Friday, April 24, 2009

Basal and Derived Taxa

Recently, I’ve been plumbing a bit of the macroecological literature and have been somewhat baffled by the usage of ‘basal’ and ‘derived’ in reference to extant species. These terms are frequently used in reference to the spatial distribution of phylogenetic diversity: does species richness within regions consist primarily of members of basal or derived clades? I am a big fan of much of this work, and I think that the patterns of phylogenetic diversity through space can tell us much about the feasibility of niche conservatism-type models for diversity gradients. However, I have a hard time wrapping my head around precisely what basal and derived mean in this context and think there is a real need for terminological clarification here.

As an example: one macroecological metric is the “root distance”: basically, the number of nodes separating a species from the root of a phylogenetic tree. Several studies have looked at mean root distances among species within regions, classify species as basal (few nodes between root and tip) and derived (lots of nodes between root and tip). Under this classification scheme, there are very interesting differences in species richness between basal and derived taxa.

I have a hard time getting over my initial visceral reaction to the use of ‘basal’ versus ‘derived’ in this context (see previous discussion on the “coffee shop phylogenetics” series). While I think these studies are on to something, my take on root-node distances is that they are a metric of diversification rate or total diversification. Regions with more “derived” species thus contain more species from clades that have undergone substantial diversification (and hence, have greater root-tip nodal distances). But I think a focus on basal and derived taxa is confusing and this literature could benefit from eliminating the use of these terms in association with extant taxa (see, for example, Crisp and Cook on this subject).


Poletarac said...

Also see Omland et al. (2008)

Jack Sullivan said...

I'm with you, but use of "basal" has taken the place of "primitive." It's an improvement, in that there's not the same connotation, and it refers to a taxon that is sister to much of the rest of whatever the reference clade is (at least that's what I mean when I use the word to modify a group). If others infer "primitive" (i.e., retains many primitive characters) when I'm not trying to imply that, then it's up to me to find a better word. So Ascaphus may be a basal frog lineage that is a mosaic of primitive and derived characters. Ditto for monotremes (except the frog part).

I also don't like the term "derived" as a modifier for a group. Maybe "apical" is better, but it's also relative. We do need more precise language, and it's been so as long as I can remember.

Don't get me started on "higher" versus "lower."

I intended to chime in on the prehistoric bird post, but life's hectic.

Vazrick said...

Another good reference is:

Krell, F.T. & Cranston, P.S., 2004. Which side of the tree is more basal?
Systematic Entomology 29: 279–281.

Salva said...

I like the piece of Krell and Cranston: there are sister groups, but each 'side' of the tree all have the same age, then no branch can be more basal or derived.

Maybe, the problem is the original analogy: it is better "twin taxa" than "sister taxa".

John Harshman said...

Generally, "basal" means "of low diversity" and "derived" means "of high diversity", though I suspect that's not what the users of those terms think they mean. That's just the way it works out. If two groups diverge at a node, the one that doesn't have many species is called the basal one (especially if it just has one species).

I do think it's a pernicious term. "Sister to the rest of the clade" would be the alternative that doesn't have odd implications.

Chris Randle said...

In this regard, I'm an operationalist rather than a philosopher. I know what people mean when they say basal and derived, so I don't bother to dispute those terms.

Aloysius Horn said...

Nodes can be basal (or apical... I like Jack's term), but calling extant species, clades, or lineages basal is wrongheaded for the reasons given here. Is there a counterargument to be made?

Dan Rabosky said...

I *think* I understand in general what is meant when these terms are used to describe extant species, but I am not convinced they are signifying what authors sometimes think they signify. It doesn't tell us anything about lineage age, which is one interpretation I have seen (somehow, 'basal' - ie low diversity- lineages are perceived as older). E.g., lots of members of "basal" clades in some region - what does this tell us?

I can't think of a good counterargument and can see lots of problems with continued usage here. Even within the set of folks posting here, who all recognize that this is technically incorrect, we find a range of interpretations.