<p>Melanin is a ubiquitous biological pigment found in bacteria, fungi, plants, and animals. It has a diverse range of ecological and biochemical functions including display, evasion, photoprotection, detoxification, and metal scavenging. Two forms of melanin produced from different molecular precursors are present in nature - eumelanin (dark brown-black in color) and pheomelanin (orange-red in color). Both eumelanin and pheomelanin are complex highly cross-linked biopolymers that are found intertwined with proteins, lipids, and metal ions in nature. </p><p> </p><p>Recent reports have used morphological evidence to suggest the presence of melanin in the fossil record. These studies have been met with criticism due to their lack of chemical evidence to support melanin identification. This dissertation describes chemical approaches to unambiguously verify the presence of melanin in the fossil record and characterize the ancient pigment. It also explores the limitations for the survival of melanin in the fossil record and the possibility that melanin acts as a protective matrix to preserve other biomolecules that are embedded in the pigment. </p><p>Melanin has unique chemical signatures that are commonly used to characterize and compare the pigment of modern organisms. We applied these chemical approaches to the study of fossil pigmentation. Analysis of the black pigmentation of two > 160 million year old (Mya) Jurassic cephalopod ink sacs provided the first conclusive evidence for eumelanin in the fossil record. The preserved fossil eumelanin was then compared to modern cephalopod eumelanin from Sepia officinalis. Using these chemical approaches we found that fossil eumelanin was chemically and morphologically identical to S. officinalis eumelanin. </p><p> Although there is mounting chemical evidence for the presence and preservation of melanin in the fossil record, there is very little data constraining its long-term survival. We applied the analytical approaches designed to study fossil melanins and techniques used to study fossil sediments to compare the fossil inks from three deposits of similar age and lithology, but different maturation histories. Specifically, two ~ 180 Mya fossil ink sacs from a site that has entered the oil window in Holzmaden, Germany were compared to the previously analyzed fossil inks from two less mature sites in southern England. The chemistry of eumelanin was shown to alter at the onset of the oil window regardless of the age of the specimen. The decrease in surviving melanin was accompanied by an increase in the relative abundance of organic macromolecular material (kerogen), but no consistent change in melanin morphology. </p><p> Finally, the role of melanin as a matrix that enhances the preservation of other biomolecules in the fossil record was considered. Proteins, commonly associated with melanin in modern organisms, were discovered in the aforementioned fossil ink sacs during full-scale chemical analysis. The amino acid profile of the protein in each fossil specimen was determined with an amino acid analyzer and compared to the amino acid profile the protein in modern S. officinalis. Statistical analysis of the amino acid distributions indicated that there is no significant difference between the amino acid profile of modern and fossil melanins. In order to verify the ancient origin of the amino acids in the fossil ink sacs, the ratio of D/L amino acid isomers was determined. While the proteins of living organisms consist of only L-amino acids, post-mortem the amino acids slowly convert from L to D form until they reach equilibrium (D/L = 1). This process is called racemization. The amino acids in the fossil ink sacs were racemized, which suggests their ancient origin. This marks the oldest determination of protein in a fossil system and provides evidence that the longevity of proteins may be enhanced when associated with melanin.</p> / Dissertation

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

No description available.

Small carnivores and middle-sized mammals (mesomammals) are ubiquitous in fossil sites in South Africa, but their taphonomy is poorly understood. This study presents an actualistic investigation of bone modification by two captive small carnivores; the caracal (Caracal caracal) and honey badger (Mellivora capensis), housed at the Johannesburg Zoo. The carnivores were fed domestic rabbit (Oryctolagus cuniculus) carcasses as proxies for mesomammals and the bone modification of the resulting refuse and scatological assemblages were assessed in terms of their skeletal part representation, breakage patterns, digestive modifications and tooth marks. The investigation revealed that skeletal part representation and breakage patterns in the caracal and honey badger assemblages resembled those reported from other small carnivores. The caracal and honey badger assemblages were distinct from other carnivores in having overall light digestive modifications and a high frequency of tooth marks. Digestion was greater and tooth marks less frequent in the caracal than in the honey badger. Results were applied to the fossil assemblage of Cooper’s D which has a large assemblage of mesomammals and small carnivores. While a taphonomic analysis of Cooper’s D has not been published, initial results suggest that small carnivores had a great potential as contributors in the formation of the assemblage. The findings of this study emphasise the need for employing a variety of bone modifications in the identification of a small carnivore as an accumulator since there is rarely a single characteristic that is diagnostic for a particular carnivore.

Thesis (M.S.)--Ohio University, August, 2009. / Title from PDF t.p. Includes bibliographical references.

This thesis uses metrical data and morphological observations to describe the comparative anatomy of the cranial base region in extant adult hominoids. The changes that occur during growth in this region have also been studied in samples of juvenile hominoids, and cross-sectional growth data for the same variables measured in the adult metrical study have been recorded. Detailed metrical and morphological observations were also made on a series of fossil hominid crania dating from the Plio- Pleistocene. The results of the two comparative studies of the cranial base region in extant hominoids were then used to assess the significance of the differences noted in the cranial base region of the fossil hominids from sites in South and East Africa. The results of the adult metrical study; and the series of soft tissue dissections, demonstrate that there are fundamental differences in the comparative anatomy of the modern human and pongid cranial bases. The results of the comparative growth study indicate that these differences are probably not the result of an overall acceleration, or retardation, in growth rates of the component bones of the human cranial base, but more likely due to a combination of increases and decreases in growth rates occurring in individual bones, as well as to differences in morphology already manifest soon after birth. The results of the study of fossil hominid specimens indicate that the 'gracile' australopithecine fossils from South Africa have a cranial base pattern similar to that of the extant pongid samples, but that the 'robust' australopithecine fossils, and those fossils attributed to early Homo have a cranial base pattern more similar hominid fossil specimens which are still of uncertain taxonomic designation. The comparative studies of the hominoid cranial base also provide a framework which enables features of this region to be used in phylogenetic analysis. to the modern Homo sapiens sample. These differences in basicranial anatomy among the fossil hominid sample provide a useful tool to assess the taxonomic status of several

In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

Final Project (M.A.)--John F. Kennedy University, 2007. / "5 January 2007"--T.p. Includes bibliographical references (p. 114-125).

Made available in DSpace on 2014-06-11T19:32:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-11-07Bitstream added on 2014-06-13T19:21:58Z : No. of bitstreams: 1 oliveira_cem_dr_rcla.pdf: 4708204 bytes, checksum: 54fa2a96be083a391a6b092441f44f30 (MD5) / A Formação Adamantina do Grupo Bauru, Cretáceo Superior, é muito rica em fósseis de vertebrados. Dentre estes fósseis, destacam-se os restos de crocodilomorfos, em especial os do gênero Baurusuchus. Neste trabalho, é relatado pela primeira vez um grande conjunto de associações de ovos e cascas de ovos de crocodilomorfos fósseis restrito em uma área relativamente pequena nesta unidade litológica na região de Jales – SP. Este conjunto de associações revela informações inéditas sobre a provável biologia reprodutiva de Baurusuchus sp que não puderam ser obtidas, até então, através da análise de materiais osteológicos. A análise da morfologia e da histoestrutura dos ovos revelou que a espessura da casca, as unidades básicas e o padrão e formato dos poros são diferentes de todos os outros ovos de crocodilomorfos fósseis já descritos na literatura. O estudo das associações de ovos sugere que: estas não foram construídas em nível de lençol freático e não sofreram transporte; que alguns ovos eclodiram; o gênero Baurusuchus provavelmente nidificava em grupo, construía ninhos principais e secundários e retornava ao mesmo local de nidificação periodicamente. / The Adamantina Formation of the Bauru Group, Upper Cretaceous, is very rich in fossils of vertebrates. Amongst these fossils, remains of crocodilomorphs are highlighted, in special of the genus Baurusuchus. In this work, it is reported for the first time, a great set of egg clutches and eggshells of fossils crocodylomorphs, restricted to a relatively small area in this lithologic unit, in the region of Jales – SP. This set of clutches discloses new information on the probably reproductive biology of Baurusuchus sp which could not have been obtained, until now, through the analysis of osteological materials. The analysis of the morphology and the histostructure of eggs unearthed that the basic thickness of the eggshells, basic units and the pattern and shape of the pores are different of all other fossil crocodylomorph eggs previously described in the literature. The study of egg clutches suggest that: these clusters were not constructed above the water table and did not suffer transport; some eggs hatched; the Baurusuchus genus probably nested in group, constructed main and secondary nests and returned to the same nesting site periodically.

The latest-Permian mass extinction was the greatest biotic crisis of the Phanerozoic. The extinction decimated both marine and terrestrial communities, and changed the evolutionary trajectory of multicellular life on the planet. The unique nature of the extinction’s aftermath has prompted attention from paleontologists seeking to understand the timing and pattern of the Triassic recovery. With this dissertation I have sought to shed additional light on the terrestrial side of the extinction by examining different patterns by which its survivors responded to the extinction. Temnospondyl amphibians were one of the few tetrapod clades that were able to take advantage of the extinction to expand their diversity. In Chapter 1 I examine the relationship between taxonomic and ecological diversity of temnospondyls across the Permian-Triassic (P-Tr) boundary in the Karoo Basin of South Africa. Ecomorphological diversity, as implied by differences in cranial shape, was incorporated into the study by the use of a landmark-based geometric morphometric analysis. Both taxonomic diversity and cranial disparity were low during the Permian and increased across the Permian-Triassic boundary. Taxonomic diversity was stable through the Triassic, but disparity showed subsequent increases during the Olenekian and Anisian. Temnospondyls were restricted in size immediately following the extinction, but size range fully rebounded by the Olenekian. Tests of phylogenetic signal demonstrate that cranial shape was heavily influenced by phylogenetic relatedness, and the observed increases in disparity may be partly the result of decreases in the net relatedness of coeval Karoo stereospondylomorph temnospondyls in younger faunas. The increase in community-level taxonomic diversity for temnospondyls in the Karoo following the latest-Permian mass extinction was likely facilitated by an influx of distantly related and ecologically distinct species from other parts of Pangea. In Chapter 2, I discuss the merits of different potential methods for quantifying rates of dispersal within clades. I then apply some of these methods to two very different scenarios, first the dispersal of crocodylians across oceanic barriers during the Late Cretaceous and Cenozoic, and second the dispersal of different groups of tetrapods across Pangea during the Permo-Triassic interval. For crocodylians, because they were dispersing across substantial geographic obstacles, I opted for a direct measurement approach utilizing the optimization of discrete dispersals onto phylogenies. I examined the history of crocodylian biogeography using both parsimony and maximum likelihood on three distinct topologies with several different methods for estimating branch lengths. Across all analyses, members of the clade Alligatoroidea consistently dispersed across oceanic barriers less frequently than did non-alligatoroids. This is consistent with the hypothesis that the greater degree of salt tolerance observed in extant crocodyloids and gavialoids played a role in shaping crocodylian biogeography. The phylogenetic and temporal distribution of high dispersal rates points to an acquisition of greater salt tolerance early in the history of Crocodyloidea and Gavialoidea, potentially near the base of Longirostres if the combined evidence topology is correct. Patterns observed for changes in dispersal rate within individual clades can be largely attributed to changes in global climate and continental configuration over their history. The greater geographic ambiguity represented by the Permo-Triassic continental configuration makes a direct measurement approach inappropriate. For this study I instead opted for a proxy measurement approach, using the phylogenetic clustering of taxa within a community, measured using the Net Relatedness Index. I examined temporal changes in the phylogenetic clustering of five major tetrapod clades that span the Permian-Triassic boundary (Stereospondylomorpha, Parareptilia, Neodiapsida, Anomodontia, and Eutheriodontia) in order to examine patterns of extinction and origination through time, as well as rates of geographic dispersal. Some clades (Stereospondylomorpha, Parareptilia, and Neodiapsida) show evidence of phylogenetically selective extinction across the boundary, but this is not a universal pattern. Only one clade, Stereospondylomorpha, shows an unambiguous increase in dispersal rate following the mass extinction event. Other clades either show no change in dispersal rate, or have results that are mixed, depending on the parameters used in the analysis. These results show that stereospondylomorph temnospondyls were dispersing between geographical regions at increased rates during the Early Triassic, and this may explain much of their apparent increase in diversity following the latest-Permian mass extinction. In Chapter 3, I perform a comparison between the timing of the Triassic recovery with that following the Cretaceous-Paleogene (K-Pg) mass extinction. Three terrestrial fossil-bearing successions were examined, the Lower Triassic Beaufort Group in South Africa and Cis-Ural succession in Russia, and the Paleocene faunas of the American northern Great Plains. A comparison of generic diversity of tetrapods through time for the post-extinction intervals reveals a temporal disparity between the length of terrestrial recovery after the latest-Permian and K-Pg extinctions. Both Permo-Triassic successions show a period of low taxonomic richness (4-5Myr) after the extinction event, followed by an eventual rise in richness. The North American K-Pg succession shows a different pattern, with an immediate rise in richness culminating in a plateau shortly after the extinction (1-3 Myr). This disparity in recovery times may result from prolonged deleterious environmental conditions following the P-Tr events, although several important differences exist between these sequential fossil assemblages that may be affecting the apparent speed of recovery.