Thesis (Ph. D.)--University of California, San Diego, 2007. / Title from first page of PDF file (viewed November 7, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.

Thesis (Ph. D.)--State University of New York at Binghamton, Department of Anthropology, 2006. / Includes bibliographical references (leaves 263-281).

Thesis (M.S.) -- Mississippi State University. Department of Sociology, Anthropology, and Social Work. / Title from title screen. Includes bibliographical references.

Thesis (Dr. Sc. Nat.)--Universität Zürich, 2003. / Includes bibliographical references (leaves 186-209). Also available online (PDF file) by a subscription to the set or by purchasing the individual file.

Thesis (Dr. Sc. Nat.)--Universität Zürich, 2003. / Includes bibliographical references (leaves 186-209).

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment of the requirements for the degree of Doctor of Philosophy / This thesis is a study of quantifiable variation in the geometric shape of the superior articular surface of the talus of higher primates, with special reference to fossil tali of Plio- Pleistocene hominids. (Abbreviation abstract ) / AC2017

Enhancer RNAs (eRNAs) are a family of long noncoding RNAs (lncRNAs) transcribed from enhancer sites by RNA polymerase II (RNAPII) as part of the process of enhancer activation. Normally, eRNAs are typically processed by the Integrator complex and incorporated into the enhancer looping machinery formed by the Mediator and Cohesin complexes. However, some eRNAs escape this processing step and are instead transcribed to produce longer, polyadenylated RNAs. Poly(A)+ eRNAs are usually targeted for exosomal degradation by the Mtr4-containing PAXT complex, but under some conditions can be exported to the cytoplasm. I n this latter option, as shown in Chapter 2 of this thesis, eRNAs that contain ORFs, of which there are a surprising number, are capable of being translated to produce functional proteins. eRNAs can gain ORFs through the process of de-novo gene birth, resulting in novel genes at sites capable of fulfilling the roles of both canonical coding genes and enhancers.This dissertation is divided into three main sections, and an additional fourth section outlining future research directions. In the first section, I review the current research on eRNAs and other lncRNAs including their origins, processing, and functions. I also review current research on proteins encoded by canonically noncoding RNAs, and the process and implications of de-novo gene birth as it relates to the aforementioned topics. In the second section, we aimed to identify translating eRNAs in the human genome using ribosome profiling compared to a database of transcribed enhancers. Using these results, we selected ten large eRNA ORFs to investigate the functions of the proteins they encode, including their subcellular localization and protein interactomes. Finally, we investigated the homologs of these eRNA ORF sequences in other species to determine their level of evolutionary conservation compared to that observed in canonical protein-coding genes. Our findings in the second section provide evidence for novel, highly-basic, arginine-rich proteins encoded by eRNAs and capable of interacting with DNA and RNA, either directly or through interactions with other associated proteins. We also present evidence that the ORFs encoding these proteins appeared relatively recently in human evolution, with most being primate-specific and exhibiting mutation rates associated with purifying selection of coding sequences across their homologs in great apes. In the third section, we present additional results from analysis of published proteomics and RNA-seq results that provide evidence for expression of ORF-containing eRNAs in differentiating stem cells. These results were also confirmed using qRT-PCR of whole-cell RNA samples isolated from these differentiating cells. These results show expression of several eRNAs identified in the second section during the early stages of human embryonic stem cell differentiation into the three germ layers and subsequent mature cell types. These results are also supported by a decrease in Mtr4 protein levels also detected in proteomics results from the same differentiations. These results indicate that expression of ORF-containing eRNAs and the Mtr4-depleted conditions leading to it are present in stem cells during differentiation, and stem cell differentiation is a promising subject of future research on the roles of eRNA-encoded proteins in normal cellular function.

M.Phil. (Anthropology) / The primary aim of this study was to undertake the description and analysis of the manual and pedal hominin phalanges from Drimolen, South Africa. The specimens were contextualized by examining their counterparts in a series of extant and extinct specimens. As Drimolen preserves the remains of both Paranthropus robustus and early Homo, it provides an opportunity to contribute to our understanding of morphological variation and differences between these taxa, as well as providing an important first step in conceptualizing their evolutionary history and palaeobiology. The first section focused on the manual and pedal phalanges, while the second focused exclusively on the first metatarsal. Numerous studies have analyzed Plio-Pleistocene manual and pedal phalanges to evaluate tool-related behaviours and locomotion in early hominins. In this dissertation nine phalanges were described and analyzed for the first time. The manual specimens consist of one proximal (DNH 9), two proximal pollical (DNH 116 and DNH 119), four intermediates (DNH 48, DNH 63, DNH 65 and DNH 66) and one distal pollical phalanx (DNH 13). There is currently only one pedal proximal phalanx (DNH 117). As at Swartkrans, assignment of postcranial elements was hampered by the fact that two hominin species have been found at the site, namely Paranthropus robustus and early Homo. To analyze the specimens, multivariate statistics (PCA and CVA) were conducted on the specimens using raw and size-adjusted data. This was done within the context of a large extinct and extant dataset to compare size and shape data. In general, PCA and CVA yielded similar results but only the raw data was useful in discriminating between taxa. There was poor discrimination in the analyses based upon size-adjusted data because of the huge degree of overlap between fossil and extant taxa. Consequently, results were not diagnostic and it wasn’t possible to assign specimens confidently to either Paranthropus or Homo. This was exacerbated by the isolated nature of the remains, the presence of two hominin taxa and taxonomic uncertainties of several Swartkrans phalanges. Despite these difficulties, these specimens do provide insight into the degree of morphological variation present in the phalanges from the Plio-Pleistocene of South Africa. The second section described the fragmentary first metatarsal and quantified it by using laser scanning and calculating the curvature of the proximal articular surface. Univariate statistics were then calculated in order to examine the degree of curvature between each of the extant taxa and whether these differences were statistically significant. Finally, a simple bivariate plot was generated using the curvature results which showed that this joint surface was most curved in chimpanzees and western gorillas, moderately curved in eastern gorillas, and flattened in modern humans and baboons. Highly curved joint surfaces in this region suggest a more mobile hallux, whereas flattened surfaces suggest reduced joint mobility. The fossil specimens SK 1813, STW 573, STW 595 and OH-8 all grouped closely with modern humans; A.L. 333-54 and SKX 5017 grouped with chimpanzees, while DNH 115 grouped with eastern gorillas. Overall, these results indicate that SKX 5017 was the most curved of the South African specimens and is attributed to Paranthropus (Susman, 1988). It grouped closely with DNH 115 which suggested that climbing activities may have continued to play an important role in the behavioral repertoire of these individuals during the Plio-Pleistocene.

Swartkrans Cave, famous for abundant hominin fossils of P. robustus and the site where the first evidence of the co-existence of two hominin species was recovered, has yielded a wealth of information on early hominin behaviour. In 2005 a new program of research and excavation began at the site, and its results form the central part of this thesis. This study has focused on the early Pleistocene Member 1 deposits which include an Earlier Stone Age industry and the late Pleistocene Member 4 Middle Stone Age deposits. The thesis has four areas of focus. First the new work has resulted in clarification and new interpretations for the formation of the hominin rich Hanging Remnant deposit of Member 1, which lacks stone tools. This extensive calcified conglomerate which spans most of the north wall of the cave is now seen as a non-homogenous unit that represents material entering from at least four avens. However, this study also established that the newly exposed central portion of the Hanging Remnant and the hominin fossil-rich northwest corner infill worked by Robert Broom in the 1940s derived from the same depositional episode. Secondly, the new excavations in the Lower Bank of Member 1 have resulted in an enlargement of the previously ambiguous Earlier Stone Age assemblage. Analysis of this new assemblage, in conjunction with recently released dating results, has now confirmed that the artefacts belong to the Oldowan Industrial Complex. Thirdly, new excavations in the Member 4 deposit have resulted in the recovery of over 3,200 Middle Stone Age (MSA) stone tools and a clearer understanding of their context. The stone tool-bearing deposits of Member 4 are now understood to derive from a surface colluvium, rather than a cave infill. This MSA assemblage consists of a high number of retouched pieces that are dominated by steep-sided scrapers and denticulated scrapers with a near-absence of points. The technology of a variety of core types suggests a superior understanding of raw material flaking qualities by the tool makers. The limited types of formal tools suggest that the site was used for one or more specific activities, rather than for a range of activities by the tool makers. Fourthly, excavation of the deposits underlying the Member 4 colluvium has resulted in the discovery of two previously unknown hominin-bearing deposits. It is now established that what was originally called Member 4 is composed of three distinct deposits. The lowest of these is an east extension of the Member 1 Lower Bank (LB East Extension), which has yielded P. robustus fossils. This is overlain by a large talus cone (TCD), which also has yielded P. robustus fossils. The latter is capped by flowstone dated to ~110,000 years, followed by the MSA-tool bearing colluvium.

M.Sc. (Geology) / The Cradle of Humankind is a 47 000 hectare demarcated area with over three dozen fossil-bearing cave sites well known for the preservation of fossil evidence of early hominin taxa such as Australopithecus Africanus, Australopithecus Sediba, Paranthropus Robustus and Early Homo. As a result, a database of precise and accurate chronological data for fossil-bearing cave deposits of the Cradle of Humankind (similar to that for East African fossil sites) is very important, but developing one has proven extremely challenging. The main challenge is that the fossil-bearing deposits at the cradle are mainly complex breccias with a chaotic, localized stratigraphy and no association to any volcanic ash beds, unlike the East African deposits which are lacustrine and fluviatile deposits interbedded with volcanic ash layers. However, substantial success has been obtained recently through the combination of U-Pb dating of CaCO₃ speleothems and palaeomagnetic dating (magnetostratigraphy) after many attempts and unconvincing results from techniques such as biostratigraphic correlations, electron spin resonance on teeth and cosmogenic burial dating of the sediments. The problem with U-Pb dating of CaCO₃ speleothems is that this requires samples that are extremely clean (i.e. detrital-free) and have an appreciable U content (close to 1 ppm), and such material is at many sites not available...