Bio 104 1-3

Absolutely — here’s your Bio 1040 Exam 1 Master Vocabulary List (Lectures 1–3) 💥

I’ve grouped everything logically (Lecture 1 → Microevolution, Lecture 2 → Speciation, Lecture 3 → Phylogeny).

Each term has a short, clear definition — and examples where they help you remember.

🧬

LECTURE 1 – INTRODUCTION & MICROEVOLUTION

🔹 Core Evolution Concepts

Term	Definition	Example
Evolution	Change in inherited traits (allele frequencies) of a population over generations.	Darwin’s finches evolving deeper beaks after drought.
Microevolution	Evolution within a population or species (small-scale).	Change in moth coloration due to pollution.
Macroevolution	Large-scale evolution above the species level; origin of new species and clades.	Evolution of mammals from reptile ancestors.
Population	Group of interbreeding individuals of one species living in a given area.	All finches on one island.
Gene Pool	Total collection of alleles in a population.	All the different alleles for beak size in a finch population.
Allele Frequency	Proportion of one allele among all alleles for a gene.	p = freq(A), q = freq(a).

🔹 Genetic Terms

Term	Definition	Example
Genotype	Genetic makeup (e.g., AA, Aa, aa).	A heterozygote Aa.
Phenotype	Physical expression of genotype.	Brown vs. white fur.
Locus	Location of a gene on a chromosome.	Hemoglobin gene locus on chromosome 11.
Allele	Variant of a gene.	A vs. a.
Homozygous / Heterozygous	Two same alleles / two different alleles.	AA vs. Aa.

🔹 Hardy–Weinberg Equilibrium (HWE)

Term	Definition	Example
HWE	Null model showing when evolution does not occur (allele frequencies remain constant).	p² + 2pq + q² = 1
Conditions for HWE	No mutation, migration, drift, or selection; random mating; infinite population.	Real populations always violate → evolution happens.
Null Model	Baseline expectation used to detect evolution.	HWE predicts no change; if data differ, evolution is occurring.

🔹 Mechanisms of Microevolution

Mechanism	Definition	Example
Mutation	Random change in DNA → new alleles.	Sickle-cell mutation in hemoglobin gene.
Migration (Gene Flow)	Movement of individuals or alleles between populations.	Wind-blown pollen carrying genes.
Genetic Drift	Random change in allele frequencies (strongest in small populations).	Bottleneck after natural disaster.
Founder Effect	Small group establishes new population → low genetic diversity.	Island colonization.
Bottleneck Effect	Population drastically reduced → loss of genetic variation.	Cheetahs after Ice Age.
Natural Selection	Nonrandom process favoring traits that increase survival/fecundity.	Peppered moths during Industrial Revolution.

🔹 Requirements for Natural Selection

Variation in traits
Heritability (traits passed to offspring)
Differential survival/fecundity
Trait correlated with success

✅ Result → Adaptation

Term	Definition	Example
Adaptation	Trait that improves survival or reproduction.	Camouflage fur.
Fecundity	Ability to produce offspring.	High egg production in fish.
Fitness (Darwinian)	Survival + fecundity.	Plants making more viable seeds.

🔹 Key Examples

Example	Concept Demonstrated
Darwin’s finches	Natural selection & heritable variation.
Chili pepper capsaicin	Coevolution (discourages mammals, attracts birds).
Artificial selection in fruit flies	Humans directing evolution by selecting traits.

🌿

LECTURE 2 – SPECIATION

🔹 Core Terms

Term	Definition	Example
Speciation	Process by which one species splits into two or more distinct species.	Ancestral finch → multiple island finch species.
Species	Group of organisms capable of interbreeding and producing fertile offspring.	Humans (Homo sapiens).
Anagenesis	Evolutionary change within a single lineage (no split).	Gradual change of a fossil lineage.
Cladogenesis	Splitting of one lineage into two (new species).	Divergence of wolves and coyotes.

🔹 Species Concepts

Concept	Definition	Key Person	Example / Notes
Biological Species Concept (BSC)	Species = populations that can interbreed and are reproductively isolated.	Ernst Mayr	Does not apply to fossils/asexuals.
Evolutionary Species Concept	Lineage evolving separately with its own historical fate.	G.G. Simpson	Useful for fossils & phylogeny.
General Lineage Concept	Species = separately evolving lineages; different criteria show separation.	Kevin de Queiroz	Modern unified concept.
Cryptic Species	Morphologically identical but genetically distinct.	Tree frogs that look the same.
Polymorphism	Multiple distinct forms within one species.	Color morphs of Hawaiian spiders.
Sexual Dimorphism	Male and female forms differ.	Peacock vs. peahen.

🔹 Reproductive Isolation

Prezygotic (before fertilization):

Temporal isolation: breed at different times. → Hawks vs. apples (Rhagoletis flies)
Habitat isolation: occupy different habitats.
Behavioral isolation: unique mating calls/courtship. → Frog calls
Mechanical isolation: incompatible reproductive organs.
Gametic isolation: sperm and egg don’t fuse.

Postzygotic (after fertilization):

Hybrid inviability: embryo dies early.
Hybrid sterility: hybrid lives but is sterile (e.g., mule = horse + donkey).
Hybrid breakdown: later generations weak or sterile.

🔹 Models of Speciation

Type	Description	Example
Allopatric Speciation	Populations separated by a physical barrier → divergence.	Isthmus of Panama split shrimp; glaciation events.
Vicariance	Barrier forms and splits an existing population.	River divides population.
Dispersal	Individuals cross a barrier and start a new population.	Hawaiian fruit flies colonizing islands.
Parapatric Speciation	Adjacent populations diverge along environmental gradient; some gene flow.	Grass near metal mines evolving tolerance.
Sympatric Speciation	Divergence within same area due to disruptive selection.	Apple maggot flies, sticklebacks, palms.
Ring Species	Populations form ring; ends can’t interbreed.	Ensatina salamanders, Larus gulls.

🔹 Polyploidy (common in plants)

Term	Definition	Example
Polyploidy	Doubling of chromosome sets → instant reproductive isolation.	Many ferns and crops.
Autopolyploidy	Within one species (chromosomes fail to separate).	Tetraploid potato species.
Allopolyploidy	Between two species (hybridization + doubling).	Brassica napus (canola).
Nondisjunction	Error in meiosis creating gametes with extra chromosomes.	Cause of polyploidy.

🔹 Key Models

Term	Definition	Example
Dobzhansky–Muller Model	Genetic incompatibility evolves between isolated populations, causing hybrid sterility.	Fly hybrid genes don’t interact properly.
Reinforcement	Selection strengthens prezygotic barriers when hybrids are less fit.	Two frog species reinforcing mating call differences.
Secondary Contact	Isolated populations meet again and may hybridize.	Hybrid zones between species.

🌳

LECTURE 3 – PHYLOGENY

🔹 Core Concepts

Term	Definition	Example
Phylogeny	Evolutionary history of a group or lineage.	Tree of Life diagram.
Phylogenetic Tree	Visual representation of evolutionary relationships.	Mammal phylogeny showing primates, rodents, etc.
Root	Common ancestor of all taxa on the tree.	Base of the tree.
Node	Branching point = speciation event.	Where one lineage splits into two.
Branch	Lineage evolving through time.	Mammal lineage.
Tip	Existing species.	Humans, chimpanzees, etc.
MRCA	Most recent common ancestor.	Humans & chimps share MRCA ~6 Mya.

🔹 Clades and Groups

Type	Definition	Example
Clade (Monophyletic Group)	Ancestor + all descendants.	Mammals.
Paraphyletic Group	Ancestor but not all descendants.	“Reptiles” (excluding birds).
Polyphyletic Group	Group without common ancestor (assembled by similarity).	“Marine mammals” (seals + whales).

🔹 Character Data

Term	Definition	Example
Character	Heritable feature used to infer relationships.	Presence of hair.
Character State	Variation of a character.	Hair: present (1) or absent (0).
Synapomorphy	Shared derived trait that defines a clade.	Feathers in birds.
Symplesiomorphy	Shared ancestral trait (uninformative).	Backbone in vertebrates.
Homology	Similarity due to shared ancestry.	Forelimb bones of bat, whale, human.
Homoplasy	Similarity due to convergence, not ancestry.	Wings of bats & birds.

🔹 Building Trees

Concept	Definition	Example
Outgroup	Closely related taxon used to determine ancestral vs. derived traits.	Non-primate mammals for primate tree.
Character Polarity	Direction of evolution (ancestral → derived).	Tails ancestral in primates.
Parsimony	Simplest tree (fewest changes) preferred.	Tree requiring 6 vs. 8 changes = 6-change tree is best.
Homoplasy Conflict	Trait evolves twice or is lost twice.	Flight in bats & birds.
Heuristic Search	Algorithm that finds best tree when too many possible trees exist.	Computer tree searches.

🔹 Molecular Models

Model	Description	Notes
Jukes–Cantor (JC)	All nucleotide substitutions equally probable.	Simplest model.
Kimura Two-Parameter (K2P)	Transitions and transversions occur at different rates.	More realistic.

🔹 Advanced Concepts

Term	Definition	Example
Orthologs	Homologous genes diverged by speciation.	Hemoglobin in humans vs. mice.
Paralogs	Homologous genes diverged by duplication.	Alpha vs. beta hemoglobin.
Incomplete Lineage Sorting (ILS)	Gene trees differ from species trees due to ancestral polymorphism.	Some bird genes show different relationships than species tree.
Deep Coalescence	Same as ILS—ancestral variation persists through speciation.	Mismatched gene histories.

🔹 Key Takeaways

Phylogeny = hypothesis of relationships.
Only shared derived traits (synapomorphies) define clades.
Outgroups determine ancestral vs. derived states.
All extant species are equally “evolved.”
You are related to every other living thing via shared ancestry.

Would you like me to make this into a printable 2-page exam study sheet (PDF format) — clean layout, perfect for quick memorization?