Skiphosoura is a derived non-pterodactyloid as predicted. This phylogeny also put Petrodactyle as a gallodactylid.

I’ve been on a bit of a run for the last few years with naming a number of new species. In particular, that has been with papers where the primary purpose of the paper was simply to get the thing described, named, and work through the various comparisons necessary to demonstrate that it is new. However, for almost every one of these that I have done (both recently and in the past), referees and editors have suggested that a phylogeny should be included in order to properly show exactly where the new taxon might fit.

This sounds immediately sensible and reasonable, but actually I think it’s rather problematic for a number of reasons. As this has come up so much, and is something I have discussed with some colleagues in the past, it roused me into writing this post about the problem. Partly, obviously, so I can moan about it. But also literally as a placeholder for the next time this comes up and so I can point to this post and not have to explain yet again why I don’t think a taxonomy paper needs a phylogeny.

So here are my reasons in no special order, though somewhat ascending in terms of complexity and importance. In theory at least, any of these can be ‘overruled’ by whatever it takes to make a paper correct and acceptable should be done, but the central argument I would make is that it’s not required at all because:

1) It’s not the paper being written. If the paper is a taxonomy one, it doesn’t need to be a systematics one. The two are obviously linked, but the fields are not synonymous and just because a species or genus is named doesn’t inherently require a phylogeny. If the definition and diagnosis is solid, that should be sufficient.

2) There may not be space. I did recently get the inevitable request to add a phylogeny in a paper that was already well over the space limit in that journal. So adding in new methods, results, and discussion sections, as well as at least one new figure is obviously adding a lot of material, and that means either cutting something else I want to include, or paying even more in excess charges.

3) The expertise may not be there. Not everyone can put together a phylogeny, and it can be a huge amount of work. Even just adding a single line to an existing matrix and coding it up and then running it is really time consuming, and not everyone has the time to do some extra big piece of work to add to a project. But if you are learning how to do this as it’s not your area, it’s then a massive ask, and it’s not as simple as ‘just get a coauthor to help’ if they don’t have the knowledge either, or you don’t want to bring someone in on the paper.

4) Critically, I would make the point to say what does a phylogeny actually add to a taxonomy paper? Unless it is some incredibly odd and aberrant or unique taxon where it is not at all clear what it is related to, as part of the descriptions and comparisons, it should be obvious what clade (even quite a narrow one) the species belongs to. This is because we now define so many clades and even single nodes on cladograms are defined by unambiguous traits that have been established through phylogenetic analyses. What were we doing with all this data if not to help define clades and work out the identity of isolated or incomplete or new material?*

So, if we already know that this new species is a member of group X because it has so many features in common with them, and likely shares unique traits, what does the phylogeny tell us?  That it might branch slightly earlier or later than one or two other species is not inherently informative about any evolutionary patterns, radiations or anything else. Unless you actually then add an analysis of rates of changes, or patterns of single traits etc., the phylogeny alone isn’t adding very much (and potentially, adding almost nothing).

The resulting cladogram will also still only be a hypothesis, and for many groups will either be entirely congruent with every other result going, or will clash with at a least one result where there are very different competing results. Yes, adding in one new line can really be crucial for resolving various clades, but that is pretty rare. Looking at my own species for example, we named Zhuchengtyrannus as a tyrannosaurine and in every analysis it has come out as one, Bellubrunnus was named as a rhamphorhynchine and in every analysis it has come out as one, and Petrodactyle was named as a ctenochasmatoid, and probably a gallodactylid and has come out as a gallodactylid. Even before we ran the analysis for Skiphosoura we were confident it would come out as a derived non-pterodactyloid monofenestratan with the proportions of the wings and tail, and so it came to be.

This adds a final relevant point here – there are new phylogenies coming constantly. It’s such a mainstay of so many studies that if a phylogeny isn’t included here, the taxon will almost certainly appear in one very soon afterwards (as indeed happened for all of the species named above, where it only took a year or so for them to be formally analysed). The odds that multiple people will code and analyse this animal with a revised and updated matrix, and do it better, and more thoroughly, in a dedicated paper, very soon is very high. So why push for what will likely be a rushed, imperfect result that will be a lot of work and probably uninformative, if something better will follow soon anyway?

All in all, I think that’s a fairly comprehensive set of solid reasons that a taxonomy paper does not inherently require a phylogeny. More importantly, I think it’s something referees and editors should stop suggesting it. It’s not the only thing like this either. I similar see or get requests on papers that say ‘just do a histological section’ or ‘just CT scan it’ or ‘just check it with method X’ like this is trivial, or even necessary. I remember for the Zhuchengtyrannus paper being asked to CT scan it by one referee, before been assured that there wasn’t even a scanner in China capable to taking the specimen! Even if there was, the time, money, software, and expertise needed to get a scan and then do something meaningful was very much out of our reach. Yes, it would have been nice, but it’s not a trivial ask by any stretch of the imagination, and not necessary to describe and name the animal.

What is good, and what is needed for what the authors are trying to do with the paper, are not the same thing. We are community, working together with different skills, support, funding, access, and time, to try and learn what we can and do effective science. Pushing for something that may even be inappropriate if it forces people to include something they are not comfortable doing, or requires a major amount of work, or to bring in additional collaborators, or means restructuring the paper isn’t a reasonable request at the best of times. When that doesn’t actually improve the paper, and will be rapidly superseded, it makes it a doubly inappropriate request.

It’s an apparent reflex that a new species needs a new phylogeny. To be fair, I have got all these papers through without needing one, so it’s not like there is a ban in play. But it is clearly a pervasive attitude that I seem to have to fight against every time, and I wonder how many phylogenies have been run and published because either the referees or editors insisted, or the authors thought the paper would not get through without it. It’s difficult enough to do good taxonomy these days without adding unnecessary barriers and I hope this is something that can be resisted.

*Yes, you can use phylogenies for lots of other things too, but all the data defining nodes is most useful for this exact thing. Also, it’s notable that when anyone publishes a new specimen of a known species, it’s assumed that the diagnostic traits are sufficient to place the new specimen with that species. No one insists on a phylogeny to make sure they come out together, with the implication that such traits are a good indicator of what is and isn’t a species, except, apparently, when one is new, when suddenly they are not enough on their own.