A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. Johannesburg, 2015. / Thrinaxodon liorhinus, a cynodont that has been of captivating importance in the evolution of therapsids, is one of the best known transitional fossil taxa from non-mammaliaform cynodonts to mammals. The species is abundant in the South African Karoo Basin and is one of the best represented taxa immediately after the Permian-Triassic mass extinction. One of the key adaptive characteristics that may have aided in their survival was fossorialism. Numerous fossils of Thrinaxodon have been found in burrows or in a curled-up position, which has provided important circumstantial evidence for the formalization of the hypothesis of Thrinaxodon as a burrower. However, finding a fossil inside a burrow or even in a curled-up position only provides firm evidence for burrow use, not for burrow creation. Direct evidence for burrowing capability can come from the understanding of the functional morphology of Thrinaxodon limbs. The present study investigates internal and external structure of the Thrinaxodon forelimb, a variety of reptiles characterized by different behavioural patterns, and other cynodonts in order to advance present knowledge about the functional morphology of the transitional phase cynodont. The study uses Geometric Morphometric analyses, forelimb metric indices, torsion and cortical thickness of humeri in order to determine the extent to which, the Thrinaxodon forelimb functionally and structurally resembles that of a fossorial mammal versus a digging reptile. Results of the study tease apart the extent to which the Thrinaxodon forelimb illustrates modifications due to gait (e.g., sprawling versus semi-sprawling) versus a fossorial lifestyle. This would indicate that Thrinaxodon retained the reptilian skeletal configuration and adapted a posture that had begun to resemble parasagittal more than sprawling or semi-sprawling gait. Nonetheless, Thrinaxodon exhibits forelimb structural similarities to digging species, whether mammals or reptiles.

The genus Kannemeyeria is one of the most important and distinctive taxa of the Triassic dicynodonts. It became the first Triassic dicynodont known to science, and thus forms the benchmark for the comparison of the evolution and morphology of other Triassic dicynodonts. An understanding of this genus forms an integral part of the biozonation of the Beaufort Group, and is pivotal in influencing the interpretation of the evolution, physiology and phylogenetic relationships of the Triassic dicynodonts. This study focuses on the detailed cranial morphology and relationships of the Kannemeyeria, and uses a rigorous morphological investigation as the basis for a meaningful elucidation of the functional and thus physiological aspects of this dicynodont. The descriptions demonstrate that variations related to the skull size, distortion or naturally occurring variation within the genus allow for the synonymy of the formerly recognised species K. latifrons Broom (1898; 1913), K. erithrea Haughton (1915) and K. wilsoni Broom (1937). This conclusion is further supported by the allometric analysis which cannot distinguish the variation observed in the holotypes with that occurring naturally within a growth series. Apart from the large specimen, the other smaller individuals are accommodated in the genus as different ontogenetic stages of the growth series represented by K. simocephalus Weithofer (1888). Several allometric variables show unusual patterns of development, indicating that Kannemeyeria can be subdivided into ontological classes, as juvenile and adult forms, separated from each other by a particular level of development. An age-related threshold level is suggested, and considered to represent an animal reaching sexual maturity. It is consequently proposed that the Kannemeyeria population was, at an age-related level, subdivided into sexually mature and immature groups but remained ecologically homogeneous. Both the descriptions and the allometric analysis of the species K. cristarhynchus Keyser & Cruickshank (1979) clearly indicate that it does not conform to the growth series of K. simocephalus and thus the differences observed between these two taxa are not constrained to size increases. Consequently, the recognition of the species K. cristarhynchus is considered valid. From the observations of the cranial morphology, tested using an allometric analysis, generic and specific diagnoses are constructed for Kannemeyeria and its two African species. Several features of Kannemeyeria are discussed in a functional context. A corrugated hom-covered snout and large caniniform processes are considered to be associated with defence and posturing behaviour. Several features of the braincase also suggest herding behaviour. Kannemeyeria also has a slightly different occipital musculature arrangement than that proposed for many other dicynodonts. Most Kannemeyeria cranial features are related to its masticatory function. From the analysis of masticatory cycle it is clear that the jaw action is described via a single pivot-point, which in Kannemeyeria approached the original, primitive position of the jaw hinge. The vertical orientation of the articulation and this pivot-point ensured that the muscle action during second phase of mastication produced an upward crushing and grinding action instead of the typical fore-and-aft motion of many other dicynodonts. It also meant that the muscle force was at their maximum, and little or no energy was lost to translation of the moment arm at the jaw articulation. Consequently, the Kannemeyeria masticatory cycle was both highly effective and extremely efficient. The morphology, and resultant physiology, of Kannemeyeria skull is considered to represent the innovative foundation for much of the success of many of the later Triassic dicynodonts.

This dissertation is an exploration of phenomena on varying scales, built on the backbone of Cenozoic mammalian biochronologic units (Land Mammal ‘Ages’): the integration of fossil and geological data to constrain spatiotemporal patterns in evolution. I develop and test hypotheses about the origins and ordinal-level relationships of the extinct South American endemic placental order Notoungulata, as well as about some more specific macroevolutionary patterns at a familial level within notoungulates. Major novel outcomes include a new biochronologic timescale for the terrestrial Cenozoic of South America, numerically calibrated through synthesis of new and existing high-precision geochronological data (particularly U-Pb and 40Ar/39Ar dating), along with an explicit logical framework for Land Mammal “Age” calibration; description of two new interatheriid notoungulate taxa from the central Chilean Andes; a new phylogenetic hypothesis for the position of Notoungulata within Placentalia; and the first ever DNA sequences obtained from the extinct musk ox relative Bootherium bombifrons. The first study, chapter two, is a review of geochronologic (radiometric and magnetostratigraphic) constraints for the South American Land Mammal “Age” timescale. I present a revised, updated timescale, and a descriptive, logical framework for the synthesis of geochronologic and biochronologic data from a variety of sources and analytical methods. Significant changes to the calibration of individual SALMAs in this update are concentrated in the Paleogene, while Neogene calibrations have remained fairly stable, with small refinements to the core age ranges of the Huayquerian, Chasicoan, Colloncuran, and Friasian. This section also investigates the influence of latitudinal biotic provinciality on correlations and chronologic calibrations, particularly as far as provinciality reflects the climatic evolution of the continent. Marked provinciality is evident at least as early as the early Eocene, with faunas like Itaboraí differing from potential correlative faunas at higher latitudes, potentially representing unique periods in mammalian evolution, both faunally and chronologically. Instead of trying to recognize and correlate the classical high latitude SALMAs to highly distinctive tropical assemblages, the SALMA timescale should allow for the development of separate mammalian biochronologic zonations for low and high latitudes. Chapter three presents and describes two new notoungulate taxa, representing the first species formally described from the Los Queñes Fauna, a late Eocene mammal assemblage from the Andean Main Range of central Chile. These two taxa, Anabalcarcel ignimbritae and Jackconrad carreterensis, represent the earliest hypsodont interatheres known. Based on ancestral state reconstructions using parsimony, hypsodonty appeared no later than the latest Eocene (34.6 ± 0.8 Ma; likely correlative with the Mustersan South American Land Mammal Age) in interatheres, a time when this dental specialization was not yet pervasive among other mammalian herbivores. Tree-based comparative analyses revealed two significant taxonomic radiations of interatheres, the early radiation of basal interatheriids and a later radiation of hypselodont taxa after the interval of dramatic global climatic change associated with the Eocene/Oligocene boundary. In chapter four, I attempted to apply some of the geochronologic methods incorporated in the first two chapters, to date a newly discovered site in Abanico Formation, central Chilean Andes. This formation yields fossil mammals in numerous areas, including at several localities in the Río Las Leñas and Río Cachapoal drainages. In the Cachapoal Valley, steeply-dipping beds have yielded fossils of Tinguirirican age, including a polydolopine marsupial and an interatheriid notoungulate. The results of this study, the first 40Ar/39Ar analysis from the Cachapoal Valley, are a date of 11.1 ± 1.8 Ma, from stratigraphically higher levels loosely constraining the minimum age for fossiliferous deposits. Chapters five and six change tack a little, and investigate analytical methods in ancient-DNA phylogenomics, time-calibrated with radiocarbon dates, using as a study system Bootherium bombifrons, the endemic North American helmeted musk ox that went extinct, along with most of its megafaunal colleagues, at the end of the Pleistocene. This switch to a North American, rather than South American, endemic mammal was driven by availability of molecular comparative material and the presence of hundreds of helmeted musk ox specimens in the American Museum paleontology collections, which I was able to sample destructively. I present the first complete mitochondrial genome of the extinct musk ox Bootherium bombifrons, and new mitochondrial sequence data from seven individuals referred to Bootherium bombifrons Additionally, I obtained new radiocarbon dates from these same specimens, of 38580 ± 720, 30240 ± 260, 44570 ± 190, 41040 ± 910, 44240 ± 1500, 39080 ± 770, 28370 ± 210, and 47190 ± 2100 calibrated 14C years BP. Phylogenetic analysis supports placement of Bootherium as sister to the living musk ox, Ovibos moschatus, in agreement with morphological taxonomy. I also tested hypotheses regarding the impact that locus choice has on divergence date estimates using tip calibrations in this taxon. Estimates of the root age of three different gene trees for Bootherium specimens ranged from 19 ka, for cytochrome B, to over 50 ka for the mitochondrial control region. The final study in this dissertation (chapter seven) is a superordinal scale approach to fitting Notoungulata into the picture of all placental mammals through synthesis and expansion of existing total-evidence matrices. Results presented here corroborate previous findings that notoungulates are most closely related to Afrotheria, but do not support afrothere and notoungulate reciprocal monophyly, suggesting a complex biogeographic relationship between South America and Africa persisting from Late Cretaceous through mid-Paleocene.

Clark’s Cave contains a large collection of late Pleistocene mammal material. In particular, it contains a sizable amount of Microtus spp. which can be valuable paleoclimate indicators. Identification techniques traditionally used to classify these species have been shown to be unreliable. Recent studies have shown that using geometric morphometric techniques on lower first molars can be more successful. By placing landmarks and running a discriminate analysis on new and previously collected material from the cave, significant differences in Microtus species proportions were found. Specifically, showing the deposit has a larger proportion of M. xanthognathus than previously reported; resulting in a subsequent drop in the number of M. pennsylvanicus and M. chrotorrhinus present. Moreover, previously unreported M. ochrogaster was determined to be an important component of the fauna. The results presented here show the importance of applying new techniques to previous studies.

The American alligator, Alligator mississippiensis, is a large extant archosaur and member of the Order Crocodilia. Crocodilian ontogeny has been studied in great detail, the skull being of particular interest. One aspect of the skull left unstudied is how individual cranial elements change through ontogeny independent of one another. This study observed morphological change in a growth series of 34 specimens of A. mississippiensis from ETSU Vertebrate Paleontology Lab collections. The premaxilla, maxilla, nasal, jugal, frontal, and parietal were analyzed using landmark morphometrics. The frontal, jugal, and parietal showed more allometric growth with the orbits reducing in size posteriorly. The premaxilla, maxilla, and nasal showed more isometric growth. This suggests the common observation that the snout elongates with age is mistaken. The cranium showed allometric growth in very early in life but more isometric growth after that. Unique to this study, the premaxilla showed almost no shape change throughout ontogeny.

An early late Campanian transgressive lag, a 'shark tooth bed', in the local base of the Demopolis Formation overlying the Coffee Formation at the Frankstown site in Prentiss County, northeastern Mississippi, reveals a diverse vertebrate fauna of fragmentary remains pertaining to a wide variety of habitats of the northern Mississippi Embayment. By comparing the Frankstown taxa to those of less mixed faunas elsewhere in America, it is possible to separate the large primary shallow-water marine fauna from the smaller secondary deep-water marine, estuarine, fluviatile and terrestrial faunas mixed with it. The site includes 53 taxa---the most diverse Cretaceous vertebrate fauna known from Mississippi, including a chimaeroid, 13 sharks, 5 rays, 15 bony fish, 6 turtles, a lizard, 5 mosasaurs, a plesiosaur, 2 crocodilians, and 4 dinosaurs. Many of these (26) are new records for the state. A review of the 42 known Mississippi Late Cretaceous vertebrate taxa not present at the site is also included, 26 of which are also new records for the state. The deep-water (pelagic) marine fauna was likely washed inshore by storms, but the other secondary faunas were probably reworked from underlying beds. By separating the various faunas of a diverse transgressive lag assemblage, a broad overview of the paleoecology of the area can be obtained from a single site. Vertebrate faunas from the base of a stratigraphic sequence are fundamentally different in nature from those of the deep-water marine (maximum transgression) middle part of a sequence, and not, as has been thought, just a poorly preserved high-energy version of the well-preserved low-energy middle sequence fauna Based on X-ray diffraction analyses done for this study, it is argued that, in an early stage of lag formation, unstable phosphate was leached from the vertebrate material of the lag, and redeposited as a more stable form in wood, rip-up clasts, and steinkerns Contrary to previous work, it is shown that the shallow-water marine vertebrate fauna of the American Cretaceous changed little through that time---there was no major faunal change after the Turonian / acase@tulane.edu

The Nile crocodile Crocodylus niloticus currently has an extensive range throughout the African continent and Madagascar, though fossil and subfossil remains show that its historic range was considerably larger and included parts of the Sahara Desert, Mediterranean coast, and Arabian Peninsula. Recent molecular studies have yielded genetically distinct populations of C. niloticus, leading to the possibility that C. niloticus is actually multiple cryptic species, while morphological variation remains unassessed. This study compares skulls of C. niloticus to other members of the genus Crocodylus in dorsal view using geometric morphometrics to evaluate intraspecific and interspecific variation. The morphometric analysis is coupled with a geographic analysis to determine if the species is morphologically variable by geographic region as well as a model-based cluster analysis to determine and morphological clusters irrespective of other factors. These analyses indicate that C. niloticus exhibits populational variation that exceeds almost every other species of Crocodylus, with differences between geographic regions statistically disctinct. These results support the presence of a cryptic species complex. Additionally, an osteological description of Crocodylus niloticus is provided.

There is general agreement that a range of paleodepths and environments are represented in the individual shell units of the middle Pliocene to earliest Pleistocene Tamiami Formation of southwest Florida, but maximum depths remain poorly constrained. Here, benthic Foraminifera abundances are used as a paleoenvironmental proxy to compare the upper Tamiami from quarries in Sarasota, Florida to Recent modern coastal, bay, and reef habitats of Florida, the Grand Cayman Islands, and Puerto Rico, ranging in depth from 0 to 55 meters. I used: (1) ordination techniques, including detrended correspondence analysis (DCA) and cluster analysis, to compare upper Tamiami foraminiferal assemblages with potential modern analogs; (2) Ammonia-Elphidium (AEI) and FORAM (FI) indices to reconstruct past oxygen levels and environmental stress levels, respectively; and (3) diversity indices and rarefaction to investigate habitat-specific diversity change through time.Results indicate that the upper Tamiami units represent several distinct environments. APAC quarry, Fruitville Member Unit 4 samples group in DCA and cluster analyses with modern shallow, tropical, mangrove-proximate lagoon samples from Puerto Rico; AEI values of both Unit 4 and these lagoonal samples are consistent with high nutrients. APAC quarry, Fruitville Member Unit 3 and Pinecrest Member units 5 and 7, however, group with tropical shallow, open coast environments up to 12 m in depth and have relatively low FORAM indices suggesting stress and AEI values comparable to modern mesotophic, shelf habitats. SMR samples group with modern mangrove environments from White Water Bay at depths approximately 0 to 0.3 m, with FORAM and AEI indices indicating low oxygen and possibly high nutrients. Species richness measured by individual rarefaction in the fossil units is highest in the lowest APAC units sampled and progressively declines in younger APAC units, while SMR beds have the lowest richness of all fossil samples. The lower portion of Unit 7 contains the highest richness of all fossil and modern units, while other fossil units have either lower or comparable richness, diversity, and evenness when compared to modern habitat analogs as identified in cluster and DCA analyses. Thus, there is no clear evidence for wide-scale decline in foraminiferal biodiversity from the Plio-Pleistocene to now. Significantly, the identification of modern habitat analogs for the upper Tamiami units make it possible to compare biodiversity trends in other fauna (e.g., mollusks) thought to have experienced significant extinction.

This thesis deals with the stratigraphy and brachiopod systematic palaeontology of the latest Devonian (Famennian) to Early Permian (Kungurian) sedimentary sequences of the Tarim Basin, NW China. Brachiopod faunas of latest Devonian and Carboniferous age have been published or currently in press in the course of the Ph.D candidature and are herein appendixed, while the Early Permian brachiopod faunas are systematically described in this thesis. The described Early Permian brachiopod faunas include 127 species, of which 29 are new and 12 indeterminate, and six new genera (subgenera) are proposed; Tarimella, Bmntonella, Marginifera (Arenaria), Marginifera (Nesiotia), Baliqliqia and Ustritskia. A new integrated brachiopod biostratigraphical zonation scheme is proposed, for the first time, for the latest Devonian-Early Permian sequences of the entire Tarim Basin on the basis of this study as well as previously published information (including the Candidate's own published papers). The scheme consists of twenty three brachiopod acm biozones, most of which replace previously proposed assemblage or assemblage zones. The age and distribution of these brachiopod zones within the Tarim Basin and their relationships with other important fossil groups are discussed. In terms of regional correlations and biostratigraphical affinities, the Late Devonian to Early Carboniferous brachiopod faunas of the Tarim Basin are closest to those from South China, while the Late Carboniferous faunas demonstrate strong similarities to coeval faunas from the Urals, central Asia, North China and South China. During the Asselian-Sakmarian, strong faunal links between the Tarim Basin and those of the Urals persisted, while at the same time links with central Asia, North China and South China weakened. On the other hand, during the Artinskian-Kungurian times, affinities of the Tarim faunas with the Urals/Russian Platform rapidly reduced, when those with peri-Gondwana (South Thailand, northern Tibet) and South China increased. Thirty lithofacies (or microfacies) types of four facies associations are recognised for the Late Devonian to early Permian sediments. Based on detailed lithostratigraphy, biostratigraphy and facies analysis, 23 third-order sequences belonging to four supcrsequences are identified for the Late Devonian to Early Permian successions, from which sea-level fluctuation curves are reconstructed. The sequence stratigraphical analysis reveals that four major regional regressions, each marking a distinct supersequence boundary, can be recognised; they correspond to the end-Serpukhovian, end-Moscovian, late Artinskian and end-Kungurian times, respectively. The development of these sequences is considered to have been formed and regulated by the interplay of both eustasy and tectonism. Using the system tract of a sequence as the mapping time unit, a succession of 47 palaeogeographical maps have been reconstructed through the Late Devonian to Early Permian. These maps reveal that the Tarim Basin was first immersed by southwest-directed (Recent geographical orientation) transgression in the late Famennian after the Caledonian Orogeny. Since then, the basin had maintained its geometry as a large, southwest-mouthed embayment until the late Moscovian when most areas were the uplifted above sea-level. The basin was flooded again in late Asselian-Artinskian times when a new transgression came from a large epicontinental sea lying to its northwest. Thereafter, marine deposition was restricted to local areas (southwestern and northwestern margins until the late Kungurian, while deposition of continental deposits prevailed and continued through the Middle and late Permian into the Triassic.

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