Tree Thinking: Core Idea (Page references in transcript)
Darwin’s idea: all species are related by common descent.
Lineages branch over time to form a Tree of Life.
Phylogenetic trees are hypotheses about evolutionary relationships among populations, species, or genes.
Trees can be rooted or unrooted; outgroups help root.
Tree Thinking: What is a Phylogenetic Tree? (Page references)
A visual representation of evolutionary history for populations, species, or genes.
A hypothesis about evolutionary relationships.
The tips represent taxa, populations, or genes; internal nodes represent hypothetical ancestors.
Tree Thinking: Tree Anatomy (Characters and States)
Trees are built from traits (characters): morphology, behavior, DNA, etc.
Taxa that share more traits are grouped together.
Characters can be shared (present in multiple taxa), derived (new in a lineage), or ancestral (present in an ancestor).
Characters are often treated as binary states: 0 or 1, with data stored in a matrix.
Example: a trait with states 0/1 can be encoded as 0,1 in a character matrix.
Tree Thinking: Forms of Representation (Page 6–7)
Trees can be drawn in multiple ways but show the same relationships.
Visual flexibility does not change the underlying relationships.
Tip labels and branch structure encode the same information across alternative drawings.
Tree Thinking: Internal Nodes and Clades (Pages 8–12)
Internal nodes represent hypothetical ancestors of the taxa,
Example: the Most Recent Common Ancestor (MRCA) of D, C, B, A.
Example: the MRCA of B and A.
Clade is defined as a group consisting of a node (ancestor) and all of its descendants.
Smaller clades are nested within larger clades.
Building Trees: Data, Characters, and Matrices (Pages 14–16)
Building trees uses data from characters of the taxa at the tips of the tree.
Character data are entered as binary states (0 or 1) in a matrix.
Taxa are grouped based on how many traits they share; those with a more recent common ancestor share more traits.
We look for shared, derived characters to define groups; these are ideally homologous.
Use outgroups to determine ancestral states of characters.
Building Trees: Challenges (Page 17–18)
Some traits mislead: convergent evolution can produce analogous traits in unrelated lineages.
Wings in insects, birds, and bats are an example of analogous traits due to convergent evolution.
These traits do not reflect common descent.
Homologous vs Analogous (Pages 20–25)
Homologous structures: present in a common ancestor; due to common descent; can be modified for different functions.
Analogous structures: not present in the common ancestor; result from convergent evolution; similar function but different underlying structures.
Forelimb bones (radius and ulna) in bats, birds, and humans are homologous because they develop from the same embryonic cell lines and genes; underlying structure remains similar.
Convergence and reversals can complicate tree interpretation:
Convergence: two lineages independently evolve similar traits (e.g., wings).
Reversal: a trait reverts to an ancestral state in a lineage.
Reading: two tick marks on a tree can indicate convergent evolution of the same trait in separate lineages; a reversal is shown as a tick mark in the same lineage.
Parsimony and Tree Selection (Page 27)
Parsimony: the best tree is the one with the fewest evolutionary steps.
An evolutionary step includes any transition from ancestral to derived states, or reversals (derived back to ancestral).
Conceptually, parsimony seeks the simplest explanation for observed trait distributions.
Rooting the Tree (Pages 28–33)
Trees can be rooted or unrooted.
Outgroup: a taxon that is distantly related to the group being studied but not part of it. It helps determine ancestral vs derived states.
The root provides directionality: which character states are ancestral and which are derived.
Example discussion:
Some traits are obvious (e.g., no placenta vs placenta in mammals) as ancestral vs derived.
Outgroup choice is crucial for interpreting character state polarity.
Kangaroo example: ancestral character state = no placenta; derived state = placenta.
Shared, derived characters define clades; rooting helps decide whether a trait is ancestral or derived.
Reading Trees (Pages 36–40)
There are many ways to draw a tree; equivalent trees can be created by swinging branches around nodes without changing relationships.
Phylogenetic trees do not depict a linear progression from simple to complex; both pines and flowering plants can descend from a common ancestor.
Reading trees:
Each tick mark represents a change in a character state (presence/absence).
All taxa above a tick share that trait.
Example question: what traits did the most recent common ancestor of Tuna and Turtle have?
Taxonomy and Phylogeny (Pages 42–46)
Taxonomy: grouping living things and naming them; historically based on shared traits; Linnaeus emphasized nested hierarchies.
Modern practice uses shared, derived characters to define taxonomic groups; good groups are monophyletic.
Monophyletic: a group that includes an organism and all of its descendants; clades are monophyletic.
Not all groups are monophyletic:
Polyphyletic: a group that does not include the most recent common ancestor of its members (e.g., “flying animals”).
Paraphyletic: a group that includes the most recent common ancestor but not all of its descendants (e.g., traditional reptiles).
Taxonomic Content and Excerpts from Transcript (Taxon Lists and Examples)
The transcript includes an extensive list of taxa, tribes, and higher groups (e.g., Incertae sedis, HESPERI, Moncini, Nymphidiini, Riodinini, Helico pini, Papilionini, Satyrini, Elymnini, Agaturinae, Leptocircini, etc.).
Some entries show hierarchical placement (e.g., Papilionini–Papilionini, Papilionini–Papilio glaucus; Leptocircini–Graphium, Leptocircini–Photographum marces).
These entries illustrate the breadth of taxa that can be placed into a phylogeny and highlight the complexity of real-world systematic work.
Extra Credit and Review Items (Pages 34, 41)
Extra Credit (LQ #1): Which would be the best outgroup when making a phylogeny of parrots?
A. A dog
B. A shark
C. A non-parrot bird
D. A non-avian dinosaur
E. A snake
Answer: best outgroup would be a taxon clearly outside the ingroup but related; typically a non-parrot bird or a more distant avian lineage would be used depending on the ingroup; the exact best choice depends on the defined parrot ingroup.
Lecture Quiz #2 (Page 41): What is the most recent common ancestor of Lizards and Salmon? (Options omitted here; think about MRCA in a vertebrate tree.)
Practical Takeaways
Phylogenetic trees are hypotheses about evolutionary history based on characters.
Homology vs analogy is a central concept for interpreting characters:
Homologous traits reflect common ancestry and can be modified for different functions.
Analogous traits arise by convergent evolution and do not reflect shared ancestry.
Outgroups are essential for rooting trees and determining ancestral vs derived character states.
Parsimony provides a criterion for choosing among competing trees by minimizing the number of character state changes.
Taxonomy now emphasizes monophyletic groups (clades); paraphyletic and polyphyletic groups are considered less informative for representing evolutionary history.
When interpreting trees, remember that rearranging branches around nodes while preserving ancestry yields equivalent trees; the topology (who is related to whom) remains constant.
Additional Notes: Reading and Examples (Selected Details)
Internal nodes symbolize hypothetical common ancestors; the MRCA concepts help identify when lineages split.
The idea of a clade requires including all descendants of a common ancestor: this is the essence of monophyly.
Binary character states (0/1) form the backbone of