Difficulty: Intermediate | Prerequisites: Basic understanding of evolutionary relationships and shared traits
Phylogenies are branching diagrams that show how species are related through common ancestors. You build them from shared derived traits, and you read them to answer questions about relatedness, homology vs. homoplasy, and whether groups are monophyletic. Species concepts (biological, morphospecies, phylogenetic) each define "species" differently, and a population can qualify under one concept but not another.
Phylogeny (phylogenetic tree)
A branching diagram showing the evolutionary relationships among a group of organisms, inferred from shared traits or genetic data. Think of it as a family tree for species.
Synapomorphy (shared derived trait)
A trait that evolved in the common ancestor of a group and is shared by its descendants. Synapomorphies are the evidence used to group species together on a phylogeny.
Monophyletic group (clade)
A group that includes a common ancestor and all of its descendants. If any descendant is left out, the group is not monophyletic. In simple terms, a complete branch snipped from the tree.
Homology
Similarity between species due to shared ancestry. Two species have homologous traits because they inherited them from a common ancestor.
Homoplasy
Similarity between species that is not due to shared ancestry. It arises from convergent evolution (independent gain of a trait) or reversal (loss of a previously evolved trait). In simple terms, two species look alike but got there independently.
Outgroup
A species or group that diverged before the group of interest. It is used to root the tree and determine which traits are ancestral vs. derived.
Basal
Refers to a lineage that diverged early from the rest of the group. A "basal" lineage is not more primitive; it has had the same amount of time to evolve as every other lineage since the root.
Biological species concept (BSC)
Defines a species as a group of organisms that can interbreed and produce fertile offspring. Think of it as the "can they have babies that also have babies" test.
Morphospecies concept
Defines a species based on measurable physical differences. If two populations look distinctly different, they may be separate morphospecies.
Phylogenetic species concept
Defines a species as the smallest monophyletic group on a phylogeny. You test this by placing individuals on a tree and checking whether they form their own exclusive clade.
Start with a character matrix: rows are species, columns are traits, and cells contain 0 (ancestral) or 1 (derived).
The outgroup has all 0s (no derived traits). This is your reference point.
Group species that share derived traits. The principle of parsimony says the tree requiring the fewest evolutionary changes is preferred.
Mark each derived trait on the branch where it first appeared. All species above that mark share the trait (unless a reversal occurred).
Example from the exam: five mollusc groups (Bivalvia, Decabranchia, Gastropoda, Krytotrochozoa, Nautiloidea) with five traits. Krytotrochozoa (all 0s) is the outgroup. Mineralized shell is the most broadly shared derived trait, so it maps to the deepest branch.
Two species are most closely related if they share a more recent common ancestor than either shares with any other species.
On a tree, look for the node that connects two species without including any others.
Example: H. floresiensis is more closely related to H. habilis than to H. sapiens, because their most recent common ancestor excludes H. sapiens.
Homology: similarity inherited from a shared ancestor. Wings in bats and arms in humans are homologous (same underlying bone structure from a common mammalian ancestor).
Homoplasy: similarity that arose independently. There are two routes to homoplasy:
Convergent evolution: two unrelated lineages independently evolve a similar trait (e.g. wings in bats and wings in insects).
Reversal: a lineage loses a trait that its ancestor had. This makes the lineage resemble a more distant relative that never had the trait.
Example: H. floresiensis had a small brain similar to chimpanzees. On the phylogeny, large brains evolved in the common ancestor of Homo, then were lost in H. floresiensis. The small-brain similarity between H. floresiensis and chimps is homoplasy (specifically, a reversal).
A monophyletic group (clade) must include an ancestor and every one of its descendants.
If even one descendant is excluded, the group is not monophyletic (it is paraphyletic or polyphyletic instead).
Example: Australopithecus does not form a monophyletic group on the Argue phylogeny, because the descendants of their common ancestor also include all of Homo.
Biological species concept: Can they interbreed and produce fertile offspring (including F2s, not just F1s)? Gough Island mice can interbreed with mainland mice and produce fertile F2 offspring, so under BSC they are not a separate species.
Morphospecies concept: Are they physically distinguishable? Gough Island mice are clearly larger, so a case can be made either way: "yes" if the size difference is enough to classify them separately, or "no" if they are otherwise very similar.
Phylogenetic species concept: Do they form a monophyletic group? You would need to build a phylogeny from morphological or genetic data and check.
Different concepts can give different answers for the same population. That is why biologists use multiple lines of evidence.
Students often say a species at the top or side of the tree is "more evolved" or "more basal" than others. Every living species has had the same amount of time to evolve since their common ancestor. Chimps are not more primitive than humans; they have simply evolved in a different direction.
Students confuse homology and homoplasy. If two species share a trait and their common ancestor also had it, that is homology. If the trait arose independently (or was lost and regained), it is homoplasy. Always check the tree.
Students forget that "monophyletic" means all descendants. Leaving out even one descendant disqualifies the group.
Students assume the biological species concept is the only valid definition. It does not work for asexual organisms, fossils, or populations that have never had the chance to interbreed. That is why multiple species concepts exist.
⚠️ You will be asked to build a phylogeny from a trait matrix. Practice identifying the outgroup, finding shared derived traits, and marking trait origins on branches.
⚠️ Expect questions asking whether a hypothesis about species relationships is consistent with a given phylogeny. This requires reading the tree to determine which species share a more recent common ancestor.
⚠️ You will need to distinguish homology from homoplasy using a phylogeny as evidence, and explain your reasoning (convergence vs. reversal).
⚠️ Know all three species concepts (biological, morphospecies, phylogenetic) and be prepared to apply each to the same scenario, reaching different conclusions.
True or False: The species at the bottom of a phylogeny is more primitive than the species at the top.
False. All extant species have evolved for the same amount of time since their common ancestor.
Fill in the blank: A group that includes a common ancestor and all of its descendants is called a ___ group.
Monophyletic (or clade)
True or False: If two species share a similar trait but their common ancestor lacked it, the similarity is an example of homoplasy.
True.
Fill in the blank: Under the biological species concept, two populations are the same species if they can interbreed and produce fertile ___.
Offspring (including F2s)
True or False: Convergent evolution and reversal are both forms of homoplasy.
True.
Q: Species A and Species B both have trait X, but their common ancestor did not. Species C, which is distantly related, also has trait X and inherited it from an ancestor it shares with A and B. Is the similarity between A and C homology or homoplasy?
A: The similarity between A and C is homoplasy (specifically convergent evolution), because the trait arose independently in A's lineage and C's lineage.
Q: On a phylogeny, Species 1 and Species 2 share a node that excludes Species 3. A colleague claims Species 1 is more closely related to Species 3. Is the colleague correct?
A: No. Species 1 and Species 2 share a more recent common ancestor (the node that excludes Species 3), so they are more closely related to each other.
Q: A population of island birds can produce fertile F1 offspring with mainland birds, but the F2 offspring are infertile. Are they the same species under the biological species concept?
A: This is borderline, but many biologists would say no under a strict BSC interpretation, because the biological species concept requires fully fertile offspring across generations, not just F1s.
Q: A genus contains three named species. On a phylogeny, the descendants of their common ancestor also include two species from a different genus. Is the original genus monophyletic?
A: No. A monophyletic group must include all descendants of the common ancestor. The two species from the other genus are descendants that fall outside the original genus, so it is not monophyletic.
Q: How would you test whether a population of large lizards on an island is a distinct species?
A: Build a phylogeny using morphological or genetic data from the island lizards and mainland relatives. If the island lizards form a monophyletic group (a clade exclusive to them), that supports recognising them as a distinct species under the phylogenetic species concept.
Phylogenetics connects directly to mechanisms of evolution: natural selection, genetic drift, and mutation drive the divergence that phylogenies depict. Understanding homology vs. homoplasy also feeds into interpreting morphological data in comparative anatomy and developmental biology.
Species concepts connect to speciation, gene flow, and reproductive isolation, topics covered later in most introductory biology courses.
Phylogeny, phylogenetic tree, cladogram, clade, monophyletic, paraphyletic, polyphyletic, synapomorphy, shared derived trait, homology, homoplasy, convergent evolution, reversal, outgroup, biological species concept, morphospecies concept, phylogenetic species concept, BIOL 180, tree thinking, common ancestor, derived trait, ancestral trait, parsimony, trait matrix, character matrix, Homo floresiensis, Australopithecus