Bridget F. B. Algee-Hewitt

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.

Modeling Bone Surface Morphology: A Fully Quantitative Method for Age‐at‐Death Estimation Using the Pubic Symphysis

The pubic symphysis is widely used in age estimation for the adult skeleton. Standard practice requires the visual comparison of surface morphology against criteria representing predefined phases and the estimation of case‐specific age from an age range associated with the chosen phase. Known problems of method and observer error necessitate alternative tools to quantify age‐related change in pubic morphology. This paper presents an objective, fully quantitative method for estimating age‐at‐death from the skeleton, which exploits a variance‐based score of surface complexity computed from vertices obtained from a scanner sampling the pubic symphysis. For laser scans from 41 modern American male skeletons, this method produces results that are significantly associated with known age‐at‐death (RMSE = 17.15 years). Chronological age is predicted, therefore, equally well, if not, better, with this robust, objective, and fully quantitative method than with prevailing phase‐aging systems. This method contributes to forensic casework by responding to medico‐legal expectations for evidence standards.

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.

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.

Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets

Significance We describe a method for identifying in distinct genetic datasets observations that represent the same person. By using correlations among genetic markers close to one another in the genome, the method can succeed even if the datasets contain no overlapping markers. We show that the method can link a dataset similar to those used in genomic studies with another dataset containing markers used for forensics. Our approach can assist in maintaining backward compatibility with databases of existing forensic genetic profiles as systems move to new marker types. At the same time, it illustrates that the privacy risks that can arise from the cross-linking of databases are inherent even for small numbers of markers. 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.

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.

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.

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 articles 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.

Linkage disequilibrium connects genetic records of relatives typed with disjoint genomic marker sets

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.

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.