Considerations for age estimation accuracy: Method-derived outcomes and practitioner interpretations.

Recent research observed 92% accuracy for age-at-death estimations by U.S. forensic anthropologists. The present study compares this case report level accuracy to method level accuracy for the most commonly used methods in U.S. casework, drawing from the Forensic Anthropology Database for Assessing Methods Accuracy (FADAMA). Method application rate (i.e., how often a method is used in casework) was analyzed for n = 641 cases and identified 15 methods with an application rate >45 cases, and the present study focused further analyses on these 15 methods. Of the 15, only four yielded accuracies greater than or equal to the 92% documented for case-report level accuracy. The other 11 methods produced accuracy rates ranging from 54% to 91%, with six of these below 70% This disconnect between highly accurate age estimations at the case report level compared to the poor performance at method level suggests that practitioner interpretation and synthesis of the methods' outcomes is a critical step for increasing the accuracy rates of the age estimations as reported on the final case report. This inference was further supported by the study's results which indicated that practitioner interpretations of frequently used method combinations improve accuracy and age range width of age estimation. The study also performed a Fisher's Exact test to assess whether case report-level accuracy differed with the number of aging methods used in a case, and found no significant differences.

Investigating identification disparities in forensic anthropology casework.

Forensic anthropology is shifting to reflect on the impact of its practices within the criminal justice context in important ways. Here, we contribute to this essential work by examining how decedent demographics as well as estimations of biological profile components are related to identification trends in forensic anthropology cases. The study uses data from more than 1,200 identified and unidentified forensic anthropology cases from three agencies (together representing a nation-wide sample). We found the following: i) multivariate analyses indicated that decedent sex, age, and race and/or ethnicity are not related to case identification rates in the pooled United States sample, ii) when identification rate differences do occur, they appear to be smaller effects, more agency-specific, and/or related to the context of a particular agency, iii) for the agency-specific sample with available data, there was no consistent evidence for a discrepancy in the duration of an identification investigation based on a decedent's sex, age, or race and/or ethnicity, iv) forensic anthropological estimations of sex, age, and ancestry can improve the odds of identification for decedents, although these are small effects, and v) reporting an ancestry estimation does not appear to impact decedent race representation among resolved unidentified person cases. Although previous studies have identified demographic discrepancies in other areas of the criminal justice system, the results presented here suggest that decedent demographic estimation practices by forensic anthropologists in general do not appear to be related to discrepancies in identification trends, but more research is needed to examine whether these findings hold. Contextual factors and practices specific to each investigative agency likely contribute to identification trends.

Applying posterior probability informed thresholds to traditional cranial trait sex estimation methods.

Sex estimation methods using traditional cranial nonmetric traits utilize predictive models to produce a final sex estimation, using the resulting model's score to classify the individual. When sex estimations are assigned from discriminant scoring alone, statistical confidence in the resultant estimate is not always assessed or reported. Although some forensic anthropologists may qualitatively report their confidence in the assessment (e.g., "probable male"), these statements are subjective, not standardized, and not necessarily based on statistical results in a uniform way. The goals of this study were to evaluate how posterior probability-informed thresholds (PPITs) impacted accuracy rates, assess the balance between sample inclusion and accuracy for the proposed PPIT approach, and make recommendations for the use and interpretation of specific thresholds in casework. Using a sample of U.S. Black and White females and males (n = 292), we examined how PPITs can standardize the decision-making process of inferring sex for two methods using nonmetric cranial traits. We found that using PPITs of at least 0.85 increased accuracy (over 92% for some PPITs) yet remained highly inclusive of the sample. PPITs < 0.75 did not produce classification accuracy rates significantly higher than chance, and when using these cranial trait sex estimation methods, cases with posterior probabilities (PPs) <0.75 should be reported as "indeterminate." The 0.75-0.84 PPIT interval had an accuracy rate of 76%, which was both statistically significantly different from chance as well as from the higher (>0.85) groups, suggesting that although sex estimation at this level may be acceptable, the results hold lower confidence.

Forensic anthropology casework performance: Assessing accuracy and trends for biological profile estimates on a comprehensive sample of identified decedent cases.

The purpose of this study was to investigate the accuracy rates and trends in forensic anthropology casework concerning the estimation of the biological profile (sex, age, ancestry, and stature). Identified cases from the Forensic Anthropology Database for Assessing Methods Accuracy (FADAMA; n = 359) were analyzed to explore the following: accuracy rates per biological profile component, case-level performance in assessing the biological profile, and factors related to inaccuracy rates. Accuracy rates for the four biological profile components ranged from 83% to 98%, with sex estimation performing the best and stature performing the poorest. While the overall sex estimation inaccuracies were the lowest of any biological profile component, we found that females are missexed approximately ten times more often than males. Inaccurate age estimates were more frequently the result of overestimation than underestimation, while the trends are reversed for stature estimation. Regarding ancestry estimation performance, African American/Black and White decedents had the lowest inaccuracy rates, while Hispanic and Asian/Pacific Islander decedents demonstrated greater inaccuracy rates. When examining accuracy rates for each case, 81% of cases had no inaccurate biological profile estimates, while 17% and 2% inaccurately estimated one and two biological profile components, respectively. The demographic trends of identified forensic anthropology cases reflect the national unidentified decedent demographics. Biological profile accuracy rates were generally comparable to previous studies. The findings highlight the current status of forensic anthropologists' casework performance, with a greater amount of case-level inaccuracy rates than previously thought, and demonstrate the potential methodological and sampling strategies that could improve accuracy rates.

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.

Technical note: A report on the Forensic Anthropology Database for Assessing Methods Accuracy.

We report on the functionality, available support, and research capability of the Forensic Anthropology Database for Assessing Methods Accuracy (FADAMA; DOJ DUBX0213). FADAMA is an online repository for case data from identified forensic skeletal cases. The goal of FADAMA is to address the lack of adequate measures for assessing accuracy and reliability of forensic anthropology methods. FADAMA requires users to apply for access with their university or organization credentials. Verified users may upload and download anonymized case data via the user interface, after signing a terms of service agreement outlining ethical behavior. Case data uploads require information about the actual biological profile of the decedent and the forensic anthropology estimations. Uploading case data takes approximately 15-25 min. FADAMA users currently have 85 methods to select from when entering case data, with the capability to add new methods as they are developed. Access to the database is free, and online video tutorials are available for users covering database functionality. Currently, the database houses anonymized case data for over 350 identified cases from across the U.S. Funding has been allocated for a database technician to assist offices with large caseloads to upload cases. As it stands, the database is easy to use, and maintains thoughtful tools to assist users. The power of the database to identify trends in both method accuracy and usage is apparent, and will continue to grow as more cases are added.

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.

Correction: Investigating the case of human nose shape and climate adaptation.

[This corrects the article DOI: 10.1371/journal.pgen.1006616.].

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.

Development and Assessment of Postcranial Sex Estimation Methods for a Guatemalan Population.

This study tests whether postcranial sex estimation methods generated from Hispanic, and mainly Mexican samples, can be successfully applied to other increasingly common migrant populations from Central America. We use a sample of postcranial data from a modern (1980s) Guatemalan Maya sample (n = 219). Results indicate a decrease in classification accuracies for previously established univariate methods when applied to the Guatemalan study sample, specifically for males whose accuracies ranged from 30 to 84%. This bias toward inaccuracies for Guatemalan males is associated with the smaller skeletal sizes for the Guatemalan sample as compared to the samples used in the tested sex estimation methods. In contrast, the tested multivariate discriminant function classification yielded less sex bias and improved classification accuracies ranging from 82 to 89%. Our results highlight which of the tested univariate and multivariate methods reach acceptable levels for accuracy for sex estimation of cases where the region of origin may include Guatemala.

Investigating the case of human nose shape and climate adaptation.

The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of genetic drift, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst-Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

Genetic Structure of First Nation Communities in the Pacific Northwest.

This study presents genetic data for nine Native American populations from northern North America. Analyses of genetic variation focus on the Pacific Northwest (PNW). Using mitochondrial, Y chromosomal, and autosomal DNA variants, we aimed to more closely address the relationships of geography and language with present genetic diversity among the regional PNW Native American populations. Patterns of genetic diversity exhibited by the three genetic systems were consistent with our hypotheses: genetic variation was more strongly explained by geographic proximity than by linguistic structure. Our findings were corroborated through a variety on analytic approaches, with the unrooted trees for the three genetic systems consistently separating inland from coastal PNW populations. Furthermore, analyses of molecular variance support the trends exhibited by the unrooted trees, with geographic partitioning of PNW populations (FCT = 19.43%, p = 0.010 ± 0.009) accounting for over twice as much of the observed genetic variation as linguistic partitioning of the same populations (FCT = 9.15%, p = 0.193 ± 0.013). These findings demonstrate a consensus with previous PNW population studies examining the relationships of genome-wide variation, mitochondrial haplogroup frequencies, and skeletal morphology with geography and language.

A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d.

Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748-12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years.

Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs.

Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct 'subfossil' lemur species, all of which were substantially larger (body mass ∼11-160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study subfossil lemur extinction biology and update our understanding of extant lemur conservation risk factors by i) reconstructing a comprehensive phylogeny of extinct and extant lemurs, and ii) testing whether low genetic diversity is associated with body size and extinction risk. We recovered complete or near-complete mitochondrial genomes from five subfossil lemur taxa, and generated sequence data from population samples of two extinct and eight extant lemur species. Phylogenetic comparisons resolved prior taxonomic uncertainties and confirmed that the extinct subfossil species did not comprise a single clade. Genetic diversity estimates for the two sampled extinct species were relatively low, suggesting small historical population sizes. Low genetic diversity and small population sizes are both risk factors that would have rendered giant lemurs especially susceptible to extinction. Surprisingly, among the extant lemurs, we did not observe a relationship between body size and genetic diversity. The decoupling of these variables suggests that risk factors other than body size may have as much or more meaning for establishing future lemur conservation priorities.

Patterns of admixture and population structure in native populations of Northwest North America.

The initial contact of European populations with indigenous populations of the Americas produced diverse admixture processes across North, Central, and South America. Recent studies have examined the genetic structure of indigenous populations of Latin America and the Caribbean and their admixed descendants, reporting on the genomic impact of the history of admixture with colonizing populations of European and African ancestry. However, relatively little genomic research has been conducted on admixture in indigenous North American populations. In this study, we analyze genomic data at 475,109 single-nucleotide polymorphisms sampled in indigenous peoples of the Pacific Northwest in British Columbia and Southeast Alaska, populations with a well-documented history of contact with European and Asian traders, fishermen, and contract laborers. We find that the indigenous populations of the Pacific Northwest have higher gene diversity than Latin American indigenous populations. Among the Pacific Northwest populations, interior groups provide more evidence for East Asian admixture, whereas coastal groups have higher levels of European admixture. In contrast with many Latin American indigenous populations, the variance of admixture is high in each of the Pacific Northwest indigenous populations, as expected for recent and ongoing admixture processes. The results reveal some similarities but notable differences between admixture patterns in the Pacific Northwest and those in Latin America, contributing to a more detailed understanding of the genomic consequences of European colonization events throughout the Americas.

Ancient DNA analysis of mid-holocene individuals from the Northwest Coast of North America reveals different evolutionary paths for mitogenomes.

To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga'a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor-descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.

Cranial morphological variation among contemporary Mexicans: Regional trends, ancestral affinities, and genetic comparisons.

Genetic research has documented geographical variation within Mexico that corresponds to trends in ancestry admixture from postcolonial times on. The purpose of this study is to determine whether craniometric variation among contemporary Mexicans is comparable to that reported in genetic studies. Standard osteometric measurements were taken on 82 male crania derived from forensic cases, with geographic origins of the specimens spanning over two-thirds of Mexico's states. To study similarities in regional clustering patterns with genetic data, k-means clustering analyses were performed, followed by chi-square tests of association between cluster assignments and geographic region of origin. Normal mixtures analyses were performed, centered on three "ancestral" sample proxies to estimate classification probability to each ancestry. The results demonstrate that the cranial morphological sample data cluster similarly to the regional groupings inferred from the genetic data. Additionally, the results indicate a gradient trend in population structure for contemporary Mexicans, with the proportion of Amerindian ancestry increasing from North to South while, conversely, European ancestry proportion estimates increase from South to North. Furthermore, the probabilities for classification of African ancestry remained low across the regions, again reflecting the results for the genetic data. Cranial morphological variation is well aligned with the genetic data for describing broad trends among Mexican populations, as well as yielding comparable estimates of general ancestry affiliations that reflect Mexico's history of Spanish contact and colonialism.

A simulation for exploring the effects of the "trait list" method's subjectivity on consistency and accuracy of ancestry estimations.

The nonmetric "trait list" methodology is widely used for estimating ancestry of skeletal remains. However, the effects of the method's embedded subjectivity on subsequent accuracy and consistency are largely unknown. We develop a mathematical simulation to test whether variation in the application of the "trait list" method alters the ancestry estimation for a given case. Our simulation explores how variations in (i) trait selection, (ii) number of traits employed, and (iii) ancestry choice thresholds affect the ancestry estimation of an unidentified skeleton. Using two temporally and geographically diverse samples, the simulation demonstrates that trait selection, trait quantity, threshold choices, and the exclusion of high-frequency traits had minimal effect on estimation of general ancestry. For all data sets and Runs, Accuracy(AS) was maintained above 90%. The authors close with a discussion on the logistical issues present when choosing traits, and how to avoid ancestry bias.