<p> This research examines the evolution, phylogenetic distribution, and functional explanations for a peculiar and often overlooked character seen in birds, herein called tracheal and esophageal displacement. Of special interest to this study is examining whether the trait was present in non-avian theropod dinosaurs. This study found that essentially all birds are characterized by a laterally displaced trachea and/or esophagus. The displacement may occur gradually along the neck, or it may happen immediately upon exiting the oropharynx. Displacement of these organs is the result of a heavily modified neck wherein muscles that create mobility restrictions in lizards, alligators, and mammals (e.g., <i>m. episternocleidomastoideus, m. omohyoideus,</i> and <i> m. sternohyoideus</i>) no longer substantially restrict positions in birds. Rather, these muscles are modified, which may assist with making tracheal movements. </p><p> An exceptionally well-preserved fossil theropod, <i>Scipionyx samniticus </i>, proved to be paramount. Its <i>in situ</i> tracheal and esophageal positions and detailed preservation (showing the hallmarks of displacement including rotation, obliquity, a strong angle, and a dorsal position in a caudad region of the neck) demonstrate that at least some theropods were characterized by tracheal and esophageal displacement. Ultimately, the presence of the trait correlates with a highly flexible neck, allowing slack and permitting for the organs to save length as they avoid the long curves of the S-shaped neck.</p>

<p> Historical biogeography has a diversity of methods for inferring ancestral geographic ranges on phylogenies, but many of the methods have conflicting assumptions, and there is no common statistical framework by which to judge which models are preferable. Probabilistic modeling of geographic range evolution, pioneered by Ree and Smith (2008, <i>Systematic Biology</i>) in their program LAGRANGE, could provide such a framework, but this potential has not been implemented until now. </p><p> I have created an R package, "BioGeoBEARS," described in chapter 1 of the dissertation, that implements in a likelihood framework several commonly used models, such as the LAGRANGE Dispersal-Extinction-Cladogenesis (DEC) model and the Dispersal-Vicariance Analysis (DIVA, Ronquist 1997, <i> Systematic Biology</i>) model. Standard DEC is a model with two free parameters specifying the rate of "dispersal" (range expansion) and "extinction" (range contraction). However, while dispersal and extinction rates are free parameters, the cladogenesis model is fixed, such that the geographic range of the ancestral lineage is inherited by the two daughter lineages through a variety of scenarios fixed to have equal probability. This fixed nature of the cladogenesis model means that it has been indiscriminately applied in all DEC analyses, and has not been subjected to any inference or formal model testing. </p><p> BioGeoBEARS also adds a number of features not previously available in most historical biogeography software, such as distance-based dispersal, a model of imperfect detection, and the ability to include fossils either as ancestors or tips on a time-calibrated tree. </p><p> Several important conclusions may be drawn from this research. First, formal model selection procedures can be applied in phylogenetic inferences of historical biogeography, and the relative importance of different processes can be measured. These techniques have great potential for strengthening quantitative inference in historical biogeography. No longer are biogeographers forced to simply assume, consciously or not, that some processes (such as vicariance or dispersal) are important and others are not; instead, this can be inferred from the data. Second, founder-event speciation appears to be a crucial explanatory process in most clades, the only exception being some intracontinental taxa showing a large degree of sympatry across widespread ranges. This is not the same thing as claiming that founder-event speciation is the <i>only</i> important process; founder event speciation as the only important process is inferred in only one case (<i>Microlophus</i> lava lizards from the Galapagos). The importance of founder-event speciation will not be surprising to most island biogeographers. However, the results are important nonetheless, as there are still some vocal advocates of vicariance-dominated approaches to biogeography, such as Heads (2012, <i>Molecular Panbiogeography of the Tropics</i>), who allows vicariance and range-expansion to play a role in his historical inferences, but explicitly excludes founder-event speciation <i> a priori.</i> The commonly-used LAGRANGE DEC and DIVA programs actually make assumptions very similar to those of Heads, even though many users of these programs likely consider themselves dispersalists or pluralists. Finally, the inclusion of fossils and imperfect detection within the same likelihood and model-choice framework clears the path for integrating paleobiogeography and neontological biogeography, strengthening inference in both. </p><p> Model choice is now standard practice in phylogenetic analysis of DNA sequences: a program such as ModelTest is used to compare models such as Jukes-Cantor, HKY, GTR+I+G, and to select the best model before inferring phylogenies or ancestral states. It is clear that the same should now happen in phylogenetic biogeography. BioGeoBEARS enables this procedure. Perhaps more importantly, however, is the potential for users to create and test new models. Probabilistic modeling of geographic range evolution on phylogenies is still in its infancy, and undoubtedly there are better models out there, waiting to be discovered. It is also undoubtedly true that different clades and different regions will favor different processes, and that further improvements will be had by linking the evolution of organismal traits (e.g., loss of flight) with the evolution of geographic range, within a common inference framework. In a world of rapid climate change and habitat loss, biogeographical methods must maximize both flexibility and statistical rigor if they are to play a role. This research takes several steps in that direction. </p><p> BioGeoBEARS is open-source and is freely available at the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/BioGeoBEARS/index.html). A step-by-step tutorial, using the <i>Psychotria</i> dataset, is available at PhyloWiki (http://phylo.wikidot.com/biogeobears). </p><p> (Abstract shortened by UMI.)</p>

The phosphatic chalks of the Anglo-Paris Basin are granular phosphorites of Santonian to early Campanian age. They were deposited in erosional cuvettes up to 1 km long, 250 m wide and 30 m deep, incised into white chalks. Most are situated in the Picardy region of northern France. Cuvettes are floored by strongly indurated and mineralized basal hardgrounds developed in intraclastic sediments. The hardgrounds are penetrated by prominent phosphatic-chalk filled Thalassinoides burrows and overlain by intraclast-pebble lags containing 'Terebella' phosphatica Leriche, Diblasus arborescens Parent and Lopha semiplana (J. Sowerby). Lithification occurred a few centimetres below the sediment/water interface in a sediment of increased permeability, and is geochemically discernible ~90 cm below the hardground surface. Glauconitization was restricted to replacement of clay minerals during the early development of the hardground, later phosphatization replacing carbonate. Actinocamax verus Miller occurs in basal phosphatic chalks and a bed of Gonioteuthis quadrata quadrata (Blainville) occurs at the summit. The Gonioteuthis Bed is commonly underlain by, but separated from, a bed of Offaster pilula (Lamarck). The proportion of faecal pellets, phosphatic ooliths, echinoderm fragments and benthonic foraminiferans decline above the basal hardgrounds as the phosphorites become finer-grained and less phosphatic. Inoceramid prisms or pelagic foraminiferans are the dominant component of poorer phosphatic chalks. Intraformational slump folds and hardground mélanges occur at the base of some successions. The palaeobiology of belemnites is considered in detail and it is concluded that the Gonioteuthis Beds were the products of massmortalities accompanying reproduction. Pelletal phosphate was formed by the replacement of carbonate during early diagenesis in an organic-rich, anoxic environment and water depths of <150 m. Current activity and subsurface anoxia were intermittent; colonization, bioturbation and winnowing alternating with quiescent, anoxic phases of mineralization. Phosphatic chalk cuvettes were eroded by a proto-Gulf Stream during a eustatic regression. Upwelling of this current was the main source of phosphate in the phosphatic chalks.

The Calama and eastern Pampa del Tamarugal Basins are located between 22°S and 23°S within the forearc of northern Chile. They are filled by sediments deposited in alluvial braidplain, fluvial, playa sandflat, lacustrine and volcaniclastic environments under a semi-arid to hyper-arid climate. The nature of the alluvial braidplain depositional environment is unusual in that it combines elements of both alluvial fan and fluvial depositional systems, in contradiction to recently published models of alluvial fan sedimentation. Detailed sedimentary logging, magnetostratigraphy and dating of 14 volcanic interbeds by the ⁴⁰Ar/³⁹Ar laser fusion method has established a lithostratigraphic and chronostratigraphic framework for the 700 m thick basin-fill. Basin formation was investigated by regional subsidence during the Late Eocene or Early Oligocene, followed by widespread alluvial braidplain deposition during the Oligocene(?). A change to fluvial and playa sandflat deposition during the Early to Mid-Miocene is considered to be coincident with a decrease in active subsidence. Sedimentation ceased and thick (25 m) gypcrete deposits developed along the eastern margin of the basin during the Mid-Miocene as a response to an increasingly arid climate. Phases of minor lacustrine, fluvial and alluvial braidplain deposition during the Late Miocene-Early-Pliocene and the Late Pliocene(?) to Pleistocene were primarily controlled by small-scale fault movements and folding events, although climatic variations may have been important in some cases. A new lithostratigraphic division of the basin-fill is proposed here, which comprises 13 different formations. The previously defined El Loa Formation comprises a number of depositional units which are spatially and temporally discrete formations, and is therefore awarded group status.

Prosaurolophus maximus is a crested hadrosaurine known from numerous specimens from the Dinosaur Park Formation of Alberta. Therefore, it is an ideal taxon to reconstruct patterns of growth and variation in hadrosaurids, and improve our understanding of their evolutionary relationships. This study describes the cranial anatomy of P. maximus, quantitatively examines its range of variation, and provides the first ontogenetic series for this taxon. A second species, P. blackfeetensis, was named based on morphological differences in the characteristic nasal crest; however, morphometric results fail to quantitatively differentiate P. blackfeetensis from P. maximus. A species-level phylogenetic analysis of hadrosaurids recovers P. maximus and P. blackfeetensis as sister taxa. Based on both the morphometric and phylogenetic data, this study supports the previous hypothesis that P. blackfeetensis is a junior synonym of P. maximus thereby substantially increasing its temporal range, and suggests a long period of morphological stasis in this taxon.

Prosaurolophus maximus is a crested hadrosaurine known from numerous specimens from the Dinosaur Park Formation of Alberta. Therefore, it is an ideal taxon to reconstruct patterns of growth and variation in hadrosaurids, and improve our understanding of their evolutionary relationships. This study describes the cranial anatomy of P. maximus, quantitatively examines its range of variation, and provides the first ontogenetic series for this taxon. A second species, P. blackfeetensis, was named based on morphological differences in the characteristic nasal crest; however, morphometric results fail to quantitatively differentiate P. blackfeetensis from P. maximus. A species-level phylogenetic analysis of hadrosaurids recovers P. maximus and P. blackfeetensis as sister taxa. Based on both the morphometric and phylogenetic data, this study supports the previous hypothesis that P. blackfeetensis is a junior synonym of P. maximus thereby substantially increasing its temporal range, and suggests a long period of morphological stasis in this taxon.

Tangasaurid eosuchians are represented by hundreds of specimens from the Permo-Triassic strata of Madagascar and Africa. The confusion surrounding the identification and anatomy of these reptiles is resolved by comparative anatomy and relative measurements, and three genera, Thadeosaurus, Tangasaurus and Hovasaurus, are described. Extensive growth series present a unique opportunity to study differences in growth strategies in two closely related Permian genera, one that was terrestrial (Thadeosaurus) and the other aquatic (Hovasaurus). The vertebrae of Youngina have a derived character state that indicates close relationship with the tangasaurids. A new genus and species of eosuchian, Acerosodontosaurus piveteaui, has a specialized feature in the carpus that is found in the Tangasauridae. The relationships between tangasaurids and other eosuchians are considered.

Thesis (Ph.D.) -- McMaster University, 1996. / Includes bibliographical references. Also available via World Wide Web.

Thesis (Ph.D.)--University of Adelaide, School of Earth and Environmental Sciences, Discipline of Geology and Geophysics, 2003? / Includes Publication list by the author as appendix A. "July 2003." Includes bibliographical references (leaves 308-324).

Thesis (M. Sc.)--Carleton University, 2004. / Includes bibliographical references (p. 137-151). Also available in electronic format on the Internet.