Biodiversity II Final Review:

Charles Darwin

1809-1882

- Theory shaped by several different fields of study and experiences: geology, economics, Beagle

- Proposed that species evolve over time through natural selection.

Alfred Russel Wallace

Naturalist in the Amazon and Southeast Asia ~ 1848

• Collected beetles

- Reached similar conclusions as Darwin

Natural Selection leads to...

Adaptations

Evidence of Evolutionary Change

• Fossil record

• Biogeography

• Observations of natural and artificial selection

• Homologies

• Anatomical

• Developmental

• Molecular

Evidence of Evolutionary Change - Fossil Records

- Fossils are preserved remains or traces of ancient organisms.

- Depth of the fossil can help inform its age

- Fossil record is incomplete, but shows gradual evolutionary change (e.g., horses)

Transitional Form

Intermediate between ancestral form and descendant

Evidence of Evolutionary Change - Biogeography

- Spatial record of evolution

It shows that organisms in similar environments but different locations evolve independently, while nearby regions tend to have related species.

- Similar species on continents that are far apart suggest past physical connection

Evidence of Evolutionary Change - Direct Observations (Natural

and Artificial Selection)

Selective breeding/ artificial selection

Breeders choose parents, over time can lead to large changes in morphology

• Made possible by genetic variation

Evidence of Evolutionary Change - Homologies: Anatomical

Refers to similarities in the physical structures of different organisms that arise from a common ancestor, even if those structures serve different functions today.

A classic example is the forelimbs of vertebrates:

- Human arm (grasping)

- Whale flipper (swimming)

- Bat wing (flying)

Evidence of Evolutionary Change - Homologies: Developmental

Refers to similarities between structures in different organisms that arise from the same embryonic origin or developmental pathway.

- Species that differ as adults often bear striking similarities during embryonic stages

- Presence of gill ridges in human embryos indicates that humans evolved from an aquatic animal with gill slits

- Human embryos have long bony tails

Evidence of Evolutionary Change - Homologies: Molecular

- The idea that DNA, RNA, or protein sequences are similar because they were inherited from a common ancestor.

- All living species use DNA to store information

- Sequences of closely related species tend to be more similar to each other than to distantly related species

Convergent Evolution

2 species from different lineages show similar

characteristics because they occupy similar

environments

The Mechanism of Natural Selection

1. Variation exists Individuals in a population are not identical—they differ in traits like size, color, behavior, or physiology. These differences often come from genetic variation (mutations, recombination).

2. Traits are heritable Some of these differences can be passed from parents to offspring through genes.

3. Overproduction and competition Organisms tend to produce more offspring than can survive. Limited resources (food, space, mates) create competition.

4. Differential survival and reproduction Individuals with traits better suited to their environment are more likely to survive and reproduce. This is often called “fitness.”

5. Accumulation of favorable traits Over generations, beneficial traits become more common in the population, because the individuals carrying them leave more offspring.

Descent with modification

A concept from the theory of evolution by natural selection stating that species change over time, with new species arising from pre-existing ones while retaining some ancestral traits.

Homology

Similarity between traits due to shared ancestry, even if the traits serve different functions.

Homologous structure

A physical feature in different species that has a common evolutionary origin but may have different functions (e.g., vertebrate forelimbs).

Analogous structure

Structures that serve similar functions but evolved independently, not from a common ancestor (e.g., wings of birds and insects).

Convergent evolution

The process where unrelated species independently evolve similar traits due to similar environmental pressures.

Fossil

Preserved remains, impressions, or traces of ancient organisms, providing evidence of past life and evolution.

Vestigial structure

A reduced or nonfunctional feature that was functional in an organism's ancestors (e.g., human tailbone).

Evolutionary tree

A diagram (also called a phylogenetic tree) showing relationships among species based on common ancestry and divergence over time.

Biogeography

The study of the geographic distribution of species and ecosystems, helping explain how evolution and Earth's history shape where organisms live.

Artificial selection

The intentional breeding of organisms by humans to enhance desired traits (e.g., dog breeding).

Adaptation

A heritable trait that increases an organism's ability to survive and reproduce in a specific environment.

Why variation is common and necessary for natural selection

Variation exists in populations because of:

Mutations (new genetic changes)

Genetic recombination during meiosis

Gene flow between populations

This variation is essential for natural selection because:

Selection can only act on existing differences

Without variation, all individuals would respond the same to environmental pressures → no evolution

Using the Hardy-Weinberg equilibrium

Key equations:

Allele frequencies: p + q = 1 (p = dominant allele, q = recessive allele)

Genotype frequencies: p^2 + 2pq + q^2 = 1

p^2 = homozygous dominant

2pq = heterozygous

q^2 = homozygous recessive

Five conditions for Hardy-Weinberg equilibrium

No mutations

Random mating

No natural selection

Extremely large population size (no drift)

No gene flow (no migration)

Four patterns of natural selection

- Directional selection

- Stabilizing selection

- Disruptive selection

- Balancing selection

Directional selection

Favors one extreme phenotype

Example: larger beak size becoming more common

Stabilizing selection

Favors intermediate traits

Reduces variation (average individuals do best)

Disruptive selection

Favors both extremes over the intermediate

Can lead to speciation

Balancing selection

Maintains multiple alleles in a population

Often due to heterozygote advantage or changing environments

Sexual selection

A type of natural selection focused on mating success rather than survival.

Types:

Intrasexual selection

Competition within the same sex (e.g., male vs male fighting)

Intersexual selection

One sex chooses mates (often female choice based on traits)

Genetic drift

- Random change in allele frequencies, especially in small populations.

Key points:

Not based on fitness (pure chance)

Can reduce genetic variation

Strongest in small populations

Examples:

Bottleneck effect: sudden population reduction

Founder effect: small group starts a new population

Biological Species Concept (BSC)

Species are groups of actually or potentially interbreeding populations that are reproductively isolated from others.

Limitation: doesn't work for asexual organisms or fossils

Morphological Species Concept

Species are defined by physical traits (appearance).

Limitation: subjective; different species can look similar (cryptic species)

Phylogenetic Species Concept

Species are the smallest group sharing a common ancestor (based on DNA/evolutionary history).

Limitation: requires detailed data; can over-split species

Why reproductive isolation is necessary

- Prevents gene flow between populations.

Without it:

Populations would keep mixing genetically

Differences would not accumulate

With isolation:

Genetic differences build up over time

Eventually leads to new species (speciation)

Eight mechanisms of reproductive isolation (Prezygotic)

Habitat isolation – live in different environments

Temporal isolation – breed at different times

Behavioral isolation – different mating behaviors

Mechanical isolation – incompatible reproductive structures

Gametic isolation – sperm and egg cannot fuse

Eight mechanisms of reproductive isolation (Postzygotic)

Reduced hybrid viability – offspring don’t survive well

Reduced hybrid fertility – offspring are sterile (e.g., mule)

Hybrid breakdown – offspring viable but weak in later generations

Sympatric speciation (same location)

Occurs without geographic separation.

Common mechanisms:

Polyploidy (extra chromosome sets, especially in plants)

Habitat differentiation within the same area

Sexual selection (mate preferences split populations)

Disruptive selection

Allopatric speciation (most common)

Happens when populations are geographically separated (mountains, rivers, distance).

Why it's most common:

Physical barriers easily stop gene flow

Populations evolve independently under different conditions

Speciation

Formation of new species

Reproductive isolation

Barriers preventing interbreeding

Biological species concept

Defines species by ability to interbreed

Allopatric speciation

Speciation due to geographic separation

Sympatric speciation

Speciation without geographic separation

Hybrid zone

Area where two species meet and interbreed

Polyploidy

Extra sets of chromosomes (common in plants)

Hybrid

Offspring of two different species

Intraspecific

Within the same species

Interspecific

Between different species

Adaptive radiation

Rapid diversification into many species from a common ancestor (often when new niches open)

How eukaryotic cells evolved from prokaryotic cells

The endosymbiotic theory.

- An ancestral prokaryotic cell engulfed smaller bacteria

- Instead of digesting them, they formed a symbiotic relationship

- These internalized bacteria evolved into organelles:

- Mitochondria (from aerobic bacteria)

- Chloroplasts (from photosynthetic bacteria, in plants/algae)

Biases of the fossil record

Hard parts preserve better (bones, shells > soft tissue)

Certain environments favor fossilization (sediments, low oxygen)

Recent fossils are more common than older ones

Geological processes (erosion, heat) destroy fossils

What we know (and don't) about the origin of life (Best Understood)

- Early Earth had simple molecules (water, methane, ammonia)

- Organic molecules can form naturally (e.g., Miller-Urey type experiments)

- RNA may have been an early genetic system (RNA world hypothesis)

What we know (and don't) about the origin of life (Less Certain)

Exact pathway from nonliving chemistry → first living cells

First self-replicating system

Exact environment where life began (deep-sea vents vs shallow pools)

Timeline of life on Earth

Earth formed about 4.6 billion years ago.

Prokaryotes: ~3.5–3.8 billion years ago

Eukaryotes: ~2.0–2.5 billion years ago

Multicellular eukaryotes: ~1.0 billion years ago

Animals: ~600 million years ago

Land plants: ~470 million years ago

Humans (Homo sapiens): ~300,000 years ago

Changes in Earth's environment and their effects

Oxygen revolution (~2.4 billion years ago)

- Photosynthetic microbes released oxygen

- Caused mass extinction of anaerobic organisms

- Enabled evolution of aerobic life

Climate changes (ice ages, warming periods)

- Alter habitats and drive natural selection

Mass extinctions (e.g., asteroid impacts)

- Wipe out species → open niches → adaptive radiations

Estimating fossil age (radiometric dating)

Basic idea:

Unstable isotopes decay at a known rate (half-life)

Measure ratio of parent → daughter isotopes

Example:

If half-life = 1 million years

50% parent left → 1 million years old

25% parent left → 2 million years old

Common isotopes:

Carbon-14 (recent fossils)

Uranium-238 (very old rocks)

Early development and evolutionary relationships

Studying embryos helps reveal shared ancestry.

- Different species often show similar early stages

- Controlled by conserved developmental genes (e.g., Hox genes)

Interpreting and drawing phylogenetic trees

How to read one:

- Root = common ancestor

- Branches = lineages through time

- Nodes = common ancestors where lineages split

- Sister taxa = closest relatives (share a recent node)

Drawing one (basic steps):

Identify shared traits (derived characteristics)

Group organisms by shared derived traits

Place the most ancestral traits near the root

Add branches where new traits appear

Trees can...

change

Phylogenetic trees are hypotheses, not final truths.

New DNA evidence or fossil discoveries can change relationships

Advances in molecular biology often lead to revisions

Monophyletic group (clade)

Includes a common ancestor and all descendants

Why monophyletic is preferred:

- Accurately reflects evolutionary history

- Matches patterns of descent in evolution

Paraphyletic group

- Includes a common ancestor but not all descendants

Polyphyletic group

- Includes organisms without their common ancestor

Principle of parsimony

The simplest explanation (fewest evolutionary changes) is most likely correct.

When choosing between trees:

- Prefer the one requiring the fewest mutations or trait changes

How neutral mutations spread

- Changes in DNA that don’t affect fitness.

They spread through populations via genetic drift:

- Random chance determines whether they increase or disappear

- Especially important in small populations

- Can eventually become common or fixed without providing an advantage

Using molecular clocks

A molecular clock uses the rate of DNA mutations to estimate how long ago two species diverged.

- Mutations accumulate at roughly constant rates in some genes

- By comparing DNA differences, scientists estimate time since a common ancestor

Basic idea:

- More genetic differences → longer time since divergence

- Calibrated using fossils or known dates

Complications in phylogenetic trees

(HGT): Horizontal gene transfer is when genes move between unrelated organisms (common in bacteria).

- Makes species appear more closely related than they are

- Creates a “web” of relationships instead of a simple tree

Convergent evolution: Convergent evolution occurs when unrelated species evolve similar traits.

- Leads to analogous structures

- Can mislead scientists into grouping species incorrectly

Binomial nomenclature & taxonomy

Binomial nomenclature

- Developed by Carl Linnaeus:

- Each species has a two-part name:

Genus (capitalized)

Species (lowercase)

Example: Homo sapiens

Taxonomic hierarchy (broad → specific):

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

Phylogeny

Evolutionary history of a species or group

Systematics

Study of classifying organisms and their relationships

Taxon

Any named group (e.g., species, genus, family)

Sister taxa

Two groups that share an immediate common ancestor

Analogy

Similarity due to convergent evolution, not shared ancestry

Homology

Similarity due to shared ancestry

Clade

A monophyletic group (ancestor + all descendants)

Monophyletic

Includes common ancestor and all descendants

Paraphyletic

Includes ancestor but not all descendants

Polyphyletic

Excludes common ancestor

Shared ancestral character

Trait inherited from a distant ancestor (not unique to a group)

Shared derived character (synapomorphy)

Trait unique to a group, used to define clades

Bacteria

Prokaryotic (no nucleus)

Cell walls contain peptidoglycan

Very diverse metabolically

Archaea

Prokaryotic

Cell walls lack peptidoglycan

Often live in extreme environments

Biochemically more similar to eukaryotes

Archaea and Eukarya are more closely related to each other than either is to Bacteria

Eukarya

Have nucleus and membrane-bound organelles

Include animals, plants, fungi, protists

Ecological roles of prokaryotes

Decomposers: break down dead organic matter, recycle nutrients

Producers: some perform photosynthesis (e.g., cyanobacteria)

Nitrogen fixers: convert N₂ → ammonia (usable by plants)

Pathogens: cause disease

Symbiosis:

Mutualistic (both benefit)

Commensal (one benefits, other unaffected)

Parasitic (one benefits, one harmed)

Horizontal gene transfer (HGT)

Transformation: uptake of free DNA from environment

Transduction: DNA transferred by viruses

Conjugation: direct transfer via cell-to-cell contact

Importance:

Rapid spread of traits (e.g., antibiotic resistance)

Contributes to genetic diversity

Played a role in early evolution and possibly in the origin of eukaryotes (e.g., gene exchange before organelles stabilized)

Bacterial Shapes

Coccus (spherical)

Bacillus (rod-shaped)

Spirillum (spiral)

Bacterial Cell wall types:

Gram-positive: thick peptidoglycan

Gram-negative: thin peptidoglycan + outer membrane

Bacterial Modes of Nutrition

Photoautotroph: light energy + CO₂

Photoheterotroph: light energy + organic carbon

Chemoautotroph: chemical energy + CO₂

Chemoheterotroph: chemical energy + organic carbon

Bacterial Oxygen Use:

Aerobic: require oxygen

Anaerobic: do not use oxygen (may be harmed by it)

Facultative anaerobes: can switch

Halophile

Thrives in high salt

Extremophile

Lives in extreme conditions

Thermophile

Thrives in high temperatures

Methanogen

Produces methane (archaea)

Nitrogen fixation

Conversion of N₂ to usable ammonia

Aerobic

Requires oxygen

Anaerobic

Does not require oxygen

Unifying characteristics of protists

Protists are grouped mainly by what they are not:

- Eukaryotic (have nucleus and organelles)

- Mostly unicellular (some multicellular or colonial)

- Do not fit into animal, plant, or fungi kingdoms

They are incredibly diverse in:

- Nutrition (autotrophs, heterotrophs, mixotrophs)

- Habitat (aquatic, moist environments)

- Structure and movement