Building a Phylogeny: Homology, Shared Derived Characters and Parsimony
Phylogenetic trees are hypotheses about common ancestry. Shared derived character states can support groups, while convergence can mislead. Parsimony compares candidate trees by the minimum character changes they require. The lowest score does not guarantee the true evolutionary history.
What a learner can do afterwards
- Separates homology from convergence using a stated character and its distribution.
- Counts the changes a candidate tree requires and compares two trees on that count.
- Explains why an ancestral state retained by every sampled member does not distinguish branching relationships within the studied group.
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Speciation introduced lineage splitting. A phylogenetic tree is a hypothesis about relationships among lineages. Homologous features come from common ancestry, such as corresponding bones in a whale flipper and a human arm. Bird and insect wings evolved separately as flight structures. Similar function alone does not establish close relationship. Compare several characters.
A character is a feature; its state might be present or absent. An ancestral state was present in the ancestor being considered. A derived state differs from it and can be a gain or a loss. Shared derived states can support a subgroup. A state retained throughout the studied group does not resolve its internal branching. An outgroup lies outside the studied group and helps infer ancestral states; it is not the group's direct ancestor.
The most recent common ancestor of L, M and N has state 0. L and M have state 1; N has state 0. Sister taxa share an immediate common ancestor. If L and M are sisters, one change on their shared ancestral branch explains both state-1 tips. If L and N are sisters, no single changed branch reaches L and M without N. At least two changes are needed, such as separate gains in L and M.
A clade contains an ancestor and all its descendants. Omitting a descendant makes the proposed group incomplete. A shared derived state is evidence for a clade, not proof: convergence or later losses can obscure its history. Hair supports mammals as a group. Backbones are ancestral within mammals and occur in other vertebrates, so they do not identify mammals alone.
Under equal-weight parsimony, gains and losses each count as changes. Find each character's minimum count on a candidate tree, then add the counts across characters. Prefer the lowest total. Equal totals leave a tie under this rule. Repeated changes can mislead, so the preferred tree remains a hypothesis.
Compare inherited character states, identify complete clades, and total gains and losses. Parsimony ranks candidate trees without proving their history.
Lesson, questions and flashcards written for this dataset.
Readings and flashcards written for this dataset. "Understanding and building phylogenetic trees" is by Khan Academy; "Discovering the tree of life" is by the California Academy of Sciences.
More to read
Comparing features and their origins
Identify the particular feature being compared before interpreting a similarity. Corresponding bones in a human arm and whale flipper are homologous because they were inherited from a common ancestor. Their present functions differ, but that does not erase their shared origin.
Bird and insect wings provide a different comparison. As flight structures, they have separate evolutionary origins. Their matching use does not establish an exclusive bird-and-insect group.
A phylogenetic study compares several characters because one resemblance can mislead. Features can evolve separately or disappear after being inherited. A proposed tree must account for those possibilities rather than treating appearance or function alone as proof.
Clades and comparison levels
To identify a clade on a candidate tree, choose an ancestor and follow every descendant branch. Include the ancestor and all its descendants. A group omitting one descendant is not that complete clade.
A character's usefulness depends on the comparison. Backbones distinguish vertebrates from many other animals, but their presence does not identify mammals alone. Within mammals, backbones are ancestral and shared throughout the group. Hair supplies evidence at a different level.
An ancestral state is not useless in every analysis. The relevant question is whether its distribution distinguishes the particular relationships being investigated. Shared derived states can support a clade, but repeated changes can complicate that inference.
Counting changes on candidate trees
Record each character's observed states and any stated ancestral condition. For each candidate tree, place changes on branches so that inheritance produces the observed tip states. Seek the minimum count consistent with the observations. Under equal-weight parsimony, a gain and a loss each count as a change.
Repeat the procedure for every character, then add the minimum counts. Different characters can favour different candidates, so compare totals rather than choosing whichever tree fits one character best. Equal totals leave a tie under this rule.
A branch point represents common ancestry; it does not require a new character to appear there. Character changes can occur along branches. A low total ranks a hypothesis under parsimony without proving its history.
A small character-counting exercise
Consider hypothetical species R, S and T. Their common ancestor lacked a stripe. R and T have a stripe; S does not. If R and T are sisters, one gain on their shared ancestral branch explains both striped species. If R and S are sisters, at least two changes are needed, such as separate gains in R and T.
The ancestral condition is stated in this exercise. In research, an outgroup provides an outside comparison that can help infer ancestral states. It is not the studied group's direct ancestor, and its current states need not match that ancestor exactly.
Sorting manufactured objects can practise recording character states. Their similarities do not, by themselves, establish biological descent.
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Where it sits
8 questions wait behind this lesson, each with its answer explained. Every answer feeds the sky: stars light as they are learned, and dim when it is time to come back.