Friday, December 20, 2013

How not to decrease the confusion about monophyly

Today this year's last issue of Australian Systematic Botany has come out, and the first paper in it is 'Defining and redefining monophyly: Haeckel, Hennig, Ashlock, Nelson and the proliferation of definitions' by Vanderlaan, Ebach, Williams and Wilkins.

It provides a historical overview of the various ways in which the term 'monophyletic' has been used over the years. A perhaps overly simplistic take is this:
  1. Haeckel introduced the term to describe a group with a common ancestor.
  2. Hennig found it important to distinguish two types of groups that have a common ancestor. Monopyletic ones include all descendants of that ancestor, paraphyletic ones only some of the descendants.
  3. Ashlock was unhappy with the redefinition of monophyletic and wanted to return to what he saw as the original definition by Haeckel. He thus used monophyletic to refer to both Hennig's monophyletic and paraphyletic and created the new term holophyletic for Hennig's monophyletic only. Because they have a vested interest in blurring the line between mono- and paraphyly, so-called Evolutionary Systematists prefer Ashlock's definitions.
Confused yet? In reality, as the authors of the present paper point out, it is even more complicated because there is some disagreement about whether a monophyletic group includes the descendants and everything back in time to the ancestor or only the descendants existing in one time-slice.

Vanderlaan et al now propose two new terms: diamonophyletic for a clade that is seen through time to include the ancestor and all, and synmonophyletic for a group of contemporaneous species that are more closely related to each other than to anything else.

Yes, definitions are important. But I still have a few issues with this paper. First, I do not have the foggiest idea why we really need to distinguish these cases. Assuming that evolution is true (and I do hope the four authors of the present paper agree), is there really any imaginable group where an extant species would be assigned to a diamonophyletic but not to a synmonophyletic group or vice versa? I cannot imagine how that would be possible.

And that means that a monophyletic group is a monophyletic group is a monophyletic group, as long as we ignore Ashlock's re-redefinition. In a phylogeny, being each others closest relatives means being descended from the same ancestor. So maybe I miss something, but I cannot imagine a situation in which I am talking about a plant group, let us say the genus Senecio, and somebody would ask back, 'do you mean including the ancestor or only the species that exist today?' That is just not a thing that happens.

The second issue here is that as recent as 2010 Podani had already suggested new terms for what (at first glance at least) appears to be precisely the same distinction: monophyly/paraphyly for phylogenies seen through time, i.e. including ancestors, and monoclady/paraclady for contemporaneous species only. The strange thing is, I vaguely remember one of the authors of today's paper (or his blog partner?) lambasting Podani over this for somewhat unclear reasons, and now he goes and does what sure looks like the same, only ignoring the previous contribution (yes, they don't even cite it).

And that is then another problem. We now have even more terms floating around than before because Vanderlaan et al have created new ones where Podani's would have been available. How that is meant to decrease the conceptual confusion instead of increasing it exponentially is not immediately clear.

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