Hawk Rim represents a new mid-Miocene site in Eastern Oregon. This time period offers a rare chance to observe dramatic climatic changes, such as sudden warming trends. The site is sedimentologically and stratigraphically consistent with the Mascall Formation of the John Day Basin to the north and east of Hawk Rim. Hawk Rim preserves taxa such as canids Cynarctoides acridens and Paratomarctus temerarius, the felid Pseudaelurus skinneri, castorids Anchitheriomys and Monosaulax, tortoises and the remains of both cormorants and owls. Hawk Rim has yielded a new genus and species of mustelid. As individuals these taxa are of interest, but the real story is told by the paleoecology. The lower reaches of the section have lacustrine diatomite layers as well as preserved logs, suggesting the presence of a wet, forested ecosystem as conformed by the structure of the paleosols. Climate data allow us to make analyses of large-scale ecological trends in mid-Miocene Oregon.

A Amazônia abriga uma grande parcela da biodiversidade mundial, no entanto, existem grandes incertezas sobre os processos de geração e manutenção dessa enorme diversidade, com várias hipóteses propostas até o momento. Diversas características como tamanho pequeno, baixa capacidade de dispersão e fidelidade ao ambiente estritamente florestal fazem de lagartos do gênero Loxopholis (Squamata: Gymnophthalmidae) candidatos ideais para rastrear a história de modificações da paisagem no norte da América do Sul durante o Neogeno. Nesta tese, revisamos a variação morfológica, taxonomia e a distribuição geográfica das espécies do gênero Loxopholis, assim como estimamos as relações filogenéticas e o tempo de divergência entre as espécies com base em sequências de DNA provenientes do genoma mitocondrial e nuclear. Com essa base de dados, construímos um modelo de como ocorreu a história evolutiva de Loxopholis, discutindo os resultados a partir de reconstruções geológicas provenientes da literatura, e fornecendo uma datação independente para eventos geológicos que potencialmente influenciaram a história evolutiva do gênero. Neste estudo, também revelamos que a atual diversidade descrita para Loxopholis está severamente subestimada. Encontramos que a espécie L. osvaldoi representa um complexo de espécies crípticas, contendo de 8 a 14 potenciais espécies novas, com profundas divergências genéticas tanto nos genomas mitocondrial e nuclear, praticamente dobrando a diversidade conhecida no gênero. No entanto, a morfologia em Loxopholis é extremamente conservada, dificultando a diagnose das espécies novas. Finalmente, descrevemos a primeira população bissexual da espécie partenogenética L. percarinatum, discutindo as implicações deste achado para o entendimento relativo a aparição da partenogênese em Loxopholis / The Amazon rainforest houses a significant portion of the world biodiversity, however, there is still a lot of uncertainty about the processes involved in its generation and maintenance, with several hypotheses proposed so far. Loxopholis lizards (Squamata: Gymnophthalmidae) are small-sized; show low vagility, and high fidelity to the humid forest environment, making them ideal to test hypotheses on the history of landscape modifications in Northern South America, during the Neogene. In this thesis, we revise the morphological variation, the taxonomy, and the geographic distribution of Loxopholis species, as well as estimated a phylogenetic hypothesis and divergence times for these species based on sequences from mitochondrial and nuclear DNA. With this dataset, we build a model for the evolutionary history of Loxopholis and compared the results with geologic reconstructions of the Amazon available in the literature, which provided independent time estimates for geological events that potentially affected the evolutionary history of genus. In this study, we also showed that the actual diversity described for Loxopholis was severely underestimated. We found that L. osvaldoi represents a complex of cryptic species with 8-14 potential new species, and strong divergences in both the mitochondrial and the nuclear genomes, virtually doubling the actual diversity in the genus. Finally, we describe the first bisexual population for the parthenogenetic species L. percarinatum, discussing its implications to the origin of parthenogenesis in the genus

The Laurentian trilobite genus Clelandia Cossmann, 1902, is represented by 12 named species that range from the late Cambrian to Early Ordovician. Species of Clelandia have been described from many localities in the United States, Canada, Scotland, and Greenland and attempts have been made to employ them as tools in biostratigraphic correlation. Nevertheless, important questions persist regarding the taxonomy and phylogeny of the group. No species-level phylogenetic analysis has been attempted for the genus and its family affinity has been unclear. Previous work often has produced limited numbers of small photographs which tend to mask subtle, but critical, morphological details and confuse taxonomic identification. New collections from the Great Basin of the western United States have resulted in material representing five new species of Clelandia, three of which are formally named. Other species of Clelandia are illustrated and the type species is redescribed. C. aspina and C. bispina are reported from a new locality in east-central Nevada. The first articulated specimens from a species of Clelandia are illustrated and demonstrate multiple synapomorphies of the thorax and pygidium that strongly indicate a unique, low-diversity clade of trilobites which persisted from the late Cambrian into the Early Ordovician with similarities to the Kingstoniidae. Phylogenetic analysis shows Clelandia to contain two distinct components. One component is characterized by species with glabellar furrows, widely flared posterior projections, and exsagittal pits of the occipital furrow. A more derived component consists of species with long glabellar spines, relatively narrow posterior fixigenae, bacculae, and a unique glabellar-occipital spine structure.

This project seeks to explore, name, and describe some of the earliest known members of Alligatoroidea. Explorations of Bottosaurus harlani and Deinosuchus reveal that early in their evolutionary history alligatoroids had attained bauplans that are highly divergent from the ancestral condition in both body size and morphology. Bottosaurus harlani preserves aspects of the skull table – including constricted supratemporal fenestrae, a linear frontoparietal suture, and a large trapezoidal dorsal supraoccipital exposure – that are similar to those of caimans. Optimal trees from phylogenetic analysis recover B. harlani in three different positions; as a sister either to the modern dwarf caimans (Paleosuchus), or either living species of Paleosuchus. That a substantial stratigraphic gap separates B. harlani from both species of Paleosuchus, which first appears in the Miocene, along with low character and nodal support raises questions about this relationship. However, should the relationships recovered here be true, Bottosaurus harlani would be the oldest known caiman. The taxon indicates that morphologies common to modern caimans date to the earliest record of the clade. In addition to the enigmatic B. harlani, the Campanian giant Deinosuchus was re-evaluated as part of this project. Recent consensus has been that the three named species of Deinosuchus (D. hatcheri, D. riograndensis, and D. rugosus) represent a single, widely ranging species. Newly-collected material from the Big Bend region of western Texas and increased sampling of the lineage from throughout North America allowed for a review of species-level systematics of Deinosuchus and helped refine its phylogenetic placement among crocodylians. Deinosuchus from western and eastern North America can be consistently differentiated and represent different species. As a result of the lack of diagnostic characters in the very incomplete holotype specimen, the name Deinosuchus is restricted to D. hatcheri. To encompass specimens formerly included in Deinosuchus a new genus, Deinosuchoides, is erected. In addition to naming a new genus, the holotype specimen for Deinosuchus rugosus is determined to be undiagnostic to species level and is therefore a nomen dubium. A new species, Deinosuchoides schwimmeri, is erected upon a cranial specimen from Mississippi. The snout of Deinosuchoides is very long and wide. Almost invariably, crocodylian snouts are either long or wide, but not both. In addition to the unusually long and wide snout, the skull table of this taxon bears hallmarks found in species of other long-snouted taxa such as Tomistoma and Gavialis. To explore the variability of the crocodylian skull table a morphometric analysis was conducted with the inclusion of fossil taxa. As the skull table is robust and likely to be recovered in the paleontological record this element was an ideal fit for a morphometric study. In addition to establishing the morphospace occupation of fossil taxa, the morphometric analysis found considerable overlap in morphospace between Alligatoroidea and Crocodyloidea – the overlap between these groups may be the product of shared ancestry. Additionally, similarities exist in the ecologies of these groups as evidenced by shared snout shape categories. This project finds association between skull table shape and snout length. As such, plotting isolated skull tables in morphospace, may indicate snout length and thus ecology of fossil taxa. When landmarks representing the supratemporal fenestrae are included in the analysis Gavialoidea is broadly separated from the other groups in morphospace. It has been long hypothesized that the size of the supratemporal fenestrae reflect the length of the snout as a result of jaw musculature attaching to their medial margins. However, this relationship is not as straightforward as previously hypothesized; the snouts of the crocodyloids Tomistoma and Euthecodon may exceed the length of the snout in gavialoids but their supratemporal fenestrae are proportionally smaller. This study suggests that a phylogenetic constraint on the size of the supratemporal fenestrae may be present in crocodyloids. In addition to exploring morphospace occupation, allometric trajectories of all extant taxa with available ontogenetic sequences were explored. The smallest extant taxa (O. tetraspis, P. palpebrosus, and P. trigonatus) demonstrate allometric trajectories that plot alongside the juveniles of the other taxa in this analysis. This may suggest that the small sizes of the skull tables in these species were achieved through paedomorphosis, or the maintenance of juvenile morphologies into adulthood.

The boletes are macrofungi which have undergone extensive taxonomic revisions since the advent of molecular tools. To further our understanding of the boletes in peninsular Florida, we sequenced two common Floridian boletes, and analyzed them with molecular phylogenetic tools. Boletus rubricitrinus, a common Florida bolete often found in lawns under Quercus, and likely has a distribution that extends to Texas. Based on ITS and LSU sequences and morphological studies, this species belongs in the genus Pulchroboletus. As the holotype is in poor condition, an epitype is established here. A thorough description of macroscopic and microscopic features is also provided for the species. Fungi in the genus Phylloporus are lamellate boletes that occur worldwide, but primarily in the tropics. Phylloporus boletinoides is a species which was described from Florida, and is found growing near Pinus spp. Based on ITS, LSU, and RPB1 sequences, we establish the novel genus Pseudophylloporus, which is allied to Bothia and Solioccasus. Morphological data are also provided from our collections, and one from Belize. Based on molecular data and a review of bolete literature, the delimitation of this genus suggests that there are three distinct lineages of boletes that have a lamellate hymenium in the Boletaceae. These molecular and morphological data will be useful to further improve our understanding of bolete taxonomy.

A consensus classification for the waterfowl (order Anseriformes) has never been reached. There have been many revisions of the relationships within the order including those of the monotypic Australian genera. The Southern Hemisphere anseriforms comprise a large number of monotypic, endemic genera which have traditionally been linked to the established genera and tribes of the Northern Hemisphere. More recently, however, with the recognition of endemic Australian radiations of marsupial mammals (Main and Bakker 1981) and passerine birds (Cracraft 1976; Sibley and Ahlquist 1985; Christidis et al. 1988; Christidis and Schodde 1991), the affinities of the six monotypic Australian genera of anseriforms have been questioned (Delacour 1954; Frith 1955, 1964a, b, 1982; Johnsgard 196la, b, 1966; Davies and Frith 1964; Fullager 1990). In particular, whether they are more closely related to one another, or whether some or all of these monotypic genera have closer affinities with the Northern Hemisphere genera. Classification of the taxonomic relationships of the aberrant Australian endemic species may also corroborate or refute the recently advanced hypothesis of a Southern Hemisphere origin for the Anseriformes (Cracraft 1976, 1980; Livezey 1986; Olson 1988). A 307bp fragment of the mitochondrial cytochrome b gene of the 19 native Australian anseriforms and four Northern Hemisphere species was enzymatically amplified by PCR and manually sequenced. The Chicken (Gallus gallus) and Muscovy Duck (Cairinia moschatd) cytochrome b sequences were obtained from Genbank. The patterns of evolutionary dynamics within the cytochrome b gene of Anseriformes appear to conform to those reported in studies of avian and other vertebrate mtDNA. A new phylogenetic classification for the Anseriformes is proposed. The phylogenetic trees generated in this study indicate that the monotypic Australian genera, the pygmygeese and the swans and geese are members of the subfamily Anserinae which appears to represent a Southern Hemisphere radiation. Within the Anserinae, the Cape Barren Goose and Freckled Duck link most closely with each other, the Pink-eared Duck appears to be closely related to the true geese, the Musk Duck is a sister taxon to the Pink-eared Duck and may be less closely related to the Oxyura than previously thought and the Magpie Goose is the most divergent member of the Anseriformes included in this study. The Maned Duck and the remaining native Australian anseriforms are members of the established European genera and tribes of waterfowl. These species probably represent a secondary radiation of recent Northern Hemisphere invaders of Australia. Finally, the data provides some support for the theory of a Southern origin for the Anseriformes.

Gnathostomes, or jawed vertebrates, make up the overwhelming majority of modern vertebrate diversity. Among living vertebrates, they comprise the chondrichthyans (“cartilaginous fishes” such as sharks, skates, rays, chimaeras) and the osteichthyans (“bony fishes” or bony vertebrates, inclusive of tetrapods). Gnathostomes appear to have originated in the early Palaeozoic Era, but their early fossil record is fairly scant. The best fossils appear first in the Late Silurian and Devonian periods. Much of gnathostome diversity owes to unique adaptations in the internal skeleton of their head (the endocranium). The endocranium is composed of the braincase, jaws, hyoid arch, and branchial arches, which sometimes fossilise when they are composed of bone or calcified cartilage. The purpose of this thesis is to describe and compare the fossilised cranial endoskeletons of a variety of different Palaeozoic gnathostomes. The objective is to test current conceptions of gnathostome interrelationships (i.e. phylogeny) and infer aspects of key morphological transformations that took place during the evolution of Palaeozoic members of this group. Two key areas are examined: the morphology and interrelationships of Palaeozoic gnathostomes and the morphology of the visceral arches in sarcopterygian fishes. New data on the visceral arches are described from the stem tetrapods Panderichthys and rhizodontids. These provide insight into the sequence of character acquisition leading to the tetrapod middle ear. Panderichthys shows key features of the tetrapod middle ear chamber were established prior to the origin fo digited limbs. New morphological data are described from the “acanthodian” fish Ptomacanthus. Ptomacanthus provides only the second example of a well-preserved braincase from any member of this group. It shows dramatic differences from that of its counterpart, Acanthodes, providing new evidence for acanthodian paraphyly. New interpretations of basal gnathostome and osteichthyan phylogeny are presented, challenging or enriching existing views of these problems.

To investigate vascular-plant phylogeny at deep levels of relationship, I collected and analyzed a large set of plastid-DNA data comprising multiple protein-coding genes and associated noncoding regions. I addressed questions relating to overall tracheophyte phylogeny, including relationships among the five living lineages of seed plants, and within two of the largest living gymnosperm clades (conifers and cycads). I also examined relationships within and among the major lineages of monilophytes (ferns and relatives), including their relationship to the remaining vascular plants. Overall, I recovered three well-supported lineages of vascular plants: lycophytes, monilophytes, and seed plants. I inferred strong support for most of the phylogenetic backbones of cycads and conifers. My results suggest that the cycad family Stangeriaceae (Stangeria and Bowenia) is not monophyletic, and that Stangeria is instead more closely related to Zamia and Ceratozamia. Within the conifers, I found Pinaceae to be the sister-group of all other conifers, and I argue that two conifer genera, Cephalotaxus and Phyllocladus (often treated as monogeneric families) should be recognized under Taxaceae and Podocarpaceae, respectively. Systematic error likely affects inference of the placement of Gnetales within seed-plant phylogeny. As a result, the question of the relationships among the five living seed-plant groups still remains largely unresolved, even though removal of the most rapidly evolving characters appears to reduce systematic error. Phylogenetic analyses that included these rapidly evolving characters often led to the misinference of the “Gnetales-sister” hypothesis (Gnetales as the sister-group of all other seed plants), especially when maximum parsimony was the inference method. Filtering of rapidly evolving characters had little effect on inference of higher-order relationships within conifers and monilophytes, and generally resulted in reduced support for backbone relationships. Within the monilophytes, I found strong support for the majority of relationships along the backbone. These were generally congruent with other recent studies. Equisetaceae and Marattiaceae may be, respectively, the sister-groups of the remaining monilophytes and of the leptosporangiate ferns, but relationships among the major monilophyte lineages are sensitive to the outgroups used, and to long branches in lycophytes.

The leafhopper genus Xyphon, included in the sharpshooters, is a widely distributed group of insects whose species are vectors for various plant diseases. Xyphon has historically contained up to 9 species. These species have been poorly delimited in the past and their identification has been difficult using published keys. The genus is revised here based on a new species level phylogenetic assessment that incorporates both morphological and molecular data. The genus Xyphon was erected to contain leafhoppers that possessed a reticulated forewing apex but lacked both a median sulcus on the crown and a carinate anterolateral crown-face margin both of which are present in the closely related genus Draeculacephala. Young (1977) revised most of the genera included in Xyphon's containing subfamily. He did not attempt a revision of Carneocephala (the genus that formerly contained most Xyphon species), but noted the need for a revision of its species. This revision of the genus Xyphon is based on the examination of approximately 8,000 specimens and includes a phylogenetic analysis of the genus that includes data from one gene (NDI) and 47 morphological characters. A generalized model of each preliminary taxonomic unit was used to test the monophyly of each species. These tests resulted in the synonomization of 4 former species: Xyphon gillettei to include X. balli; and X. reticulatum to include X. diductum, X. dyeri, and X. sagittiferum. Parsimony and Bayesian techniques were used to infer relationships among species. These analyses resulted in almost identical tree topologies. In all analyses Xyphon was monophyletic and Draeculacephala was its sister genus although clade support for the genus was generally low. The analyses found that X. flaviceps and X. fulgidum form a basal clade within Xyphon, above which X. gillettei and X. n. sp. 1 (new species 1) form a clade that is sister to a third clade containing X. triguttatum, X. nudum, and X. reticulatum.

The tribe Leucophoropterini (Miridae: Phylinae) is a diverse assemblage of primarily Indo-Pacific and Australian bugs which are united by simple, small genitalia and a trend towards ant-mimetic body forms. Previous to this work, the relationship of the Leucophoropterini to the other tribes of Phylinae, as well as the generic relationships within the lineage, was unresolved. Further, the characters initially proposed to unite the tribe are brought into question with the addition of several recently discovered taxa from Australia. The Leucophoropterini is first re-evaluated within a phylogenetic analysis of the subfamily Phylinae, using a combined molecular and morphological dataset to test the monophyly of the lineage, re-test the character synapomorphies supporting it, and to determine the closest relatives to the tribe. The molecular dataset includes 4 genes (COII, 16S, 28S, and 18S), and 123 morphological characters for 104 taxa, which is analyzed in a parsimony analysis using Tree analysis using New Technology [TNT], a model-based analysis in RAxML, and a Bayesian analysis in Mr. Bayes. All three methods resulted in phylogenetic trees with nearly identical generic and tribal groupings, and a lineage containing Pseudophylus Yasunaga, Decomia Poppius and Tuxedo Schuh being sister-group to the Leucophoropterini. With the closest relatives to the Leucophoropterini determined for outgroup selection, a generic revision of the tribe including both Australian and Indo-Pacific taxa is accomplished using 137 morphological characters and is analyzed in an un-weighted and implied weighted parsimony analysis using TNT for 86 leucophoropterine taxa. The Indo-Pacific taxa of Leucophoropterini are found to be related to the Australian Leucophoropterini, and at least two genera within the tribe (Sejanus Distant, Leucophoroptera Poppius) were found to be paraphyletic. Lastly, taxa are revised within the context of the generic-level phylogenetic analysis, with new genera and species from Australia and the Indo-Pacific being described.