Phylogenetics (gen)

Objectives and Key Concepts

  • Objectives for today include understanding:
    • What phylogenetic trees are
    • How trees show relationships between species
    • The meanings of ancestral and derived states
    • How trees are used to name groups
    • How to construct a phylogenetic tree based on homologous traits
  • Tree thinking emphasizes evolutionary relationships as a branching history rather than a linear progression.
  • Key terms to know: ancestral state, derived state, homologous characters, analogous characters, outgroup, monophyletic, clade, polyphyletic, paraphyletic, parsimony.

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 0,10,1 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).
  • Specific examples include:
    • Troidini, Papillonini, Papilionini, Vinopalpini, Zerynthini, Luehdorfini, Pamassini, Pamas, Leptocircini, Satyrini, Elymnini, Victorini, Coeini, Pierini, Appl, Adhochar, Appias tytho, ORINAE, Neme, Semonesia, Dia carte, I wan, Theope, mphidium onseum, Mesen, Nymphidiini, Symmachi, Emesidin, Erynnini, Carcharodini, Passov, peates petata, Euchsemoninas, Coelades, Hedylidae groups (e.g., Hedylus Macrosoma, Hedylidne Macrosoma), Troidini, Pachilopts aristolochiae, Baus polydemas, Baronia (Baronia brew), etc.
  • 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