Bio Final

Genetic Diversity

Variation in alleles within a population; increases adaptability.

Species Diversity

Number of species + their relative abundance in an area

Functional Diversity

Range of biological traits and ecological roles in a community

Ecosystem Diversity

Variety of ecosystems, habitats, and ecological processes

Why Africa avoided mass extinctions

Humans evolved there —> animals co-evolved with humans —> developed anti-predator behaviors

Why islands have more extinctions

Small populations, limited resources, native species, high endemism

Leading cause of extinction

HIPPO: Habitat loss, Invasive species, Pollution, Population Growth, Overexploitation

Extrinsic Value of Biodiversity

Benefits to humans (ecosystem services, medicine, food)

Intrinsic Value of Biodiversity

Species have value simple because they exist

Biological Species Concept

Interbreeding populations reproductively isolated from others

Pros: testable

Cons: not for fossils/asexuals

Morphospecies Concept

Species defined by physical traits

Pros: widely application

Cons: subjective

Phylogenetic Species Concept

Smallest monophyletic group on a phylogeny

Pros: precise

Cons: requires genetic data

Cladogram labeling

Made up of root, nodes, branches, tips, and outgroup

Tools for phylogenies

Morphology, DNA sequences, protein sequences, and fossils

Synapomorphy

Shared derived trait unique to a clade

Sympleiomorphy

Shared ancestral trait, not useful for defining clades

Monophyletic group

Common ancestor + All descendants

Paraphyletic Group

Common Ancestor + Some descendants

Polyphyletic Group

Group lacking a common ancestor, grouped by convergent traits

Convergent evolution

Independent evolution of similar traits, misleading because traits are not inherited from a common ancestor

Parsimony Limitations

Can be misled by convergent evolution or rapid evolution

Molecular Clock

Uses mutation rates to estimate divergence times

Interpreting Cladograms

Cladograms show relationships, not “progress” or “complexity”

Constructing Cladograms

Group by shared derived traits, build from outgroup —> ingroup

Why are viruses are particles?

They lack metabolism, homeostasis, and independent reproduction

Virus origins

Escape hypothesis, reduction hypothesis, virus-first hypothesis

How do new viruses emerge?

Mutation, recombination, and host switching

Two basic viral structures

Genetics Material (DNA/RNA) + capsid, some have envelopes

Virus Classification

Genome type, capsid shape, envelope presence, host range

Lytic Cycle

Virus replicates —> bursts cell

Lysogenic Cycle

Viral DNA integrates into host genome, dormant until triggered

Virus Entry

Receptor binding, Membrane fusion, and endocytosis

Virus Exit

Lysis, budding, and ecosytosis

What viruses co-opt

Host ribosomes, enzymes, and machinery to make viral proteins

Antigenic Shift

Major genome reassortment —> new viral strains —> pandemics

Why do phylogenies matter for viruses?

Track transmission, evolution, outbreaks, and vaccine targets

What structural features do Bacteria and Archaea share?

Both are prokaryotic, lack a nucleus, have circular DNA, ribosomes, and cell walls.

How do Bacteria and Archaea differ in cell membrane structure?

Archaea have ether‑linked lipids; Bacteria have ester‑linked lipids.

How do Bacteria and Archaea differ in cell wall structure?

Bacteria have peptidoglycan; Archaea lack peptidoglycan and use pseudopeptidoglycan or protein walls.

Why does archaeal membrane structure explain extremophily?

Ether bonds and branched isoprenoids resist heat, acid, and salinity.

Why was Carl Woese’s chosen molecule important for discovering Archaea?

He used 16S rRNA, which evolves slowly and reveals deep evolutionary relationships.

What does the modern Tree of Life look like?

A two‑domain tree: Bacteria and Archaea, with Eukaryotes nested within Archaea.

Which domain is the outgroup?

Bacteria.

What phylogenetic term describes Archaea relative to eukaryotes?

Paraphyletic (Eukarya branch from within Archaea).

How is bacterial/archaeal reproduction different from genetic recombination?

Reproduction = binary fission (clonal).

Recombination = exchange of DNA without reproduction.

What role does horizontal gene transfer play in evolution?

It blurs lineage boundaries, accelerates adaptation, and complicates phylogenies.

How do Bacteria & Archaea accomplish genetic recombination?

Transformation, transduction, conjugation.

What is the difference between gram‑positive and gram‑negative bacteria?

Gram+ = thick peptidoglycan, no outer membrane.
Gram– = thin peptidoglycan + outer membrane with LPS.

Why is this important for microbiologists and healthcare workers?

Determines antibiotic susceptibility and pathogenicity.

What should you know about bacteria responsible for diseases discussed in class?

Identify which species causes which disease (e.g., Vibrio cholerae, Borrelia burgdorferi, etc.).

What types of bacterial/archaeal metabolism should you understand?

Autotrophy, heterotrophy, chemolithotrophy, photoautotrophy, anaerobic vs. aerobic respiration.

What role do bacteria play in the nitrogen cycle?

Nitrogen fixation, nitrification, denitrification, ammonification.

What is eutrophication?

Nutrient enrichment → algal blooms → oxygen depletion.

Why is eutrophication problematic?

Causes dead zones, fish kills, and ecosystem collapse.

What are characteristics of a healthy microbiome?

High diversity, stability, beneficial metabolic activity.

How does it relate to overall health?

Influences immunity, digestion, inflammation, mental health.

How is bioremediation used in ecological restoration?

Microbes break down pollutants (oil, toxins, heavy metals).

What issues does antibiotic resistance present to pharmaceutical companies?

Reduced drug effectiveness, costly R&D, rapid resistance evolution.

Why are the 5 major Bacteria phyla significant?

Known for roles in disease, nitrogen fixation, photosynthesis, decomposition, and biotechnology.

Why are the 2 major Archaea phyla and 1 supergroup significant?

Known for extremophily, methane production, and being ancestral to eukaryotes.

What were the 2 primary endosymbiosis events?

Ancestral archaeal host engulfed α‑proteobacterium → mitochondria.

Early eukaryote engulfed cyanobacterium → chloroplasts.

What are the 5 pieces of evidence for endosymbiosis?

Own circular DNA

Double membranes

Bacterial ribosomes

Replicate by fission

Gene similarity to bacteria

What was the secondary endosymbiosis event?

A eukaryote engulfed a photosynthetic eukaryote (red or green alga).

What protists cause diseases discussed in class?

Examples: Plasmodium, Trypanosoma, Giardia, Entamoeba.

Why are the 12 major protist phyla significant?

Roles in photosynthesis, decomposition, symbiosis, disease, and food webs.

What is the phylogeny of protists relative to plants, fungi, and animals?

Protists are paraphyletic and ancestors of all three multicellular lineages.

What does amitochondriate mean?

Lacking mitochondria (or having reduced forms like mitosomes).

What Amitochondriate examples were discussed?

Giardia, Trichomonas.

What factors influence red tide events?

Nutrient runoff, warm water, calm seas, algal species composition.

What factors influence coral bleaching?

Temperature rise, acidification, pollution, UV stress.

What is alternation of generations?

Life cycle alternating between haploid gametophyte and diploid sporophyte.

Why is it evolutionarily important?

Increases genetic diversity and allows adaptation to land.

Q: What are the three major Plantae lineages?

A: Red algae, green algae, land plants.

Q: What is Rhodophyta?

A: Red algae; marine, contain phycoerythrin.

Q: What defines green algae?

A: Chlorophyll a & b, cellulose walls, starch storage.

Q: What are Charophytes?

A: Stoneworts; closest relatives of land plants.

Q: What are Bryophytes?

A: Mosses; nonvascular, gametophyte‑dominant.

Q: What are Lycophytes?

A: Club mosses; early vascular plants.

Q: What are Pteridophytes?

A: Ferns; vascular, seedless.

Q: What are gymnosperms?

A: Seed plants with “naked” seeds (no fruit).

Q: What are angiosperms?

A: Flowering plants with seeds enclosed in fruit.

Q: What is the synapomorphy of Plantae?

A: Chloroplasts from primary endosymbiosis with cyanobacteria.

Q: Where do red algae sit on the Plantae tree?

A: Early‑branching lineage.

Q: Why are red algae ecologically important?

A: Reef building, food, agar, carrageenan.

Q: What pigment gives red algae their color?

A: Phycoerythrin.

Q: Why do red algae dominate deep water?

A: Phycoerythrin absorbs blue/green light that penetrates deepest.

Q: What are green algae synapomorphies?

A: Chlorophyll a & b, cellulose walls, starch.

Q: Why are charophytes important?

A: Sister group to land plants.

Q: What evidence links land plants to green algae?

A: Same pigments

Stacked thylakoids

Cellulose + peroxisome enzymes

Flagellated sperm

Starch storage

Q: What are land plant synapomorphies?

A: Cuticle, stomata, embryo retention, alternation of generations.

Q: What advantages did land offer?

A: More sunlight, CO₂, nutrients; no herbivores; less competition.

Q: What challenges did plants face on land?

A: Desiccation, UV radiation, structural support, water transport, reproduction without water.

Q: What is the cuticle?

A: Waxy layer preventing water loss.

Q: What are stomata?

A: Pores for gas exchange.

Q: What do guard cells do?

A: Regulate stomatal opening.

Q: What protects plants from UV?

A: Flavonoids.

Q: Spores are produced by what process?

A: Meiosis.

Q: What does the embryo receive from the parent?

A: Nutrients via placental transfer cells.

Q: What is sporopollenin?

A: Tough polymer coating spores/pollen.

Q: Where do mosses live?

A: Moist forests, bogs, tundra.