AP Biology Unit 7 Notes: Speciation, Phylogenetic Trees, and Extinction

Phylogeny

Phylogeny is the evolutionary history and relationships among organisms—essentially, a hypothesis about “who is related to whom” and how those relationships formed through descent with modification. In AP Biology, phylogeny matters because natural selection acts on populations over time, and the evidence of that evolutionary change is written into traits, DNA sequences, and patterns of common ancestry. Understanding phylogeny helps you connect microevolution (changes in allele frequencies within populations) to macroevolution (large-scale patterns like the origin of new species and major lineages).

How scientists represent phylogeny: trees and clades

A phylogenetic tree (often shown as a cladogram) is a branching diagram that represents inferred evolutionary relationships. It is not a “ladder of progress.” Instead, it’s like a family tree: branches indicate lineages splitting from common ancestors.

Key parts of a tree:

Node: a branching point representing a common ancestor of the descendant lineages.
Branch: a lineage through time.
Clade: a group consisting of an ancestor and all of its descendants. A clade is also called a monophyletic group.
Sister taxa: two lineages that share an immediate common ancestor.

Why clades matter: evolution is about branching. If you want groups to reflect evolution, they should be clades. Many traditional groupings don’t do this. For example, “reptiles” sometimes exclude birds in everyday language, but birds evolved within reptiles—so excluding birds makes “reptiles” a non-clade.

What evidence builds a phylogeny?

Phylogenies are hypotheses built from data. In AP Biology, you’re expected to understand that different data sources can support (or sometimes conflict with) one another.

Morphological (structural) data
Scientists compare traits such as bone structures, embryological features, or observable characteristics. The most useful traits for building phylogenies are homologous structures—features shared due to common ancestry.

A common pitfall is confusing homology with analogy:

Homologous traits: similar because of shared ancestry (e.g., the forelimb bones of humans, bats, and whales).
Analogous traits: similar because of convergent evolution, not shared ancestry (e.g., bird wings and insect wings).

Analogous traits are examples of homoplasy (similarity not due to common ancestry). Homoplasy can mislead tree-building if you treat convergent traits as evidence of close relatedness.

Molecular (DNA/protein) data
Comparing DNA sequences, RNA sequences, or amino acid sequences often provides large datasets and can resolve relationships that morphology alone can’t. In general, more similar sequences suggest more recent common ancestry—but you must remember that:

Different genes evolve at different rates.
Selection can speed up or slow down changes.
Shared DNA segments can sometimes be shaped by processes other than vertical inheritance (especially in microbes, where horizontal gene transfer can occur).

Shared derived characters: the logic behind cladistics

A major method for building trees is cladistics, which groups organisms by shared derived characters.

Character: a heritable trait you can compare (e.g., presence of a backbone).
Ancestral character: an older trait inherited from distant ancestors.
Derived character: a newer trait that evolved in a lineage.
Shared derived character (synapomorphy): a derived trait shared by members of a clade; this is especially informative for identifying clades.

To decide whether a trait is ancestral or derived, scientists often use an outgroup—a species or group known to be outside the clade of interest. If the outgroup has the trait, it is more likely ancestral; if only the ingroup has it, it may be derived.

How to read a phylogenetic tree correctly

Students often miss points not because the biology is hard, but because tree reading is a skill. Here are the core rules.

Relatedness is determined by the most recent common ancestor
Two taxa are more closely related if they share a more recent node.
The order of tips across the page is not meaningful
Branches can rotate around nodes without changing relationships. If you “spin” a node, the tree may look different but represent the same evolutionary hypothesis.
“More evolved” is not a scientific interpretation
All lineages have been evolving for the same amount of time since their last common ancestor. A lineage that looks “simple” today is not an ancestral form; it is a modern lineage with its own evolutionary history.
Branch lengths may or may not represent time/change
Some trees are just branching order diagrams; others are scaled so branch length represents time or amount of genetic change. You must look for cues (scale bars, tick marks, labels) before interpreting lengths.

Building trees: parsimony and model-based approaches

When multiple trees could explain the same data, scientists need a way to choose among them.

Maximum parsimony favors the tree with the fewest evolutionary changes (the simplest explanation). This is intuitive but can be misled when many changes occur over long time spans (multiple substitutions at the same site can hide history).
In modern biology, likelihood and Bayesian methods are also common; they use explicit models of sequence evolution. For AP Biology, you mainly need to understand that phylogenies are inferences supported by evidence and that different methods can be used.

“Molecular clocks” (conceptually)

A molecular clock is the idea that some DNA or protein sequences accumulate changes at a roughly predictable rate over time, allowing scientists to estimate when lineages diverged. The key word is “roughly”—rates can vary among genes, lineages, and environments, so molecular clock estimates usually require calibration (for example, using fossil evidence).

Example: interpreting a tree (what conclusions are valid?)

Imagine a tree with taxa A, B, and C where B and C share a node that A does not share with them.

Valid conclusion: B and C are sister taxa and share a more recent common ancestor with each other than either does with A.
Invalid conclusion: “B evolved from C” or “C is the ancestor of B.” Tips represent modern taxa, not ancestors.

Now imagine a trait (like “hair”) appears on the branch leading to the B+C clade.

Valid conclusion: hair is a shared derived character of B and C (a synapomorphy) and likely evolved in their common ancestor.
Common misconception: thinking the trait evolved separately in B and C because both have it. The tree suggests one origin unless data indicate otherwise.

Exam Focus

Typical question patterns:
- Interpret relatedness from a tree (identify sister taxa, most recent common ancestor, or which taxa form a clade).
- Map traits onto a tree (identify where a derived trait most likely evolved; detect convergent evolution).
- Compare trees built from different datasets (morphology vs DNA) and justify which is better supported.
Common mistakes:
- Using tip order to infer relatedness instead of nodes—always trace back to the common ancestor.
- Saying one modern species is the ancestor of another—modern taxa share ancestors; they don’t “turn into” each other.
- Treating analogous traits as evidence of close relationship—convergent evolution can produce misleading similarity.

Speciation

Speciation is the process by which one ancestral population splits into two or more species. In evolutionary terms, speciation matters because it is the main way biodiversity increases over time. Natural selection can shift traits within a population, but speciation explains how separate evolutionary lineages form—why there are multiple kinds of finches, frogs, flowers, or bacteria rather than just one continuously varying group.

To understand speciation, you need two big ideas:

Gene flow (movement of alleles between populations) tends to make populations more similar.
Reproductive isolation reduces gene flow, allowing populations to diverge via selection, drift, and mutation.

What is a “species”? (and why definitions matter)

A species concept is a way of defining what counts as a species. Different concepts are useful in different situations.

Biological Species Concept (BSC)
Under the biological species concept, a species is a group of populations whose members can interbreed in nature and produce viable, fertile offspring, and are reproductively isolated from other such groups.

Why the BSC is powerful: it ties directly to evolution. If gene flow is blocked, populations can evolve independently.

Limitations (important for exam reasoning):

It can’t be applied to fossils.
It doesn’t work well for asexual organisms.
It can be hard to test in nature (some populations never meet, but could interbreed if they did).

Other concepts you may see:

Morphological species concept: species defined by physical traits; useful for fossils but can miss cryptic species.
Phylogenetic species concept: species defined as the smallest monophyletic group on a phylogeny; emphasizes diagnosable differences.

AP Biology typically emphasizes the BSC and reproductive isolation mechanisms, but it’s useful to know why species boundaries can be “fuzzy.”

Reproductive isolation: how speciation is maintained

Reproductive isolation is any feature that prevents gene flow between populations. It can happen before fertilization (prezygotic) or after (postzygotic).

Prezygotic barriers (prevent mating or fertilization)

These barriers stop zygotes from forming.

Habitat (ecological) isolation: populations live in different habitats and rarely encounter each other.
Temporal isolation: populations breed at different times (day/night, different seasons, different years).
Behavioral isolation: differences in courtship signals (songs, dances, pheromones).
Mechanical isolation: mismatched reproductive structures.
Gametic isolation: sperm/pollen can’t fertilize eggs due to molecular incompatibility.

Prezygotic barriers are especially important because they prevent wasted reproductive effort.

Postzygotic barriers (after fertilization)

These occur when a zygote forms but gene flow still doesn’t effectively occur.

Reduced hybrid viability: hybrids fail to develop properly or are frail.
Reduced hybrid fertility: hybrids survive but are sterile (a classic example is the mule).
Hybrid breakdown: first-generation hybrids are viable and fertile, but later generations have reduced fitness.

A common misconception is that hybrids “prove” two groups are the same species. Under the BSC, occasional hybridization can occur, but if hybrids have low fitness or if hybridization is rare, the populations can still remain distinct species.

Modes of speciation: how new species form

Speciation is usually explained by geography and gene flow.

Allopatric speciation (geographic separation)

Allopatric speciation occurs when a population is separated by a physical barrier (mountains, rivers, islands, glaciers), reducing gene flow.

How it works step by step:

A once-interbreeding population becomes split into isolated populations.
Mutation, genetic drift, and natural selection cause allele frequencies to diverge.
Over time, reproductive barriers evolve.
Even if the barrier disappears, the populations may no longer interbreed successfully.

Why it’s common: it’s straightforward to stop gene flow with geography.

Example (illustrative): populations on different islands often diverge rapidly because migrants are rare. If each island has different resources, natural selection can push traits in different directions.

Sympatric speciation (same geographic area)

Sympatric speciation happens without geographic separation. Gene flow must be reduced by other forces.

Mechanisms that can drive sympatric speciation:

Polyploidy (especially in plants): a sudden change in chromosome number can create immediate reproductive isolation. A polyploid individual may be unable to produce fertile offspring with the original diploid population but can reproduce with other polyploids.
Disruptive selection combined with assortative mating: if individuals at opposite trait extremes have higher fitness and preferentially mate with similar individuals, gene flow between extremes decreases.
Host shift and habitat preference: if a subset of a population starts using a different host or microhabitat and mates there, gene flow can drop.

Example: polyploidy in plants
A plant species might produce an unreduced gamete (with a full set of chromosomes). If two unreduced gametes fuse, the offspring can be polyploid. If that polyploid is fertile with other polyploids but not with the original population, reproductive isolation can occur in a single generation.

Sympatric speciation can feel counterintuitive, so on exams you often need to explain how gene flow is reduced despite overlapping ranges.

Parapatric speciation and hybrid zones (often extension ideas)

In parapatric speciation, neighboring populations diverge while maintaining limited contact and gene flow across a boundary. A hybrid zone can form where ranges meet and interbreeding occurs.

Hybrid zones can have different outcomes:

Reinforcement: if hybrids have low fitness, selection favors stronger prezygotic barriers.
Fusion: if barriers are weak, populations may merge.
Stability: hybrids continue to form and persist, sometimes because the zone is maintained by environmental gradients.

Adaptive radiation: rapid speciation into many niches

Adaptive radiation is the rapid evolution of many species from a common ancestor when new ecological opportunities arise (new habitats, reduced competition, or after extinctions open niches).

How it connects to natural selection:

Different environments favor different traits.
Selection drives divergence as populations specialize.
Reproductive isolation evolves as differences accumulate.

Example: island colonization can set the stage for adaptive radiation because one ancestral population encounters many unoccupied niches.

Ring species (a helpful way to see speciation as a process)

A ring species is a pattern where populations are distributed in a geographic ring around a barrier; neighboring populations can interbreed, but populations at the ends of the ring cannot. This illustrates that speciation can be gradual, with reproductive isolation increasing over time.

The key takeaway for AP Bio: speciation isn’t always a clean, instant event. It’s often a process with intermediate stages.

Example: diagnosing reproductive isolation in a scenario

Suppose two populations of frogs live in the same region, but one breeds in early spring and the other breeds in summer. Even if they could produce fertile offspring in a lab, in nature they rarely mate.

The isolating mechanism is temporal isolation (prezygotic).
Evolutionary consequence: reduced gene flow allows divergence.

If a question adds that hybrids are produced occasionally but are sterile, then you also have reduced hybrid fertility (postzygotic). Many exam questions combine barriers and ask you to identify them precisely.

Exam Focus

Typical question patterns:
- Identify whether a barrier is prezygotic or postzygotic from a description (timing, behavior, hybrid sterility, etc.).
- Distinguish allopatric vs sympatric speciation using geographic and reproductive information.
- Predict what happens in hybrid zones (reinforcement, fusion, stability) given hybrid fitness.
Common mistakes:
- Treating “cannot interbreed” as the only criterion—often the scenario describes reduced gene flow rather than absolute impossibility.
- Misclassifying barriers (e.g., calling sterile hybrids “prezygotic” when it is postzygotic).
- Assuming sympatric speciation is impossible—remember mechanisms like polyploidy and assortative mating can strongly reduce gene flow.

Extinction

Extinction is the permanent loss of a species. It might feel like the opposite of speciation, but in evolution they are tightly linked: speciation increases biodiversity, extinction decreases it, and the balance between them shapes the diversity you observe today.

Extinction matters for three major reasons:

It reshapes ecosystems by removing species interactions (predation, pollination, competition).
It alters evolutionary trajectories by opening ecological niches—often setting the stage for adaptive radiations.
It is a key reason the fossil record and phylogenetic trees show branching patterns where many lineages end.

Extinction as a natural process (background extinction)

Most extinctions are not sudden global catastrophes. Background extinction refers to the ongoing, “normal” rate of extinction caused by typical ecological and evolutionary processes.

Common contributors include:

Environmental change (climate shifts, habitat changes)
Competition (a species being outcompeted for resources)
Predation or disease pressure
Small population size leading to vulnerability (genetic drift, inbreeding, demographic stochasticity)

A crucial evolutionary idea: extinction is not “failure” in a moral sense. It is often a predictable outcome when environments change faster than a population can adapt or migrate.

Mass extinctions: rare but transformative

A mass extinction is a relatively short interval (in geologic terms) when extinction rates rise dramatically and many lineages are lost. AP Biology emphasizes the concept and its evolutionary consequences more than memorizing specific dates.

Why mass extinctions matter to phylogeny and speciation:

They prune the tree of life—many branches end.
Survivors may diversify rapidly because many niches become available.
Traits that were once advantageous may become irrelevant, and new selection pressures dominate.

Mechanisms: why species go extinct

Extinction usually results from a mismatch between a species’ biology and its environment.

Environmental change and niche loss

If temperature, precipitation, salinity, or seasonality changes, organisms adapted to narrow conditions can lose their niche.

Specialists (narrow niche) often face higher risk when conditions shift.
Generalists (broad niche) may persist longer across variable conditions.

Population size, genetic diversity, and extinction risk

Small populations are vulnerable even when the environment seems stable.

Genetic drift can remove beneficial alleles or fix harmful ones by chance.
Inbreeding can increase the frequency of harmful recessive alleles.
Random demographic events (a poor breeding year, skewed sex ratio) can push populations below a viable threshold.

Students sometimes think natural selection “will save” a species. Selection can only act on existing variation, and adaptation takes time. If change is too rapid or variation too limited, extinction can occur.

Coextinction and ecosystem dependence

Coextinction occurs when one species goes extinct and another dependent species also disappears (for example, a specialized parasite losing its host, or a plant losing a specific pollinator). This highlights that extinction is not only about individual species, but about networks of interactions.

Extinction and phylogenetic trees: what you can infer

On phylogenetic trees, extinction is represented when a lineage ends before the present. You can connect extinction to tree interpretation in two important ways:

Extant taxa are not “ancestors”: even if one lineage looks similar to an ancestral form, it is still a modern species. Extinction of intermediate forms can make modern species appear more “isolated” on a tree.
Diversity patterns reflect both speciation and extinction: a lineage with few surviving species might have low speciation, high extinction, or both.

Example: extinction opening niches (linking to natural selection)

Imagine a large predator goes extinct in an ecosystem. Smaller predators that were previously suppressed by competition or predation may expand their range and population size.

Ecological effect: prey populations and competition networks shift.
Evolutionary effect: new selection pressures can favor traits suited to the newly available niche.
Long-term outcome: if different populations specialize on different prey or habitats, speciation becomes more likely.

This is one reason extinction and speciation are often discussed together: extinction can “reset” ecological opportunity.

Human impacts (conceptually)

Modern extinction risk is strongly influenced by human activity (habitat loss and fragmentation, invasive species, pollution, overharvesting, and climate change). For AP Biology, the key is connecting these pressures to mechanisms you already know:

Habitat fragmentation reduces gene flow and shrinks population size, increasing drift and inbreeding.
Rapid environmental change can outpace adaptation.
Invasive species can change selection pressures abruptly.

Even without memorizing statistics, you should be able to explain why these factors raise extinction risk using evolutionary reasoning.

Exam Focus

Typical question patterns:
- Given a scenario (habitat loss, invasive species, climate shift), explain mechanistically why extinction risk increases using population size, genetic diversity, and selection.
- Connect extinction to adaptive radiation (predict diversification after niches open).
- Interpret trees that include extinct lineages or discuss how extinction affects observed diversity.
Common mistakes:
- Claiming organisms “adapt because they need to”—adaptation depends on existing variation and differential reproduction, not intention.
- Ignoring population genetics: many extinctions involve small-population problems (drift, inbreeding) as much as selection.
- Treating extinction as separate from evolution—extinction changes selective environments and shapes future evolutionary pathways.