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

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

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 aim 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, in that we expected genetic variation to be more strongly explained by geographic proximity than 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, the AMOVA tests 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 compared with 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

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

A novel method of estimating facial ancestry using 3D images

Zaidi A., Claes P., Daniels K., Yao W., Hughes C.E., Malhi R.S., Shriver M.D., ''A novel method of estimating facial ancestry using 3D images'', American journal of physical anthropology, vol. 153, pp. 280-281, 2014 (83rd annual meeting of the American Association of Physical Anthropologists (AAPA), April 8-12, 2014, Calgary, Alberta, Canada).status: publishe

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

<div><p>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.</p></div

TMRCA estimates for the putative common ancestors of haplogroup C1d and subhaplogroup C1d3.

<p>BSP: Bayesian skyline plot. See Tables A and B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141808#pone.0141808.s004" target="_blank">S2 Text</a> for further details.</p><p>TMRCA estimates for the putative common ancestors of haplogroup C1d and subhaplogroup C1d3.</p