Elliptical Fourier Analysis of Lateral Skull Profiles As a Tool to Aid Skeletal Identification Jodi Caple Bforensicsc, Bbiomedsc(Hons)
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Elliptical Fourier analysis of lateral skull profiles as a tool to aid skeletal identification Jodi Caple BForensicSc, BBiomedSc(Hons) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 Faculty of Medicine Abstract When dealing with the identification of skeletonised human remains, osteological features can be used to reduce the pool of individuals to whom the remains may belong by estimating biological factors such as ancestry and sex. While pre-existing quantitative methods for estimating ancestry and sex can achieve considerable accuracy, they typically use sparsely located landmarks, risking the loss of meaningful information between the data points. These methods also require substantial levels of manual input, which is time consuming and often requires specialised recording equipment. This also acts to restrict use of analytical methods to the laboratory. The overarching aim of this thesis is to determine if morphology of the skull, specifically its outline in norma lateralis as viewed in a 2D photograph, can be used to accurately estimate the ancestry and sex of skeletons. When capturing lateral 2D views of 3D skulls, anatomical characters that are positioned more laterally act to obscure morphologies of interest due to the camera viewpoint. To evaluate the level of information retained in 2D lateral views, the 'anterior profile line' visible as the skull margin was traced in a 3D view. This also resulted in a reworking of the pre-existing craniometric terminology used to describe skulls in 2D views (also extended herein to faces). A standardised photography protocol was developed to acquire images of skulls in norma basalis, frontalis, lateralis, and verticalis, and applied to adult skulls of known sex from different populations sourced from: the Pretoria Bone Collection, the Hamann-Todd Human Osteological Collection, the WM Bass Donated Skeletal Collection, the Robert J Terry Anatomical Skeletal Collection, the Chiba Bone Collection, and the Khon Kaen Osteological Collection. Photographs were taken in a manner that permitted the profile line to always be in focus in a lateral view, with a single setup using: a full-frame Canon 6D camera body fitted with a 100 mm macro lens, and with a set subject-to-camera distance of 1.20 m. To visualise the average morphology of each sex and ancestry group in photographic resolution (i.e., centroids of data), means were calculated of anterior and lateral skull photographs using Psychomorph. These depictions of group means serve as texture mapped versions of group centroids for the skull outlines, and thus provide high-quality visual representations for group comparisons with an unknown skull. Skull and cranial outlines were specifically extracted from the photographs and analysed with elliptical Fourier analysis (EFA) using 40 harmonics on partial Procrustes aligned coordinates. Both size-retained and size-normalised methods were employed. EFA coefficients were subject to principal component (PC) analysis to reduce the data and to assess variations in size and shape of the outlines. The PCs were statistically significant overall by ancestry and sex, for skull and cranial outlines both with and without size information (p < 0.01). Linear discriminant function analysis ii was used to derive group classification models, and using five-fold cross-validation to estimate classification accuracy. Using skull outlines, size-retained data correctly classified ancestry and sex 73 % of the time with all seven groups included in the comparison. This accuracy decreased to 60 % with size normalisation. Cranial outlines for the seven group comparison correctly classified 73 % and 62 % with size-included and size-normalised analyses respectively. A four-way assessment of ancestry and sex for Black and White females and males using size-retained skull outlines achieved 67-89 % correct classifications, with an overall accuracy of 78 %. For comparison, analysis in FORDISC 3.1 using 14 measurements visible in norma lateralis achieved 66-80 % accuracy (74 % overall); and stepwise selection of the eight best performing variables achieved 70-84 % correct classifications (79 % overall). Accuracy of out-of-group ancestry and sex estimation was assessed using nine DNA-identified skulls from the Defense POW/MIA Accounting Agency (DPAA) Laboratory. When compared to all seven groups, eight of the nine identified skulls (89 %) correctly classified as White male with size retained, with one misclassification as White female (for both skull and cranial comparisons). These results indicate that skull and cranial outlines captured in norma lateralis contain enough morphological information to enable correct ancestry and sex estimation most of the time. The portable and user-friendly nature of the EFA protocol make this method viable for use at skeletal recovery sites. This would help to mitigate risk of erroneous repatriation of unknown human remains, which is especially pertinent where large distances and expenses are involved. This sex and ancestry estimation method has been scripted in R and is freely available as SkullProfiler at CRANIOFACIALidentification.com. iii Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my research higher degree candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis. iv Publications during candidature Peer-reviewed Papers Caple JM and Stephan CN (2015). A standardized nomenclature for craniofacial and facial anthropometry. International Journal of Legal Medicine 130(3):863-879, doi: 10.1007/s00414- 015-1292-1 Caple JM and Stephan CN (2016). Photo-realistic statistical skull morphotypes: new exemplars for ancestry and sex estimation in forensic anthropology. Journal of Forensic Sciences 62(3):562- 572, doi: 10.1111/1556-4029.13314 Caple JM, Byrd J, and Stephan CN (2017). Elliptical Fourier analysis: fundamentals, applications, and value for forensic anthropology. International Journal of Legal Medicine doi:10.1007/s00414-017-1555-0 Conference Abstracts Caple JM and Stephan CN (2016). Photo-Realistic Statistical Exemplars of Skulls: Visualizing Average Sex and Ancestry in High-Resolution for Forensic Anthropology. 8th International Symposium of Clinical and Applied Anatomy. Budapest, Hungary: Argentine Journal of Clinical Anatomy 8(3):170-207. v Publications included in this thesis No publications have been included verbatim as part of this thesis; however, the following publications were reworked and reworded to serve as components of larger chapters. 1. Caple JM, Byrd JE, and Stephan CN (2017). Elliptical Fourier analysis: fundamentals, applications, and value for forensic anthropology. International Journal of Legal Medicine. doi: 10.1007/s00414-017-1555-0 – this paper has been reworked and included in Chapters 2 and 4. Contributor Statement of contribution Author Jodi Caple (Candidate) Conceptualisation (40 %) Data collection and analysis (70 %) Wrote paper (55 %) Author John Byrd Conceptualisation (20 %) Data collection and analysis (10 %) Wrote paper (15 %) Author Carl Stephan Conceptualisation (40 %) Data collection and analysis (20 %) Wrote paper (30 %) 2. Caple JM and Stephan CN (2015). A standardized nomenclature for craniofacial and facial anthropometry. International Journal of Legal Medicine 130(3):863-879. doi: 10.1007/s00414-015- 1292-1 – portions of the paper have been reworked and included in Chapters 2 and 6. Contributor Statement of contribution Author Jodi Caple (Candidate) Conceptualisation (30 %) Data collection and analysis (80 %) Wrote paper (70 %) Author Carl Stephan Conceptualisation (70 %) Data collection and analysis (20 %) Wrote paper (30 %) vi 3. Caple JM and Stephan CN (2016). Photo-realistic statistical skull morphotypes: new exemplars for ancestry and sex estimation in forensic anthropology. Journal of Forensic Sciences 62(3):562- 572. doi: 10.1111/1556-4029.13314 – portions of this paper have been reworked and included in Chapter 8. Contributor Statement of contribution Author Jodi Caple (Candidate) Conceptualisation (30 %) Data collection and analysis (80 %) Wrote paper (70 %) R programming