Difficulty: Introductory to Intermediate | Prerequisites: Basic understanding of evolution, shared ancestry, and what a "trait" is
Phylogenetics is the study of evolutionary relationships among organisms, represented as branching "trees" (phylogenies). In BIOL 180, you will need to build simple phylogenies from trait data, read and interpret published phylogenies, and use them to answer questions about how species are related. This topic ties together everything you learn about evolution: natural selection, speciation, homology, and the history of life. If you can read a tree accurately, you can reason about almost any evolutionary question the exam throws at you.
A phylogeny is a hypothesis about how organisms are related through common ancestry. You build one by grouping species that share derived traits (synapomorphies). Reading a tree means understanding which groups share a more recent common ancestor, whether a group is monophyletic, and whether shared traits are due to common descent (homology) or independent evolution (homoplasy).
Phylogeny (phylogenetic tree)
A branching diagram showing the inferred evolutionary relationships among a group of organisms. Think of it as a family tree for species.
Synapomorphy (shared derived trait)
A trait that is shared by two or more taxa and was inherited from their most recent common ancestor. These are the traits used to group organisms on a phylogeny. In simple terms, it is a new feature that evolved once and was passed down to descendants.
Monophyletic group (clade)
A group consisting of an ancestor and all of its descendants. Think of it as snipping one complete branch off the tree, with everything attached. If you leave out even one descendant, the group is not monophyletic.
Paraphyletic group
A group that includes an ancestor and some but not all of its descendants. It is an incomplete branch.
Homology
Similarity between organisms that is due to shared ancestry. The trait was inherited from a common ancestor. For example, the forelimbs of bats and whales are homologous because both inherited the basic limb structure from the same ancestor.
Homoplasy (convergent evolution / analogy)
Similarity between organisms that is not due to shared ancestry. The trait evolved independently in separate lineages, often because of similar selective pressures. For example, wings in bats and wings in insects.
Outgroup
A taxon that is closely related to the group being studied but falls outside it. It is used as a reference point to determine which traits are ancestral and which are derived.
Basal
Refers to a lineage that branches off near the root of the tree. It does not mean "primitive" or "less evolved."
Derived trait
A trait that has changed from the ancestral condition. It is new relative to what came before. Coded as "1" in a trait matrix (ancestral = "0").
Most recent common ancestor (MRCA)
The nearest shared ancestor of two or more taxa on a phylogeny. It is the node where their lineages diverge.
Parsimony
The principle that the simplest explanation, requiring the fewest evolutionary changes, is preferred when building a phylogeny.
You are given a table of taxa (rows) and traits (columns), with 0 = ancestral state and 1 = derived state.
Start by identifying the outgroup: the taxon with all zeros (or the most zeros). This is the root of your tree.
Group taxa that share derived traits (1s) together. A trait shared by a subset of taxa marks where that branch splits off.
Place trait changes (synapomorphies) on the branches. Each derived trait should ideally appear just once on the tree (parsimony).
Example from the exam: five mollusc groups (Bivalvia, Decabranchia, Gastropoda, Krytotrochozoa, Nautiloidea) with five traits. Krytotrochozoa has all zeros, so it is the outgroup. Mineralized shell (shared by all except Krytotrochozoa) goes on the first branch. Then you work out which subgroups share each remaining trait.
The tips of the tree are living (or recently extinct) taxa. The nodes (branching points) represent hypothetical common ancestors.
Two taxa that share a more recent node are more closely related to each other than either is to a taxon that branches off earlier.
You can rotate branches around any node without changing the meaning of the tree. The branching pattern (topology) is what matters, not the left-to-right order of tips.
A monophyletic group (clade) includes an ancestor and all of its descendants.
To test whether a group is monophyletic, trace back to the most recent common ancestor of all the members and check whether every descendant of that ancestor is included.
Example: on the Homo phylogeny, Australopithecus is not monophyletic if some descendants of their common ancestor (like Homo species) are excluded from the group.
If two taxa share a trait because they inherited it from a common ancestor, it is homology.
If two taxa share a trait because it evolved independently in each lineage, it is homoplasy (convergent evolution).
To distinguish them, look at the phylogeny. If the trait requires only one evolutionary origin (on the branch leading to their common ancestor), it is homology. If it requires two or more independent origins, it is homoplasy.
Example: H. floresiensis had a small brain similar in size to a chimpanzee's. On the phylogeny, H. floresiensis nests within Homo (large-brained species), well separated from chimps. The small brain in H. floresiensis must have evolved independently (a secondary reduction), making the similarity with chimps homoplasy, not homology.
"Basal" describes a lineage that diverges near the root, but it does not mean that species is more primitive or ancestral.
All living species on a phylogeny have been evolving for the same amount of time since their last common ancestor.
Chimps are the outgroup on a hominid phylogeny, but they are not "more basal" than other species in an absolute sense. They are simply the first lineage to branch off within the group shown.
A phylogeny can be used to test competing hypotheses about relationships.
If someone claims species A descended from species B, check whether A nests as a close relative (or sister taxon) of B on the tree. If A branches off from a completely different part of the tree, the hypothesis is not supported.
Example: the hypothesis that H. floresiensis is a diseased population of H. sapiens is not consistent with Argue's phylogeny, because H. floresiensis does not group with H. sapiens. Instead, it branches off much earlier, near H. habilis.
Students often think the leftmost taxon on a phylogeny is the "most primitive." It is not. Branch order on a page is arbitrary; what matters is the branching pattern.
Students sometimes say one living species "evolved from" another living species (e.g., "humans evolved from chimps"). Living species share a common ancestor; neither descended from the other.
Students confuse homology with homoplasy. Two species sharing a trait does not automatically mean they inherited it from a common ancestor. Always check the phylogeny to see whether one origin or multiple origins are required.
Students often assume that "basal" means "ancestral" or "less evolved." Chimps have been evolving just as long as humans have since their last shared ancestor.
⚠️ You will be asked to construct a phylogeny from a trait matrix. Practise identifying the outgroup and placing synapomorphies on branches.
⚠️ Expect questions asking whether a named group is monophyletic. Remember: ancestor plus all descendants.
⚠️ Homology vs homoplasy is a classic exam question. The answer always depends on the phylogeny, not on how similar the traits look.
⚠️ Be ready to evaluate whether a phylogeny is consistent with a specific hypothesis about relationships.
True or false: A monophyletic group can exclude some descendants of the group's common ancestor.
False. A monophyletic group must include the ancestor and all of its descendants.
Fill in the blank: A trait shared by two species due to independent evolution rather than common ancestry is called ___.
Homoplasy (or convergent evolution)
True or false: The outgroup is the taxon that has the most derived traits.
False. The outgroup typically has the most ancestral traits (the most zeros in a trait matrix).
Fill in the blank: When building a phylogeny, the principle of ___ favours the tree requiring the fewest evolutionary changes.
Parsimony
True or false: If species A is drawn to the left of species B on a phylogeny, species A is more primitive.
False. The horizontal order of tips on a phylogeny is arbitrary.
Q: Given a trait matrix with five taxa and five traits, how do you determine which taxon is the outgroup?
A: The outgroup is the taxon with all (or the most) ancestral character states, coded as 0. It branches off first, at the root of the tree.
Q: You are told that Australopithecus species share a common ancestor on a phylogeny, but some Homo species also descend from that same ancestor. Do Australopithecus species form a monophyletic group?
A: No. A monophyletic group must include the common ancestor and all of its descendants. If Homo species also descend from that ancestor but are excluded from the group, Australopithecus is paraphyletic.
Q: H. floresiensis had a brain about the size of a chimpanzee's, yet it nests well within the genus Homo on the phylogeny. Is the similar brain size between H. floresiensis and chimps an example of homology or homoplasy? Explain.
A: Homoplasy. On the phylogeny, the common ancestor of chimps and Homo likely had a small brain, but brain size increased in the lineage leading to Homo. H. floresiensis then underwent a secondary reduction in brain size. The small brains of chimps and H. floresiensis were not inherited from the same recent ancestor via a continuous line of small-brained descendants; rather, the trait was lost and re-acquired (or reduced) independently.
Q: Some experts argued that H. floresiensis was descended from Homo erectus. Argue's phylogeny places H. floresiensis branching off near H. habilis, well before H. erectus. Is the phylogeny consistent with the H. erectus descent hypothesis?
A: No. If H. floresiensis descended from H. erectus, it should be nested within or as a sister to H. erectus on the tree. Instead, it branches off much earlier, which is inconsistent with that hypothesis.
Q: Is it correct to say that chimps are the "most basal species" on a phylogeny of primates? Why or why not?
A: It is not quite right. Chimps are the outgroup in this phylogeny, meaning they branch off first relative to the other taxa shown. But "basal" does not mean more primitive. Chimps have been evolving for the same amount of time as every other species since their last common ancestor.
Phylogenetics connects to population genetics (allele frequencies and mutations drive the divergence that phylogenies depict), speciation (species concepts define what sits at the tips of the tree), and mechanisms of evolution (natural selection and drift shape the traits used to build trees). Understanding homology and homoplasy is also essential for comparative anatomy and developmental biology.
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