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

The humanitarian crisis on the US-Mexico 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-Mexico and Texas-Mexico border regions, where demographic trends for immigrants attempting to cross into the United States have shifted dramatically. The demographic change and volume of immigrants seeking shelter in the United States present 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, this study investigated how genetic variation inferred from forensically significant microsatellites can provide valuable information on regions of origin for unidentified remains at the group level. To explore how to mobilize these genetic data to inform identification strategies, the authors conducted a comparative genetic analysis of identified and unidentified immigrant cases from the Arizona- and Texas-Mexico 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-Mexico immigrants have the strongest relationship (>80%) with groups from El Salvador, Guatemala, Mexico, and an indigenous group from southern Mexico. Texas-Mexico immigrants have the strongest relationships (>80%) with groups from Belize, Colombia, Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua. These findings agree with, and are discussed in comparison with, previously reported demographic trends, population genetics research, and population history analyses. The authors emphasize the utility and necessity of coupling genetic variation research with a nuanced anthropological perspective for identification processes in the US-Mexico border context.

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 approximate 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, identifying specific single-nucleotide polymorphisms (SNPs) that influence specific regions of the face. This study assesses the translation of these regions to craniometric dimensions (interlandmark 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 to encourage interdisciplinary work within the forensic sciences. We examined a selection of candidate SNPs currently identified in the literature to examine correlations between interlandmark distances and these SNPs within the same individual. A series of 99 craniometric landmarks were collected from 17 documented skulls from the Texas State Donated Skeletal Collection using a three-dimensional Microscribe digitizer. Criteria for inclusion in this study included European American ancestry, presence of intact skulls, and presence of associated donor blood cards collected at the time of body donation. Using these blood cards, DNA from each individual was extracted, amplified, and sequenced through next-generation sequencing for the chosen SNPs. Bioinformatics tests were then applied to observe the presence or absence of the major or minor alleles in 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 modeling between variables that demonstrated significant correlation; a principal components analysis on the craniometric data (interlandmark measurements) and genetic data (SNP presence/absence) to check homogeneity of each data set; and a pairwise Procrustes analysis on the correlation of the two data sets as different groups. The results indicate correlations of varying degrees between the targeted craniofacial regions and the targeted SNPs. Eleven SNPs showed significant correlation (p < 0.05), but the correlations were not as expected and showed some interesting results. By group level there was no significant correlation, but 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 not previously reported. Combining craniometric and DNA analyses to leverage genotype-phenotype associations has great potential to expand the discourse of current facial approximation and thereby to provide new investigative tools for human identification in forensic anthropology.

Cadaveric blood cards: Assessing DNA quality and quantity and the utility of STRs for the individual estimation of trihybrid ancestry and admixture proportions.

As part a body donation program, blood samples were collected and stored on untreated (non-FTA) blood cards. The blood cards were evaluated in terms of DNA preservation and STR typing success with resulting profiles assessed with special consideration given to profile matching for positive identification and biogeographic ancestry estimation. While STR profiles were successfully generated for all samples, results indicate that the time interval between date of death and sample collection have an impact on DNA quantity and quality. There is a statistically significant decrease in relative fluorescent unit (RFU) values with increasing time interval between date of death and sample collection, indicating degradation in the blood card samples related to the post-mortem interval prior to sample collection. The STR profiles were used to estimate ancestry and admixture using the program STRUCTURE, demonstrating utility of these markers beyond individual identification purposes, with caveats for application based on population history.

A Study on the Asymmetry of the Human Left and Right Pubic Symphyseal Surfaces Using High-Definition Data Capture and Computational Shape Methods.

The pubic symphysis is among the most commonly used bilateral age indicators. Because of potential differences between right and left sides, it is necessary to investigate within-individual asymmetry, which can inflate age estimation error. This study uses 3D laser scans of paired pubic symphyses for 88 documented White males. Scan data are analyzed by numerical shape algorithms, proposed as an alternative to traditional visual assessment techniques. Results are used to quantify the within-individual asymmetry, evaluating if one side produces a better age-estimate. Relationships between the asymmetry and advanced age, weight, and stature are examined. This analysis indicates that the computational, shape-based techniques are robust to asymmetry (>80% of paired differences are within 10 years and >90% are within 15 years). For notably more asymmetric cases, differences in estimates are not associated with life history factors. Based on this study, either side can be used for age-at-death estimation by the computational methods.

Understanding (Mis)classification Trends of Latin Americans in Fordisc 3.1: Incorporating Cranial Morphology, Microgeographic Origin, and Admixture Proportions for Interpretation.

Assigning correct population affinity to a skeleton can contribute important information to an investigation-yet recent work highlights high error rates when classifying Latinos with a traditional tool, Fordisc 3.1 (FD3). Our study examines whether misclassification trends exist, and whether these can be used to infer population affinity. We examine the relationships among ancestry, geography, and FD3 misclassifications of Latinos using canonical variate analysis and unsupervised model-based clustering of craniometrics. Northern Mexicans appear more strongly associated with FD3 references samples with elevated amounts of European ancestry (e.g., American Blacks and Whites), while Southern Mexicans are more strongly associated with FD3 reference samples with reduced amounts of European ancestry (e.g., Guatemalans and Native Americans). FD3 classifications revealed that Latinos exhibited lower posterior probabilities when compared to other common case demographics (Whites and African Americas), even when the classification was "correct." We make recommendations for practitioner interpretation of FD3 reports for casework.

Testing Reliability of the Computational Age-At-Death Estimation Methods between Five Observers Using Three-Dimensional Image Data of the Pubic Symphysis.

In an effort to standardize data collection and analysis in age estimation, a series of computational methods utilizing high-dimensional image data of the age indicator have recently been proposed as an alternative to subjective visual, trait-to-phase matching techniques. To systematically quantify the reproducibility of such methods, we investigate the intrascan variability and within- and between-observer reliability in initial scan data capturing and editing using 3D laser scans of the Suchey-Brooks pubic symphysis casts and five shape-based computational methods. Our results show that (i) five observers with various training background and experience levels edited the scans consistently for all three trials and the derived shape measures and age estimates were in excellent agreement among observers, and (ii) the computational methods are robust to a measured degree of scan trimming error. This study supports the application of computational methods to 3D laser scanned images for reliable age-at-death estimation, with reduced subjectivity.

Statistical Detection of Relatives Typed with Disjoint Forensic and Biomedical Loci.

In familial searching in forensic genetics, a query DNA profile is tested against a database to determine whether it represents a relative of a database entrant. We examine the potential for using linkage disequilibrium to identify pairs of profiles as belonging to relatives when the query and database rely on nonoverlapping genetic markers. Considering data on individuals genotyped with both microsatellites used in forensic applications and genome-wide SNPs, we find that ∼30%-32% of parent-offspring pairs and ∼35%-36% of sib pairs can be identified from the SNPs of one member of the pair and the microsatellites of the other. The method suggests the possibility of performing familial searches of microsatellite databases using query SNP profiles, or vice versa. It also reveals that privacy concerns arising from computations across multiple databases that share no genetic markers in common entail risks, not only for database entrants, but for their close relatives as well.

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

The Combined DNA Index System (CODIS) loci comprise a standard microsatellite marker set widely used for distinguishing among individuals in forensic DNA identity testing for medicolegal 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. Longstanding arguments have been made that small ancestry panels, including the CODIS loci specifically, are not suitable for ancestry inference in admixed populations, due to high heterozygosity and limited number of 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 medicolegal 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 to make direct comparisons of the outcomes, the authors produced ancestry estimates from (a) a small CODIS/CODIS-proxy locus panel and (b) a robust and validated microsatellite ancestry-informative panel. They found evidence (e.g., ρ = 0.80-0.88) 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 results of studies using CODIS on Latin American populations: 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, this study also highlights the limitations of CODIS for making individual-level inferences of ancestry: the associated estimates for an acceptable level of statistical confidence (95%) are too broad to make any nuanced inferences regarding an individual's actual ancestry composition.

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

In this study, we investigated, 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 derived 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 were selected from the Howells data set and more recently collected samples from Europe and Asia. Using unsupervised clustering, we investigated 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 used 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 microgeographic regions, revealing at the country level how different population dynamics-whether 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 found that population of origin explains 38-51% of the variation in each ancestry component, and we detected significant differences among the Asian samples in their quantities of ancestry. Filipinos appear considerably admixed, as they carry almost 20% less Asian ancestry than the average quantity (90%) estimated for the other Asian groups. We also revealed 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; the Manila cemetery sample had the highest level of Asian ancestry, and, as we might expect, the Negrito sample had the greatest quantity of African ancestry. We performed additional analyses that introduced craniometrics from the Howells Australo-Melanesian series, 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 that, with craniometrics just as with genetic loci, patterns of affinity are informative of the complex history of Southeast Asia, as they suggest 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 are of fundamental importance in forensic anthropology, because it contributes to the identity parameters used in a medicolegal death investigation. However, reliable estimates are difficult because many traditional aging methods depend on 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 Latinx, 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 whether population-specific aging methods among Latinx groups are needed. The authors obtained data from two skeletal collections representing modern individuals of Mexican and Puerto Rican origin. They examined five newly developed computational shape-based techniques using 3D laser scans of the pubic symphysis and one traditional bone-to-phase technique. 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 subsample. Results suggest that traditional and computational aging techniques applied to the pubic symphysis perform best with individuals within 35-45 years of age. Levels of bias and inaccuracy increase as chronological age increases, with overestimation of individuals younger than 35 years and underestimation of individuals older than 45 years. New regression models provided error rates comparable to, and in some occasions outperformed, the original computational models developed on white American males, but age estimates did not significantly improve. This study shows that population-specific models do not necessarily improve age estimates in Latinx samples. Results do suggest that computational methods can ultimately outperform the Suchey-Brooks method and provide improved objectivity when estimating age at death in Latinx samples.

Testing inter-observer reliability of the Transition Analysis aging method on the William M. Bass forensic skeletal collection.

OBJECTIVES: Skeletal age estimation is an integral part of the biological profile. Recent work shows how multiple-trait approaches better capture senescence as it occurs at different rates among individuals. Furthermore, a Bayesian statistical framework of analysis provides more useful age estimates. The component-scoring method of Transition Analysis (TA) may resolve many of the functional and statistical limitations of traditional phase-aging methods and is applicable to both paleodemography and forensic casework. The present study contributes to TA-research by validating TA for multiple, differently experienced observers using a collection of modern forensic skeletal cases. MATERIALS AND METHODS: Five researchers independently applied TA to a random sample of 58 documented individuals from the William M. Bass Forensic Skeletal Collection, for whom knowledge of chronological age was withheld. Resulting scores were input into the ADBOU software and maximum likelihood estimates (MLEs) and 95% confidence intervals (CIs) were produced using the forensic prior. Krippendorff's alpha was used to evaluate interrater reliability and agreement. Inaccuracy and bias were measured to gauge the magnitude and direction of difference between estimated ages and chronological ages among the five observers. RESULTS: The majority of traits had moderate to excellent agreement among observers (≥0.6). The superior surface morphology had the least congruence (0.4), while the ventral symphyseal margin had the most (0.9) among scores. Inaccuracy was the lowest for individuals younger than 30 and the greatest for individuals over 60. Consistent over-estimation of individuals younger than 30 and under-estimation of individuals over 40 years old occurred. Individuals in their 30s showed a mixed pattern of under- and over-estimation among observers. DISCUSSION: These results support the use of the TA method by researchers of varying experience levels. Further, they validate its use on forensic cases, given the low error overall.

Geographic substructure in craniometric estimates of admixture for contemporary American populations.

OBJECTIVES: This study investigates heterogeneity in craniometrically-derived estimates of admixture in order to reveal population substructure in a sample of Black, White, Hispanic, and Native American individuals from the FDB. It reports evidence of spatial trends in population-specific patterns of admixture and contextualizes its results in terms of demographic diversity in the United States. MATERIALS AND METHODS: The FDB was sampled to capture the population variation within forensic casework, skeletal collections, and the U.S. population-at-large. Individuals were selected for the availability of population identifier, sex, and geographic information. Variation in inferred admixture proportions was evaluated, per population and by sex, for evidence of geographic substructure. Comparative data was sourced from the U.S. Census. RESULTS: This analysis identifies significant associations between the estimated Black, Native American and White component memberships and place of birth and recovery. The sampled populations differ significantly in admixture proportions, in a systematic way. Admixture patterns vary in accordance with the densities and relative proportions of the U.S. census populations. DISCUSSION: There is considerable variation in admixture estimates, not just between, but notably within, all four of the populations. This substructure can be explained by differences in geography, including regions, divisions, and states. This article's findings agree with census trends and speak broadly to admixture dynamics and ancestral diversity among contemporary Americans. They are also specifically relevant to those cases in the FDB. The presence of subpopulations has implications for cranial research, forensic identification, and studies of biological variation in the United States.

Temporal trends in craniometric estimates of admixture for a modern American sample.

OBJECTIVES: Temporal trends in craniometric estimates of admixture are investigated for three U.S. populations in the FDB. Patterns of association between birth years and posterior probabilities of cluster membership are identified to assess how these proportions of admixture have changed over recent time. Demographic and genetic data correlates, patterns of morphological expression, and shifts in source populations are evaluated. MATERIALS AND METHODS: Estimates of three-way admixture were obtained for 1,521 individuals of documented population, sex, and birth years that span the 20th century. Correlations were calculated between birth years and admixture proportions for members of each FDB population. Population and sex-specific admixture variation was further assessed by ANOVA and regression. Correlation analysis was used to identify, per population, which of the cranial measurements change in dimension under increased or decreased admixture. RESULTS: Admixture proportions differ significantly by population and change over time. No sex differences are detected. Analysis of the relationship between admixture proportions and ILDs finds that admixture drives morphological change in areas of the cranium known to vary among populations. Results agree with prior work on secular change. DISCUSSION: Findings reveal a progressive increase in White-European population admixture for the self-identified Black individuals, a recent demographic shift toward the increased representation of Hispanic individuals carrying greater Native American ancestry, and reduction in admixture for White individuals that suggest a loss of diversity over time. Changes in admixture produce tractable differences in morphological expression. Both sexes exhibit similar admixture proportions and self-identification patterns. Observed diachronic trends are corroborated by information on recent U.S. demographic change.

Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets.

Combining genotypes across datasets is central in facilitating advances in genetics. Data aggregation efforts often face the challenge of record matching-the identification of dataset entries that represent the same individual. We show that records can be matched across genotype datasets that have no shared markers based on linkage disequilibrium between loci appearing in different datasets. Using two datasets for the same 872 people-one with 642,563 genome-wide SNPs and the other with 13 short tandem repeats (STRs) used in forensic applications-we find that 90-98% of forensic STR records can be connected to corresponding SNP records and vice versa. Accuracy increases to 99-100% when ∼30 STRs are used. Our method expands the potential of data aggregation, but it also suggests privacy risks intrinsic in maintenance of databases containing even small numbers of markers-including databases of forensic significance.

A Computational Framework for Age-at-Death Estimation from the Skeleton: Surface and Outline Analysis of 3D Laser Scans of the Adult Pubic Symphysis.

In forensic anthropology, age-at-death estimation typically requires the macroscopic assessment of the skeletal indicator and its association with a phase or score. High subjectivity and error are the recognized disadvantages of this approach, creating a need for alternative tools that enable the objective and mathematically robust assessment of true chronological age. We describe, here, three fully computational, quantitative shape analysis methods and a combinatory approach that make use of three-dimensional laser scans of the pubic symphysis. We report a novel age-related shape measure, focusing on the changes observed in the ventral margin curvature, and refine two former methods, whose measures capture the flatness of the symphyseal surface. We show how we can decrease age-estimation error and improve prior results by combining these outline and surface measures in two multivariate regression models. The presented models produce objective age-estimates that are comparable to current practices with root-mean-square-errors between 13.7 and 16.5 years.

Better together: Thinking anthropologically about genetics.

What are the effects that genetics has had on Anthropological research and how can we think anthropologically about Genetics? Just as genetic data have encouraged new hypotheses about human phenotypic variation, evolutionary history, population interaction, and environmental effects, so too has Anthropology offered to genetic studies a new interpretive locus in its history and perspective. This introduction examines how the fields of Anthropology and Genetics have arrived at a crucial moment at which their interaction requires careful examination and critical reflection. The papers discussed here exemplify how we may engage in such a trans-disciplinary conversation. They speak to the future of thoughtful interaction between genetic and anthropological literature and seek a new integration that embodies the holism of the human biological sciences.

Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

Population inference from contemporary American craniometrics.

OBJECTIVES: This analysis delivers a composite picture of population structure, admixture, ancestry variation, and personal identity in the United States, as observed through the lens of forensic anthropological casework and modern skeletal collections. It tests the applicability of the probabilistic clustering methods commonly used in human population genetics for the analysis of continuous, cranial measurement data, to improve population inference for admixed individuals without prior knowledge of sample origins. MATERIALS AND METHODS: The unsupervised model-based clustering methods of finite mixture analysis are used here to reveal latent population structure and generate admixture proportions for craniofacial measurements from the Forensic Anthropology Data Bank (FDB). Craniometric estimates of ancestry are also generated under a three contributor model, sourcing parental reference populations from the Howells Craniometric Dataset. Tests of association are made among the coefficients of cluster memberships and the demographic information documented for each individual in the FDB. Clustering results are contextualized within the framework of conventional approaches to population structure analysis and individual ancestry estimation to discuss method compatibility. RESULTS: The findings reported here for contemporary American craniometrics are in agreement with the expected patterns of intergroup relationships, geographic origins and results from published genetic analyses. DISCUSSION: Population inference methods that allow for the model-bound estimation of admixture and ancestry proportions from craniometric data not only enable parallel-skeletal and genetic-analyses but they are also shown to be more informative than those methods that perform hard classifications using externally-imposed categories or seek to explain gross variation by low-dimensional projections. Am J Phys Anthropol 160:604-624, 2016. © 2016 Wiley Periodicals, Inc.