Phylogeny Friday -- 16 March 2007

New Terms in Phylogenetics

I'm a cladist, and as a cladist I want all of my taxa monophyletic. That means anything given a name (animals, plants, vertebrates, insects, etc.) should include all the organisms that descend from the most recent common ancestor (MRCA) shared by the organisms you claim are in that group. Confused? Well, allow me to direct you to Wilkins's post on clades and this handy diagram:

In the tree above, grouping species A, B, C, and D into a single taxon results in a monophyletic clade. But if we exclude species A (calling species B, C, and D a single taxon), we create a paraphyletic taxon. For a real world example, think of birds and reptiles. Birds are a monophyletic taxon, but reptiles (if one excludes birds from the group) are not. To make reptiles monophyletic, we must include birds in that taxon.

There are other terms one must become familiar with when describing trees, such as sister taxa (that would be species A and B), which refers to lineages that are each other's closest relatives amongst the taxa sampled in the tree. But these terms only apply to rooted trees -- those trees where we can identify the location of the MRCA of all taxa. In our tree above, the root is located on the vertical branch connecting species E to species A, B, C, and D. But not all trees are rooted.

When working with unrooted trees, it becomes difficult (or impossible) to identify monophyletic groups because the location of the root determines whether a particular taxon contains all descendents of a MRCA or not. In the unrooted tree shown above, if the root of the tree were placed on the branch leading to taxon C, then taxa A, B, and D would be monophyletic. If, however, the root were placed on the branch connecting taxa A and B with taxa C and D, then A and B would be monophyletic and C and D would be monophyletic.

Because the terms 'monophyletic' and 'sister taxa' lose meaning when applied to unrooted phylogenies, a group of biologists from the Natural History Museum in London, the National University of Ireland, and the University of Newcastle upon Tyne have proposed alternate terminology for unrooted trees. They suggest using the term 'clan' as the unrooted equivalent of clade, and 'adjacent group' for sister groups in unrooted trees.

If one splits a tree along any branch, one produces two clans, at least one of which would be monophyletic were the tree rooted. This allows for many different possible clans (although the amount is finite) from any given unrooted tree. The authors point out that, for some unrooted trees, we have an idea where the root may be located. In those cases, we can limit ourselves to the clans that are realistic given other knowledge.

In our example unrooted tree, we can create a split between taxa A and B and taxa C and D, creating two clans: A/B and C/D. There are three possible adjacent groups for clan A/B: taxon C, taxon D, or clan C/D. If we assume that clan A/B is a monophyletic clade, then one of those adjacent groups would be a sister taxon, but we cannot say for certain which one. The root of the tree could be place either on the branch connecting clan A/B and clan C/D, on the branch leading to taxon C, or on the branch leading to taxon D. While sister taxon is an absolute term for a rooted tree, adjacent groups are dynamic.

While this may seem like mere semantics, these distinctions are important because unrooted trees lack information present in a rooted tree. Without a root, a tree lacks direction and MRCAs are unclear. That's why we need to be clear when describing evolutionary relationships in unrooted trees. Providing explicit terms for unrooted trees that differ from those used in rooted phylogenies allows for such clear descriptions.

Wilkinson M, McInerney JO, Hirt RP, Foster PG and Embley TM. 2007. Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends Ecol Evol 22: 114-115. doi: 10.1016/j.tree.2007.01.002