Sexual dimorphism in white South African crania

Original published work submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2016Sexual dimorphism is one of four critical factors assessed by forensic anthropologists when compiling biological profiles. The current study used geometric morphometric methods to analyse various aspects of sexual dimorphism in white South African crania to significantly contribute to current forensic standards for this underrepresented population. As edentulous crania are a major contributing factor to the low number of publications on white South African populations, the question arose as to how tooth loss affects cranial structures and the accuracy of sex and ancestry estimation. Two hundred and twenty nine crania were digitised using landmarks and sliding semilandmarks, both globally and for a number of cranial subsets. Although a number of effects were identified when the skull was analysed globally, only the maxillary alveolar ridges were significantly affected when subsets were analysed individually. As both upper facial height and palate shape were significantly altered by tooth loss, the effects of tooth loss on cranial structures and sex and ancestry estimations were investigated. Next, to parse out the mechanisms by which sexual dimorphism causes morphological variation, overall sexual dimorphism, common allometry and nonallometric sexual dimorphism were individually assessed. Global and subset data were studied and the effects of sexual dimorphism and allometry were found to be universal, with significant differences being observed between the sexes both globally and regionally. A significant non-allometric component was, however, only found to contribute to the shape of the zygomatic bone. Finally, the accuracy of 17 widely used traditional cranial measurements was compared to all possible interlandmark distances (ILDs) attainable from 45 fixed landmarks. Discriminant functions derived using the ILDs compared well to those of previous work on white South Africans, thus demonstrating the similarity between traditional and 3-D methods. Finally, custom discriminant functions were created for a number of cranial subsets and for the cranium in its entirety. The subsets achieved sexing accuracies ranging between 71.8% and 83.7%, with the nasomaxilla proving most accurate. The overall cranial function attained a cross-validated sexing accuracy of 88.2%. These functions are critical for sex estimation not only for intact crania, but also for the innumerable fragmentary cranial remains recovered regularly in South Africa.MT201

Virtual Morphology and Evolutionary Morphometrics in the new millenium.

EDITED VOLUME; abstract N/

Drivers of cetacean diversity: Evidence from the past and present

In just 8-12 million years, cetaceans (whales, dolphins, and porpoises) underwent profound changes in adaptive zone. Their evolution from land-dwellers to aquatic inhabitants is an exemplar of macroevolutionary change. However, there has been little study of evolutionary dynamics that span their entire 50-million-year history. Using 3D geometric morphometrics and a rich dataset of 201 living and fossil species spanning Cetacea’s evolutionary history, I quantify cranial morphology and investigate shifts in evolutionary rates and disparity. I find three key waves of diversification throughout cetacean evolution. The first is in archaeocete (early whales) evolution as cetaceans evolved rapidly to fill a largely vacant aquatic niche. The second, in the mysticetes (baleen whales) and odontocetes (toothed whales) which diverged ~39-36 Mya and followed unique evolutionary pathways, facilitated by key innovations: echolocation in odontocetes and filter-feeding in mysticetes. The third wave, in the Miocene, is mostly an odontocete signal (~18-10 Mya). Further, I find asymmetry related to echolocation in odontocetes is driven by the pressures of acoustically complex environments, and that multiple ecological factors influence skull shape. I find climate fluctuations drive cranial evolution through deep-time. Importantly, ocean productivity drives evolutionary rates in mysticetes, whereas in odontocetes, these are driven by rates of temperature change. Finally, I switch from morphological to taxonomic diversity and investigate environmental and anthropogenic impacts on diversity in shallow-time, reinforcing the importance of long-term strandings data to monitor impacts. My results highlight the idiosyncrasies of species responses to environmental and anthropogenic impacts. Differences in diversity between suborders reflects their different early innovations and resultant ‘ecospace’ occupation. Importantly, this work highlights the differences in drivers behind mysticete and odontocete evolutionary rates, particularly with regards to climate change. The different historical responses of extant suborders highlight a requirement for separate, tailored conservation and mitigation of climate impacts for toothed and baleen whales

Causal Inference from Statistical Data

The so-called kernel-based tests of independence are developed for automatic causal discovery between random variables from purely observational statistical data, i.e., without intervention. Beyond the independence relations, the complexity of conditional distriubtions is used as an additional inference principle of determining the causal ordering between variables. Experiments with simulated and real-world data show that the proposed methods surpass the state-of-the-art approaches

Registration of non-rigidly deforming objects

This thesis investigates the current state-of-the-art in registration of non-rigidly deforming shapes. In particular, the problem of non-isometry is considered. First, a method to address locally anisotropic deformation is proposed. The subsequent evaluation of this method highlights a lack of resources for evaluating such methods. Three novel registration/shape correspondence benchmark datasets are developed for assessing different aspects of non-rigid deformation. Deficiencies in current evaluative measures are identified, leading to the development of a new performance measure that effectively communicates the density and distribution of correspondences. Finally, the problem of transferring skull orbit labels between scans is examined on a database of unlabelled skulls. A novel pipeline that mitigates errors caused by coarse representations is proposed

Craniofacial integration, plasticity and biomechanics in the mouse masticatory system

The craniomandibular skeleton is a complex, dynamic structure, housing many vital tissues and required to perform critical functions. This region is however subject to substantial morphological change during development, and required to adapt to its environment and individual variance. The capacity of this region to maintain correlated form and appropriate functional performance despite these challenges is not fully understood. The sample consists of three strains of mice; a wild-type strain and two mutant strains from the same genetic background strain. Both mutations selectively affect chondrocranial growth, and thus influence of both are limited to the crania. The brachymorph mutant phenotype is characterised by a shortened cranium, while the pten is elongated. This sample therefore allows exploration of a potential plastic response in terms of the mandible, the masticatory lever system, and in turn mechanical advantage, when cranial length and the out-lever are varied. Three dimensional landmarks were applied to micro-CT scans and partial-least-squares analysis carried out to determine covariance between crania and mandibles. Mechanical advantage was calculated as a ratio of muscle in-lever and jaw out-lever for three key masticatory muscles. A common pattern of both variance and covariance was found among all three strains, with mandibular morphology in each strain covarying with cranial phenotypes. Jaw out-lever lengths were found to be significantly different in all three strains, and yet little significant difference between strains was found in mechanical advantage for any muscles. This maintenance of mechanical advantage is attributed to plastic adaptation in regions influencing muscle in-lever length, the latter which were found to be significantly different in the three strains. These results show the potential of the craniomandibular complex to plastically adapt to maintain both correlated form and functionality when variation occurs in one region, and thus these results have significant implications for the evolvability of the complex

Age Estimation with Decision Trees: Testing the Relevance of 94 Aging Indicators on the William M. Bass Donated Collection

Anthropologists have been estimating ages-at-death of skeletons for a long time. A variety of different age indicators has been studied and age estimation methods have been developed in an attempt to standardize the process. Even with all the work that has gone into developing age estimation methods, age estimation of mature skeletons is still very imprecise. This research investigates various age indicator definitions and their performance on an elderly skeletal sample. Using 176 individuals from the William M. Bass Donated Collection curated in the Department of Anthropology at the University of Tennessee, Knoxville, data were collected on age indicators gathered from fifteen age estimation methods. Ninety-four variables were tested with various decision trees to show patterns among the variables. Regression equations were built using the same variables as the decision trees, and the performance between the two methodologies were compared. The decision trees performed slightly better, with a mean absolute error of prediction of around five years. Variable occurrence was tabulated across various decision tree models. The most common variables are pit shape of the sternal rib end morphology and the phase of the auricular phase. These two variables, along with others commonly selected, present best candidates for building an age estimation method that pertains to older populations

Understanding the brain through its spatial structure

The spatial location of cells in neural tissue can be easily extracted from many imaging modalities, but the information contained in spatial relationships between cells is seldom utilized. This is because of a lack of recognition of the importance of spatial relationships to some aspects of brain function, and the reflection in spatial statistics of other types of information. The mathematical tools necessary to describe spatial relationships are also unknown to many neuroscientists, and biologists in general. We analyze two cases, and show that spatial relationships can be used to understand the role of a particular type of cell, the astrocyte, in Alzheimer's disease, and that the geometry of axons in the brain's white matter sheds light on the process of establishing connectivity between areas of the brain. Astrocytes provide nutrients for neuronal metabolism, and regulate the chemical environment of the brain, activities that require manipulation of spatial distributions (of neurotransmitters, for example). We first show, through the use of a correlation function, that inter-astrocyte forces determine the size of independent regulatory domains in the cortex. By examining the spatial distribution of astrocytes in a mouse model of Alzheimer's Disease, we determine that astrocytes are not actively transported to fight the disease, as was previously thought. The paths axons take through the white matter determine which parts of the brain are connected, and how quickly signals are transmitted. The rules that determine these paths (i.e. shortest distance) are currently unknown. By measurement of axon orientation distributions using three-point correlation functions and the statistics of axon turning and branching, we reveal that axons are restricted to growth in three directions, like a taxicab traversing city blocks, albeit in three-dimensions. We show how geometric restrictions at the small scale are related to large-scale trajectories. Finally we discuss the implications of this finding for experimental and theoretical connectomics