Learn to be sceptical by seeing how the sausage is made
Years ago, when I was young and stupid, I used to read papers containing phylogenetic analyses and think, “Oh, right, I see now, Euhelopus is not a mamenchisaurid after all, it’s a titanosauriform”. In other words, I believed the result that the computer spat out. Some time after that, I learned how to use PAUP* and run my own phylogenetic analysis and realised how vague and uncertain such result are, and how easily changed by tweaking a few parameters.
These days good papers that present phylogenetic analysis are very careful to frame the results as the tentative hypotheses that they are. (Except when they’re in Glam Mags, of course: there’s no space for that kind of nuance in those venues.)
It’s common now for careful work to present multiple different and contradictory phylogenetic hypotheses, arrived at by different methods or based on different matrices. For just one example, see how Upchurch et al.’s (2015) redescription of Haestasaurus (= “Pelorosaurus“) becklesii presents that animal as a camarasaurid (figure 15, arrived at by modifying the matrix of Carballido at al 2011), as a very basal macronarian (figure 16, arrived at by modifying the continuous-and-discrete-characters matrix of Mannion et al. 2013), and as a basal titanosaur (figure 17, arrived at by modifying the discrete-characters-only matrix from the same paper). This is careful and courageous reporting, shunning the potential headline “World’s oldest titanosaur!” in favour of doing the work right.) [1]
But the thing that really makes you understand how fragile phylogenetic analyses are is running one yourself. There’s no substitute for getting your hands dirty and seeing how the sausage is made.
We need to get away from a mystical or superstitious view of peer-review as a divine seal of approval. We need to push back against wise-sounding pronouncements such as “Good reporting would have noted that the paper has not yet been peer-reviewed” as though this one bit of information is worth much.
Yeah, I said it.
References
- Carballido, Jose L., Oliver W. M. Rauhut, Diego Pol and Leonardo Salgado. 2011. Osteology and phylogenetic relationships of Tehuelchesaurus benitezii (Dinosauria, Sauropoda) from the Upper Jurassic of Patagonia. Zoological Journal of the Linnean Society 163:605–662. doi:10.1111/j.1096-3642.2011.00723.x
- Huber, Juergen, Sabiou Inoua, Rudolf Kerschbamer, Christian König-Kersting, Stefan Palan and Vernon L. Smith. 2022. Nobel and novice: author prominence affects peer review. https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4190976
- Mannion, Philip D., Paul Upchurch, Rosie N. Barnes and Octávio Mateus. 2013. Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms. Zoological Journal of the Linnean Society 168(1):98–206. doi:10.1111/zoj.12029
- Upchurch, Paul, Philip D. Mannion and Michael P. Taylor. 2015. The Anatomy and Phylogenetic Relationships of “Pelorosaurus” becklesii (Neosauropoda, Macronaria) from the Early Cretaceous of England. PLOS ONE 10(6):e0125819. 51 pages. doi: 10.1371/journal.pone.0125819
Notes
- Although I am on the authorship of Upchurch et al. (2015), I can take none of the credit the the comprehensiveness and honesty of the phylogenetics section: all of that is Paul and Phil’s work.
Source: https://svpow.com/2022/09/16/learn-to-be-sceptical-by-seeing-how-the-sausage-is-made/
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