Sunday, May 10, 2015

A new classification of all living organisms

Of course, the day after I write that there is a near-unanimous consensus that taxa should be monophyletic, I get an alert that a new classification of all of life has been suggested, and it turns out to be proudly non-phylogenetic (Ruggiero et al. 2015, A higher level classification of all living organisms, PLOS One 10: e0119248).

Interestingly, the authors describe their classification as "neither phylogenetic nor evolutionary". There are two ways to read this. Either they don't know what they are talking about, because 'evolutionary' classification is what the proponents of paraphyletic taxa call theirs, and Ruggiero et al's classification has paraphyletic taxa and is consequently 'evolutionary' in that twisted sense; or they mean to indicate that their classification is pragmatic and theory-free.

The latter interpretation would fit with the repeated mention of "serving ... database providers" and "its immediate use as a management tool". In other words, this is about archiving, not science, which is fine as far as it goes. Weirdly, however, the abstract also claims that the new classification would be "immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory 'backbone' for biodiversity databases, museum collections, libraries, and textbooks". But that is precisely what a non-phylogenetic classification is not useful for. Naming incomplete, non-natural groups is downright misleading to subsequent taxonomic and biodiversity research, it misinforms the public, and it would misinform students if used in textbooks.

So, how much non-monophyly is there in this system? Lots. They recognise the prokaryotes, although it seems fairly clear now that the archaea are at least more closely related and more similar to the eukaryotes than to the bacteria if not paraphyletic to the eukaryotes. They recognise various groups of algae that are paraphyletic to the land plants; the crustaceans, which are paraphyletic to the insects; the paraphyletic reptiles. And that is just scratching the surface. If somebody were to interpret this as a summary of our knowledge of the tree of life they would be seriously mislead.

As always when somebody proposes a non-phylogenetic classification, I have a particular interest in their justification. So what are the authors' arguments against circumscribing natural groups?
There is currently no consensus among the world's taxonomists concerning which classification scheme to use for the overall hierarchy of life, in part because of the confusion resulting from Hennig's redefinition of previous terminology of classification, which has not been universally accepted;
Yes, Ernst Haeckel, who only died as recently 1919, called groups with a common ancestor monophyletic. Realising that this definition is quite meaningless because any random collection of species on this planet has a common ancestor, Willi Hennig (1913-1976) restricted the meaning of the term to groups encompassing all descendants of the common ancestor. Today, Hennig's definition is used in university courses, it is used in textbooks, it is used in journal articles, and it is used in conference presentations. It is even used on Wikipedia, and everybody knows how vulnerable that site is to people who promote fringe positions but have a lot of time on their hands. Scaly things living under damp rocks use Hennig's definition, and conversely most people have never heard of Haeckel's.

There is precisely zero confusion. The only people who prefer Haeckel's definition are those who want to accept paraphyletic taxa, and even then only some of them. If I lost a few fingers in a freak lab accident tomorrow I could still use the remaining ones to count off the number of papers I have seen that seriously use the word monophyletic in Haeckel's sense, and I have never heard it used like that at a conference.

What else?
the separate goals of cladification and classification
and later:
there is still strong debate over their accounting for evolutionary divergence or information content other than the branching pattern
and yet later:
In this sense it summarizes overarching aspects of the tree of life, including both paraphyletic and monophyletic groups, both being important in facilitating meaningful communication among scientists and between the scientific community and society.
I have argued before that you can either have phylogenetic information content or phenetic information content in a classification, but if you try to get both you will have neither because the end user cannot be sure which of the two criteria was used to define any given group.

And if there is even just one paraphyletic group in your system, then by definition you are not summarising the tree of life. The sentence cited above is fully equivalent to the claim that I am boiling water when I put it into the -80C freezer. So put me down as not convinced.
conflicting or unresolved evidence for phylogenetic relationships
If there is no clear evidence for what the relationships are, then nobody knows if the classification is non-phylogenetic. So this is irrelevant as a justification for deliberate non-monophyly.

Then there are parts that indicate that the authors may be genuinely confused about about the meaning of monophyly, but not in a Haeckel versus Hennig way.
We have therefore named only groups generally considered to have had a monophyletic origin, even though some of them may be paraphyletic...
There is a tree of life, and then a systematist goes and circumscribes a group, and depending on how well they do it the group turns out either monophyletic or paraphyletic. The only way to make sense of the above sentence is by supposing that the authors have fallen prey to some kind of circular reasoning whereby paraphyletic groups are assumed to be natural entities, but whether they are is obviously the point of contention.
...and others, e.g., Euglenozoa, Rhizaria, Cercozoa, include subgroups (such as Euglenophyceae, Chlorarachnea, and Paulinella) that evolved by the symbiogenetic merger of two fundamentally different lineages, while others have had infusions of genes from elsewhere and therefore do not conform to any purely formal definition of monophyly. [...] For practical purposes we treat Proteobacteria and Cyanobacteria as holophyletic phyla even though both exclude their mitochondrial and chloroplast descendants, neither of which is now a bacterium but an evolutionarily chimaeric cell organelle.
To me the idea that the eukaryotes are not monophyletic because they have taken up endosymbionts makes about as much sense as the claim that a human ceases to be the same individual when they receive a kidney transplant. Conversely, if there is any "practical" reason not to classify mitochondria and chloroplasts into their lineages I have never seen it. Everybody knows that chloroplasts for example are cyanobacteria, but nobody ever seriously thought that that should have consequences for the systematic position of plants.
This argument, however, overemphasizes cladistic level compared with phenotypic disparity, and is contrary to traditional assignment of phylum (or division) status to the main bryophyte, "pteridophyte" and seed-plant subgroups.
Ah, tradition. Traditionally, we believed that the sun goes around the Earth and that diseases were caused by demonic possession. And then science marched on.

Here we have perhaps the fundamental conflict in contemporary biological systematics, and the real reason for why the present classification looks the way it does. There are systematists who see themselves primarily as scientists and thus strive to update classifications as our knowledge advances. And then there are other systematists who see themselves primarily as archivists and thus want a neat, unchanging classification. They have grown up with paraphyletic reptiles so they will now fight tooth and claw to keep reptiles paraphyletic; if they had grown up with Linnaeus' 1735 Systema Naturae, they would now fight tooth and claw to keep whales classified as fish, for the sake of stability, ease of communication, and "information content".

Other sciences do not seem to have to deal with that. Where are the medical researchers who, when presented with evidence that symptoms they had previously diagnosed as one disease can really have two possible causes, will reject the new system with reference to tradition? They would be laughed out of the room. But in systematics and taxonomy a surprising number of people seems to think one should avoid drawing consequences from new knowledge because it would make a database harder to manage. I can see where they are coming from, but shouldn't we be scientists first?

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