That editorial in Cladistics

On the weekend, a colleague made me aware of the recent editorial in Cladistics clarifying that all papers in the journal need to use parsimony methods, and she indicated that it had already produced a lot of harsh criticism. Today I read the editorial and several responses including the ones on the Twitter hash tag #parsimonygate. At the moment I am somewhat in two minds about the affair.

To summarise the Cladistics editorial:

• Authors should always show parsimony trees. Alternative phylogenies can be shown in addition if they are different and there is "a pertinent reason" to do so. This is not really new, as when I published a paper in Cladistics a few years ago I was already asked to do the same. In other journals I have seen the reviewers or editors demand likelihood analyses. I am a methods pragmatist and can live with either. If the data are strong, the results will be the same anyway.

• The editors consider parsimony analysis to be preferable to other methods for "philosophical" reasons. As far as I can tell, most biologists would be more impressed by biological and pragmatic reasons; I know I am. They also stress repeatability, intelligibility and clarity, implying somewhat that model based methods don't have those. This I find odd except perhaps in the case of certain Bayesian analyses suffering from an over-abundance of unknowable priors.

• The editors point out that all methods have their weaknesses, and that we have to live with not knowing the truth for certain. Seems obvious.

• The editors think that they are doing something right because the journal has a high impact factor. Well... let's just say that I have very mixed feelings about impact factors.

To summarise the criticism, let's go through #parsimonygate as of today 10:49 Sydney time:

• 8x Equating the Cladistics editors to religious fundamentalists or calling them otherwise dogmatic. 

• 3x Mocking Cladistics as too traditional and/or stuck in the 1980ies. 

• 1x Some analogy to physics that I don't quite understand. 

• 3x Ridicule without argument. 

• 1x Call for boycott. 

• 1x A different journal advertises itself as accepting all phylogenetic approaches. 

• 5x Meta, as in expressing amusement at somebody else's comment.

Elsewhere I have seen another call for boycott and somebody mocking the sentence about how we cannot know The Truth with complete certainty, strangely equating this stance with creationism. I think that is exactly backwards, because it is creationists who crave certainty, and it is good scientists who accept that conclusions are tentative and open to future falsification. But okay, it is at least clear the main arguments are that parsimony is outdated and that accepting only papers using a certain approach is dogmatic.

Types of phylogenetic tree diagrams

This post has two motivations. First, it can serve as a future reference point if I need to mention tree types again, and of course it can be found via search engine by anybody who needs to look this stuff up. The second is my recent observation that some 'evolutionary' systematists have the tendency to call all phylogenetic trees cladograms, perhaps conflating ways of displaying evolutionary relationships with their dubious claim that cladists do not accept the existence of ancestors. I would like to take the opportunity to explain the different ways we can draw trees, what they mean, and what a cladogram really is.

Phylogenetic trees are simple non-cyclical graphs connecting terminals - often species - to show how the terminals are related. In species trees, the internal internodes are common ancestors, and the nodes where branches meet are speciation events. In gene trees, they would be ancestral alleles and mutation events, respectively.

Perhaps the oldest truly phylogenetic tree was drawn by Charles Darwin in his notebook, the famous "I think" diagram. But it was in that case an abstract model to help him visualise for himself common descent, not yet a concrete hypothesis about any specific organisms.

So we have a tree connecting terminals. I will further assume that the tree is outgroup-rooted, so that it has an explicit directionality: In the following examples, the arrow of time points from the left to the right. It could be different. All that follows would work just as well if the trees were turned by 90 degrees and the arrow of time pointed from bottom to top, or if the tree was circular as in the case of Darwin's sketch. What this post is about is simply what the branch lengths on the tree diagram mean, if anything.

Aubert's analysis of phylogenetic terminology, part 6: empirical falsification

Continuing the discussion of this paper from here, here, here, here, and here, and working through the main claims of the paper as I see them:

• The various definitions provided in the paper are in some way better than the ones that are currently accepted.

• There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)

• A strictly phylogenetic classification is formally impossible.

• Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".

• Cladism is built on biologically unrealistic assumptions that have been empirically falsified.

• There exists an objective approach to delimiting paraphyletic groups.

• It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

Have the assumptions underlying cladism been empirically falsified?

The abstract of the present paper claimed that the "biologically unrealistic assumptions on which cladism is based ... have been empirically falsified". I was curious what this would be about. As far as I can tell, the only subsection of the paper dealing with the claim is 10.4., Unformitarianism and Punctualism.

Aubert's analysis of phylogenetic terminology, part 5: is cladism anti-realist?

Continuing the discussion of this paper from here, here, here, and here, and working through the main claims of the paper as I see them:

• The various definitions provided in the paper are in some way better than the ones that are currently accepted.

• There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)

• A strictly phylogenetic classification is formally impossible.

• Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".

• Cladism is built on biologically unrealistic assumptions that have been empirically falsified.

• There exists an objective approach to delimiting paraphyletic groups.

• It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

What assumptions is cladism based on?

The section of Aubert's paper most relevant to the claim of cladism being anti-realist and metaphysical is #10, Analysis of the Cladist Doctrine. But before we come to the supposed structuralist influence, it is interesting to examine how the cladist "doctrine" is described:

Cladism as it was founded by Hennig

Okay, let's stop right here for a moment. Aubert wants to recognise paraphyletic taxa, and mainstream systematics today recognises only monophyletic ones. Question is now, are we talking about cladism as founded by Hennig, or are we talking about Phylogenetic Systematics as practised today, by hundreds of people publishing papers to circumscribe groups as monophyletic? Because finding a mistake made by Hennig personally will not necessarily address the underlying disagreement with all the latter, who still want to make taxa monophyletic even as they may or may not agree with Hennig's species concept and phylogenetic methodology.

This is a bad start, comparable to a creationist rejecting modern evolutionary biology because of Darwin's now outdated ideas on inheritance. Let's see where this is going, but it is important to realise that today's phylogenetic systematists do not treat Willi Hennig like an infallible prophet. Practises have changed since 1966.

Aubert's analysis of phylogenetic terminology, part 4: cladism impossible?

Continuing the discussion of this paper from here, here, and here, and working through the main claims of the paper as I see them:

• The various definitions provided in the paper are in some way better than the ones that are currently accepted.

• There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)

• A strictly phylogenetic classification is formally impossible.

• Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".

• Cladism is built on biologically unrealistic assumptions that have been empirically falsified.

• There exists an objective approach to delimiting paraphyletic groups.

• It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

So today is going to be about the claim that a strictly cladistic classification is formally impossible.

Staying at first at the abstract level, imagine a group Aides. Its ancestral species A split into species B and C. Subsequently, B split into species D and E, while C split into F and G. The following is a strictly cladistic classification, and it does not look impossible:

Aides = { A, Bides = { B, D, E }, Cides = {C, F, G } }

Realistically, we will probably not know the ancestral species in most cases, so in practice we will be dealing with synchronous classifications like this:

Aides = { Bides = { D, E }, Cides = {F, G } }

Again, this is a strictly cladistic classification, and it is not self-evidently impossible. So what is going on?

Botany picture #221: Hibiscus divaricatus (and two other miscellaneous photos)

Close-up of the flower of Hibiscus divaricatus (Malvaceae), taken today at the Australian National Botanic Gardens. The five stigmatic branches are clearly visible, as is the fact that the stamens are forming a tube around the style in Malvaceae, at least s.str. The filaments of the stamens are fused while the anthers are free; in the Asteraceae, the opposite has happened, and the tube is made from fused anthers while the filaments are free!

We also went down into the ANBG's rainforest gully, where they were spraying mist at the time. Quite an interesting atmosphere.

Finally, one of the rare moments where I show an animal on this blog. This praying mantis was sitting on a sculpture near the rock garden.

Aubert's analysis of phylogenetic terminology, part 3: Different kinds of relationships

Continuing the discussion of this paper from here and here, and working through the main claims of the paper as I see them:

• The various definitions provided in the paper are in some way better than the ones that are currently accepted.

• There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)

• A strictly phylogenetic classification is formally impossible.

• Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".

• Cladism is built on biologically unrealistic assumptions that have been empirically falsified.

• There exists an objective approach to delimiting paraphyletic groups.

• It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

One of the claims made repeatedly in Damien Aubert's paper (and in a recent comment here) is that the same definitions and approaches apply to all levels of biological diversity. In this post, I would like to take the opportunity to discuss in detail why I disagree. I do believe that the relationships between individuals of the same biological species are not equivalent to the relationships between species or groups of species. Importantly, the same stance underlies phylogenetic systematics, AKA cladism.