Tuesday, November 29, 2016

Cladistics textbook

In my office I have two 'proper' phylogenetics textbooks, that is counting only those that cover the principles and theory as opposed to offering only a practical how-to manual. One is Felsenstein's, who is strongly associated with likelihood phylogenetics, although his book covers all approaches. The second is:

Kitching IJ, Forey PL, Humphries CJ, Williams DM, 1998. Cladistics second edition - the theory and practice of parsimony analysis. The Systematics Association Publication No. 11. Oxford Science Publications.

As the title implies, it is entirely about parsimony phylogenetics.

Having recently looked into Kitching et al., I noticed two short sections that I found interesting enough to discuss here. I will start with the question of ancestors. Proponents of paraphyletic taxa often make claims on the lines of cladists "not accepting the existence of ancestral species", of "ignoring ancestors", or of "treating all species as sister taxa".

Here now we have a textbook written by cladists, in other words the official version, to the degree that an official version exists. It is, of couse, not as easy as that because the only thing that unites cladists in the sense of what paraphylists argue against is that supraspecific taxa should be monophyletic. Many other details differ from cladist to cladist, and in the sense of what paraphylists argue against the concept of cladist includes those who use e.g. Bayesian phylogenetics.

I also do not want to give the impression that I, personally, take what Kitching et al. promote on this or that detailed question to necessarily be The Correct View. It is well possible that I, a cladist, find myself in disagreement with some chapter of that textbook. I am not even arguing here, in this instance, that making taxa monophyletic is the way to go (although of course I do believe that).

No, the point of the post is merely this: if Kitching et al. argue not-XYZ, then this demonstrates decisively that any claim of all cladists arguing XYZ is nonsense.

So, about ancestors, and turning to page 14 of the textbook:
In fact, to date, Archaeopteryx has no recognized autapomorphies. Indeed, if there were, Achaeopteryx would have to be placed as the sister-group to the rest of the birds.
It does not matter here whether more recent analyses have demonstrated Archaeopteryx to have autapomorphies and to actually have been a side branch relative to modern birds. We should here simply think of any species that looks exactly like the ancestral species of a later-existing clade is inferred to have looked like.

It should be clear that the above section is correct. An ancestral species would not have any systematically useful characters relative to its descendants, because that descendant clade would have started out as that species. My view - and here other cladists may differ - is actually that the ancestral species and the clade are one and the same. The ancestral species has over time turned (diversified) into the clade.
In terms of unique characters, Archaeopteryx simply does not exist. This is absurd, for its remains have been excavated and studied. To circumvent this logical dilemma, cladists place likely ancestors on the cladogram as the sister-group to their putative descendants and accept that they must be nominal paraphyletic taxa (Fig. 1.9c). Ancestors, just like paraphyletic taxa in general, can only be recognized by a particular combination of characters that they have and characters that they do not have. The unique attribute of possible ancestors is the time at which they lived.
Here is the reason why paraphylists complain about ancestors being treated as sister to their descendants: they are treated like that, crucially, so that we can do the analysis. It is a practical, not a philosophical reason.

Note also that at least the cladists who wrote the textbook do not have any problem with paraphyletic species. Whether we think that this use of the word paraphyletic makes sense or not (as do I), it is discussions like this one which make me groan in frustration whenever I read a paraphylist claim that cladists only accepted paraphyletic species as a cop-out once they could no longer deny that they existed. No, cladism was founded on the principle that monophyly applies above the species level, so it never had to backpedal like that.
After a cladistic analysis has been completed the cladogram may be reinterpreted as a tree (see below)
What they mean here is that they see a cladogram as such (merely) as a different visualisation of the data from the data matrix, while the "tree" is the cladogram's interpretation in terms of evolutionary relationships, of actual genealogical relatedness of the terminals.
and at this stage some palaeontologists may choose to recognize these paraphyletic taxa as ancestors, particularly when they do not overlap in time with their putative descendants (see Smith 199a for a discussion).
And this is the main point. Here we have a group of senior cladists who wrote, to put it in the simplest possible terms, "we need to treat every species as a terminal to get a cladogram, but then if you wish you can interpret a terminal without autapomorphies as an ancestor".

It is as if the people who claim that cladists do not accept the existence of ancestors haven't even bothered to figure out what any cladists really think.

Next time I will look at a short section of the textbook that I definitely disagree with.


  1. Alex, you might find my slides from a recent presentation I gave at GSA interesting, as they are on this topic. They even touch on Archaeopteryx as an ancestor.


    1. Thanks! Interesting, although obviously a bit hard for me to judge, not being a palaeobotanist and not having heard your audio.

      Wonder what Wagner meant with ancestors potentially having autapomorphies - how could they possibly have those relative to their own descendants? Perhaps need to check the reference.

      Although I am not totally comfortable with the morphospecies / composite species concept in theory, it seems clear why it would be the default species concept in palaeontology, as shown in your slides. I assume "it looks the same, so it is the same species" is pretty much the dominant view among palaeontologists?

      Interesting that your analysis found no anagenesis, given how important that process is in the theoretical considerations and argumentation of some people.

  2. Well, to save you the time, Wagner explained that if there was any probability of character reversal, than an ancestor might have autapomorphies not present in its descendants. Thus, if we allow for the possibility of reversal, autapomorphies are an imperfect proxy for ancestral status at best.

    Yes, most paleontologist use the morphospecies concept, or something like it (i.e. chronospecies). Some hold to a strict phylogenetic species concept (e.g. Smith 1994 argued for something like that).

    Well, note that what I call 'anagenesis' isn't necessarily what everyone else calls anagenesis. I'm using the vernacular particular to the majority of invertebrate paleontologists. I'm saying that the evidence is that morphospecies don't originate without a branching event initiating them, and that the ancestral morphospecies doesn't terminate when branching occurs (so, budding 'cladogenesis', not 'bifurcating' or 'anagenesis').