<p>[Missing page v]</p> / <p>This thesis reports an attempt to extract DNA from the skeletal remains of five young children who died approximately 1,900 years ago and who were recovered from an Italian archaeological site, Isola Sacra. These skeletons have been tentatively diagnosed as thalassemics based on morphological observations, but alternative diagnoses are also possible. DNA diagnosis was used to attempt to identify thalassemia mutations from the human globin genes extracted from these skeletons.</p> <p>Successful extraction of the human globin genes is largely dependent on two factors: retrieving sufficient amounts of ancient DNA without PCR (Polymerase Chain Reaction) inhibitors, and no contamination from modern DNA. To improve the chances of success, a more efficient and rapid method of extracting DNA from ancient skeletons was developed using a silica-based spin column technique to maximize the yield of amplifiable DNA from ancient skeletons and minimize the risk of the contamination with modern DNA. In a single step, the DNA is concentrated and separated from non-DNA substances that could inhibit PCR. This sufficiently removed PCR inhibitors but without an increased risk of contamination. A comparison test proved that this new approach is superior to current commonly used methods.</p> <p>Upon application of the new method, the evidence suggests that ancient human p-globin genes were extracted from three of the five individuals from Isola Sacra. DNA diagnosis for two of the most common Italian thalassemia mutations, IVS 1-11 a and codon 39 (more than 50% of current Italian thalassemia mutations),revealed that these three individuals did not have these two mutations. However, the present results cannot totally exclude the possibility of thalassemia from these specimens since five other untested mutations might occur in these specimens.</p> <p>Precautions were taken to minimize the risk of contamination. Contamination was also monitored by mtDNA analysis of each individual. No systemic contamination took place in this study but a sporadic contamination was identified with one specimen. The further analysis clearly indicated that the contamination came from the author.</p> <p>This thesis has shown that DNA diagnosis of diseases from ancient remains can be a new, powerful approach to the study of health and disease in past human populations. Technical improvements and revised research strategies are expected to advance DNA diagnoses of ancient diseases.</p> / Doctor of Philosophy (PhD)

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ReFace (Reality Enhancement Facial Approximation by Computational Estimation) is a prototype facial approximation software program developed by the Federal Bureau of Investigation (FBI) in conjunction with GE Global Research. The prototype extrapolates an “approximation” of a face from a skull using a database of computed tomography (CT) scans of living individuals. The test set consisted of CT scans of 53 articulated human skulls from the William M. Bass Donated Skeletal Collection and the William M. Bass Forensic Skeletal Collection, which are curated at the University of Tennessee in Knoxville. Through the Federal Bureau of Investigation’s Visiting Scientist Program, an educational opportunity administered by the Oak Ridge Institute of Science and Education (ORISE), the researcher conducted an independent validation of this software in two phases. Phase 1 tested and evaluated the software performance, resulting in improvements to the software and the development of standardized protocol for articulation, packaging, and preparation of human skulls for CT scans. Phase 2 validated the accuracy of the software in the production of facial approximations from human skulls using face pools and resemblance ratings. In Phase 2, computerized facial approximations were visually compared with antemortem photographs by four participant groups (N = 103). Ten test subjects of European ancestry (six females and four males) were selected for a photographic validation by face pool and resemblance rating validation tests. Participants were asked to choose the face pool photograph that most closely resembled the facial approximation produced by ReFace. In the second test, the same volunteers were asked to rate (on a scale of 1 to 5) how closely ReFace facial approximations of target subjects resembled an antemortem photograph. In the Face Pool Validation Test, nine out of ten target subjects were correctly identified above random chance, and the frequency distribution was statistically above chance expectations for nine out of ten target subjects (p < .01). The mean hit rate for all subjects was 24% (10% above random chance). There were no significant differences in the hit rates between male participants (67%) and females participants (33%), or between participant groups. All participants were non-experts. Male target subjects received higher numbers of correct responses than female target subjects. The overall ratings for the Resemblance Rating Validation Test were 13% none, 24% slight, 22% approximate, 25% close, and 16% strong. The majority of subjects were rated as close resemblance (six subjects), strong resemblance (one subject), approximate resemblance (one subject), and slight resemblance (one subject). The foil comparison received an equal number of ratings for no resemblance (30.5%) and slight resemblance (30.5%).

Determining sex from skeletal remains is important in forensic and archaeological settings. Though using the pelvis to determine sex is ideal, often remains are fragmentary or incomplete, requiring sex to be estimated from other skeletal elements. Many individual bones have been studied to evaluate sexual dimorphism and the extent to which they can be used to determine sex of an unknown individual. However, sexual dimorphism in the vertebral column has only been examined to a limited extent. The purpose of this study is to examine the extent of sexual dimorphism throughout the entire vertebral column and, if present, to establish a method by which sex can be determined from any given vertebra, even if the exact vertebral number is not known. A total of 16 different measurements were taken on the vertebrae from a sample of 119 individuals from the William M. Bass Skeletal Collection. Given the small representation of African American individuals in the collection, only individuals of European descent were considered in this study. Since possible effects of aging were to be considered, equal numbers of males and females were randomly selected and matched for age groups. First MANOVA analyses were performed on each vertebrae and vertebral grouping, i.e. cervical C3-C7, thoracic, lumbar, and vertebral column C3-L5, to determine if each was significant for sex for each measurement taken. A stepwise analysis and then discriminant function analysis was performed to select the most sexually dimorphic measurements for each vertebra or vertebral grouping and equations were developed to allow sex to be determined from an unknown individual for each vertebra, or if the vertebral number is not known, from the vertebral grouping.

Food choices can create and maintain group membership, also distinguishing groups based on dietary preferences and the perceived social value of foods. The food behaviors of social elites within complex societies are often governed by differential access and cultural factors determining the menu within a regional ecology. This study employs bioarchaeological and stable isotopic analyses to investigate the evidence for dietary variation of social elites within the Late Horizon (A.D. 1470–1532) cemetery of Huaca Las Abejas at Túcume using stable nitrogen and carbon isotopes. Paired teeth (early life diet) and bones (later life diet) were sampled from 23 individuals to examine consistency in food behaviors related to age, biological sex, and change over the life course. In total, 25 bone collagen, 33 bone apatite, 32 dentin collagen, and 30 enamel apatite samples were analyzed (n=120). Results suggest a mixed diet containing a high proportion of C4 resources and a dietary protein source elevated in δ13C. This research revealed statistically significant differences between bone and tooth δ15N and δ13Csc, adult and juvenile dentin δ15N and δ13Ccol, male and female bone δ15N, δ13Ccol, and dentin δ13Ccol. Paired tissues displayed statistically significant differences between δ15N and δ13Csc. The results of this multi-isotope and multi-tissue study indicate individual dietary patterns shifted through life and gendered dietary variation existed at Túcume during the Late Horizon. These results enhance the limited published isotopic literature on Andean Late Horizon north coast dietary variation, offering new insight into the food behaviors of social elites living under Inca administration.

Bioarchaeological analysis can help identify patterns of mortuary ritual and social experience of ancient Maya peoples. However, there is limited bioarchaeological and mortuary evidence for the relationship between the development of social complexity and social experience. Particularly, how is social organization reflected in patterns of burial practice and skeletal markers of stress. This thesis uses osteobiographies to contextualize the mortuary and biological profiles of 20 individuals interred at the Maya site of Holtun, Guatemala to examine bioarchaeological variation during the Preclassic (800 B.C. – 250 A.D.) and Late Classic (550 A.D. – 900 A.D.) periods. This work highlights the integration of comparative osteobiographic analyses from small samples into the exploration of individual identities and social experiences. By incorporating architectural contexts, mortuary evidence, and osteology, the individual becomes the focus of study. When each individual is examined for mortuary features, sex, age, and evidence of stress, these lives in focus become salient portraits of ancient humans as complex social beings with intertwined identities at Holtun, essentially deploying a bioarchaeology of personhood. Results of this thesis identified common trends of the mortuary program and biological health status of individuals throughout the chronology of Holtun. Individuals were most commonly interred in simple graves or cists in an extended supine position with head oriented to the north. Additionally, very few indicators of childhood stress or systemic pathology were identified, though females at Holtun seemed to disproportionately suffer from carious lesions compared to males. In addition to these trends, evidence for intentional body modification, individual mortuary assemblages, and daily activity stress markers all indicate variation in the social identities of these individuals. Overall, this study affirms the strength that a small sample can have in contributing to the exploration of social organization and identity reflected through a contextualized osteobiographic approach. These results enhance our understanding of increasing mortuary and biological variation during the Preclassic and Late Classic period southern Maya lowlands, and offer new insight into the complex development of social organization and individual social experience at Holtun, Guatemala.

Alzheimer's disease is a prevalent disease that affects roughly 5.4 million individuals each year (Fisher et al., 2018). Understanding the prevalence of Alzheimer's disease within the bioarchaeological record can help anthropologists gain an understanding of a population's health while also understanding the potential social ramifications. Trace element analysis is a valuable tool that allows bioarchaeologists to gain insight into individuals' health and development within the context of the past. In bioarchaeological studies, hair analysis has been used to map the nutritional status and migration patterns of individuals of past peoples, with recent studies focusing on disease prevalence. Analysis of hair as a biosource of information for trace element analysis is highly useful for various reasons such as its ability to withstand taphonomic processes, the high concentration of elements within its structure, and the expanded time frame of an individual's life it represents. This study uses ICP-MS to conduct the trace element analysis of copper (Cu), zinc (Zn), manganese (Mn), iron (Fe), selenium (Se), and aluminum (Al) to create a profile of hair from 13 bioarchaeological individuals from Romano-Christian Kellis 2 cemetery) in the Dakhleh Oasis, Egypt and 13 modern individuals from the Florida State Willed Body Program at The University of Central Florida Medical School with confirmed or suspected Alzheimer's disease to conduct a comparative analysis between the two samples. High levels of the aforementioned elements have been noted as resulting in a high toxicity level within the brains of individuals with Alzheimer's disease (Dormandy, 1989). Results indicate that eight individuals from Kellis may have had neurological diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and mood disorders (e.g., depression, anxiety, and ADD/ADHD). Additionally, health profiles for each individual from Kellis were constructed and show the possibility of other pathological conditions such as cardiovascular disease, kidney/liver disease, anemia, and diabetes mellitus. This research provides a deeper understanding of health and illness in the Dakhleh Oasis during the Romano-Christian period, in conjunction with a holistic understanding of the social care practices as discussed through the theoretical framework of the Bioarchaelogy of Care theory.

Crime scenes involving human skeletal remains in obstructed wooded environments are challenging to document. One potential option to include with the crime scene processing protocol is 3D documentation utilizing close-range photogrammetry (CRP). This method results in the generation of realistic 3D models and accurate plan-view maps of the crime scene. The purpose of this research was to explore the use of CRP to preserve contextual information of simulated scenes involving scattered human remains in obstructed wooded environments. The main goal was to improve CRP methodology as well as demonstrate how to incorporate this method into the forensic archaeology documentation protocol. Photographs were collected freehand and models were processed using Agisoft Metashape Professional. The first phase of the research included recording one skeletal scatter four times with varying amounts of individual coded targets in addition to photogrammetric scale bars to test whether using additional coded targets improved 3D model accuracy. Accuracy was assessed through visual analysis, root-mean square (RMS) reprojection errors and total scale bar errors. The results indicated that including extra coded targets did not improve the accuracy of models significantly enough to warrant using the extra targets in conjunction with photogrammetric scale bars. For the second phase of the research, two larger skeletal scatters were documented to test the capabilities of CRP in an obstructed environment. While visual errors were present when zoomed in, the RMS reprojection and scale bar errors still indicated highly accurate models. However, the wooded environment presented numerous challenges that made utilizing CRP more difficult. Therefore, guidelines were outlined for documenting skeletal scatters in wooded environments using CRP, with a focus on addressing variables that can affect image quality. Overall, CRP is a viable method for documenting complex scenes in wooded environments which should be incorporated into forensic archaeological protocols.

The documentation of outdoor forensic crime scenes involving human remains poses multiple challenges to law enforcement officials documenting the context of the scene. More rigorous protocols for the documentation of these scenes are needed, and recent advances in technology open up the possibility of three-dimensional (3D) documentation of the scene. More commonly used in archaeological contexts, close-range photogrammetry (CRP) creates reliable 3D models through triangulation of overlapping points between multiple photographs. This documentation technique allows for the preservation of the entire 3D context and the virtual manipulation without evidence destruction. However, CRP has only been preliminarily used in the field of forensic archaeology. To further refine data collection and processing protocols for the use of CRP on forensic scenes, four mock crime scenes on different complex ground surfaces involving a surface scatter of human remains were created. Photographs were collected using a Nikon D7200 camera and processed using Agisoft Metashape Professional. The first scene, a mixed surface dominated by leaves, was used to test the number of images that should be incorporated into a 3D scene. The second (mixed surface dominated by grass), third (mixed surface dominated by pine needles), and fourth (ground surface of mixed leaves and dirt) scenes were used to test data collection techniques, the capability of documenting a scene using CRP on different complex surfaces, as well as to illustrate complex variables that may affect the final model. Accuracy was determined through an estimation of the final root mean square error (RMSE) and visual analysis of qualitative errors. Results show that CRP can be used to accurately and reliably document the 3D context of real-life scenes in a time-efficient and cost-effective manner. This new methodology should be integrated into current forensic crime scene documentation and may eventually replace current methods of mapping the scene context.

This research involves the examination of the contribution of stable isotope analysis to the forensic anthropological objective of human identification. Oxygen isotopes, which vary in water in a predictable manner according to climatological and geographical factors, can be used to determine the region of origin of an unidentified individual following isotopic analysis of human skeletal remains. However, stable oxygen isotopes from human remains recovered from various aqueous environments may be altered by diagenetic processes that occur following deposition. The focus of this research is to determine potential diagenetic changes in the oxygen isotopic value (d18O) of Sus scrofa (domestic pig) ribs, used as a proxy for human remains. Bone samples (n=50) were exposed to different aqueous environments, including distilled water, fresh water, and brackish water, for a period of one, three, and six months, simulating distinct aqueous conditions that may be encountered by forensic anthropologists working in Florida. Results of this study suggest that submersion in fresh, brackish, and distilled can significantly alter the isotopic composition of bone over a period of six months. However, the observed significant shifts in isotopic composition occur over only a 1‰ range, suggesting that oxygen isotopic data derived from bone that was previously submerged in low salinity water for six months or less may be cautiously used to narrow the geographic origin of unidentified individuals in forensic investigations. This study provides a meaningful contribution to forensic research regarding stable isotope analysis as well as the body of literature regarding early diagenetic changes in aqueous contexts.