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Understanding phylogenies

Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time.

Phylogeny showing relationship between sharks, ray-finned fish, amphibians, primates, rodents & rabbits, crocodiles, and diniosaurs & birds. Dinosaurs & birds and crocodiles share a common ancestor and two post-orbital fenestrae. Primates and Rodents & rabbits share a common ancestor and hair. The above four groups share another common ancestors and an amniotic egg. Amphibians and the previous four groups share a common ancestor and four limbs. Ray-finned fish and the previous five groups share a common ancestor and a bony skeleton. Sharks and the previous six groups share a common ancestor and vertebrae.

When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.

This image shows two parallel line connected at the bottom point by a horizontal bar. From a point in the middle of the horizontal bar, a blue line descends directly downward. The point in the middle of the horizontal bar that connects with the blue bar is the speciation event. The blue bar is the ancestral lineage.

Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.

A phylogeny with descendents A, B, and C. A shares a speciation event with B and C. B shares a speciation event with C. There is a dotted line moving from the bottom of the phylogeny towards the speciation event of B and C; this represents the shared history of B and C. The line leading to B is green, representing the unique history of B. The line leading to C is blue, representing the unique history of C.

Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

Shows the same phylogeny of A, B, and C as the previous one. The point representing the speciation event of A and B&C also represent the common ancestor of A, B, and C. The point showing the speciation event of B and C also represents the common ancestor of B and C. A point along the line to C represents a unique ancestor of C.

A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.

Four different phylogenies. Top left shows a clade (comprised of three descendents with two speciation events) highlighted in green. Top right shows another clade (only one descendent) highlighted in blue. Bottom left shows two descendents connected by a common ancestor and another descendent that is physically close in the phylogeny but not connected all highlighted red and labeled "not a clade." Boottom right shows another "not-clade," which is all but one descendent of the phylogeny highlighted in orange.

Clades are nested within one another — they form a nested hierarchy. A clade may include many thousands of species or just a few. Some examples of clades at different levels are marked on the phylogenies below. Notice how clades are nested within larger clades.

Left, one small clade highlighted yellow. Middle, a clade highlighted blue that has the yellow clade nested within it. Right, a clade highlighted red that has both the yellow and blue clades nested within it.

So far, we’ve said that the tips of a phylogeny represent descendent lineages. Depending on how many branches of the tree you are including however, the descendants at the tips might be different populations of a species, different species, or different clades, each composed of many species.

Get the basics on understanding evolutionary trees in this primer.

In some phylogenies, more than two daughter lineages arise from a single ancestral lineage. Find out how to interpret these trees.

Teach your students about evolutionary relationships and phylogenetics:

Find additional lessons, activities, videos, and articles that focus on phylogenetics.

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The family tree

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Trees, not ladders