Hostname: page-component-76fb5796d-vvkck Total loading time: 0 Render date: 2024-04-25T20:59:13.645Z Has data issue: false hasContentIssue false
  • English
  • Français

The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

Published online by Cambridge University Press:  06 December 2018

Emanuel TSCHOPP  and
Paul UPCHURCH
Emanuel TSCHOPP*
Affiliation:
Division of Paleontology, American Museum of Natural History, Central Park West @ 79th Street, New York, NY 10024, USA. Email: etschopp@amnh.org Dipartimento di Scienze della Terra, Università di Torino, Via Valperga Caluso 35, 10125 Torino, Italy. Museu da Lourinhã, Rua João Luís de Moura 95, 2530-157 Lourinhã, Portugal.
Paul UPCHURCH
Affiliation:
Department of Earth Sciences, University College London, Gower Street, London, WC1E 6BT, UK.
*
*Corresponding author
Get access Rights & Permissions [Opens in a new window]

Abstract

Specimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

Keywords

character weightingcladisticsspecies delimitationvariabilityvertebrate morphology
Type
Articles
Information
Earth and Environmental Science Transactions of The Royal Society of Edinburgh , Volume 109 , Issue 1-2: Fossils, Function and Phylogeny: Papers on Early Vertebrate Evolution in Honour of Professor Jennifer A. Clack , March 2018 , pp. 301 - 323
Copyright
Copyright © The Royal Society of Edinburgh 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

8. References

Adams, B. J. 2001. The species delimitation uncertainty principle. Journal of Nematology 33, 153–60.Google Scholar
Ahmadzadeh, F., Flecks, M., Rödder, D., Böhme, W., Ilgaz, Ç., Harris, D. J., Engler, J. O., Üzüm, N. & Carretero, M. A. 2013. Multiple dispersal out of Anatolia: biogeography and evolution of oriental green lizards. Biological Journal of the Linnean Society 110, 398–408.Google Scholar
Alroy, J., Aberhan, M., Bottjer, D. J., Foote, M., Fürsich, F. T., Harries, P. J., Hendy, A. J. W., Holland, S. M., Ivany, L. C., Kiessling, W., Kosnik, M. A., Marshall, C. R., McGowan, A. J., Miller, A. I., Olszewski, T. D., Patzkowsky, M. E., Peters, S. E., Villier, L., Wagner, P. J., Bonuso, N., Borkow, P. S., Brenneis, B., Clapham, M. E., Fall, L. M., Ferguson, C. A., Hanson, V. L., Krug, A. Z., Layou, K. M., Leckey, E. H., Nürnberg, S., Powers, C. M., Sessa, J. A., Simpson, C., Tomašových, A. & Visaggi, C. C. 2008. Phanerozoic trends in the global diversity of marine invertebrates. Science 321, 97–100.Google Scholar
Arbour, V. M. & Currie, P. J. 2012. Analyzing taphonomic deformation of ankylosaur skulls using retrodeformation and Finite Element Analysis. PLOS ONE 7, e39323.Google Scholar
Arbour, V. M. & Currie, P. J. 2016. Systematics, phylogeny and palaeobiogeography of the ankylosaurid dinosaurs. Journal of Systematic Palaeontology 14, 385–444.Google Scholar
Arnold, E. N., Arribas, O. & Carranza, S. 2007. Systematics of the Palaearctic and Oriental lizard tribe Lacertini (Squamata: Lacertidae: Lacertinae), with descriptions of eight new genera. Zootaxa 1430, 3–86.Google Scholar
Bacon, C. D., McKenna, M. J., Simmons, M. P. & Wagner, W. L. 2012. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). BMC Evolutionary Biology 12, 23.Google Scholar
Barbadillo, L. J. & Sanz, J. L. 1983. Análisis osteométrico de las regiones sacra y presacra de la columna vertebral en los lagartos Ibéricos Lacerta viridis Laurenti, Lacerta lepida Daudin y Lacerta schreiberi Bedriaga. Amphibia-Reptilia 4, 215–39.Google Scholar
Baum, D. A. 1998. Individuality and the existence of species through time. Systematic Biology 47, 641–53.Google Scholar
Bell, C. J., Gauthier, J. A. & Bever, G. S. 2010. Covert biases, circularity, and apomorphies: a critical look at the North American Quaternary Herpetofaunal Stability Hypothesis. Quaternary International 217, 30–36.Google Scholar
Bell, M. A. & Lloyd, G. T. 2014. Strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence: a tutorial. Dryad Digital Repository 1–14. DOI: 10.5061/dryad.4k078.Google Scholar
Bell, M. A. & Lloyd, G. T. 2015. Strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence. Palaeontology 58, 379–89.Google Scholar
Benson, R. B. J., Evans, M. & Druckenmiller, P. S. 2012. High diversity, low disparity and small body size in plesiosaurs (Reptilia, Sauropterygia) from the Triassic–Jurassic boundary. PLOS ONE 7, e31838.Google Scholar
Benson, R. B. J., Campione, N. E., Carrano, M. T., Mannion, P. D., Sullivan, C., Upchurch, P. & Evans, D. C. 2014. Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage. PLOS Biology 12, e1001853.Google Scholar
Benson, R. B. J., Butler, R. J., Alroy, J., Mannion, P. D., Carrano, M. T. & Lloyd, G. T. 2016. Near-stasis in the long-term diversification of Mesozoic tetrapods. PLOS Biology 14, e1002359.Google Scholar
Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21, 163–93.Google Scholar
Bhullar, B.-A. S., Marugán-Lobón, J., Racimo, F., Bever, G. S., Rowe, T. B., Norell, M. A. & Abzhanov, A. 2012. Birds have paedomorphic dinosaur skulls. Nature 487, 223–26.Google Scholar
Böhmer, C., Rauhut, O. W. M. & Wörheide, G. 2015. Correlation between Hox code and vertebral morphology in archosaurs. Proceedings of the Royal Society B 282, 20150077.Google Scholar
Bonnan, M. F. 2007. Linear and geometric morphometric analysis of long bone scaling patterns in Jurassic neosauropod dinosaurs: their functional and paleobiological implications. The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology 290, 1089–111.Google Scholar
Boyd, C. A., Brown, C. M., Scheetz, R. D. & Clarke, J. A. 2009. Taxonomic revision of the basal neornithischian taxa Thescelosaurus and Bugenasaura. Journal of Vertebrate Paleontology 29, 758–70.Google Scholar
Brazeau, M. D. 2011. Problematic character coding methods in morphology and their effects. Biological Journal of the Linnean Society 104, 489–98.Google Scholar
Bremer, K. 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42, 795–803.Google Scholar
Bremer, K. 1994. Branch support and tree stability. Cladistics 10, 295–304.Google Scholar
Brinkman, D., Rabi, M. & Zhao, L. 2017. Lower Cretaceous fossils from China shed light on the ancestral body plan of crown softshell turtles (Trionychidae, Cryptodira). Scientific Reports 7, 6719.Google Scholar
Brochu, C. A. 1996. Closure of neurocentral sutures during crocodilian ontogeny: implications for maturity assessment in fossil archosaurs. Journal of Vertebrate Paleontology 16, 49–62.Google Scholar
Brummitt, R. K. 2002. How to chop up a tree. Taxon 51, 31–41.Google Scholar
Brusatte, S. L. 2010. Representing supraspecific taxa in higher-level phylogenetic analyses: guidelines for palaeontologists. Palaeontology 53, 1–9.Google Scholar
Brusatte, S. L., Benton, M. J., Desojo, J. B. & Langer, M. C. 2010. The higher-level phylogeny of Archosauria (Tetrapoda: Diapsida). Journal of Systematic Palaeontology 8, 3–47.Google Scholar
Burnell, A., Collins, S. & Young, B. A. 2012. Vertebral morphometrics in Varanus. Bulletin de la Societe Geologique de France 183, 151–58.Google Scholar
Butler, R. J., Upchurch, P. & Norman, D. B. 2008. The phylogeny of the ornithischian dinosaurs. Journal of Systematic Palaeontology 6, 1–40.Google Scholar
Butler, R. J. & Upchurch, P. 2007. Highly incomplete taxa and the phylogenetic relationships of the theropod dinosaur Juravenator starki. Journal of Vertebrate Paleontology 27, 253–56.Google Scholar
Campbell, J. A., Ryan, M. J., Holmes, R. B. & Schröder-Adams, C. J. 2016. A re-evaluation of the chasmosaurine ceratopsid genus Chasmosaurus (Dinosauria: Ornithischia) from the Upper Cretaceous (Campanian) Dinosaur Park Formation of Western Canada. PLOS ONE 11, e0145805.Google Scholar
Campione, N. E., Brink, K. S., Freedman, E. A., McGarrity, C. T. & Evans, D. C. 2013. ‘Glishades ericksoni', an indeterminate juvenile hadrosaurid from the Two Medicine Formation of Montana: implications for hadrosauroid diversity in the latest Cretaceous (Campanian-Maastrichtian) of western North America. Senckenbergiana Lethaea 93, 65–75.Google Scholar
Cano, A., Nguyen, D. T., Ventura, S. & Cios, K. J. 2016. ur-CAIM: improved CAIM discretization for unbalanced and balanced data. Soft Computing 20, 173–88.Google Scholar
Carballido, J. L., Salgado, L., Pol, D., Canudo, J. I. & Garrido, A. 2012. A new basal rebbachisaurid (Sauropoda, Diplodocoidea) from the Early Cretaceous of the Neuquén Basin; evolution and biogeography of the group. Historical Biology 24, 631–54.Google Scholar
Carballido, J. L. & Sander, P. M. 2014. Postcranial axial skeleton of Europasaurus holgeri (Dinosauria, Sauropoda) from the Upper Jurassic of Germany: implications for sauropod ontogeny and phylogenetic relationships of basal Macronaria. Journal of Systematic Palaeontology 12, 335–87.Google Scholar
Carpenter, K. 2017. Comment (Case 3700) – opposition against the proposed designation of Diplodocus carnegii Hatcher, 1901 as the type species of Diplodocus Marsh, 1878 (Dinosauria, Sauropoda). The Bulletin of Zoological Nomenclature 74, 47–49.Google Scholar
Carr, T. D., Varricchio, D. J., Sedlmayr, J. C., Roberts, E. M. & Moore, J. R. 2017. A new tyrannosaur with evidence for anagenesis and crocodile-like facial sensory system. Scientific Reports 7, 44942.Google Scholar
Carr, T. D. & Williamson, T. E. 2004. Diversity of late Maastrichtian Tyrannosauridae (Dinosauria: Theropoda) from western North America. Zoological Journal of the Linnean Society 142, 479–523.Google Scholar
Carstens, B. C., Pelletier, T. A., Reid, N. M. & Satler, J. D. 2013. How to fail at species delimitation. Molecular Ecology 22, 4369–83.Google Scholar
Cau, A. 2017. Specimen-level phylogenetics in paleontology using the Fossilized Birth-Death model with sampled ancestors. PeerJ 5, e3055.Google Scholar
Chamero, B., Buscalioni, Á. D., Marugán-Lobón, J. & Sarris, I. 2014. 3D geometry and quantitative variation of the cervico-thoracic region in Crocodylia. The Anatomical Record 297, 1278–91.Google Scholar
Chinsamy-Turan, A. 2005. The microstructure of dinosaur bone. Baltimore, MD: Johns Hopkins University Press, 216 pp.Google Scholar
Chippindale, P. T. & Wiens, J. J. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Systematic Biology 43, 278–87.Google Scholar
Cleary, T. J., Moon, B. C., Dunhill, A. M. & Benton, M. J. 2015. The fossil record of ichthyosaurs, completeness metrics and sampling biases. Palaeontology 58, 521–36.Google Scholar
Close, R. A., Benson, R. B. J., Upchurch, P. & Butler, R. J. 2017. Controlling for the species-area effect supports constrained long-term Mesozoic terrestrial vertebrate diversification. Nature Communications 8, 1–11.Google Scholar
Congreve, C. R. & Lamsdell, J. C. 2016. Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices. Palaeontology 59, 447–62.Google Scholar
Cormack, D. H. 1987. Ham's histology. 9th edn. Philadelphia, PA: Lippincott Williams & Wilkins, 732 pp.Google Scholar
De Laet, J. 1997. A reconsideration of three-item analysis, the use of implied weights in cladistics, and a practical application in Gentianaceae. PhD Dissertation, Catholic University of Leuven, Belgium. 214 pp.Google Scholar
D'Emic, M. D. 2012. The early evolution of titanosauriform sauropod dinosaurs. Zoological Journal of the Linnean Society 166, 624–71.Google Scholar
de Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation. In Howard, D. J. & Berlocher, S. H. (eds) Endless forms: species and speciation, 57–75. Oxford: Oxford University Press.Google Scholar
de Queiroz, K. & Donoghue, M. J. 1990a. Phylogenetic systematics and species revisited. Cladistics 6, 83–90.Google Scholar
de Queiroz, K. & Donoghue, M. J. 1990b. Phylogenetic systematics or Nelson's version of cladistics? Cladistics 6, 61–75.Google Scholar
Dettman, J. R., Jacobson, D. J., Turner, E., Pringle, A. & Taylor, J. W. 2003. Reproductive isolation and phylogenetic divergence in neurospora: comparing methods of species recognition in a model eukaryote. Evolution 57, 2721–41.Google Scholar
Donoghue, M. J. 1985. A critique of the biological species concept and recommendations for a phylogenetic alternative. The Bryologist 88, 172–81.Google Scholar
Donoghue, M. J., Olmstead, R. G., Smith, J. F. & Palmer, J. D. 1992. Phylogenetic relationships of dipsacales based on rbcL sequences. Annals of the Missouri Botanical Garden 79, 333–45.Google Scholar
Farris, J. S. 1969. A successive approximations approach to character weighting. Systematic Biology 18, 374–85.Google Scholar
Farris, J. S. 1983. The logical basis of phylogenetic analysis. In Platnick, N. & Funk, V. A. (eds) Advances in cladistics Vol. 2, proceedings of the second meeting of the Willi Hennig Society, 7–36. New York: Columbia University Press.Google Scholar
Foth, C., Evers, S. W., Pabst, B., Mateus, O., Flisch, A., Patthey, M. & Rauhut, O. W. M. 2015. New insights into the lifestyle of Allosaurus (dinosauria: Theropoda) based on another specimen with multiple pathologies. PeerJ 3, e940.Google Scholar
Gauthier, J. A., Kearney, M., Maisano, J. A., Rieppel, O. & Behlke, A. D. B. 2012. Assembling the squamate tree of life: perspectives from the phenotype and the fossil record. Bulletin of the Peabody Museum of Natural History 53, 3–308.Google Scholar
Gilmore, C. W. 1925. A nearly complete articulated skeleton of Camarasaurus, a saurischian dinosaur from the Dinosaur National Monument, Utah. Memoirs of the Carnegie Museum 10, 347–84.Google Scholar
Giovanardi, S. 2017. Evaluation of Several cladistic methodologies and their impact on a paleontological dataset: the case of Diplodocidae (dinosauria: Sauropoda). Master's Thesis, Università di Torino, Italy. 56 pp.Google Scholar
Godinho, R., Crespo, E. G., Ferrand, N. & Harris, D. J. 2005. Phylogeny and evolution of the green lizards, Lacerta spp. (Squamata: Lacertidae) based on mitochondrial and nuclear DNA sequences. Amphibia-Reptilia 26, 271–85.Google Scholar
Goloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9, 83–91.Google Scholar
Goloboff, P. A. 1995. Parsimony and weighting: a reply to Turner and Zandee. Cladistics 11, 91–104.Google Scholar
Goloboff, P. A. 2014. Extended implied weighting. Cladistics 30, 260–72.Google Scholar
Goloboff, P. A., Farris, J. S., Källersjö, M., Oxelman, B., Ramírez, M. J. & Szumik, C. A. 2003. Improvements to resampling measures of group support. Cladistics 19, 324–32.Google Scholar
Goloboff, P. A., Mattoni, C. I. & Quinteros, A. S. 2006. Continuous characters analyzed as such. Cladistics 22, 589–601.Google Scholar
Goloboff, P. A., Farris, J. S. & Nixon, K. C. 2008a. TNT, a free program for phylogenetic analysis. Cladistics 24, 774–86.Google Scholar
Goloboff, P. A., Carpenter, J. M., Arias, J. S. & Esquivel, D. R. M. 2008b. Weighting against homoplasy improves phylogenetic analysis of morphological data sets. Cladistics 24, 758–73.Google Scholar
Goloboff, P. A., Torres, A. & Arias, J. S. 2018. Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics 34, 407–37.Google Scholar
Goloboff, P. A. & Farris, J. S. 2001. Methods for quick consensus estimation. Cladistics 17, S26–34.Google Scholar
Hastings, A. K. & Hellmund, M. 2015. Rare in situ preservation of adult crocodylian with eggs from the Middle Eocene of Geiseltal, Germany. PALAIOS 30, 446–61.Google Scholar
Hauser, D. L. & Presch, W. 1991. The effect of ordered characters on phylogenetic reconstruction. Cladistics 7, 243–65.Google Scholar
Hillis, D. M. & Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42, 182–92.Google Scholar
Hoso, M., Asami, T. & Hori, M. 2007. Right-handed snakes: convergent evolution of asymmetry for functional specialization. Biology Letters 3, 169–73.Google Scholar
Huelsenbeck, J. P. 1991. When are fossils better than extant taxa in phylogenetic analysis? Systematic Zoology 40, 458–69.Google Scholar
Ji, Q., Wu, X. & Cheng, Y. 2010. Cretaceous choristoderan reptiles gave birth to live young. Naturwissenschaften 97, 423–28.Google Scholar
Jiang, F. & Sui, Y. 2015. A novel approach for discretization of continuous attributes in rough set theory. Knowledge-Based Systems 73, 324–34.Google Scholar
Källersjö, M., Albert, V. A. & Farris, J. S. 1999. Homoplasy increases phylogenetic structure. Cladistics 15, 91–93.Google Scholar
Kearney, M. & Clark, J. M. 2003. Problems due to missing data in phylogenetic analyses including fossils: a critical review. Journal of Vertebrate Paleontology 23, 263–74.Google Scholar
Kimura, Y., Flynn, L. J. & Jacobs, L. L. 2016. A palaeontological case study for species delimitation in diverging fossil lineages. Historical Biology 28, 189–98.Google Scholar
Klein, N. & Sander, M. 2008. Ontogenetic stages in the long bone histology of sauropod dinosaurs. Paleobiology 34, 247–63.Google Scholar
Kopuchian, C. & Ramírez, M. J. 2010. Behaviour of resampling methods under different weighting schemes, measures and variable resampling strengths. Cladistics 26, 86–97.Google Scholar
Lehman, T. M. 1990. The ceratopsian subfamily Chasmosaurinae: sexual dimorphism and systematics. In Carpenter, K. & Currie, P. J. (eds) Dinosaur systematics: approaches and perspectives, 211–29. Cambridge: Cambridge University Press.Google Scholar
Longrich, N. 2015. Systematics of Chasmosaurus – new information from the Peabody Museum skull, and the use of phylogenetic analysis for dinosaur alpha taxonomy. F1000Research 4, 1468.Google Scholar
Maddison, W. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics 5, 365–77.Google Scholar
Makovicky, P. J. 2010. A redescription of the Montanoceratops cerorhynchus holotype, with a review of referred material. In Ryan, M. J., Chinnery-Allgeier, B. J. & Eberth, D. A. (eds) New perspectives on Horner dinosaurs: the Royal Tyrrell Museum Ceratopsian Symposium, 68–82. Bloomington and Indianapolis, IN: Indiana University Press.Google Scholar
Mannion, P. D., Upchurch, P., Barnes, R. N. & Mateus, O. 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, 98–206.Google Scholar
Mannion, P. D., Upchurch, P., Benson, R. B. J. & Goswami, A. 2014. The latitudinal biodiversity gradient through deep time. Trends in Ecology & Evolution 29, 42–50.Google Scholar
Mannion, P. D., Benson, R. B. J., Carrano, M. T., Tennant, J. P., Judd, J. & Butler, R. J. 2015. Climate constrains the evolutionary history and biodiversity of crocodylians. Nature Communications 6, 9438.Google Scholar
Mannion, P. D., Allain, R. & Moine, O. 2017. The earliest known titanosauriform sauropod dinosaur and the evolution of Brachiosauridae. PeerJ 5, e3217.Google Scholar
Mannion, P. D. & Upchurch, P. 2010. Completeness metrics and the quality of the sauropodomorph fossil record through geological and historical time. Paleobiology 36, 283–302.Google Scholar
Marx, F. G. 2011. The more the merrier? A large cladistic analysis of Mysticetes, and comments on the transition from teeth to baleen. Journal of Mammalian Evolution 18, 77–100.Google Scholar
Marzahn, E., Mayer, W., Joger, U., Ilgaz, Ç., Jablonski, D., Kindler, C., Kumlutaş, Y., Nistri, A., Schneeweiss, N., Vamberger, M., Žagar, A. & Fritz, U. 2016. Phylogeography of the Lacerta viridis complex: mitochondrial and nuclear markers provide taxonomic insights. Journal of Zoological Systematics and Evolutionary Research 54, 85–105.Google Scholar
Mayer, W. & Pavlicev, M. 2007. The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiadinae. Molecular Phylogenetics and Evolution 44, 1155–63.Google Scholar
McIntosh, J. S., Miles, C. A., Cloward, K. A. & Parker, J. R. 1996. A new nearly complete skeleton of Camarasaurus. Bulletin of the Gunma Museum of Natural History 1, 1–87.Google Scholar
McIntosh, J. S. & Carpenter, K. 1998. The holotype of Diplodocus longus, with comments on other specimens of the genus. Modern Geology 23, 85–110.Google Scholar
Mounier, A. & Caparros, M. 2015. The phylogenetic status of Homo heidelbergensis – a cladistic study of Middle Pleistocene hominins. BMSAP 27, 110–34.Google Scholar
Morrison, D. A. 2005. Networks in phylogenetic analysis: new tools for population biology. International Journal for Parasitology 35, 567–82.Google Scholar
Morschhauser, E. M., You, H., Li, D. & Dodson, P. 2014. Juvenile cranial material of Auroraceratops rugosus (Ceratopsia: Ornithischia) and implications for the phylogenetic placement of juvenile specimens. Journal of Vertebrate Paleontology, Program and Abstracts 2014, 192.Google Scholar
Müller, J., Scheyer, T. M., Head, J. J., Barrett, P. M., Werneburg, I., Ericson, P. G. P., Pol, D. & Sánchez-Villagra, M. R. 2010. Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes. Proceedings of the National Academy of Sciences 107, 2118–23.Google Scholar
Nanda, P. & Singh, B. N. 2012. Behavioural reproductive isolation and speciation in Drosophila. Journal of Biosciences 37, 359–74.Google Scholar
Nixon, K. C. & Carpenter, J. M. 1993. On outgroups. Cladistics 9, 413–26.Google Scholar
Norell, M. A. & Gao, K. 1997. Braincase and phylogenetic relationships of Estesia mongoliensis from the Late Cretaceous of the Gobi Desert and the recognition of a new clade of lizards. American Museum Novitates 3211, 1–25.Google Scholar
O'Reilly, J. E., Puttick, M. N., Parry, L., Tanner, A. R., Tarver, J. E., Fleming, J., Pisani, D. & Donoghue, P. C. J. 2016. Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data. Biology Letters 12, 20160081.Google Scholar
Otero, R. A., Soto-Acuña, S., O'Keefe, F. R., O'Gorman, J. P., Stinnesbeck, W., Suárez, M. E., Rubilar-Rogers, D., Salazar, C. & Quinzio-Sinn, L. A. 2014. Aristonectes quiriquinensis, sp. nov., a new highly derived elasmosaurid from the upper Maastrichtian of central Chile. Journal of Vertebrate Paleontology 34, 100–25.Google Scholar
Palmer, A. R. 1996. From symmetry to asymmetry: phylogenetic patterns of asymmetry variation in animals and their evolutionary significance. Proceedings of the National Academy of Sciences 93, 14279–86.Google Scholar
Palmer, A. R., Strobeck, C. & Chippindale, A. K. 1994. Bilateral variation and the evolutionary origin of macroscopic asymmetries. In Markow, T. A. (ed.) Developmental instability: its origins and evolutionary implications, 2, 203–20. Netherlands: Springer.Google Scholar
Parker, W. G. 2016. Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets. PeerJ 4, e1583.Google Scholar
Pisani, D., Feuda, R., Peterson, K. J. & Smith, A. B. 2012. Resolving phylogenetic signal from noise when divergence is rapid: a new look at the old problem of echinoderm class relationships. Molecular Phylogenetics and Evolution 62, 27–34.Google Scholar
Pleijel, F. & Rouse, G. W. 2000. Least-inclusive taxonomic unit: a new taxonomic concept for biology. Proceedings of the Royal Society of London B: Biological Sciences 267, 627–30.Google Scholar
Poe, S. & Wiens, J. J. 2000. Character selection and the methodology of morphological phylogenetics. In Wiens, J. J. (ed.) Phylogenetic analysis of morphological data, 20–36. Washington, DC: Smithsonian Institution Press.Google Scholar
Pol, D. & Escapa, I. H. 2009. Unstable taxa in cladistic analysis: identification and the assessment of relevant characters. Cladistics 25, 515–27.Google Scholar
Prendini, L. 2001. Species or supraspecific taxa as terminals in cladistic analysis? Groundplans versus exemplars revisited. Systematic Biology 50, 290–300.Google Scholar
Prevosti, F. J. & Chemisquy, M. A. 2010. The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries. Cladistics 26, 326–39.Google Scholar
Purvis, A. & Garland, T. 1993. Polytomies in comparative analyses of continuous characters. Systematic Biology 42, 569–75.Google Scholar
Puslednik, L. & Serb, J. M. 2008. Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology. Molecular Phylogenetics and Evolution 48, 1178–88.Google Scholar
Rae, T. C. 1998. The logical basis for the use of continuous characters in phylogenetic systematics. Cladistics 14, 221–28.Google Scholar
Rothschild, B. M. & Martin, L. D. 2006. Skeletal impact of disease. New Mexico Museum of Natural History and Science Bulletin 33, 1–226.Google Scholar
Sampson, S. D., Loewen, M. A., Farke, A. A., Roberts, E. M., Forster, C. A., Smith, J. A. & Titus, A. L. 2010. New horned dinosaurs from Utah provide evidence for intracontinental dinosaur endemism. PLOS ONE 5, e12292.Google Scholar
Sander, P. M. 2012. Reproduction in early amniotes. Science 337, 806–08.Google Scholar
Sansom, R. S. 2015. Bias and sensitivity in the placement of fossil taxa resulting from interpretations of missing data. Systematic Biology 64, 256–66.Google Scholar
Sansom, R. S., Wills, M. A. & Williams, T. 2017. Dental data perform relatively poorly in reconstructing mammal phylogenies: morphological partitions evaluated with molecular benchmarks. Systematic Biology 66, 813–22.Google Scholar
Sansom, R. S., Choate, P. G., Keating, J. N. & Randle, E. 2018. Parsimony, not Bayesian analysis, recovers more stratigraphically congruent phylogenetic trees. Biology Letters 14, 20180263.Google Scholar
Satler, J. D., Carstens, B. C. & Hedin, M. 2013. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus). Systematic Biology 62, 805–23.Google Scholar
Sato, T., Cheng, Y., Wu, X., Zelenitsky, D. K. & Hsiao, Y. 2005. A pair of shelled eggs inside a female dinosaur. Science 308, 375.Google Scholar
Saunders, I. W., Tavaré, S. & Watterson, G. A. 1984. On the genealogy of nested subsamples from a haploid population. Advances in Applied Probability 16, 471–91.Google Scholar
Scannella, J. B., Fowler, D. W., Goodwin, M. B. & Horner, J. R. 2014. Evolutionary trends in Triceratops from the Hell Creek Formation, Montana. Proceedings of the National Academy of Sciences 111, 10245–50.Google Scholar
Scheyer, T. M., Klein, N. & Sander, P. M. 2010. Developmental palaeontology of Reptilia as revealed by histological studies. Seminars in Cell & Developmental Biology 21, 462–70.Google Scholar
Schmidt-Lebuhn, A. N., de Vos, J. M., Keller, B. & Conti, E. 2012. Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species. Molecular Phylogenetics and Evolution 65, 23–34.Google Scholar
Schwarz, D., Ikejiri, T., Breithaupt, B. H., Sander, P. M. & Klein, N. 2007. A nearly complete skeleton of an early juvenile diplodocid (Dinosauria: Sauropoda) from the Lower Morrison Formation (Late Jurassic) of north central Wyoming and its implications for early ontogeny and pneumaticity in sauropods. Historical Biology 19, 225–53.Google Scholar
Sites, J. W., Davis, S. K., Guerra, T., Iverson, J. B. & Snell, H. L. 1996. Character congruence and phylogenetic signal in molecular and morphological data sets: a case study in the living iguanas (Squamata, Iguanidae). Molecular Biology and Evolution 13, 1087–105.Google Scholar
Sites, J. W. & Marshall, J. C. 2004. Operational criteria for delimiting species. Annual Review of Ecology, Evolution, and Systematics 35, 199–227.Google Scholar
Tennant, J. P., Mannion, P. D. & Upchurch, P. 2016a. Environmental drivers of crocodyliform extinction across the Jurassic/Cretaceous transition. Proceedings of the Royal Society B 283, 20152840.Google Scholar
Tennant, J. P., Mannion, P. D. & Upchurch, P. 2016b. Sea level regulated tetrapod diversity dynamics through the Jurassic/Cretaceous interval. Nature Communications 7, 12737.Google Scholar
Thiele, K. 1993. The Holy Grail of the perfect character: the cladistic treatment of morphometric data. Cladistics 9, 275–304.Google Scholar
Townsend, J. P., Su, Z. & Tekle, Y. I. 2012. Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny. Systematic Biology 61, 835–49.Google Scholar
Tschopp, E. 2016. Nomenclature of vertebral laminae in lizards, with comments on ontogenetic and serial variation in Lacertini (Squamata, Lacertidae). PLOS ONE 11, e0149445.Google Scholar
Tschopp, E., Russo, J. & Dzemski, G. 2013. Retrodeformation as a test for the validity of phylogenetic characters: an example from diplodocid sauropod vertebrae. Palaeontologia Electronica 16, 2T.Google Scholar
Tschopp, E., Mateus, O. & Benson, R. B. J. 2015. A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda). PeerJ 3, e857.Google Scholar
Tschopp, E., Wings, O., Frauenfelder, T. & Rothschild, B. 2016. Pathological phalanges in a camarasaurid sauropod dinosaur and implications on behaviour. Acta Palaeontologica Polonica 61, 125–34.Google Scholar
Tschopp, E., Brinkman, D., Henderson, J., Turner, M. A. & Mateus, O. 2018a. Considerations on the replacement of a type species in the case of the sauropod dinosaur Diplodocus Marsh, 1878. Geology of the Intermountain West 5, 245–62.Google Scholar
Tschopp, E., Tschopp, F. A. & Mateus, O. 2018b. Overlap indices: tools to quantify the amount of anatomical overlap among groups of incomplete terminal taxa in phylogenetic analyses. Acta Zoologica 99, 169–76.Google Scholar
Tschopp, E., Villa, A., Camaiti, M., Ferro, L., Tuveri, C., Rook, L., Arca, M. & Delfino, M. 2018c. The first fossils of Timon (Squamata: Lacertinae) from Sardinia (Italy) and potential causes for its local extinction in the Pleistocene. Zoological Journal of the Linnean Society 184, 825–56. DOI: 10.1093/zoolinnean/zly003.Google Scholar
Tschopp, E. & Mateus, O. 2016. Case 3700 Diplodocus marsh, 1878 (Dinosauria, Sauropoda): proposed designation of D. carnegii Hatcher, 1901 as the type species. Bulletin of Zoological Nomenclature 73, 17–24.Google Scholar
Tschopp, E. & Mateus, O. 2017. Osteology of Galeamopus pabsti sp. nov. (Sauropoda: Diplodocidae), with implications for neurocentral closure timing, and the cervico-dorsal transition in diplodocids. PeerJ 5, e3179.Google Scholar
Turner, H. & Zandee, R. 1995. The behaviour of Goloboff's tree fitness measure F. Cladistics 11, 57–72.Google Scholar
Upchurch, P. 1998. The phylogenetic relationships of sauropod dinosaurs. Zoological Journal of the Linnean Society 124, 43–103.Google Scholar
Upchurch, P., Tomida, Y. & Barrett, P. M. 2004. A new specimen of Apatosaurus ajax (Sauropoda: Diplodocidae) from the Morrison Formation (Upper Jurassic) of Wyoming, USA. National Science Museum Monographs 26, 1–118.Google Scholar
Villa, A., Tschopp, E., Georgalis, G. L. & Delfino, M. 2017. Osteology, fossil record and palaeodiversity of the European lizards. Amphibia-Reptilia 38, 79–88.Google Scholar
Vrana, P. & Wheeler, W. 1992. Individual organisms as terminal entities: laying the species problem to rest. Cladistics 8, 67–72.Google Scholar
Wedel, M. J. 2003. The evolution of vertebral pneumaticity in sauropod dinosaurs. Journal of Vertebrate Paleontology 23, 344–57.Google Scholar
Wedel, M. J., Cifelli, R. L. & Sanders, R. K. 2000. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45, 343–88.Google Scholar
Whitlock, J. A. 2011. A phylogenetic analysis of Diplodocoidea (Saurischia: Sauropoda). Zoological Journal of the Linnean Society 161, 872–915.Google Scholar
Wiens, J. J. 1995. Polymorphic characters in phylogenetic systematics. Systematic Biology 44, 482–500.Google Scholar
Wiens, J. J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Systematic Biology 47, 625–40.Google Scholar
Wiens, J. J. 2000. Coding morphological variation within species and higher taxa for Phylogenetic Analysis. In Wiens, J. J. (ed.) Phylogenetic analysis of morphological data, 115–45. Washington, DC: Smithsonian Institution Press.Google Scholar
Wiens, J. J. 2003. Incomplete taxa, incomplete characters, and phylogenetic accuracy: is there a missing data problem? Journal of Vertebrate Paleontology 23, 297–310.Google Scholar
Wiens, J. J. 2006. Missing data and the design of phylogenetic analyses. Journal of Biomedical Informatics 39, 34–42.Google Scholar
Wiens, J. J. & Penkrot, T. A. 2002. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology 51, 69–91.Google Scholar
Wiens, J. J. & Tiu, J. 2012. Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLOS ONE 7, e42925.Google Scholar
Wiley, E. O. & Lieberman, B. S. 2011. Phylogenetics: theory and practice of phylogenetic systematics. Hoboken, NJ: John Wiley & Sons, 497 pp.Google Scholar
Wilkinson, M. 1992. Ordered versus unordered characters. Cladistics 8, 375–85.Google Scholar
Wilkinson, M. 1995. More on reduced consensus methods. Systematic Biology 44, 435–39.Google Scholar
Wilkinson, M. 2003. Missing entries and multiple trees: instability, relationships, and support in parsimony analysis. Journal of Vertebrate Paleontology 23, 311–23.Google Scholar
Wilkinson, M., Thorley, J. L. & Upchurch, P. 2000. A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses. Systematic Biology 49, 754–76.Google Scholar
Wilson, J. A. 1999. A nomenclature for vertebral laminae in sauropods and other saurischian dinosaurs. Journal of Vertebrate Paleontology 19, 639–53.Google Scholar
Wilson, J. A. 2002. Sauropod dinosaur phylogeny: critique and cladistic analysis. Zoological Journal of the Linnean Society 136, 215–75.Google Scholar
Wilson, J. A. 2012. New vertebral laminae and patterns of serial variation in vertebral laminae of sauropod dinosaurs. Contributions from the Museum of Paleontology, University of Michigan 32, 91–110.Google Scholar
Wilson, J. A. & Upchurch, P. 2009. Redescription and reassessment of the phylogenetic affinities of Euhelopus zdanskyi (Dinosauria: Sauropoda) from the Early Cretaceous of China. Journal of Systematic Palaeontology 7, 199–239.Google Scholar
Wiman, C. 1929. Die kreide-dinosaurier aus shantung. Palaeontologia Sinica 6, 1–67.Google Scholar
Woodruff, D. C., Fowler, D. W. & Horner, J. R. 2017. A new multi-faceted framework for deciphering diplodocid ontogeny. Palaeontologia Electronica 20, 1–53.Google Scholar
Wright, A. M. & Hillis, D. M. 2014. Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data. PLOS ONE 9, e109210.Google Scholar
Yates, A. M. 2003. The species taxonomy of the sauropodomorph dinosaurs from the Löwenstein Formation (Norian, Late Triassic) of Germany. Palaeontology 46, 317–37.Google Scholar
Zander, R. H. 2004. Minimal values for reliability of bootstrap and jackknife proportions, decay index, and Bayesian posterior probability. Phyloinformatics 2, 1–13.Google Scholar
Supplementary material: File

Tschopp and Upchurch supplementary material

Tschopp and Upchurch supplementary material 1

Download Tschopp and Upchurch supplementary material(File)
File 15.9 KB