The reality of the dead in Brazil: perspectives on identification in forensic anthropology (editorial)

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Understanding the Relationship between Genetic Markers and Skeletal Remains: Implications for Forensic Anthropology and Phenotype-Genotype Studies

Human identification techniques have been a leading tool to hold perpetrators accountable, give families closure, and reconstruct faces on skulls. This project is a pilot study to critically examine three disciplines that fall under the human identification umbrella: forensic anthropology, forensic genetics, and forensic art. Current facial research in genetics focuses on data from living individuals where specific single-nucleotide polymorphisms (SNPs) that influence specific regions of the face have been found. This study assesses the translation of these same regions to craniometric dimensions (inter-landmark distances) of the underlying skull itself. The goal of this project is to provide information regarding the correlation of craniometric measurements and SNPs, as well as encourage interdisciplinary work within the forensic sciences. We examined a selection of candidate SNPs currently identified in the literature to determine if there were correlations between inter-landmark distances and those SNPs within the same individual. A series of 98 craniometric landmarks were collected from 17 documented skulls from the Texas State Donated Skeletal Collection using a 3D Microscribe digitizer. Criteria for inclusion in this study included European American ancestry, the presence of intact skulls, and presence of associated donor blood cards collected at the time of body donation. Using these blood samples, DNA from each individual was extracted, amplified, and sequenced through Next Generation Sequencing for the specific chosen SNPs. Afterward, bioinformatics tests were applied to observe the presence or absence of the major or minor alleles in the specific locations on the genome. After determining the presence or absence of an SNP (minor allele), a set of statistical tests were performed including: Spearman’s correlation between the craniometric measurements and the individual’s genetic data variables; two-way hierarchical clustering and Bootstrap Forest modelling between variables that demonstrated significant correlation; a principal component analysis was performed on the craniometric data (inter- landmark measurements) and genetic data (SNP presence/absence) in order to check the homogeneity of each data set; and finally, a pair-wise Procrustes analysis was completed on the correlation of the two data sets as different groups. The results indicate a correlation in various degrees between the targeted craniofacial regions and the targeted SNPs. There were 11 SNPs that showed significant correlation (p \u3c0.05). However, the correlations were not as expected and showed some interesting results. By group level there was no significant correlation, however, there was correlation at the individual level. While some SNPs affected the soft tissues only, others showed correlations with the skull (hard tissue), a finding that had not been previously known. By combining craniometric and DNA analyses to leverage genotype-phenotype associations, there is great potential to expand the discourse of current facial approximation and to, thereby, provide new investigative tools for human identification in forensic anthropology

Population Identifiability from Forensic Genetic Markers: Ancestry Variation in Latin America

The Combined DNA Index System (CODIS) loci are a standard microsatellite marker set widely used for distinguishing among individuals in forensic DNA identity testing for medico-legal casework in the United States and in other countries. In anthropological genetic research, CODIS markers have become an important tool for uses extending beyond case investigations to quantify ancestry proportions, reveals patterns of admixture and trace population histories. These investigations are especially prevalent in studies of Latin American population structure. Nevertheless, the accuracy of the ancestry estimates computed from the CODIS loci for highly admixed Latino populations has not been formally tested. Long-standing arguments have been made that small ancestry panels, including the CODIS loci specifically, are not suitable for ancestry inference in admixed populations, due to the high heterozygosity and limited number of the loci used. Recent studies on ancestry inference using the CODIS loci suggest that these do confer more information of population-level identifiability than recognized in forensic genetic scholarship and by the medico-legal community. Here, we formally test the ability of CODIS and CODIS-Proxy (e.g. high heterozygosity and individual identifiability loci) marker panels to accurately estimate admixture proportions of individuals, including a sample of Latinos with a wide range of ancestry proportions. Using the same individuals in order to make direct comparisons of the outcomes, we produce ancestry estimates from 1) a small CODIS/CODIS Proxy loci panel and 2) a robust and validated microsatellite ancestry informative panel. We find evidence (e.g. ρ = 0.80 to 0.88) that supports the use of CODIS/CODIS-Proxy loci to capture the general ancestry estimation trends of a sample. This finding is in line with what studies using CODIS on Latin American populations have found, in that the ancestry estimations generated by CODIS present trends supported by documented population histories (e.g. colonialism and population movements) and microevolutionary events (e.g. gene flow) in Latin America. However, the present study also highlights the limitations of CODIS for making individual-level inferences of ancestry, as the associated estimates for an acceptable level of statistical confidence (95%) are demonstrated here to be too broad to make any nuanced inferences regarding the individual’s actual ancestry composition

An Admixture Approach to Trihybrid Ancestry Variation in the Philippines with Implications for Forensic Anthropology

In this study, we investigate, for the first time from a forensic anthropological perspective, the question of mixed ancestry estimation for modern Filipinos with geographic origins in the Philippines. We derive estimates of continental ancestry using craniometrics from four sources: a new documented collection of current forensic significance from the Manila North Cemetery; the Howells cranial series representing a sample of unclaimed individuals from Manila but said largely to originate from more remote areas, with dates of death before 1940; the Hanihara sample aggregated from various locations and time periods across the Philippines; and the Hanihara series capturing various local indigenous, ethnic groups that are together identified as Philippine Negrito. Parental craniometrics are selected from the Howells dataset and more recently collected samples from Europe and Asia. Using unsupervised clustering, we investigate the algorithmically defined three-cluster, or trihybrid admixture, model to infer continental ancestry for each individual, reporting their relative proportions of Asian, European, and African admixture. We employ similar clustering procedures to identify more complex models, with a larger number of clusters, to explore patterns of affinity between our four Philippine samples and the recently acquired samples from Vietnam, Thailand, China (Hong Kong), Japan, and Korea. These analyses give insight into the relationships between both macro and micro geographic regions, such that, at the country level, we reveal how different population dynamics – whether geo-political, -economic, -historical and/or -social – structure the ancestral makeup of Asian peoples, especially in the degree of European and African admixture. From these ancestry estimates, we find that population of origin explains 38-51% of the variation in each ancestry component and we detect significant differences among the Asian samples in their quantities of ancestry. Filipinos appear considerably admixed, as they appear to carry almost 20% less Asian ancestry than the average quantity (90%) estimated for the other Asian groups. We also reveal substructure within our representation of modern Filipinos, such that differences in the patterns of three-way admixture exist between each of the four Philippine samples, finding that the Manila cemetery sample has the highest level of Asian ancestry and, as we might expect, that the Negrito sample has the greatest quantity of African ancestry. We perform additional analyses that introduce craniometrics from the Howells Australo-Melanesian series in order to more fully investigate their relationship to the Asian samples and to better understand the African contributions common to the Philippine Negritos especially, as well as the other Southeast Asians and the Spanish and Portuguese groups. By mapping the cluster patterns on a global scale, these analyses reveal, with craniometrics just as with genetic loci, patterns of affinity that are informative of the complex history of Southeast Asia, as they are suggestive of the vestiges of migration, trade, and colonialism, as well as more recent periods of isolation, marginalization, and occupation

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

Comparing Genetic Variation among Latin American Immigrants: Implications for Forensic Casework in the Arizona- and Texas-México Borderlands

The humanitarian crisis on the United States-México border is a long standing and evolving crisis in which nearly 8,000 deaths have been reported in the last two decades. These deaths are largely distributed across the Arizona-México and Texas-México border regions where demographic trends for immigrants attempting to cross into the U.S. have shifted dramatically. The demographic change and volume of immigrants seeking shelter in the U.S. presents new challenges for the forensic practitioners entrusted with the identification of individuals who lose their lives during the final segment of their journey. Within this Border context, the present study investigates how genetic variation inferred from forensically significant microsatellites can provide valuable information on regions of origin for unidentified remains on the group level. To explore how we can mobilize these genetic data to inform identification strategies, we conduct a comparative genetic analysis of identified and unidentified immigrant cases from the Arizona- and Texas-México contexts, as well as 27 other Latin American groups. Allele frequencies were utilized to calculate FST, and relationships were visually depicted in a multidimensional scaling plot. A Spearman correlation coefficient analysis assessed the strength and significance of population relationships and an agglomerative clustering analysis assessed population clusters. Results indicate that Arizona-México immigrants have the strongest relationship (\u3e80%) with groups from El Salvador, Guatemala, México, and an indigenous group from Southern México. Texas-México immigrants have the strongest relationships (\u3e80%) with groups from Belize, Colombia, Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua. These findings agree with, and are discussed in comparison to, previously reported demographic trends, population genetics research, and population history analyses. We emphasize the utility and necessity of coupling genetic variation research with a nuanced anthropological perspective for identification processes in the U.S-México border context

GlobalFiler Express DNA amplification kit in South Africa: Extracting the past from the present

In this study, the GlobalFiler Express amplification kit was evaluated for forensic use in 541 South African individuals belonging to the Afrikaaner, amaXhosa,1 amaZulu,1 Asian Indian and Coloured population groups. Allelic frequencies, genetic diversity parameters and forensic informative metrics were calculated for each population. A total of 301 alleles were observed ranging between 5 and 44.2 repeat units, 43 were rarely observed partial repeats and seven were novel. The combined match probability (CMP) ranged from 2.21x10 (Coloured) to 5.21x10 (AmaZulu), and the combined power of exclusion (CPE) 0.9999999978 (Afrikaaner) to 0.99999999979 (AmaZulu) respectively. No significant departures from Hardy-Weinberg equilibrium (HWE) were observed after Bonferroni correction. Strong evidence of genetic structure was detected using the coancestry coefficient? Analysis of Molecular Variance (AMOVA) and an unsupervised Bayesian clustering method (STRUCTURE). The efficiency of assignment of individuals to population groups was evaluated by applying likelihood ratios with WHICHRUN, and the individual ancestral membership probabilities inferred by STRUCTURE. Likelihood ratios performed the best in the assignment of individuals to population groups. Signs of positive selection were detected for TH01 and D13S317 and purifying/balancing selection for locus SE33. These three loci also displayed the largest informativeness for assignment (In) values. The results of this study supports the use of the GlobalFiler STR profiling kit for forensic applications in South Africa with the additional capability to predict ethnicity or continental origin of a random sample.IS

Acts of Aesthetics: Publishing as Recursive Agency in the Long Eighteenth Century

Of primary concern to late eighteenth-century society was the sheer volume of printed work being produced in England. The response of authors troubled by this perceived crisis was an outpouring of works on taste, aesthetics, genre and literature, which attempted to describe and provide corrective solutions to the problem of over-publication. Yet this response itself, of course, only added to the number of works within Britain. How did the solution to a deluge of print become more printed materials? Did these authors envision print’s agency as a self-corrective process? And, if so, how can we recover and perhaps even model the connections between works that encompassed the responses to print? This essay outlines a potential solution to this problem by sampling a highly focused selection of digitized texts that raise the issue of over-publication. Through a quantitative analysis of these texts, it identifies the lexical patterns that may reveal the ways in which authors of the period envisioned the work of aesthetics. In particular, this article identifies an emerging consensus on how printed objects became agents within the socio-cultural world of the long eighteenth century: both as objects which could act on readers and as objects which could act on other printed texts. By comparing the language that these clusters of texts deploy to discuss the agency of print to their traditional generic, theoretical or historical groupings, we can begin to examine the process by which the potential power of print became the solution to the dangers it, itself, presented