Saturday, May 30, 2020

It's finally January 1, 200n and Phylonyms is published!

Ah the PhyloCode, the so-called future of biological nomenclature whose release has always kept on slipping ever more distantly into the future.  After 20 years of waiting, we now have Phylonyms: A Companion to the PhyloCode, by de Queiroz et al. (2020), "a turning point in the history of phylogenetic nomenclature" according to its introduction.  As the book states "Phylonyms serves as the starting point for phylogenetic nomenclature governed by the PhyloCode. According to the preamble, “This code will take effect on the publication of Phylonyms: A Companion to the PhyloCode, and it is not retroactive.” Thus, names and definitions published here have precedence over any competing names and definitions published either before (or after) the publication of Phylonyms."  So for anyone invested in standardized phylogenetic nomenclature, this is it.  Nothing better is coming down the pipeline in our lifetimes, so let's see what we're stuck with.

First of all, it's expensive.  You can get an ebook for $222 on Amazon or a hardcover sometime after June 9th for $234.  I found an electronic version for $169 plus tax on VitalSource, but you have to use their reader.  It's 1323 pages though, so isn't a bad deal.  That's less than five $37.95 Cretaceous Research pdfs, and I figure this is one of those historical volumes it's good to have, like Sibley and Ahlquist's bird phylogeny book.

The format is an encyclopedia-style list of clades in phylogenetic order with Registration Number, Definition, Etymology, Reference Phylogeny, Composition, Apomorphies, Synonyms, Comments and Literature Cited.  Rather like my Theropod  Database, so no complaints there.  Well, one complaint is really more to do with the PhyloCode itself where they decided to abbreviate definitions with the non-standard del/nabla triangle symbol ∇.  If you want people to start using your format, you might want to choose symbols that exist on a standard keyboard.  Alt+2207 is supposed to generate it in Windows, but results in ƒ here in Blogger.  Anyone know the correct Unicode numbers?

On to the substance, where Phylonyms covers all life.  Dinosaurs are the last section of the book, and non-avian dinosaurs get all of four definitions-

Dinosauria R. Owen 1842 [M. C. Langer, F. E. Novas, J. S. Bittencourt, M. D. Ezcurra, and J. A. Gauthier], converted clade name

Registration Number: 194

Definition: The smallest clade containing Iguanodon bernissartensis Boulenger in Beneden 1881 (Ornithischia/Euornithopoda) Megalosaurus bucklandii Mantell 1827 (Theropoda/Megalosauroidea) and Cetiosaurus oxoniensis Phillips 1871 (Sauropodomorpha).

I'm glad we've standardized which theropod, ornithischian and sauropodomorph are used (or so I thought, see below), but otherwise there's not much to say.  The caveats around which apomorphies are also found in Nyasasaurus and at least some silesaurs illustrate why apomorphy-based definitions are bad.  The reference phylogeny for this and Saurischia is Lloyd et al.'s (2008) supertree, which is quite outdated and has a lot of artifacts from being a supertree.

Saurischia H. G. Seeley 1888 [J. A. Gauthier, M. C. Langer, F. E. Novas, J. Bittencourt, and M. D. Ezcurra], converted clade name

Registration Number: 195

Definition: The largest clade containing Allosaurus fragilis Marsh 1877 (Theropoda/Carnosauria) and Camarasaurus supremus Cope 1877 (Sauropodomorpha), but not Stegosaurus stenops Marsh 1887 (Ornithischia/Stegosauridae).

It's rather odd the same authors didn't choose the same specifiers for each dinosaurian clade as they did in the previous definition, leaving us without a neat node-stem triplet.  Instead they went with the Kischlatian approach of using taxa"mentioned and figured as examples of their respective groups by Seeley (1888)."  This is funny because I don't think this rationale is ever suggested in the PhyloCode, whereas Dinosauria and Saurischia are actually the official examples used for Recommendation 11F encouraging node-stem triplets ("If it is important to establish two names as applying to sister clades regardless of the phylogeny, reciprocal maximum-clade definitions should be used in which the single internal specifier of one is the single external specifier of the other, and vice versa").  Specifically- "If one wishes to define the names Saurischia and Ornithischia such that they will always refer to sister clades, Saurischia might be defined as the largest clade containing Megalosaurus bucklandii Mantell 1827 but not Iguanodon bernissartensis Boulenger in Beneden 1881, and Ornithischia would be defined as the largest clade containing Iguanodon bernissartensis but not Megalosaurus bucklandii. To stabilize the name Dinosauria as referring to the clade comprising Saurischia and Ornithischia, Dinosauria should be defined as the smallest clade containing Megalosaurus bucklandii and Iguanodon bernissartensis." 

Ornithoscelida and its consequences are mentioned, but I'm glad more time is not taken up with it as I expect the hypothesis to fall away as Baron's phylogenetic mistakes are not followed by future authors.

Sauropodomorpha F. R. von Huene 1932 [M. Fabbri, E. Tschopp, B. McPhee, S. Nesbitt, D. Pol, and M. Langer], converted clade name

Registration Number: 295

Definition: The largest clade containing Saltasaurus loricatus Bonaparte and Powell 1980 (Sauropodomorpha) but not Allosaurus fragilis Marsh 1877 (Theropoda) and Iguanodon bernissartensis Boulenger in Beneden 1881 (Ornithischia).

I dislike the use of Saltasaurus as the internal specifier, which is a holdover of Sereno's weird use of deeply nested OTUs when others would be more historically relevant and/or eponymous.  Fabbri et al. defend the choice because "Fossil specimens referred to Saltasaurus loricatus are abundant, the species is well known, and its phylogenetic position is consistent among phylogenetic analyses", but this would be even more true for e.g. Camarasaurus supremus used in Saurischia's definition.  The other specifiers are a mix of those in Dinosauria's and Saurischia's definition, so there's absolutely no consistency.  The reference phylogeny is Otero et al.'s (2015) Sefapanosaurus description using Yates' matrix, so is fine.

There's a rare error in the comments for this entry.  Fabbri et al. state "Segnosaurus galbinensis from the Cretaceous was briefly thought to be a relatively early diverging sauropodomorph (Paul, 1984; Gauthier, 1986; Olshevsky, 1991). More material referable to that species and the discovery of closely related taxa later showed that Segnosaurus galbinensis is part of the Therizinosauria", but material of S. galbinensis besides that initially recovered in the 1970s is not known.

Theropoda O. C. Marsh 1881 [D. Naish, A. Cau, T. R. Holtz, Jr., M. Fabbri, and J. A. Gauthier], converted clade name

Registration Number: 216

Definition: The largest clade containing Allosaurus fragilis Marsh 1877 (Theropoda) but neither Plateosaurus engelhardti Meyer 1837 (Sauropodomorpha) nor Heterodontosaurus tucki Crompton and Charig 1962 (Ornithischia).

Here we've chosen two completely different specifiers for Sauropodomorpha and Ornithischia, so again we have no consistency.  The reference phylogeny is Cau (2018), which is ideal. 

What about the rest?  It's a HUGE volume, and obviously most of Pan-Biota is outside my area of expertise.  One obvious issue is the wildly varying coverage of different clades.  Apparently nobody could be bothered with the vast majority of vertebrates (euteleosts) or animals (insects, except one definition for Trichoptera), and Molluska doesn't even get a definition.  But we do get several entries for edrioasterid taxa down to subfamily-level, generally obscure Paleozoic echinoderms.  Closer to dinosaurs, there's nothing at all for pan-crocs, but we get an entry for Pterosauromorpha for which only Scleromochlus is given as a plausible non-pterosaurian example (perhaps wrongly- Bennett, 2020). 

Then there are the apomorphy-based definitions which will cause headaches in the future.  Look at Apo-Chiroptera- "Definition: The clade for which the unique modifications of the hand, forearm, humerus, scapula, hip, and ankle (see Diagnostic Apomorphies) associated with flapping flight, as inherited by Vespertilio murinus Linnaeus 1758, are apomorphies."  Then you go down to the nine listed sets of Diagnostic Apomorphies like "Modification of the scapula: Scapular spine originates at the posterior edge of the glenoid fossa. Long axis of scapular spine offset 20–30 degrees from axis of rotation of the humeral head. Scapular spine reduced in height—acromion process appears more strongly arched and less well supported than in other mammals. Presence of at least two facets in infraspinous fossa."  These are all going spread out as more stem bats are discovered, and indeed the authors already note "Simmons and Geisler (1998) included the absence of claws on wing digits III-V with this suite of modifications; however, the presence of claws on all the wing digits of Onychonycteris suggests that claws were present primitively in Apo-Chiroptera."

Ungulata is defined by Archibald as "The least inclusive crown clade containing Bos primigenius Bojanus 1827 (= Bos taurus Linnaeus 1758) (Artiodactyla) and Equus ferus Boddaert 1785 (= Equus caballus Linnaeus 1758) (Perissodactyla), provided that this clade does not include Felis silvestris Schreber 1777 (= Felis catus Linnaeus 1758) (Carnivora), Manis pentadactyla Linnaeus 1758 (Pholidota), Vespertilio murinus Linnaeus 1758 (Chiroptera), or Erinaceus europaeus Linnaeus 1758 (Lipotyphla)." But this doesn't exist in molecular studies, including those of ultraconserved elements, which consistently place carnivorans, pangolins and bats closer to perrisodactyls.  So this is likely to be a historical footnote, as well established molecular relationships end up trumping morphological relationships in every example I know of.

Finally, we get Pan-Lepidosauria for the total group of lepidosaurs, which has been Lepidosauromorpha for over thirty years.  Yet Archosauromorpha is retained as "The least inclusive clade containing Gallus (originally Phasianus) gallus (Aves) (Linnaeus 1758), Alligator (originally Crocdilus) mississippiensis (Daudin 1802) (Crocodylia), Mesosuchus browni Watson 1912 (Rhynchosauria), Trilophosaurus buettneri Case 1928 (Trilophosauridae), Prolacerta broomi Parrington 1935 (Prolacertiformes), and Protorosaurus speneri von Meyer 1830 (Protorosauria)" even though Pan-Archosauria is also used for the total group of archosaurs, traditionally the definition of Archosauromorpha.  I agree our new Archosauromorpha deserved a name for being a generally recognized group, whereas whether e.g. choristoderes or sauropterygians fell out closer to lizards or birds is highly unstable.  But I would have rather kept the tradition of -omorpha for the stem clades and gave this a new name.

Overall, I'm not very impressed for something 20 years in the making that intends to be so important.  How do you contradict your own example for choosing specifiers in four papers, where two share the same author list, the other two share another author (Fabbri), and each of those shares an author with both of the first two (Langer and Gauthier)?  And one of those is an editor for the volume.  Nothing could be negotiated in over two decades?  But it's what we have to work with now, and in the name of consistancy I'll adopt the definitions proposed.  Now to see what happens when RegNum goes online.

References- Lloyd, Davis, Pisani, Tarver, Ruta, Sakamoto, Hone, Jennings and Benton, 2008. Dinosaurs and the Cretaceous terrestrial revolution. Proceedings of the Royal Society B. 275, 2483-2490.

Otero, Krupandan, Pol, Chinsamy and Choiniere, 2015. A new basal sauropodiform from South Africa and the phylogenetic relationships of basal sauropodomorphs. Zoological Journal of the Linnean Society. 174, 589-634.

Cau, 2018. The assembly of the avian body plan: A 160-million-year long process. Bollettino della Società Paleontologica Italiana. 57(1), 1-25.

Bennett, 2020. Reassessment of the Triassic archosauriform Scleromochlus taylori: Neither runner nor biped, but hopper. PeerJ. 8:e8418.

de Queiroz, Cantiono and Gauthier, 2020. Phylonyms: A Companion to the PhyloCode, 1st Edition. Taylor & Francis Group. 1323 pp.