Clades in a Phylogenetic Tree: What They Are and How to Identify Them

A clade is a group of organisms that includes an ancestor and all descendants of that ancestor (UC Berkeley, Understanding Evolution). On a phylogenetic tree, that means one node plus everything that branches from it. This guide gives a repeatable test for finding clades on a tree you are reading, and shows how to check and extract one in R with the ape package.

What is a clade in a phylogenetic tree?

A clade is a branch of the tree: a node and all of its descendants. Berkeley’s Understanding Evolution calls it “a branch on the tree of life”, and the Digital Atlas of Ancient Life states that a monophyletic group is also a clade, defined by a node plus all of its descendants. “Clade” and “clades” in a phylogenetic tree mean the same thing; the word names the group, not a particular tree style.

Clade versus monophyletic, paraphyletic and polyphyletic

Whether a group is a clade depends on whether it contains its common ancestor and every descendant of it. The Digital Atlas of Ancient Life describes three cases:

Group type	What it contains	Clade?
Monophyletic	A single common ancestor and all of its descendants, none left out	Yes
Paraphyletic	A single ancestor and only some of its descendants	No
Polyphyletic	Members not defined by a single common ancestor; their common ancestor lies outside the group	No

How to identify clades in a phylogenetic tree

To identify a clade, pick a node and check that the group you are naming is exactly the set of tips that descend from it. Follow these steps on any rooted tree.

1. Find the root, the oldest node, so you know which direction is “descendant”.
2. Choose an internal node (a branch point) as the candidate ancestor.
3. List every tip that descends from that node.
4. Compare that list with the group you are testing. If they are identical, the group is a clade.
5. If the group lacks some descendants of the node, it is paraphyletic. If the group’s common ancestor lies outside it, as when you join tips from separate branches, it is polyphyletic.
6. Before you rely on the clade, look at its support value; a clade drawn on the tree is only as reliable as the evidence for that node (see how to read a phylogenetic tree).

Worked example (illustrative tree)

This is an invented teaching tree, not real data. Take five taxa written in Newick format as (((A,B)N1,C)N2,(D,E)N3)N4;. N4 is the root; N2 holds A, B and C; N3 holds D and E; N1 holds A and B.

Group tested	Result	Why
A, B	Clade	Exactly the tips descending from N1
A, B, C	Clade	Exactly the tips descending from N2
D, E	Clade	Exactly the tips descending from N3
A, C	Not a clade	Their common ancestor, N2, also has B as a descendant, which is left out
A, B, D	Not a clade	The common ancestor is the root N4, which also has C and E as descendants

Testing and extracting a clade in R (ape)

What it is used for in research

The R package ape tests whether a set of tips forms a clade and pulls a clade out of a larger tree, which is useful when a paper claims a group is monophyletic or when you need a subtree for a separate analysis.

Install or access

ape is distributed through CRAN, the R package repository. In R, run install.packages("ape") and then library(ape).

Step by step

1. Read the tree: tr <- read.tree(text = "(((A,B)N1,C)N2,(D,E)N3)N4;"). For a file, use read.tree("yourtree.nwk").
2. Test a group: is.monophyletic(tr, c("A","B","C")). The usage is is.monophyletic(phy, tips, reroot = !is.rooted(phy), plot = FALSE, ...), where phy is a tree of class “phylo” and tips is a numeric or character vector of tips to test. Add plot = TRUE to highlight the tips.
3. Extract the clade: extract.clade(tr, "N2"). The usage is extract.clade(phy, node, root.edge = 0, collapse.singles = TRUE, interactive = FALSE); node is a node number or label. It keeps all tips descending from that node and drops the rest. With interactive = TRUE you click the node on a plotted tree.

Output and how to read it

is.monophyletic returns TRUE or FALSE. On the example tree, c("A","B","C") and c("D","E") should return TRUE, while c("A","C") and c("A","B","D") should return FALSE, matching the table above. extract.clade returns a smaller tree containing only the descendants of the node you named.

Troubleshooting

• Unrooted tree. The ape documentation says a rooted tree is used as is, but an unrooted tree is rerooted arbitrarily, so the test asks whether the tips could be monophyletic under some rooting. A TRUE on an unrooted tree does not confirm a clade in your chosen rooting; root the tree on an outgroup first.
• Wrong node. If extract.clade returns the wrong subtree, check the node number or label, or use interactive = TRUE on a plotted tree.

Free alternatives

For building the tree that you then inspect, the site’s guides cover free tools:

Tool	Role	Guide
ape (R)	Test and extract clades, as above	This page
IQ-TREE	Infer a maximum-likelihood tree to test	IQ-TREE guide

For the full building workflow see how to make a phylogenetic tree; for the taxonomy side of naming groups, see the NCBI Taxonomy guide.

Frequently asked questions

How to identify clades in phylogenetic tree?

Pick a node, list every tip that descends from it, and check that your group is exactly that set. If it is, the group is a clade; if it leaves out descendants it is paraphyletic, and if its common ancestor lies outside it, it is polyphyletic.

What is a clade in a phylogenetic tree?

A group made of an ancestor and all of its descendants, which appears on a tree as a node with everything that branches from it.

Are clades and monophyletic groups the same?

Yes. The Digital Atlas of Ancient Life states that a monophyletic group is also a clade.

Sources

• UC Berkeley, Understanding Evolution, Reading trees (read 2026-11-08).
• Digital Atlas of Ancient Life, 2.4 Phylogenetic Trees and Classification (read 2026-11-08).
• R package ape reference, is.monophyletic and extract.clade (drop.tip page) (read 2026-11-08).