The Development and Use of Computational Tools in Forensic Science

Modern computational resources make available a rich toolkit of statistical methods that can be applied to forensic questions. This toolkit is built on the foundation of statistical developments dating back to the 19th century. To fully and effectively exploit these developments, both the makers and users of software must be keenly aware of the quality, i.e., the accuracy and precision, of the data being modeled or analyzed, and end-users must be sufficiently familiar with the underlying theory to understand the process and results of any analysis or software they use. This is especially important for medico-legal personnel who might be called upon to testify in a court of law and be subject to cross-examination. With respect to the development of computational tools, it is increasingly important that they be made available as open-source code to avoid the pitfalls of commercial software support and the potential dependence of end-users on orphaned software

Image data banks and geometric morphometrics

This paper examines the opportunities offered by recent advances in digital image processing to allow access to natural history museum collections without direct handling of specimens. It specifically refers to two- and three-dimensional data recording and analysis in the frame of geometric morphometrics

The Mesoamerican Corpus of Formative Period Art and Writing

This project explores the origins and development of the first writing in the New World by constructing a comprehensive database of Formative period, 1500-400 BCE, iconography and a suite of database-driven digital tools. In collaboration with two of the largest repositories of Formative period Mesoamerican art in Mexico, the project integrates the work of archaeologists, art historians, and scientific computing specialists to plan and begin the production of a database, digital assets, and visual search software that permit the visualization of spatial, chronological, and contextual relationships among iconographic and archaeological datasets. These resources will eventually support mobile and web based applications that allow for the search, comparison, and analysis of a corpus of material currently only partially documented. The start-up phase will generate a functional prototype database, project website, wireframe user interfaces, and a report summarizing project development

Anthropology Takes Control of Morphometrics

There has been a startling change over the last decade in the intellectual context of morphometrics. In the 1990’s, this field, which has not altered its focus upon the quantitative analysis of biomedical shape variation and shape change, was principally centered around concerns of medical image analysis; but now it is driven mainly by the demands of researchers in human variability, physical anthropology, primatology, and paleoanthropology instead. This essay celebrates that change and tries to account for it by reference to cognitive and intellectual aspects of the new home

Age-at-Death Estimation for Modern Populations in Mexico and Puerto Rico Through the Use of 3D Laser Scans of the Pubic Symphysis

Reliable age-at-death estimates from the adult skeleton is of fundamental importance in forensic anthropology, as it contributes to the identity parameters used in a medico-legal death investigation. However, reliable estimates are made difficult by the fact that many traditional aging methods are dependent upon a set of population-specific criteria derived from individuals of European and African descent. The absence of information on the potential differences in the aging patterns of underrepresented, especially Hispanic populations, may hinder our efforts to produce useful age-at-death estimates. In response to these concerns, this study explores the utility of currently available aging techniques, and explores the need, if any, for population- specific aging method among Hispanic groups. The current study obtained data from two skeletal collections representing modern individuals of Mexican and Puerto Rican origin. Five newly developed computational-shape based techniques utilizing 3D laser scans of the pubic symphysis and one traditional bone-to-phase technique were examined. A validation test of all computational and traditional methods was implemented, and new population-specific equations using the computational algorithms were generated and tested against a sub-sample. Estimated mean ages from the traditional and computational techniques were compared in order to offer practical recommendations for age estimation on cases of Hispanic identity and, in particular, cases presumed to be of Mexican or Puerto Rican individuals. Results from this study suggest that traditional and computational aging techniques applied to the pubic symphysis perform the best with individuals within 35-45 years of age. Levels of bias and inaccuracy increase as chronological age increases, with overestimation of individuals under 35 years of age, and underestimation of individuals over 45 years of age. New regression models provided error rates comparable, and in some occasions, outperformed the original computational models developed on White American males, but age estimates did not significantly improve. This study has shown that population specific models do not necessarily improve age estimates in Hispanic samples. Results do suggest that computational methods can ultimately outperform the Suchey Brooks method and provide improvement in objectivity when estimating age-at-death in Hispanic samples

The morphometry of soft tissue insertions on the tibial plateau: Data acquisition and statistical shape analysis

This study characterized the soft tissue insertion morphometrics on the tibial plateau and their inter-relationships as well as variabilities. The outlines of the cruciate ligament and meniscal root insertions along with the medial and lateral cartilage on 20 cadaveric tibias (10 left and 10 right knees) were digitized and co-registered with corresponding CT-based 3D bone models. Generalized Procrustes Analysis was employed in conjunction with Principal Components Analysis to first create a geometric consensus based on tibial cartilage and then determine the means and variations of insertion morphometrics including shape, size, location, and inter-relationship measures. Step-wise regression analysis was conducted in search of parsimonious models relating the morphometric measures to the tibial plateau width and depth, and basic anthropometric and gender factors. The analyses resulted in statistical morphometric representations for Procrustes-superimposed cruciate ligament and meniscus insertions, and identified only a few moderate correlations (R 2: 0.37-0.49). The study provided evidence challenging the isometric scaling based on a single dimension frequently employed in related morphometric studies, and data for evaluating cruciate ligament reconstruction strategies in terms of re-creating the native anatomy and minimizing the risk of iatrogenic injury. It paved the way for future development of computer-aided personalized orthopaedic surgery applications improving the quality of care and patient safety, and biomechanical models with a better population or average representation

Coordinate data of crocodylian crania (pre-superimposed)

Coordinate data of 78 three-dimensional landmarks from 204 cranial specimens of 10 extant crocodylian species. All specimens, with the exception of Gavialis and Tomistoma, are from non-captive individuals. Raw coordinate data were collected with a G2 Microscribe digitzer (Immersion Corporation, CA, USA) by the principal author (A.W.). The coordinate data is in NTSYS format, in which the digitized specimens have been aligned according to PC axes (x axis = anteroposterior; y axis = mediolateral; z axis=dorsoventral), but still retain their original size. The coordinate points, therefore, have not been subjected to generalized Procrustes superimposition, allowing the user to calculate centroid size. Specimens are labeled in the file with species ID (first three letters of generic and specific names; e.g., allmis = Alligator mississippiensis) followed by their respective institutional specimen number. Please refer to the main article and associated supplementary text file for description of landmarks and additional information on the acquisition and treatment of data

Data from: The utility of cranial ontogeny for phylogenetic inference: a case study in crocodylians using geometric morphometrics

The degree to which the ontogeny of organisms could facilitate our understanding of phylogenetic relationships has long been a subject of contention in evolutionary biology. The famed notion that ‘ontogeny recapitulates phylogeny’ has been largely discredited, but there remains an expectation that closely related organisms undergo similar morphological transformations throughout ontogeny. To test this assumption, we used three-dimensional geometric morphometric methods to characterize the cranial morphology of 10 extant crocodylian species and construct allometric trajectories that model the post-natal ontogenetic shape changes. Using time-calibrated molecular and morphological trees, we employed a suite of comparative phylogenetic methods to assess the extent of phylogenetic signal in these trajectories. All analyses largely demonstrated a lack of significant phylogenetic signal, indicating that ontogenetic shape changes contain little phylogenetic information. Notably, some Mantel tests yielded marginally significant results when analysed with the morphological tree, which suggest that the underlying signal in these trajectories is correlated with similarities in the adult cranial morphology. However, despite these instances, all other analyses, including more powerful tests for phylogenetic signal, recovered statistical and visual evidence against the assumption that similarities in ontogenetic shape changes are commensurate with phylogenetic relatedness and thus bring into question the efficacy of using allometric trajectories for phylogenetic inference

PermuTree

Python program for performing a permutational regression analysis on trees. It takes a NEWICK string file and a CSV file of a single continuous variable and tests for significant correlation between phenotypic and phylogenetic distances. Please note that this script was written in Python version 2.7, thus some commands may not run properly (e.g., print function). In addition, the script requires the tree.py module to run, which can be downloaded through Peter Beerli's website (see README), as well as matplotlib and scipy Python packages