Reading up on biogeography part 5: time-slices

Today finishes up, at least for the moment and until the next special issue comes out, the little series on panbiogeography and vicariance geography. The last paper is

Corral-Ross V, Morrone JJ, 2017. Analysing the assembly of cenocrons in the Mexican transition zone through a time-sliced cladistic biogeographic analysis. Australian Systematic Botany 29: 489-501.

It uses area cladograms, as did one of the papers already discussed, but as the title indicates it does so in a way that examines different "time slices".

Before I get to the methodology I would like to establish an analogy.

Imagine you read a recipe for what are supposed to be very amazing pancakes. The instructions are as follows: (1) mix eggs and milk; (2) place the concrete in the deep freezer; (3) pour the mixture into the frying pan. Looking at such instructions you may well wonder first what concrete has to do with anything - not only would you not expect concrete to be part of pancake-making in the first place, but it does not even seem to be used for anything. Next you may notice that there is no mention of flour, although some kind of flour would appear to be necessary to produce pancakes.

There are now at least three possibilities. One is that the authors of this recipe have no idea how to make pancakes and merely pretend they do. Another is that they do in fact know what they are doing in the kitchen but merely wrote very incomplete and confusing instructions. Finally, there is the possibility that we, the readers, are just too ignorant or blinkered to understand the brilliance of the approach.

Some of the papers in cladistic biogeography and panbiogeography are very clear in their methodology, and I can immediately understand what they did and perhaps even what their logic is, even if I may have concerns. But with others I feel as if I am confronted with the above pancake recipe. Either the authors have no idea how to do biogeography, or the methods section could be clearer, or I have no idea how to do biogeography.

In the present case, the authors assembled 49 phylogenies ("cladograms") of various groups of organisms occurring in the Mexican biota that they were interested in. They then, as usual for area cladistics, replaced the names of the terminal taxa in the phylogenies with the areas those terminals occur in, and then extracted "paralogy-free subtrees" for analysis.

To this point it is the same approach as in the previous area cladistics paper, and once again I am a bit uncertain how precisely it works and, more importantly, how it could possibly be justified. When a molecular phylogeneticist removes paralogous alleles from the analysis they do so because we understand a lot about gene duplication, gene families, pseudogenes and suchlike. When an area cladist picks subtrees out of a larger area cladogram, what is the parallel? What is the theory behind it? How do they explain the existence of what they call paralogy in a way that does not make the whole idea of having area cladograms appear absurd? I cannot help but wonder if it is anything more than "this is too complicated so we will ignore it". Maybe I just haven't seen the proper justification, but the papers I have looked at so far seem to limit themselves to saying that paralogy exists and needs to be removed.

But now for the time-slicing. This is now really the pancake recipe: if it works the way I believe I understand the methods then it doesn't make any sense. But if it works in a different way that actually makes sense then it isn't explained well enough for me, at least, to understand. The way it looks to me is that the authors assigned each group of organisms for which they had a phylogeny in their analysis to a "cenocron", which they defined as a "set of taxa that share the same biogeographical history, which is recognised as a subset within a biota".

They then conducted three different analyses supposedly corresponding to the Miocene, the Pliocene and the Pleistocene, using phylogenies from only one, two and then all three cenocrons, respectively. In other words (again, if I understand correctly), the idea seems to be that only organisms from one of the cenocrons would have been in the study area in the Miocene, with the others arriving later. I think.

The conclusion after all this effort is that "the Mexican Transition Zone is a complex area that differs in delimitation from one analysis to another. The present study showed that the results may depend on the assemblage of the taxa analysed, with time-slicing being an adequate strategy for deconstructing complex patterns in cladistic biogeography". That is not exactly the most concrete conclusion I have ever seen. What is more, the second paragraph of the introduction already explained that "the Mexican transition zone, as defined by Halffter (1987), is a complex area", so at this moment I am not really on top of what new insights the analysis produced.

But my more important question is this one: How does the claim work that the "Miocene analysis" examines the Miocene time-slice when the authors appear to have used phylogenies of contemporary (that is Pleistocene) species? The Miocene was 5 to 23 million years ago. The species in the phylogeny would not have existed yet, only their distant ancestors would have, with potentially very different geographic ranges. We are talking the time of our common ancestor with the chimps and waaay beyond!

Do the authors assume that all contemporary species existed 20 Mya ago and have remained utterly static since that time? Where is the flour that one would absolutely need to get a pancake out of this? (Time-calibration of all the phylogenies they used followed by ancestral area estimation, in case that isn't immediately clear.)

Again: maybe I am missing something, perhaps even something that will be obvious to many others, which would make sense of this approach. But at the moment I pointlessly have a lump of concrete sitting in the freezer, and the promised pancake looks very much like a watery omelet to me.