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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.

Clavicles and interclavicles are plesiomorphically present in Reptilia. However, several groups show reduction or even loss of these elements. Crocodylimorpha, e.g., lost the clavicles, whereas dinosaurs are generally interpreted to only preserve the clavicles, the theropod furcula representing an unique case of fused clavicles. In sauropods, reports of clavicles are relatively frequent in non-titanosauriforms. These elements are elongated, curved, and rather stout bones with a spatulate and a bifurcate end. However, they were always found as single bones, and differ from the relatively short and unbifurcated clavicles found articulated with the scapulae of basal sauropodomorphs.
Elements from the Howe Quarry (Late Jurassic; Wyoming, USA) shed new light on these interpretations. Besides the elongated, curved bones (herein named morphotype A), also pairs of symmetric, L-shaped bones were recovered (morphotype B), associated with diplodocid dorsal and cervical vertebrae. Elements resembling morphotype B - articulated between the scapulae - have recently been reported from a diplodocid found near Tensleep, Wyoming. Taphonomic evidence, as well as the fact that they were preserved in symmetrical pairs, therefore implies that morphotype B represents the true sauropod clavicles.
Contrary to earlier reports, morphotype A elements from the Howe Quarry, as well as of previously reported specimens show a symmetry plane following the long axis of the elements. It is thus possible that the morphotype A elements were single bones from the body midline. The only such element present in the pectoral girdle of tetrapods are the interclavicle and the furcula. Comparison with crocodilian and lacertiform interclavicles indicates that the bifurcate end of the sauropod elements might represent the reduced transverse processes of the anterior end, and the spatulate end would have covered the coracoids or sternal plates ventrally.
The presence of both clavicles and interclavicles in the pectoral girdle stiffens the anterior trunk, and enhances considerably its stability. Such an enforcement might have been needed in diplodocids due to the strong lateral forces induced to the fore-limbs by the posteriorly placed center of mass (due to shorter fore- than hind-limbs), as well as lateral movements of the enormously elongated necks and tails. The absence of clavicles and interclavicles in titanosauriforms coincides with the development of wide-gauge locomotion style.
The presence of interclavicles in sauropods supports the recently proposed homology of the furcula with the interclavicle, instead of representing fused clavicles. Interclavicles were thus not lost, but may have remained cartilaginous or have yet to be found in basal dinosauriforms.

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.

ABSTRACT Diplodocid sauropods had a unique skull morphology, with posteriorly retracted nares, an elongated snout, and anteriorly restricted, peglike teeth. Because of the lack of extant analogs in skull structure and tooth morphology, understanding their feeding strategy and diet has been difficult. Furthermore, the general rarity of sauropod skulls and the fragility of their facial elements resulted in a restricted knowledge of cranial anatomy, in particular regarding the internal surface of the facial skull. Here, we describe in detail a well-preserved diplodocid skull visible in medial view. Diagnostic features recognized in other skulls observable in lateral view, such as the extended contribution of the jugal to the antorbital fenestra, are obliterated in medial view due to extensive overlapping joints between the maxilla, jugal, quadratojugal, and the lacrimal. These overlapping joints permitted limited anterior sliding movement of the snout, which likely served as a kind of ?shock-absorbing? mechanism during feeding. Diplodocid skulls therefore seem to have evolved to alleviate stresses inflicted on the snout during backward movements of the head, as would be expected during branch-stripping or raking.ABSTRACT Diplodocid sauropods had a unique skull morphology, with posteriorly retracted nares, an elongated snout, and anteriorly restricted, peglike teeth. Because of the lack of extant analogs in skull structure and tooth morphology, understanding their feeding strategy and diet has been difficult. Furthermore, the general rarity of sauropod skulls and the fragility of their facial elements resulted in a restricted knowledge of cranial anatomy, in particular regarding the internal surface of the facial skull. Here, we describe in detail a well-preserved diplodocid skull visible in medial view. Diagnostic features recognized in other skulls observable in lateral view, such as the extended contribution of the jugal to the antorbital fenestra, are obliterated in medial view due to extensive overlapping joints between the maxilla, jugal, quadratojugal, and the lacrimal. These overlapping joints permitted limited anterior sliding movement of the snout, which likely served as a kind of ?shock-absorbing? mechanism during feeding. Diplodocid skulls therefore seem to have evolved to alleviate stresses inflicted on the snout during backward movements of the head, as would be expected during branch-stripping or raking.

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.

Ossified gastralia, clavicles and sternal ribs are known in a variety of reptilians, including dinosaurs. In sauropods, however, the identity of these bones is controversial. The peculiar shapes of these bones complicate their identification, which led to various differing interpretations in the past. Here we describe different elements from the chest region of diplodocids, found near Shell, Wyoming, USA. Five morphotypes are easily distinguishable: (A) elongated, relatively stout, curved elements with a spatulate and a bifurcate end resemble much the previously reported sauropod clavicles, but might actually represent interclavicles; (B) short, L-shaped elements, mostly preserved as a symmetrical pair, probably are the real clavicles, as indicated by new findings in diplodocids; (C) slender, rod-like bones with rugose ends are highly similar to elements identified as sauropod sternal ribs; (D) curved bones with wide, probably medial ends constitute the fourth morphotype, herein interpreted as gastralia; and (E) irregularly shaped elements, often with extended rugosities, are included into the fifth morphotype, tentatively identified as sternal ribs and/or intercostal elements. To our knowledge, the bones previously interpreted as sauropod clavicles were always found as single bones, which sheds doubt on the validity of their identification. Various lines of evidence presented herein suggest they might actually be interclavicles – which are single elements. This would be the first definitive evidence of interclavicles in dinosauromorphs. Previously supposed interclavicles in the early sauropodomorph Massospondylus or the theropods Oviraptor and Velociraptor were later reinterpreted as clavicles or furculae. Independent from their identification, the existence of the reported bones has both phylogenetic and functional significance. Their presence in non-neosauropod Eusauropoda and Flagellicaudata and probable absence in rebbachisaurs and Titanosauriformes shows a clear character polarity. This implicates that the ossification of these bones can be considered plesiomorphic for Sauropoda. The proposed presence of interclavicles in sauropods may give further support to a recent study, which finds a homology of the avian furcula with the interclavicle to be equally parsimonious to the traditional theory that furcula were formed by the fusion of the clavicles. Functional implications are the stabilizing of the chest region, which coincides with the development of elongated cervical and caudal vertebral columns or the use of the tail as defensive weapon. The loss of ossified chest bones coincides with more widely spaced limbs, and the evolution of a wide-gauge locomotor style.

Diplodocids are among the best known sauropod dinosaurs. Numerous specimens of currently 15 accepted species belonging to ten genera have been reported from the Late Jurassic to Early Cretaceous of North and South America, Europe, and Africa. The highest diversity is known from the Upper Jurassic Morrison Formation of the western United States: a recent review recognized 12 valid, named species, and possibly three additional, yet unnamed ones. One of these is herein described in detail and referred to the genus \textit{Galeamopus}. The holotype specimen of \textit{Galeamopus pabsti} sp. nov., SMA 0011, is represented by material from all body parts but the tail, and was found at the Howe-Scott Quarry in the northern Bighorn Basin in Wyoming, USA. Autapomorphic features of the new species include a horizontal canal on the maxilla that connects the posterior margin of the preantorbital and the ventral margin of the antorbital fenestrae, a vertical midline groove marking the sagittal nuchal crest, the presence of a large foramen connecting the postzygapophyseal centrodiapophyseal fossa and the spinopostzygapophyseal fossa of mid- and posterior cervical vertebrae, a very robust humerus, a laterally placed, rugose tubercle on the concave proximal portion of the anterior surface of the humerus, a relatively stout radius, the absence of a distinct ambiens process on the pubis, and a distinctly concave posteroventral margin of the ascending process of the astragalus. In addition to the holotype specimen SMA 0011, the skull USNM 2673 can also be referred to \textit{Galeamopus pabsti}. Histology shows that the type specimen SMA 0011 is sexually mature, although neurocentral closure was not completed at the time of death. Because SMA 0011 has highly pneumatized cervical vertebrae, the development of the lamination appears a more important indicator for individual age than neurocentral fusion patterns. SMA 0011 is one of very few sauropod specimens that preserves the cervico-dorsal transition in both vertebrae and ribs. The association of ribs with their respective vertebrae shows that the transition between cervical and dorsal vertebrae is significantly different in \textit{Galeamopus pabsti} than in \textit{Diplodocus carnegii} or \textit{Apatosaurus louisae}, being represented by a considerable shortening of the centra from the last cervical to the first dorsal vertebra. Diplodocids show a surprisingly high diversity in the Morrison Formation. This can possibly be explained by a combination of geographical and temporal segregation, and niche partitioning.

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.

A new taxon of diplodocid sauropod, Kaatedocus siberi gen. et sp. nov., is recognized based on well-preserved cervical vertebrae and skull from the Morrison Formation (Kimmeridgian, Late Jurassic) of northern Wyoming, USA. A phylogenetic analysis places it inside Diplodocinae (Sauropoda: Flagellicaudata: Diplodocidae), as a sister taxon to a clade uniting Tornieria africana and the classical diplodocines Barosaurus lentus and Diplodocus. The taxon is diagnosed by a unique combination of plesiomorphic and derived traits, as well as the following unambiguous autapomorphies within Diplodocidae: frontals separated anteriorly by a U-shaped notch; squamosals restricted to the post-orbital region; presence of a postparietal foramen; a narrow, sharp and distinct sagittal nuchal crest; the paired basal tuber with a straight anterior edge in ventral view; anterior end of the prezygapophyses of mid- and posterior cervical vertebrae is often an anterior extension of the pre-epipophysis, which projects considerably anterior to the articular facet; anterodorsal corner of the lateral side of the posterior cervical vertebrae marked by a rugose tuberosity; posterior margin of the prezygapophyseal articular facet of posterior cervical vertebrae bordered posteriorly by conspicuous transverse sulcus; posterior cervical neural spines parallel to converging. The inclusion of K. siberi and several newly described characters into a previously published phylogenetic analysis recovers the new taxon as basal diplodocine, which concurs well with the low stratigraphical position of the holotype specimen. Dinheirosaurus and Supersaurus now represent the sister clade to Apatosaurus and Diplodocinae and therefore the most basal diplodocid genera. The geographical location in the less known northern parts of the Morrison Fm., where K. siberi was found, corroborates previous hypotheses on faunal provinces within the formation. The probable subadult ontogenetic stage of the holotype specimen allows analysis of ontogenetic changes and their influence on diplodocid phylogeny.

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.