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Tschopp, E., Tschopp F. A., & Mateus O. (2017).  Overlap Indices: Tools to quantify the amount of anatomical overlap among groups of incomplete terminal taxa in phylogenetic analyses. Acta Zoologica. 99(2), 169-176. Abstracttschopp_et_al-2017-acta_zoologica_overlap_indices_tools_to_quantify_the_amount.pdfWebsite

Phylogenetic analyses of morphological data are often characterized by missing data due to incomplete operational taxonomic units, as in fossils. This incomplete knowledge derives from various reasons, including—in the case of fossils—the numerous filters an organism has to pass through during taphonomy, fossilization, weathering and collecting. Whereas several methods have been proposed to address issues raised by the inclusion of incomplete terminal taxa, until recently no tool existed to easily quantify the amount of anatomical overlap within a particular clade. The Overlap Indices provide such values and might prove useful for comparative cladistics. We herein describe these new indices and their applications in detail and provide an example file for their calculation. A case study of diplodocid sauropod dinosaurs shows how the Overlap Indices will help to explore and quantify, which one of a number of conflicting tree topologies is supported by more anatomical traits, which skeletal regions are underrepresented in a particular phylogenetic matrix, and which taxon would improve character state score completeness.

Tschopp, E., & Mateus O. (2016).  Diplodocus Marsh, 1878 (Dinosauria, Sauropoda): proposed designation of D. carnegii Hatcher, 1901 as the type species. Bulletin of Zoological Nomenclature. 73(1), 17-24. Abstracttschopp_mateus_2016_-_case_3700_-_diplodocus_type.pdf

The purpose of this application, under Articles 78.1 and 81.1 of the Code, is to replace Diplodocus longus Marsh, 1878 as the type species of the sauropod dinosaur genus Diplodocus by the much better represented D. carnegii Hatcher, 1901, due to the undiagnosable state of the holotype of D. longus (YPM 1920, a partial tail and a chevron). The holotype of D. carnegii, CM 84, is a well-preserved and mostly articulated specimen. Casts of it are on display in various museums around the world, and the species has generally been used as the main reference for studies of comparative anatomy or phylogeny of the genus. Both species are known from the Upper Jurassic Morrison Formation of the western United States. The genus Diplodocus is the basis for the family-level taxa diplodocinae Marsh, 1884, diplodocidae Marsh, 1884, diplodocimorpha Marsh, 1884 (Calvo & Salgado, 1995) and diplodocoidea Marsh, 1884 (Upchurch, 1995). It is also a specifier of at least 10 phylogenetic clades. With the replacement of D. longus by D. carnegii as type species, Diplodocus could be preserved as a taxonomic name with generally accepted content. Taxonomic stability of the entire clade diplodocoidea, and the proposed definitions of several clades within Sauropoda, could be maintained.

Tschopp, E., Mateus O., & Benson R. B. J. (2015).  A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda). PeerJ. 3, e857., 4 Abstracttschopp_et_al_2015_brontosaurus_peerj-857.pdfWebsite

Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., ‘\textit{Diplodocus}’ \textit{hayi} or \textit{Dyslocosaurus polyonychius}), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera \textit{Apatosaurus} and \textit{Diplodocus} are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for \textit{Apatosaurus}, but is here performed for the first time for the entire clade of Diplodocidae.The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters.The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like \textit{Apatosaurus} and \textit{Diplodocus} are generically distinct. Of particular note is that the famous genus \textit{Brontosaurus} is considered valid by our quantitative approach. Furthermore, “\textit{Diplodocus}” hayi represents a unique genus, which will herein be called \textit{Galeamopus} gen. nov. On the other hand, these numerical approaches imply synonymization of “\textit{Dinheirosaurus}” from the Late Jurassic of Portugal with the Morrison Formation genus \textit{Supersaurus}. Our use of a specimen-, rather than species-based approach increases knowledge of intraspecific and intrageneric variation in diplodocids, and the study demonstrates how specimen-based phylogenetic analysis is a valuable tool in sauropod taxonomy, and potentially in paleontology and taxonomy as a whole.

Mateus, O., Maidment S., & Christiansen N. (2009).  A new long-necked 'sauropod-mimic' stegosaur and the evolution of the plated dinosaurs. Proceedings of the Royal Society of London B. 276, 1815-1821., Jan Abstractmateus_et_al_2009_stegosaur_miragaia_complete_with_suppl.pdfWebsite

Stegosaurian dinosaurs have a quadrupedal stance, short forelimbs, short necks, and are generally considered to be low browsers. A new stegosaur, Miragaia longicollum gen. et sp. nov., from the Late Jurassic of Portugal, has a neck comprising at least 17 cervical vertebrae. This is eight additional cervical vertebrae when compared with the ancestral condition seen in basal ornithischians such as Scutellosaurus.
Miragaia has a higher cervical count than most of the iconically long-necked sauropod dinosaurs. Long neck length has been achieved by ‘cervicalization’ of anterior dorsal vertebrae and probable lengthening of centra. All these anatomical features are evolutionarily convergent with those exhibited in the necks of
sauropod dinosaurs. Miragaia longicollum is based upon a partial articulated skeleton, and includes the only known cranial remains from any European stegosaur. A well-resolved phylogeny supports a new clade that unites Miragaia and Dacentrurus as the sister group to Stegosaurus; this new topology challenges the common view of Dacentrurus as a basal stegosaur.

Mateus, O. (2008).  Two ornithischian dinosaurs renamed: Microceratops Bohlin 1953 and Diceratops Lull 1905. Journal of Paleontology. 82, 423., Number 2 Abstractmateus_2008_two_ornithischians_renamed__microceratops_bohlin_1953_and_diceratops_lull_.pdfWebsite

dinosaur genera Diceratops Lull, 1905 and Microceratops Bohlin, 1953 are preoccupied by the Hymenoptera insects, Diceratops Foerster, 1868 and Microceratops Seyrig, 1952, respectively. Therefore, the name of the ceratopsian dinosaur Diceratops Lull, 1905 from the Late Cretaceous of United States is a junior homonym of the hymenoptera Diceratops Foerster, 1868. Diceratus n. gen. (Greek di ‘‘two,’’ Greek ceratos ‘‘horned’’) is proposed as the replacement name of Diceratops Lull, 1905. Some workers have considered Diceratops synonymous with Triceratops (e.g., Dodson and Currie, 1990) but it was reinstated by Forster (1996) after analysis of the characteristics of all existing ceratopsid skulls, and recent reviews (e.g., Dodson et al., 2004) have considered Diceratops a valid genus.
Due to preoccupation, the name of the ceratopsian dinosaur Microceratops Bohlin, 1953 from the Cretaceous of the Gobi is
a junior homonym of the insect Microceratops Seyrig, 1952. Microceratus n. gen. (Greek micro ‘‘small,’’ Greek ceratos ‘‘horned’’) is proposed as the replacing name of Microceratops Bohlin, 1953.
Sereno (2000:489) has declared Microceratops a nomen dubium since the holotype material lacks any diagnostic features, a
convention followed by You and Dodson (2004:480). However, the name is still used by Le Loeuff et al. (2002), Lucas (2006),
Alifanov (2003) and Xu et al. (2002), and such practice justifies the renaming of the genus.
In order to preserve some stability, the names chosen here deliberately preserve the same prefixes.

Mateus, O., Walen A., & Antunes M. T. (2006).  The large theropod fauna of the Lourinhã Formation (Portugal) and its similarity to the Morrison Formation, with a description of a new species of Allosaurus. New Mexico Museum of Natural History and Science Bulletin. 36, 123-129. Abstractmateus_walen_antunes_-_2006_-_the_large_theropod_fauna_of_the_lourinha_formation__portugal__and_its_similarity_to_the_morrison_formation__with_a_description_of_a_new_species_of_allosaurus.pdf

Late Jurassic theropod dinosaurs have been known in Portugal since 1863 but only now are they being fully understood, with the recognition of genera such as Allosaurus, Aviatyrannis, Ceratosaurus, Lourinhanosaurus, and Torvosaurus from the Lourinhã and Alcobaça Formations (Kimmeridgian/Tithonian). Ceratosaurus dentisulcatus can now be reported from Portugal. It represents the only occurrence of this species outside the Morrison Formation.
New cranial elements confirm the presence of Torvosaurus tanneri, in Portugal. Torvosaurus was the largest Late Jurassic land carnivore. New postcranial and cranial elements allow the erection of a new species from Portugal, Allosaurus europaeus n.sp. The theropod assemblage of Portugal is similar to that of the Morrison Formation.