*L1 Tree of Life

Biodiversity

The total variety of organisms present in different ecosystems. • Produced by genetic divergence over time.

Why are common names problematic?

• Vary from place to place • The same common name can refer to different species • Lead to identification mistakes • Science needs a precise, universal way to name species

Binomial nomenclature

Two-word naming system developed by Linnaeus that gives every species a scientific name: Genus + species.

How is a scientific name written?

Genus capitalized, species lowercase, and the whole name italicized (or underlined if handwritten). Ex: Homo sapiens

Advantage of binomial nomenclature

Precise and standardized worldwide — avoids the confusion caused by common names.

Hierarchical ranks

"Nested sets" of similar organisms used in the historical classification system.

Hierarchical ranks, broadest to most specific

Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species • Mnemonic: Dear King Phylum Cares Only For Green Spinach

The trouble with historical classification

It is subjective — humans decide which similarities matter, so grouping depends on human judgment rather than on evolutionary history.

Why does evolution provide a more objective way to group species?

Evolution produces real patterns of common ancestry, and those relationships can be represented as branches on a cladogram.

Speciation

The evolution of new species: an ancestral population splits, the groups stop exchanging DNA, and they become reproductively isolated.

"Forks in the road": what happens after an ancestral population splits?

• Groups can no longer exchange DNA • Mutations and other changes accumulate independently • Populations become increasingly different • Eventually reproductive isolation = 2 non-interbreeding species

How does speciation produce the branching pattern of a cladogram?

Ancestral population splits → groups stop exchanging DNA → they diverge → reproductive isolation → separate lineages branch away from their common ancestor.

Branch point (node)

The point where an ancestral lineage split. • Represents the LAST common ancestor of the lineages coming off it.

Cladogram

A branched diagram showing hypothesized evolutionary relationships — a diagram of evolutionary splits. Also called the Tree of Life.

Are cladograms facts?

NO — they are HYPOTHESES of evolutionary history, not absolute statements of what happened.

Common misconception about evolution

Modern organisms do NOT "come from" other modern organisms. Modern taxa share common ancestors; one living taxon is not the ancestor of another.

Clade

A biologically meaningful evolutionary grouping containing: a common ancestor + ALL of its descendants + nothing else.

Why are clades biologically meaningful?

They represent actual evolutionary lineages produced by common ancestry.

Artificial (non-clade) group

A group that does NOT include a common ancestor and ALL of its descendants, OR that groups organisms by general similarity rather than ancestry.

How is an artificial group created?

By leaving out one or more descendants of the group's common ancestor (or by grouping on superficial similarity).

Quick test for whether a group is a clade

Find the common ancestor of the group. If the group includes that ancestor + ALL its descendants → clade. If any descendant is left out → NOT a clade.

Why can grouping organisms by appearance be misleading?

Similar traits can evolve independently (convergence), so similar appearance does not always mean shared ancestry.

Sister taxa

The taxa that share the MOST RECENT common ancestor with each other.

How do you find a sister taxon on a cladogram?

Go down the branch to the nearest branch point, then follow the other branch back up (everything on that other branch is the sister group).

How do you tell which taxa are more closely related?

Taxa that share a MORE RECENT common ancestor are more closely related.

Does physical distance between names on a cladogram indicate relatedness?

NO. Only branching order and how recently taxa share a common ancestor matter.

Can branches rotate around a branch point?

YES — rotating a branch does not change the evolutionary relationships shown.

Can equivalent cladograms look different?

YES — trees can be drawn sideways, angled, upside down, or with rotated branches and still say the same thing.

What must be the same for two cladograms to be equivalent?

Same branching order, same sister relationships, same clades.

How do you check whether two trees are equivalent?

Compare sister relationships and branching order. If the same taxa/clades have the same sisters and branching order, the trees "say the same thing."

Why is scale important in a tree?

You must choose which taxa to include, and relationships are only interpreted within the group being examined.

Trait transitions

Can be mapped onto the branches of a cladogram to show where a trait evolved.

Main goal when determining evolutionary relationships

Identify CLADES: common ancestor + ALL descendants + nothing else.

Basic assumption when using traits to build trees

Similarity between organisms is assumed to be due to inheritance from a common ancestor.

Shared-derived character

A NEW (derived) trait that evolved in a common ancestor and is shared by its descendants.

Why are shared-derived characters useful?

They identify organisms that inherited a NEW trait from a common ancestor → they identify clades.

Lecture example of a shared-derived character

Hinged jaws — evolved in a common ancestor and passed to its descendants, so it marks a clade.

Shared-ancestral character

A trait that evolved BEFORE the common ancestor of the clade being examined, so it is already shared broadly within the group.

Why are shared-ancestral characters not useful within a clade?

Every member already has the trait, so it cannot distinguish which members are more closely related.

Walking legs example

Frog, turtle, and leopard all have walking legs, so within that group the trait is shared-ancestral and cannot resolve their relationships.

Unique character

A derived trait found in only ONE of the taxa being compared.

Why are unique characters not useful for grouping?

The trait is not shared with any other taxon, so it cannot reveal a shared evolutionary relationship.

Which character type is most useful for building cladograms?

SHARED-DERIVED characters.

Homology

Similarity due to inheritance from a COMMON ANCESTOR.

Structural homology

Structural similarity resulting from the same evolutionary and developmental origin, inherited from a common ancestor. • Lecture example: forelimb bones

Must homologous structures perform the same function?

NO — functions can be the same or completely different (ex: forelimb bones of a bat, whale, and human).

Convergence

Similarity that evolved INDEPENDENTLY, not inherited from a common ancestor.

Why does convergent evolution happen?

Different groups independently evolve similar adaptations, usually because of similar selective pressures or lifestyles.

Homology vs. convergence

HOMOLOGY = similarity inherited from a common ancestor (useful evidence). CONVERGENCE = similarity evolved independently (misleading).

Why are convergent traits not useful for building cladograms?

They have different evolutionary/developmental origins, so they do not show inheritance from a common ancestor.

Lecture examples of convergence

• Bat wings vs. fly wings (both fly, different origins) • Marsupial "mole" vs. placental mole • Gliders vs. flying squirrels • Limblessness in the eastern glass lizard vs. the coral snake

If two distantly related organisms independently evolve the same useful trait, is it homologous or convergent?

Convergent.

How can a cladogram tell you whether a trait is homologous or convergent?

Map the trait onto the tree. If it can be explained by a single origin in a common ancestor → homologous. If it must have evolved separately in different lineages → convergent.

Two major sources of characters used to build cladograms

1. Morphology/structure 2. Genetics

Morphology

The physical structure/form of an organism; useful for treebuilding when the traits are homologous.

Why is genetic information useful for evolutionary relationships?

More closely related organisms tend to have more similar gene sequences.

What genetic features can act as shared-derived characters?

Unique gene families or other genomic features shared by the members of a clade.

Can whole genomes be used to construct cladograms?

YES.

Ingroup

The group of taxa whose evolutionary relationships you are trying to determine.

Outgroup

A closely related species that is NOT part of the ingroup, whose relationship to the ingroup is already known.

Why are outgroups useful?

They approximate the ANCESTRAL condition, which lets you determine whether a character state in the ingroup is ancestral or derived.

If a trait is absent in the outgroup but present in ingroup members, what does that suggest?

The trait is likely DERIVED within the ingroup (and therefore potentially useful for identifying a clade).

Two problems when starting to build a cladogram

1. The traits of the common ancestor are unknown 2. Convergence is possible

Three basic steps for simple treebuilding

1. Identify an outgroup (establishes directionality) 2. Develop potentially informative (shared-derived) characters 3. Favor the tree requiring the fewest evolutionary changes

Parsimony: which tree is favored?

The tree requiring the FEWEST total evolutionary changes, because it is the simplest explanation of the observed character distribution.

Full procedure: given a set of taxa, how do you build a cladogram?

1. Identify an outgroup 2. Identify potentially informative shared-derived characters 3. Group taxa into clades based on those characters 4. Choose the tree requiring the fewest total changes 5. Keep splitting until the tree is resolved (2-way splits)

Why is a cladogram a testable hypothesis?

It proposes relationships that can be tested with additional evidence and can be used to make predictions.

How can a cladogram be used to make a prediction?

If taxa share a proposed common ancestor, you predict they should share additional inherited characteristics; new data can test that prediction.

Historical classification: 2 kingdoms

Plants + Animals

Historical classification: 5 kingdoms (by the 1960s)

Plants, Animals, Fungi, Protists, Bacteria (Monera)

Modern classification of life

Three major clades: Bacteria, Archaea, Eukarya. • Archaea is SISTER to Eukarya

Why are "protists" not a clade?

"Protists" lumps together many separate major eukaryotic lineages — it is not one common ancestor plus ALL of its descendants.

ESSAY: Why is historical classification subjective but a cladogram objective?

Historical ranks group organisms by similarities that PEOPLE choose as important, so which traits matter is a judgment call. Cladograms group by common ancestry produced by the real process of speciation, so the grouping reflects evolutionary history rather than human opinion.

ESSAY: How is speciation represented on a cladogram?

An ancestral population splits → the groups stop exchanging DNA → mutations and other changes accumulate independently → reproductive isolation develops → two non-interbreeding species result. On the tree: the branch point = the last common ancestor, and the branches = the diverging lineages.

ESSAY: Contrast a clade with an artificial group

CLADE = common ancestor + ALL descendants + nothing else; represents a real evolutionary lineage and is biologically meaningful. ARTIFICIAL GROUP = leaves out one or more descendants, or is based on superficial/convergent similarity; does not represent evolutionary history. Ex: "prokaryotes" and "protists" are artificial.

ESSAY: Distinguish shared-derived, shared-ancestral, and unique characters

SHARED-DERIVED = new trait shared by multiple descendants of the ancestor in which it evolved → identifies clades, the only useful type. SHARED-ANCESTRAL = evolved earlier and already shared broadly → cannot resolve relationships within the group. UNIQUE = present in only one taxon → cannot link it to any other taxon.

ESSAY: Contrast homology and convergence

HOMOLOGY = similarity from the same evolutionary/developmental origin, inherited from a common ancestor (forelimb bones); valid evidence for relationships. CONVERGENCE = similarity evolved independently under similar selective pressures (bat vs. fly wings, marsupial vs. placental moles); invalid for treebuilding because it does not indicate shared ancestry.

ESSAY: Explain the sources of data used to build cladograms

1. MORPHOLOGY — structural traits, useful only when homologous (same evolutionary/developmental origin), so convergence must be ruled out. 2. GENETICS — closely related organisms have more similar sequences; unique gene families and other genomic features act as shared-derived characters, and whole genomes can be used to build trees. Both are strongest when they agree.

ESSAY: Explain how an outgroup is used to build a cladogram

The outgroup is a closely related taxon outside the ingroup whose relationship is already known; it approximates the ancestral condition. Comparing ingroup taxa to it tells you which character states are ancestral and which are derived. Shared-derived states are then used to identify clades within the ingroup.

ESSAY: Contrast historical classifications of Life with the modern system

Historically 2 kingdoms (Plants, Animals), later 5 kingdoms (Plants, Animals, Fungi, Protists, Bacteria) based on chosen similarities. The modern system uses evolutionary history: 3 clades — Bacteria, Archaea, Eukarya — with Archaea sister to Eukarya. Older groupings like "prokaryotes" and "protists" turn out to be artificial, not clades.

PRACTICE (do on paper, not as a flashcard)

Given a character matrix and an outgroup, draw the most parsimonious tree; then circle every clade, name the sister taxon of each terminal, and redraw the same tree in a different style to prove you can recognize equivalence.