the first organisms to successfully colonize land 

What Defines a Plant?

• Kingdom: _________

• Characteristics

  • (Unicellular/Multicellular) (Prokaryotes/Eukaryotes)

  • Photosynthetic using _________

  • Cell walls made of _________

  • Alteration of generations 

• Evidence for evolution 

  • Molecular _________

  • Cell _________

  • _________ Traits 

What Defines a Plant?

• Kingdom: Plantae 

• Characteristics

  • Multicellular Eukaryotes 

  • Photosynthetic using chloroplasts 

  • Cell walls made of cellulose 

  • Alteration of generations 

• Evidence for evolution 

  • Molecular phylogenetics

  • Cell Structure 

  • Reproductive Traits 

Life on Land (mechanisms to combat challenges) 

• ________: Outer waxy layer that's used to reduce water loss

  • The trade off is that it limited the ability to __________________________

  • Stomata: ____________________________________

  • Multicellular embryos: Allows for more ___________________________

Life on Land (mechanisms to combat challenges) 

• Cuticle: Outer waxy layer that's used to reduce water loss

  • The trade off is that it limited the ability to exchange gases (can’t get carbon dioxide in if its sealed off) 

  • Stomata: Have pores that allow gas exchange in photosynthetic tissues 

  • Multicellular embryos: Allows for more investment in embryos early on 

Alternation of Generations

• Order of steps 

  • Step 1:

  • Step 2:

  • Step 3:

  • Step 4:

  • Step 5:

Alternation of Generations

• Order of steps (Dip happy game fer Z)

  • Step 1: Diploid sporophyte produces spores by meiosis 

  • Step 2: Haploid spores grows into gametophyte 

  • Step 3: Gametophyte produces gametes by mitosis 

  • Step 4: Fertilization fuses gamete → zygote 

  • Step 5: Zygote (2n) grows into sporophyte 

Alternation of Generations

• Evolutionary Importance:

  • Dispersal (_________) 

  • Reproduction (_________) 

  • Growth (_________) 

• Alternation of Generations turns these into _________ _________, allowing the plant to __________________________

Alternation of Generations

• Evolutionary Importance:

  • Dispersal (spores) 

  • Reproduction (Gametophyte) 

  • Growth (Sporophyte) 

• Alternation of Generations turns these into separate stages, allowing the plant to dedicate more resources to each stage 

Nonvascular Plants (Bryophytes)

• Major Groups: Mosses, liverworts, hornworts 

• Key Traits:

  • Lack ________ ________

  • (Small/large) size

  • __________ dominant life cycle 

Nonvascular Plants (Bryophytes)

• Major Groups: Mosses, liverworts, hornworts 

• Key Traits:

  • Lack vascular tissue

  • Small size

  • Gametophyte dominant life cycle 

Nonvascular Plants (Bryophytes)

• Importance: 

  • _________ Species

  • Important for ___________ (_______________________)

  • Helps with _________ _________ in the environments 

• Limitations

  • Transport constraints (relies on _________, which limits their height/size) 

  • Reproductive constraint (sperm requires _________ to _________________, so they’re restricted to high _________ areas) 

Nonvascular Plants (Bryophytes)

• Importance: 

  • Pioneer Species

  • Important for soil formation (breaking matters down and making them available for other organisms use) 

  • Helps with moisture retention in the environments 

• Limitations

  • Transport constraints (relies on diffusion, which limits their height/size) 

  • Reproductive constraint (sperm requires water to swim to the egg, so they’re restricted to high moisture areas) 

Evolution of Vascular Tissue

• Xylem

  • Conducts ________ and ________

  • Contains lignin for ____________ (plants can _______ _______) 

• Phloem

  • Conducts ________ in ________ ________

Evolution of Vascular Tissue

• Xylem

  • Conducts water and minerals 

  • Contains lignin for structural support (plants can grow taller) 

• Phloem

  • Conducts sugars in organic compounds 

Seedless Vascular Plants

• Ex. ferns

• Dominant _________ stage 

• Tends to be much _________ and _________ lived than gametophyte 

• Reproductive limitation: Requires _________ for fertilization 

Seedless Vascular Plants

• Ex. ferns

• Dominant sporophyte stage 

• Tends to be much larger and longer lived than gametophyte 

• Reproductive limitation: Requires water for fertilization 

Seeds as a Major Evolutionary Innovation

• Seed: Embryo with a protective coating that contains _______ _______

• Advantages:

  • _______ resistant (no longer need to be in a _______ _______ environment) 

  • Allows for _______ (Can grow when ________________________) 

  • Long distance _______ (Can _________________) 

Seeds as a Major Evolutionary Innovation

• Seed: Embryo with a protective coating that contains stored nutrients 

• Advantages:

  • Desiccation resistant (no longer need to be in a very wet environment) 

  • Allows for dormancy (Can grow when conditions are favorable) 

  • Long distance dispersal (Can colonize new areas) 

Gymnosperms

• “The _______ _______ _______”

  • Seeds are ________________________ (Ex. conifers)

• Well adapted for _______/_______ environments

Pollen

• Pollen grains: Used to transport the _______ _______

• Dispersed by wind or animals 

  • Wind: Don’t have to rely on _______ _______, but a lot of gametes need to be produced and where they go is random 

• Key advantage: Allows fertilization without _______ _______

Gymnosperms

• “The naked seed plants”

  • Seeds are not enclosed in any kind of fruit (Ex. conifers)

• Well adapted for cold/dry environments

Pollen

• Pollen grains: Used to transport the male gametes

• Dispersed by wind or animals 

  • Wind: Don’t have to rely on animal populations, but a lot of gametes need to be produced and where they go is random 

• Key advantage: Allows fertilization without standing water 

Angiosperms: Flowering Plants

• Key traits: Flowers, fruits inclosing their seeds, double ________ (Plant only invests in ________ ________ ________ after ________ has occurred, not preemptively) 

• (#)% of modern plant species 

• Close relationship with ________

  • Flower structure is shaped by their pollinators and vice versa 

• ________ (like honeybees) or ________ pollinators 

  • ________: More likely to get fertilized but if something happens to the pollinator there’s a direct effect on the plant 

Angiosperms: Flowering Plants

• Key traits: Flowers, fruits inclosing their seeds, double fertilization (Plant only invests in nutrient rich tissue after fertilization has occurred, not preemptively) 

• 90% of modern plant species 

• Close relationship with pollinators 

  • Flower structure is shaped by their pollinators and vice versa 

• Generalist (like honeybees) or specialist pollinators 

  • Specialist: More likely to get fertilized but if something happens to the pollinator there’s a direct effect on the plant 

Fruits and Seed Dispersal

• Allows for further dispersal, reducing competition

  • If a plant drops seeds right under them, they’re creating competition for themselves

• Seeds allow for transportation and then drop off with the fertilizer they need to grow (animal poop) 

Ecological Impact of Plants

• ________ ________: Base of the terrestrial food webs 

• Important in habitat formation: Forest, grasslands, wetlands 

• Important in climate regulation: oxygen production and CO2 uptake 

• ________ ________: important in soil formation, roots can break down rock, organic matter accumulation, 

• Sets stage for: Fungal ________, herbivore evolution, terrestrial animal ________

Ecological Impact of Plants

• Primary producers: Base of the terrestrial food webs 

• Important in habitat formation: Forest, grasslands, wetlands 

• Important in climate regulation: oxygen production and CO2 uptake 

• Ecosystem Engineers: important in soil formation, roots can break down rock, organic matter accumulation, 

• Sets stage for: Fungal mutualisms, herbivore evolution, terrestrial animal diversification 

• Fungi are (eukaryotic/prokaryotic) organisms 

• Grow as _______ or _______

• One of the three multicellular terrestrial lineages (_______, _______, _______) 

• Importance for study

  • Human health (fungi can infect humans) 

  • Agriculture and food systems (both infecting food and producing foods like beer or cheese) 

  • Ecosystem function (_______ _______) 

• Fungi are eukaryotic organisms 

• Grow as single-celled or multicellular 

• One of the three multicellular terrestrial lineages (Plants, animals, fungi) 

• Importance for study

  • Human health (fungi can infect humans) 

  • Agriculture and food systems (both infecting food and producing foods like beer or cheese) 

  • Ecosystem function (nutrient cycling) 

Fungi as Decomposers

• __________ Fungi are the decomposers

  • Important in __________ __________

    • (Not many organisms can) 

  • And plants decomposition

    • (Can break down __________ & __________ which is a rare trait) 

Fungi as Decomposers

• Saprophytic Fungi are the decomposers

  • Important in wood decomposition

    • (Not many organisms can) 

  • And plants decomposition

    • (Can break down cellulose & lignin which is a rare trait) 

Fungal Growth Forms

• Yeasts: _________________

• Multicellular fungi have bodies called ________

  • The fungus itself is under the ground, the mushroom is only the ________ ________

• Dimorphic: _________________

  • Environmental influences: Temperature, nutrient availability, host environment 

• Mycelia: _________________

Fungal Growth Forms

• Yeasts: Single celled fungi 

• Multicellular fungi have bodies called mycelia 

  • The fungus itself is under the ground, the mushroom is only the reproductive structure

• Dimorphic: Can switch between single celled and multicellular

  • Environmental influences: Temperature, nutrient availability, host environment 

• Mycelia: Enormous surface area to volume ratio makes it very efficient 

Predatory Fungi

• Can trap microscopic animals (________) using modifications to the ________

• Expands their range so that they’re not only restricted to ________ or ________

Reproductive Structures vs. Feeding Structures

• Mycelium: ________ and ________

  • ________ function

• Reproductive Structures: Dense multicellular structures (like the ________) 

  • Specialized for ________ ________

Predatory Fungi

• Can trap microscopic animals (nematodes) using modifications to the hyphae 

• Expands their range so that they’re not only restricted to plant material or dead things 

Reproductive Structures vs. Feeding Structures

• Mycelium: Feeding and growth

  • Absorptive function

• Reproductive Structures: Dense multicellular structures (like the mushroom) 

  • Specialized for spore production

Fungal Diversity: Why It’s Hard to Measure

• Hidden Diversity: ________________________________

  • Like only the mushroom reproductive structure being above ground

• They also are too soft to ________

• Studying Fungi

  • Morphological approaches (______________________) 

  • Molecular approaching (Ex. ________________________) 

Fungal Diversity: Why It’s Hard to Measure

• Hidden Diversity: Many of them live in soil, or inside plants or animals, so we can’t make direct observations about them

  • Like only the mushroom reproductive structure being above ground

• They also are too soft to fossilize

• Studying Fungi

  • Morphological approaches (looking at the structures we can see) 

  • Molecular approaching (Ex. DNA or direct env. sequencing) 

Four Types of Fungi Sexual Reproductive Structures 

• __________________: Has flagella which allows for active dispersal 

• ___________: Spore producing structures formed when hyphae are yoked

  • Allows them to __________________

• ___________: Club-shaped cells where meiosis occurs, forming four spores 

  • Enhances __________________

• ___________: Sac-like cells where meiosis and one round of mitosis occur, forming eight spores 

  • Shoots spores out from the structure, allowing for rapid and widespread ____________ (Like the puff mushrooms)

Four Types of Fungi Sexual Reproductive Structures 

• Swimming Gametes and spores: Has flagella which allows for active dispersal 

• Zygosporangia: Spore producing structures formed when hyphae are yoked

  • Allows them to survive harsh conditions 

• Basidia: Club-shaped cells where meiosis occurs, forming four spores 

  • Enhances long distance spread

• Asci: Sac-like cells where meiosis and one round of mitosis occur, forming eight spores 

  • Shoots spores out from the structure, allowing for rapid and widespread colonization (Like the puff mushrooms)

Fungi Reproductive Structures 

• They can also be asexual, throwing out tons of ________ into the environment 

  • No reliance on sexual reproduction means rapid ________ without reliance on a ________

  • Issue is the lack of ________ ________

Fungi Reproductive Structures 

• They can also be asexual, throwing out tons of spores into the environment 

  • No reliance on sexual reproduction means rapid colonization without reliance on a mate

  • Issue is the lack of genetic variation 

Phylogeny of Fungi

• Evidence of similarity between _________ and fungi

  • Molecular evidence

  • Shared traits

    • _________ production

    • Posterior _________

    • _________ as storage carbohydrate 

• Fungi also evolved from an _________ _________

• The close relationship with animals makes it difficult to treat (how to target fungi without targeting our own _________) 

Phylogeny of Fungi

• Evidence of similarity between animals and fungi

  • Molecular evidence

  • Shared traits

    • Chitin production

    • Posterior flagella

    • Glycogen as storage carbohydrate 

• Fungi also evolved from an aquatic ancestor 

• The close relationship with animals makes it difficult to treat (how to target fungi without targeting our own tissue) 

Fungi as Symbionts

• Most ________ interact with fungi 

• Relationships can be ________ or ________

• Mycorrhizal Fungi: ____________________________________

  • Mutualistic exchange where plants provide ________ to the fungi, and fungi provide ________ (__, __) 

Fungi as Symbionts

• Most plants interact with fungi 

• Relationships can be mutualistic or parasitic 

• Mycorrhizal Fungi: Fungi that live in close association with plant roots

  • Mutualistic exchange where plants provide sugars to the fungi, and fungi provide nutrients (N, P) 

• The Wood Wide Web: Root networks between ________ and ________ can move ________ and ________ ________ around (resource sharing)

• Larger plants can send nutrients to seedlings

• Parent trees can send nutrients to shaded/stressed offspring

• They can also communicate

  • They can warn other plants that they’re being attacked by herbivores

  • This causes the other plants to invest in defenses even though they’re not being attacked 

• Fungi can favor plants that provide more ________, and not give as much ________ to those who don't provide as much ________

• The Wood Wide Web: Root networks between plants and fungi can move nutrients and chemical signals around (resource sharing)

• Larger plants can send nutrients to seedlings

• Parent trees can send nutrients to shaded/stressed offspring

• They can also communicate

  • They can warn other plants that they’re being attacked by herbivores

  • This causes the other plants to invest in defenses even though they’re not being attacked 

• Fungi can favor plants that provide more sugar, and not give as much nutrients to those who don't provide as much sugar 

Types of Mycorrhizae

• EMF:

  • Hyphae that penetrate ________ ________

  • Form sheaths ________ ________

  • Common in ________ ________ (Mainly associated with ________)

  • Shape ________, ________ forest systems

• AMF

  • Hyphae that penetrate ________ ________

  • Branch inside ________ ________

  • Extremely widespread in ________ (more than EMF) 

  • Rapid uptake of ________ ________

  • Drive productivity and diversity in more ________ ecosystems 

Types of Mycorrhizae

• EMF:

  • Hyphae that penetrate between cells 

  • Form sheaths around roots

  • Common in temperate forests (Mainly associated with trees)

  • Shape stable, nutrient-conserving forest systems

• AMF

  • Hyphae that penetrate cell walls 

  • Branch inside root cells 

  • Extremely widespread in plants (more than EMF) 

  • Rapid uptake of inorganic nutrients 

  • Drive productivity and diversity in more dynamic ecosystems 

Other Fungal Symbioses

• Lichens: _________ species 

• Insect associations with fungi

  • _________ _________ that aid in digestion 

Why Fungi Are Such Effective Decomposers

• They have _________ _________

• Can break down _________

Spores and Reproductive Strategy

• Spores are _________ units 

• Spores can withstand _________ _________

Other Fungal Symbioses

• Lichens: Pioneer species 

• Insect associations with fungi

  • Gut fungi that aid in digestion 

Why Fungi Are Such Effective Decomposers

• They have extracellular digestion 

• Can break down lignin 

Spores and Reproductive Strategy

• Spores are dispersal units 

• Spores can withstand harsh conditions 

What is an Animal?

• Animals are a monophyletic group (One common ancestor and all of its lineages) 

• Shared Traits

  • Multicellular eukaryotes

  • Cells lack cell walls

  • Extensive extracellular matrix 

  • Heterotrophic 

• Multicellularity + Heterotrophy + Movement = purpose is consumption 

• Closest lineage is choanoflagellates (sister taxa) 

What is an Animal?

• Animals are a ___________ group (One common ancestor and all of its lineages) 

• Shared Traits

  • Multicellular eukaryotes

  • Cells lack ___________ ___________

  • Extensive ___________ ___________

  • Heterotrophic 

• ___________ + ___________ + ___________ = purpose is consumption 

• Closest lineage is ___________ (sister taxa) 

The Cambrian Explosion

• Beginning of the Cambrian period, 541 million years ago 

• Beginning of first discovered _________ _________

• Established _________ _________ in this time that have stayed very consistent across time

  • _________ spaces have been filled

  • Developing a brand new novel _________ is very rare 

The Cambrian Explosion

• Beginning of the Cambrian period, 541 million years ago 

• Beginning of first discovered animal fossils 

• Established body plans in this time that have stayed very consistent across time

  • Niche spaces have been filled

  • Developing a brand new novel structure is very rare 

Major Animal Lineages

• Animalia → _________ & _________ → _________ & _________

  • Other lineages are not less evolved than humans, they’re ___________________

Major Animal Lineages

• Animalia → Bilateria & Non-Bilateria → Protosomes & Deuterosomes

  • Other lineages are not less evolved than humans, they’re on another evolutionary track 

Origin of Multicellularity (Sponges-first hypothesis) 

• Animals are monophyletic (one common ancestor) 

• Sponges-first hypothesis: 

  • Suggests that _______________________________

• Living sponges are not ancestors, they’re a _________ _________ with a long independent history 

Origin of Multicellularity (Sponges-first hypothesis) 

• Animals are monophyletic (one common ancestor) 

• Sponges-first hypothesis: 

  • Suggests that sponges branched off first (earliest branching ancestor or animals) 

• Living sponges are not ancestors, they’re a modern lineage with a long independent history 

Choanoflagellates and Sponges

• Shared traits between Choanoflagellates and Sponges

  • ______, ______ lifestyle

  • Similar ______ cells 

• Sponges: 

  • Multiple ______ ______ ______

  • Organized tissue and extracellular matrix 

  • Some possess a true ______

• Sponges have genes for:

  • Cell ______

  • Signaling

  • Apoptosis

  • ______ Immunity

Choanoflagellates and Sponges

• Shared traits between Choanoflagellates and Sponges

  • Sessile, benthic lifestyle

  • Similar feeding cells 

• Sponges: 

  • Multiple specialized cell types

  • Organized tissue and extracellular matrix 

  • Some possess a true epithelium 

• Sponges have genes for:

  • Cell adhesion

  • Signaling

  • Apoptosis

  • Innate Immunity

Alternative Hypothesis: Ctenophores-First

• Very strongly debated

  • ______ ______ had to evolve more than once in evolution 

• Sponge-First has the most ______

  • Nervous system and ______ evolved once

Alternative Hypothesis: Ctenophores-First

• Very strongly debated:

  • Nervous system had to evolve more than once in evolution 

• Sponge-First has the most parsimony

  • Nervous system and muscle evolved once

Body Symmetry

• Radial symmetry: Appears in earlier groups

  • Ex. Jellyfish & ctenophores

• Bilateral symmetry: Associated with directional movement and head first interactions w/ environment 

Body Symmetry

• Radial symmetry: Appears in ______ ______

  • Ex. Jellyfish & ctenophores

• Bilateral symmetry: Associated with ______ ______ and ______ ______ interactions w/ environment 

Bilateral Symmetry and the Nervous System

• Radial symmetry: Usually means a _________ _________ is present 

• Bilateral symmetry: Concentration of the nervous system creates the _________ _________ _________

• Cephalization: Concentration at the _________ end of the body 

  • Located in the head because ____________________________

Bilateral Symmetry and the Nervous System

• Radial symmetry: Usually means a nerve net is present 

• Bilateral symmetry: Concentration of the nervous system creates the central nervous system 

• Cephalization: Concentration at the anterior end of the body 

  • Located in the head because animals lead with their head 

Origin of the Gut and the “Tube-within-a-Tube” Plan

• Earlier animals have a _____-like body plan (________ ________ where the food comes in and waste gets excreted) 

• Later animals evolved “Tube-within-a-Tube” (two openings, mouth and anus) 

  • Allowed us to separate ingestion & excretion (________ ________)

  • Allowed for ________ ________

Origin of the Gut and the “Tube-within-a-Tube” Plan

• Earlier animals have a sac-like body plan (one opening where the food comes in and waste gets excreted) 

• Later animals evolved “Tube-within-a-Tube” (two openings, mouth and anus) 

  • Allowed us to separate ingestion & excretion (directional flow)

  • Allowed for regional specialization 

Protostomes vs. Deuterostomes

• Fate of the _________ determines whether something is a proto or deutero 

  • Protostomes: _________________________________

  • Deuterostomes: ________________________________

• _________ are more developmental flexibility → greater diversity 

Protostomes vs. Deuterostomes

• Fate of the blastopore determines whether something is a proto or deutero 

  • Protostomes: Blastopore becomes the mouth and the anus develops second

  • Deuterostomes: Blastopore becomes the anus and the mouth develops second

• Protostomes are more developmental flexibility → greater diversity 

Segmentation

• Repetition of body units along an axis 

• Likely due to a shared ______________

  • _________ also have a segmented body plan

• Morphology evolved (independently/codependently)

• Segmentation allowed for __________

Segmentation

• Repetition of body units along an axis 

• Likely due to a shared genetic tool kit

  • Humans also have a segmented body plan

• Morphology evolved independently 

• Segmentation allowed for diversification 

What is a virus?

• Classified as: ___________________

  • Rely on host for _________

• Traits:

  • (Not made/Made) up of cells

  • (Don’t have/Have) metabolism

  • (Can’t exist/Exist) as infectious particles outside host cells

  • (Can’t/Can) replicate independently

  • (Don’t strongly/Strongly) shape life on earth

  • (Don’t evolve/Evolve) and have genomes 

What is a virus?

• Classified as: Obligate intracellular parasite

  • Rely on host for replication 

• Traits:

  • Not made up of cells

  • Don’t have metabolism

  • Exist as infectious particles outside host cells

  • Can’t replicate independently

  • Strongly shape life on earth

  • Evolve and have genomes 

Why do biologists study viruses?

• Medical importance: ______________________________

• Evolutionary importance: ______________________________

• Genetic importance: ______________________________

Why do biologists study viruses?

• Medical importance: Can cause widespread disease in animals, plants, and humans

• Evolutionary importance: Strong agent of natural selection on host (Developing resistance to viruses) 

• Genetic importance: Responsible for a lot of lateral gene transfer (Virus infects host A, may accidentally pick up some of host A’s DNA, infect host B, and inert the DNA into host A’s genome) 

Viruses and Disease: Population-Level Effects

• Epidemic: Widespread _________________

• Pandemic: Widespread _________________

Are Viruses Alive? (TRUE OR FALSE)

• No ribosomes ___

• No ATP production ___

• Independent transcription or translation ___

Viruses and Disease: Population-Level Effects

• Epidemic: Widespread within a particular regions 

• Pandemic: Widespread across multiple regions

Are Viruses Alive? (TRUE OR FALSE)

• No ribosomes (T)

• No ATP production (T)

• Independent transcription or translation (F)

Size and abundance of viruses 

• Incredibly small (20-300 nanometers) 

• Oceans contain ten times more viruses than they do ________

• Two basic categories

  • Naked viruses (_________ only) 

  • Enveloped viruses (________ + ________)

Size and abundance of viruses 

• Incredibly small (20-300 nanometers) 

• Oceans contain ten times more viruses than they do cells

• Two basic categories

  • Naked viruses (protein capsid only) 

  • Enveloped viruses (capsid + membranous envelope)

Transmission to New Hosts

• Within organism pathways:

  • _____________

  • _____________

• Between organism pathways:

  • _____________

  • _____________

  • _____________

• This is the virus equivalent of _____________

Transmission to New Hosts

• Within organism pathways:

  • Bloodstream

  • Lymphatic System

• Between organism pathways:

  • Respiratory droplets 

  • Bodily fluids

  • Vectors

• This is the virus equivalent of dispersal

Viruses can go into types of dormant stages

• Lysogeny - in bacteriophages (viruses in bacteria) 

  • Go into a dormant state, and then can get activated) 

• Latency - in animal viruses 

  • Virus persists silently to avoid detection

Viruses can go into types of dormant stages

• Lysogeny - in bacteriophage viruses

  • Method: Go into a dormant state, and then can get activated

• Latency - in animal viruses 

  • Method: Virus persists silently to avoid detection

Viruses as Evolutionary Agents

• _________ _________

  • Host evolves defenses

  • Virus evolves counter defenses (_________ _________ _________) 

• _________ _________

  • High mutation rates

  • Short generation times

Viruses as Evolutionary Agents

• Natural Selection

  • Host evolves defenses

  • Virus evolves counter defenses (coevolutionary arms race) 

• Rapid Evolution

  • High mutation rates

  • Short generation times

Origins of Viruses (Hypotheses- no general consensus) 

• Escaped-genes hypothesis: _______________________

• Degeneration hypothesis: _______________________

• RNA-world hypothesis: _______________________

Origins of Viruses (Hypotheses- no general consensus) 

• Escaped-genes hypothesis: Viruses evolve from mobile genetic elements

• Degeneration hypothesis: Viruses descended from parasitic cells

• RNA-world hypothesis: Viruses predate cellular life 

Emerging Viruses

• New diseases infecting humans for the first time

• Zoonotic jumps: Viruses moving from animal hosts to humans 

• Phylogenetics plays an important role in understanding which and how viruses might infect humans in the future 

Emerging Viruses

• New diseases infecting humans for the first time

• Zoonotic jumps: Viruses moving from animal hosts to humans 

• Phylogenetics plays an important role in understanding which and how viruses might infect humans in the future 

What is Global Ecology?

• Ecosystem = __________ + __________

  • Linked by the ______ of energy and the ______ of nutrients 

  • All connected in the biosphere 

• Ecosystem services: (4)

  • __________________________

  • __________________________

  • __________________________

  • __________________________

What is Global Ecology?

• Ecosystem = Interacting species + abiotic environment 

  • Linked by the flow of energy and the cycling of nutrients 

  • All connected in the biosphere 

• Ecosystem services: (4)

  • Provisioning (Ex. Food, timber) 

  • Regulating (Processes that regulate like flood control) 

  • Cultural (Processes that help with recreation & mental/physical health) 

  • Supporting (Ex. Primary Productivity, Nutrient Cycling) 

    • Enable all other services

Energy Flow through Ecosystems

• Energy enters via _________ _________

  • This happens mainly through _________, but some ecosystems use _________ (Ex. Thermal vents)

• Energy is not created, it just _________ through the system 

• Primary Productivity

  • Gross primary productivity (GPP): _______________________

  • Net primary productivity (NPP): ________________________

  • NPP = _____ - _____

    • ____ is respiration & Heat loss 

Energy Flow through Ecosystems

• Energy enters via primary producers

  • This happens mainly through photosynthesis, but some ecosystems use chemosynthesis (Ex. Thermal vents)

• Energy is not created, it just flows through the system 

• Primary Productivity

  • Gross primary productivity (GPP): Total chemical energy produced by photosynthesis produced per unit area per time 

  • Net primary productivity (NPP): Energy that gets stored as new biomass (energy that isn’t lost)

  • NPP = GPP - R

    • R is respiration & Heat loss 

• Reasons why photosynthesis is inefficient 

  • Limited ___________ absorbed 

  • ___________ light variation 

  • ___________ sensitivity in enzymes (limits how much they can actually convert)

  • ___________ stress limits CO2 uptake 

• Reasons why photosynthesis is inefficient 

  • Limited wavelengths absorbed 

  • Seasonal light variation 

  • Temperature sensitivity in enzymes (limits how much they can actually convert)

  • Water stress limits CO2 uptake 

Energy Dissipation

• Energy flows (one direction/two directions)

  • ___% transferred each step, ___% lost 

• Energy Dissipation limits the number of ________________ and ____________________

Pyramids of Productivity

• More efficient for humans to feed at (lower/higher) tropic levels (feeding more people from rice then growing corn to feed chickens to feed humans) 

Energy Dissipation

• Energy flows one direction

  • 10% transferred each step, 90% lost 

• Energy Dissipation limits the number of trophic levels and population sizes of top predators 

Pyramids of Productivity

• More efficient for humans to feed at lower tropic levels (feeding more people from rice then growing corn to feed chickens to feed humans) 

• Biomagnification: ______________________________

  • _____________ increases (Herring heats a lot of zooplankton, Salmon eat a lot of Herring, etc.) 

• ________ ________ are most affected, including _________

• Biomagnification: Pollutants become magnified as they move through the trophic levels 

  • Concentration increases (Herring heats a lot of zooplankton, Salmon eat a lot of Herring, etc.) 

• Top predators are most affected, including humans 

Global Patterns of Productivity

• Terrestrial: Generally higher ________ ________ than marine environments

  • Limiting factors: ________ & ________ availability 

• Marine: Highest productivity is ________ ________ and ________ ________

  • Limiting factors: ________ & ________ availability

• Human Appropriation of NPP: 

  • We use about (#)% of NPP

  • Mechanisms: Direct ________, land-use change (ex. converting forests into agriculture), and disturbances (ex. forest fires) 

Global Patterns of Productivity

• Terrestrial: Generally higher net productivity than marine environments

  • Limiting factors: Nutrient & water availability 

• Marine: Highest productivity is coral reefs and algal beds 

  • Limiting factors: Light & nutrient availability

• Human Appropriation of NPP: 

  • We use about 20% of NPP

  • Mechanisms: Direct harvesting, land-use change (ex. converting forests into agriculture), and disturbances (ex. forest fires) 

Nutrient Cycling within Ecosystems

• Uptake → assimilation → consumption 

• Death & Waste → detritus

• Decomposition → break up of nutrients 

• Control Rate:

  • ___________

  • ___________ availability

  • ___________ availability 

• Rapid cycling in places like ___________ ___________, slower cycling in places like ___________ ___________

Nutrient Cycling within Ecosystems

• Uptake → assimilation → consumption 

• Death & Waste → detritus

• Decomposition → break up of nutrients 

• Control Rate:

  • Temperature

  • Moisture availability

  • Oxygen availability 

• Rapid cycling in places like tropical rainforests, slower cycling in places like boreal forests 

The Global Water Cycle

• Four Major Reservoirs: _________, _________, _________, _________

• _________ drives the entire water cycle → precipitation gives us fresh water system → transpiration (plants releasing water) controls _________ → runoff moves nutrients and shapes landscapes → percolation (_____________________)

The Global Water Cycle

• Four Major Reservoirs: Ground water, atmosphere, ice, and ocean 

• Evaporation drives the entire water cycle → precipitation gives us fresh water system → transpiration (plants releasing water) controls climate → runoff moves nutrients and shapes landscapes → percolation (water soaking into soil) 

The Global Nitrogen Cycle

• Plants cannot consume _________ _________, so they go through nitrogen fixation to make it usable 

• Nitrogen fixation methods:

  • N2 → either ______ or ______ (_________ or _________) 

• _________ and _________ both drive nitrogen fixation 

The Global Nitrogen Cycle

• Plants cannot consume atmospheric nitrogen, so they go through nitrogen fixation to make it usable 

• Nitrogen fixation methods:

  • N2 → either NH4+ or NO3- (Ammonium or Nitrate) 

• Bacteria and lightning both drive nitrogen fixation 

The Global Carbon Cycle

• Four Major Reservoirs: _________, _________, _________, _________

• ___________ removes CO2, ___________ releases CO2

Global Climate Change

• Interruptions to the carbon cycle are increasing ___________ ___________ and ___________ the planet 

The Global Carbon Cycle

• Major Reservoirs: Oceans, sediments/rocks, terrestrial biomass, atmosphere

• Photosynthesis removes CO2, Respiration releases CO2

Global Climate Change

• Interruptions to the carbon cycle are increasing greenhouse gasses and insulating the planet