Author Interview: The phylogenetic nomenclature of ornithischian dinosaurs
PeerJ spoke to Daniel Madzia about the recently published article “The phylogenetic nomenclature of ornithischian dinosaurs”. Daniel is an assistant professor at the Institute of Paleobiology of the Polish Academy of Sciences.
Can you tell us a bit about yourself?
I’m an assistant professor at the Institute of Paleobiology of the Polish Academy of Sciences. My interests are rather broad but most of my research projects are generally designed around aspects related to the evolutionary history of Mesozoic vertebrates, especially dinosaurs and plesiosaurs.
Can you briefly explain the research you published in PeerJ?
In our recent PeerJ paper Victoria Arbour, Clint Boyd, Andrew Farke, Penélope Cruzado-Caballero, David Evans and I revised the phylogenetic nomenclature of ornithischian dinosaurs. In 2020, the International Society for Phylogenetic Nomenclature published a long-awaited set of rules aimed to govern phylogenetic nomenclature – the International Code of Phylogenetic Nomenclature, better known as the PhyloCode.
The ‘traditional’ rank-based nomenclature, as governed by the zoological, botanical, and bacteriological codes, does not have the tools to provide explicit connection between taxon names and clades they are intended to ‘cover’ and researchers may therefore use the same taxon names in different ways. For example – what do we mean when we say ‘dinosaur’? If we don’t have tools to make the meaning of the name unambiguous, how do we know, for example, what’s the oldest dinosaur? Where is the nomenclatural boundary? There is a group of dinosauromorphs named silesaurids. According to some studies they are part of the ornithischian lineage. However, other studies suggest that they are nested outside the ‘traditional’ dinosaur groups (ornithischians, theropods, and sauropodomorphs). We can easily agree that if they are nested within Ornithischia, they are dinosaurs, but if they are outside the ‘traditional’ groups, are they still dinosaurs? Some researchers could say that they are but others would disagree. Can we ensure, somehow, that everyone uses names like Dinosauria and Silesauridae in the same way? We can – that’s what phylogenetic nomenclature is for.
In phylogenetic nomenclature, the names of groups of organisms, such as Dinosauria, Mammalia, Aves etc. have clear and unambiguous meaning because they possess phylogenetic definitions. Once a name is phylogenetically defined it becomes explicitly connected with a clade of organisms. There are a few types of phylogenetic definitions and each of them specifies, in different ways, what taxa are representatives of the group to be named and what are not. For example, the name Dinosauria is formally defined as pertaining to “the smallest clade containing Iguanodon bernissartensis, Megalosaurus bucklandii, and Cetiosaurus oxoniensis”. If something falls within this clade, it’s a dinosaur; if it’s not the last ancestor of Iguanodon, Megalosaurus, and Cetiosaurus, or a descendent of that ancestor, it’s outside Dinosauria. Since the three taxa that serve as so called internal specifiers in the phylogenetic definition of Dinosauria represent ‘traditional’ members of Ornithischia, Theropoda, and Sauropodomorpha, respectively, we can safely say whether silesaurids are dinosaurs under certain phylogenetic hypotheses, or aren’t. This definition makes it absolutely clear that if they fall outside the smallest clade comprising ornithischians, theropods, and sauropodomorphs, they are not dinosaurs.
This is just one of many reasons why phylogenetic nomenclature is useful while discussing evolutionary history of groups of organisms. Another example may be more relatable. How many times have someone claimed that they’ve described the ‘oldest’ or ‘earliest diverging’ representative of a group? What if two different teams of researchers claim to have described the oldest mammal? Under rank-based nomenclature, slightly different criteria may be applied to consider an animal to be a mammal, such as different suites of morphological characters. This cannot happen under phylogenetic nomenclature. Under the formal definition of Mammalia, you need to be the last common ancestor of humans, common opossum, and short-beaked echidna, or the descendent of that ancestor to be a mammal. And that’s it.
The publication of the PhyloCode was a really big deal because researchers across different fields have been adhering to the theory of phylogenetic nomenclature since the last thirty years. However, since phylogenetic nomenclature had not been governed until mid-2020, all of the previously proposed phylogenetic definitions remained informal in the light of the code.
What we have just done was a revision of the use of names applied to clades of ornithischian dinosaurs. We have looked at the phylogenetic definitions that have been used in the past and, when necessary, applied some changes – just to make sure that the proposed definitions reflect the current knowledge of the phylogenetic relationships within Ornithischia, and comply with provisions of the Articles of the PhyloCode.
What was significant about your study?
We propose a few new names for well-supported ornithischian clades that we hope will prove useful in phylogenetic studies and discussions of the ornithischian evolutionary history.
Our study may be important for two reasons – first, it is the first such extensive study that revises the use of dinosaur clade names after the publication of the PhyloCode, and, second, it provides examples of solutions to some difficult nomenclatural cases. Not all names can be easily defined – some may require considerable efforts to come up with an appropriate phylogenetic definition. Ornithischians are well-researched but many of their clades are poorly supported and phylogenetic analyses often offer strikingly different tree topologies. We had to take this into account.
What do you hope your readers take away from the research?
We hope that our study will show that phylogenetic nomenclature can deal with some very difficult cases. Sometimes we know very little about the phylogenetic relationships within and between the groups we discuss and still can ensure that their names can be applied unambiguously.
How did you first hear about PeerJ, and what persuaded you to submit to us?
I don’t remember how did I first hear about PeerJ but I’ve been familiar with the journal since its launch in 2013. PeerJ seemed innovative and I wanted to give it a try.
How was your experience publishing with PeerJ?
My first PeerJ paper was published in 2016. Since that time, I’ve published five other papers there. I like that I don’t have to spend a lot of time formatting my manuscripts; the peer-review has always been very fast and constructive, and when I needed to ask anything, the staff have always been very helpful.
Would you submit again, and would you recommend that your colleagues submit?
Yes, I will happily publish with PeerJ again, and yes, I’ve been recommending PeerJ to colleagues since my first experience with the journal.
Anything else you would like to add?
Perhaps, I would just want to thank you for the opportunity to discuss our latest paper with you. I’m extremely delighted that it has gained wide interest!