Biological Ancestry Research Articles

The Evolution of Forensic Genomics: Regulating Massively Parallel Sequencing.

Forensic genomics now enables law enforcement agencies to undertake rapid and detailed analysis of suspect samples using a technique known as massively parallel sequencing (MPS), including information such as physical traits, biological ancestry, and medical conditions. This article discusses the implications of MPS and provides ethical analysis, drawing on the concept of joint rights applicable to genomic data, and the concept of collective moral responsibility (understood as joint moral responsibility) that are applicable to law enforcement investigations that utilize genomic data. The widespread and unconstrained use of this technology without appropriate legal protections of individual moral rights and associated accountability mechanisms, could potentially not only involve violations of individual moral rights but also lead to an unacceptable shift in the balance of power between governments and the citizenry. We argue that in light of the rights of victims and the security benefits for society, there is a collective moral responsibility for individuals to submit their DNA to law enforcement and for MPS to be used where other, less invasive techniques are not effective. However, this application should be limited by legislation, including that any data obtained should be directly relevant to the investigation and should be destroyed at the conclusion of the investigation.

The Evolving Taxonomy of Progressive Creation

This essay is a critique of a version of progressive creation developed by Michael Chaberek, O. P. He holds that there are exceptions to evolutionary descent due to the supernatural production of “natural species,” taxa that allegedly do not have biological ancestry, are theologically identified with biblical kinds, and are metaphysically characterized by distinct substantial forms. Chaberek’s assertion that these natural species correspond “roughly” to the Linnaean taxa of biological families contradicts modern scientific conclusions regarding the continuity of evolutionary descent. To illustrate this conflict, I examine some of the extensive evidence for the evolutionary origins of families within the Feliformia sub-order. I conclude that Chaberek’s assertion of supernatural progressive creation is a God-of-the-gaps theology burdened by a defensive stance with respect to scientific progress.

Inclusive Heathens Practice Ancestor Veneration, But Not Pride in Ancestry

Ancestor veneration need not entail a focus on biological ancestry, but inclusive Heathens are troubled that white supremacists are attracted to Heathenry because of a perceived connection between ancestor veneration and pride in ancestry. The Canadian Heathens of Raven’s Knoll identify themselves as inclusive, and endeavor to exclude racists from their groups and events. Previous research has often distinguished between folkish (often racist) versus universalist (not racist) practitioners of Heathenry or Ásatrú. Inclusive Heathens welcome people of all backgrounds so long as they do not discriminate against others on the basis of spurious categories such as race, gender, or sexual orientation. Inclusive Heathens venerate a variety of ancestors, not just ancestors of blood or biological ancestors, but also ancestors of affinity or imagination, and ancestors of place. This contributes to a sense of relatedness and moral community beyond the intrahuman, and the development of ecological conscience at Raven’s Knoll.

The Magic of the Margins: Rethinking Healing from the Perspective of Queer Exile

The Magic of the Margins: Rethinking Healing from the Perspective of Queer Exile

Ashkenazi Anxieties: A Transnational Social History of Jewish Genetic Admixture Modeling, 1971-1986.

During the late 1970s and early 1980s, population geneticists sought computational solutions to integrate greater numbers of genetic traits into their debates about the ancestral relationships of human groups. At the same time, geneticists' longstanding assumptions about Jewish communities, especially Ashkenazim, were challenged by a series of social, political, and intellectual developments. In Israel, the entrenched cultural and political dominance of Ashkenazi Jews faced major social upheaval. Meanwhile, to counteract lingering anti-Semitism in Europe and the United States, Arthur Koestler's The Thirteenth Tribe and Raphael Patai and Jennifer Patai Wing's The Myth of the Jewish Race argued that Jewish identity was not connected to biological ancestry from the ancient Israelites. Drawing on scientific publications and archived correspondence, this article reconstructs a transnational social history showing how geneticists responded to these shifting claims about Ashkenazi identity and ancestry. Many argued that these claims could be tested using new statistical models, which provided allegedly more "objective" estimates of ancestral gene frequencies and histories of population admixture. However, they simultaneously engaged in heated debates over the relative superiority of competing statistical approaches. These debates reveal how the transnational reverberations of Israeli ethnic politics and Euro-American anti-Semitism affected the development of new calculations for genetic admixture, permanently shifting the assumptions of population genetic research on Jewish populations as well as other human groups.

Drogowskaz na rozdrożu. Życie i myśl Józefa Karola Potockiego (1854–1898)

Józef Karol Potocki vel Marian Bohusz (1854–1898) was very important and influential although forgotten thinker. His ideas of evolutionary socialism and ethnic nationalism were fundamental for both main Polish political formations of the 1st half of 20th century: Polish Socialist Party (and broader Piłsudski’s camp) and National Democracy. The very fundament of Potocki’s world-view was idea of any “cosmic energy” as prime mover of evolution. The evolution leads towards broader and broader, deeper and deeper integration, towards more complex societies. In opinion of Potocki socialism (as a system based on cooperation) would be natural result of this evolution. Historical and cultural heritage transform society into nation – community bonded by biological ancestry, economic cooperation and culture. This ethnic meaning of the Polish nation excluded Jewish minority. On the other hand, the real nation are the working people (especially peasants), not ruling classes. Nation needs an independent state as instrument of autonomous development, therefore Potocki was bitterly anti-Russian. Potocki tried to propagate the idea of a common front of socialists and nationalists for independence. Polarization of Polish public opinion in the end of 19th century made his efforts unsuccessful.

DIREITO DE CONHECIMENTO DA ASCENDÊNCIA BIOLÓGICA COMO DIREITO FUNDAMENTAL DA PERSONALIDADE

The present study seeks to understand the fundamental and inherent characteristics of the human personality. In this way, besides asking about the right of knowledge of biological ancestry, other fronts of questioning are opened. The research in question is composed of the following specific objectives: knowledge of access to genetic truth; understand the degree of relevance to human life when it comes to knowledge of genetic characteristics; to ascertain also the need to preserve the family nucleus, established through affective ties, essentially the security, protection and preservation of socio-affective affiliation; analyze the limits of the fundamental right to identity.

Identity and community structure in Neolithic Man Bac, northern Vietnam

This paper explores the evidence for social structuring principles and other aspects of identity at Man Bac, an early Neolithic (2066–1523 cal. BCE) community in northern Vietnam. Drawing on a wealth of work over the past 15 years, we examine identity with respect to three fundamental classes of data: intrinsic biological variables (age-at-death, sex, kin group, biological ancestry), mortuary treatment, and body modification (patterned tooth removal, or ablation). We find that kin groups, biologically and affinally defined, likely played a substantive structuring role at Man Bac. Moreover, a political tension between genetically and phenotypically distinct groups inhabiting Man Bac appears to be visible in the mortuary record. Social organization aside, shells appear to have had a significant role in referencing cosmological and gendered aspects of identity. Nephrite, with regard to some artefact types, would appear to cite magico-religious and/or elite status components of identity. While unique items, such as a ceramic copy of a barrel drum, may have spoken to exchanges of shamanistic beliefs between northern Vietnam and what is now southern China. Identity at Man Bac would appear to have been complex, fluid, negotiable, and ever changing; or just what one might expect.

Hispanic/Latinos and Skincare: Disparities in Product Development, Marketing, and Toxicity.

“Hispanic” and “Latino” (also known as Mestizo) describe a diverse racial and ethnic group, with a range of cultures, languages, and biological ancestry. It includes individuals of Mexican, Central-to-South American, and Spanish-Caribbean (eg, Cuban, Puerto Rican, and Dominican) descent.1 Individuals of Hispanic/Latino race and ethnicity represent a heterogenous group of people with different skin tones and Fitzpatrick phototypes. Hispanic/Latinos are the fastest growing population in the United States (US) - projected to increase from 55 million in 2014 to 119 million in 2060, an increase of 115%.2 By 2060, more than one-quarter (29%) of the US is projected to be Hispanic/Latino.2.

An overview of synthetic biology

Synthetic Biology is the combination of basic sciences with engineering. The aim of Synthetic Biology is to create, design, and redesign biological systems and devices to understand biological processes and to achieve useful and sophisticated functionalities to improve human welfare. When the engineering community took part in the discussion for the definition of Synthetic Biology, the idea of extraction and reassembly of “biological parts” along with the principles of abstraction, modularity, and standardization was introduced. Genetic Engineering is one of the many essential tools for synthetic biology, and even though they share the DNA manipulation basis and approach to intervene in the complexity of molecular biology, they differ in many aspects, and the two terms should not be used interchangeably. Some of the applications that have already been done by Synthetic Biology include the production of 1,4-butanediol (BDO), the antimalarial drug artemisinin, and the anticancer compound taxol. The potential of Synthetic Biology to design new genomes without immediate biological ancestry has raised ontological, political, economic, and ethical concerns based on the possibility that synthetic biology may be intrinsically unethical.

Going to the Root

This paper presents an attempt to reconstruct the most basic features of the language of Homo Sapiens, following the principle of monogenesis, namely the viewpoint that since humans share a common biological ancestry, they also share a common linguistic one. Considering this issue, the basic methods of comparative linguistics are briefly presented first, along with the methodological approach utilized herein, named Qualitative Inquiry. The results of the reconstructing process are presented, classified in terms of phonological, morphological, lexical, grammatical and syntactic aspects. Only bordering to the scope of this paper, a brief comparison of this treatise to previous studies reveals both convergence and discrepancy concerning the features of the language.

Three-dimensional (3D) geometric morphometric analysis of human premolars to assess sexual dimorphism and biological ancestry in Australian populations.

This study aimed to investigate size and shape variation of human premolars between Indigenous Australians and Australians of European ancestry, and to assess whether sex and ancestry could be differentiated between these groups using 3D geometric morphometrics. Seventy dental casts from each group, equally subdivided by sex, were scanned using a structured-light scanner. The 3D meshes of upper and lower premolars were processed using geometric morphometric methods. Seventy-two landmarks were recorded for upper premolars and 50 landmarks for lower premolars. For each tooth type, two-way ANOVA was used to assess group differences in centroid size. Shape variations were explored using principal component analysis and visualized using 3D morphing. Two-way Procrustes ANOVA was applied to test group differences for ancestry and sex, and a "leave-one-out" discriminant function was applied to assess group assignment. Centroid size and shape did not display significant difference between the sexes. Centroid size was larger in Indigenous Australians for upper premolars and lower second premolars compared to the Australians of European ancestry. Significant shape variation was noted between the two ancestral groups for upper premolars and the lower first premolar. Correct group assignment of individual teeth to their ancestral groups ranged between 80.0 and 92.8% for upper premolars and 60.0 and 75.7% for lower premolars. Our findings provide evidence of significant size and shape variation in human premolars between the two ancestral groups. High classification rates based on shape analysis of upper premolars highlight potential application of geometric morphometrics in anthropological, bioarcheological and forensic contexts.

Ancestry, Diversity & Finance: Evidence from Transition Economies

In this paper, we analyze the growth effects of historical and biological ancestry, diversity and financial development in transition economies. We show that the common indicators of ethnolinguistic fractionalization, state history and genetic distance yield significant results and to some extent transform the impact of finance on growth in East-Central Europe and the former Soviet Union. Deep ethnolinguistic cleavages produce insignificant results, whereas at intermediate and lower levels of aggregation diversity is likely to significantly improve the effect of finance on growth. Similarly to finer ethnolinguistic cleavages, genetic distance from the United States also favorably increases the relevance of financial development for growth. However, state history as a proxy for long-run ancestral exposure to institutions, political organization and centralization reinforces the negative growth effect of financial development. We argue that financial development is inclined to resolve problems arising from coordination failures and absence of trust in diverse societies by easing liquidity constraints and offering incentives for entrepreneurship to minority groups. In contrast, long state history is likely to generate extractive institutions that facilitate the provision of soft budget constraints. Genetic distance from the United States induces higher reliance on continental rather than AngloSaxon financing practices, and therefore increases dependence on banks rather than bonds or equity for external liquidity purposes.

Quantification of Maxillary Dental Arcade Curvature and the Estimation of Biological Ancestry in Forensic Anthropology.

Previous studies suggest that palate shape is a useful indicator of biological ancestry in human remains. This study evaluates interobserver error in ancestry estimation using palate shape and explores palate shape variation in Gullah (descendants of West Africans) and Seminole (Indigenous American) population samples using geometric morphometric analysis. Ten participants were asked to ascribe biological ancestry and shape to 28 dental casts based on a classification scheme employed in previous studies. The mean correct classification was 42.0%, indicating that the likelihood of assigning the correct ancestry is very poor and not significantly different from random assignment (p = 0.12). The accuracy analysis based on categorical classification of the casts was complemented by geometric morphometric analysis of nine 3D landmarks reflecting palate shape of 158 casts. Principal component analysis results show no difference between populations regarding palate shape, and cross-validated discriminant function analysis correctly classified only 62.0% of the specimens. Combined, these results show that previous methods to estimate ancestry are inaccurate and that this inaccuracy is probably due to a lack of palate shape differences between groups, rather than limitation of the analytical method per se. Therefore, we recommend caution should be used when choosing to apply the analysis of palate shape in forensically relevant contexts.

Abstract 3886: Comparing the mutational landscape of African American and Caucasian lung cancers

Abstract Background: The overall death rate from lung cancer is higher in African-Americans (AA) compared to Caucasians (CAU). Understanding differences in the prevalence and type of somatic alterations between races may illuminate differences in prognosis and lead to the reduction of outcome disparities by more precisely targeting patients’ treatment. Methods: Formalin-fixed paraffin embedded tumor samples were collected from Baptist Cancer Center, Memphis, TN. DNA was extracted and sonicated to 250 bp following Covaris FFPE DNA Extraction & Purification protocol and further purified using Agencourt AMPure XP beads. The OncoPanel_v2 target enrichment panel (Agilent SureSelect) was used for hybrid capture of 502 cancer-related genes. Samples were pooled and sequenced on an Illumina HiSeq2500 to a mean depth of coverage of 210x. Tumors with >30x sequencing depth over >80% of targeted bases were considered for analysis. MuTect and SomaticIndelDetector were used to identify somatic single nucleotide variants (SNVs) and short insertions or deletions (indels), respectively. As matched normal DNA was not available for these samples, analysis was limited to variants previously observed in tumors as described in the Catalogue of Somatic Mutations in Cancer (COSMIC) database, and variants were excluded if found in the germline dataset of the Exome Sequencing Project (ESP). Results: 510 tumor specimens from 242 Black and 268 White patients (with self-reported race) were analyzed including 320 adenocarcinomas and 142 squamous cell carcinomas. Pathological classification was independently reviewed and confirmed for 374 of 472 cases for an overall concordance rate of 79%. Using principle component analysis (PCA) on germline SNVs, we observed that the biological ancestry was different than the self-reported race for 1.5% of patients. Mutational frequencies for genes with known roles in adenocarcinoma such as KRAS and EGFR were not significantly different between tumors from Black and White patients (Fisher's exact p-value > 0.05). Amplification rates for NKX2-1, MET, MDM2, and MYC and homozygous deletion rates for CDKN2A were also not significantly different between populations. Translocations involving ALK and ROS1 were detected in tumors from Black patients demonstrating that these events are present in both populations. Similarly, mutational frequencies for genes such as PIK3CA and PTEN were not significantly different across populations in squamous cell carcinomas. Conclusions: These results demonstrate that lung cancers from Black patients are more similar to Whites than East Asians with respect to genes such as EGFR, and suggest that clinical trials of targeted therapies could significantly benefit patients in both populations. Citation Format: Joshua Campbell, Christopher Lathan, Lynette Sholl, Matthew Ducar, Mikenah Vega, Ling Lin, Aaron Thorner, Nick Faris, Paul van Hummelen, Raymond Osarogiagbon, Matthew Meyerson, Laura MacConaill. Comparing the mutational landscape of African American and Caucasian lung cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3886. doi:10.1158/1538-7445.AM2015-3886

Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities.

This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person’s physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically different levels of African or European ancestry. Genetic analysis of individual ancestry shows that some self-identified African Americans have up to 99% of European ancestry, whereas some self-identified European Americans have substantial admixture from African ancestry. Similarly, African ancestry in the Latino population varies between 3% in Mexican Americans to 16% in Puerto Ricans. The implication of this is that, in African American or Latino populations, self-reported ancestry may not be as accurate as direct assessment of individual genomic information in predicting treatment outcomes. To better understand human genetic variation in the context of health disparities, we suggest using “ancestry” (or biogeographical ancestry) to describe actual genetic variation, “race” to describe health disparity in societies characterized by racial categories, and “ethnicity” to describe traditions, lifestyle, diet, and values. We also suggest using ancestry informative markers for precise characterization of individuals’ biological ancestry. Understanding the sources of human genetic variation and the causes of health disparities could lead to interventions that would improve the health of all individuals.

Viral meningitis epidemics and a single, recent, recombinant and anthroponotic origin of swine vesicular disease virus.

Swine vesicular disease virus (SVDV) is a close relative of the human Enterovirus B serotype, coxsackievirus B5. As the etiological agent of a significant emergent veterinary disease, several studies have attempted to explain its origin. However, several key questions remain, including the full biological ancestry of the virus, and its geographical and temporal origin. We sequenced near-complete genomes of 27 SVDV and 13 coxsackievirus B5 samples, all originally isolated between 1966 and 2006, and analysed these in conjunction with existing sequences and historical information. While analyses incorporating 24 additional near-complete SVDV genomic sequences indicate clear signs of within-SVDV recombination, all 51 SVDV isolates remain monophyletic. This supports a hypothesis of a single anthroponotic transfer origin. Analysis of individual coding and non-coding regions supports that SVDV has a recombinant origin between coxsackievirus B5 and another Enterovirus B serotype, most likely coxsackievirus A9. Extensive Bayesian sequence-based analysis of the time of the most recent common ancestor of all analysed sequences places this within a few years around 1961. Epidemiological evidence points to China as an origin, but there are no available samples to test this conclusively. Historical investigation and the clinical aspects of the involved Enterovirus B serotypes, makes the current results consistent with a hypothesis stating that SVDV originated through co-infection, recombination, and a single anthroponotic event, during large viral meningitis epidemics around 1960/1961 involving the ancestral serotypes. The exact geographical origin of SVDV may remain untestable due to historical aspects.

Forensic STR loci reveal common genetic ancestry of the Thai-Malay Muslims and Thai Buddhists in the deep Southern region of Thailand.

Among the people living in the five deep Southern Thai provinces, Thai-Malay Muslims (MUS) constitute the majority, while the remaining are Thai Buddhists (BUD). Cultural, linguistic and religious differences between these two populations have been previously reported. However, their biological relationship has never been investigated. In this study, we aimed to reveal the genetic structure and genetic affinity between MUS and BUD by analyzing 15 autosomal short tandem repeats. Both distance and model-based clustering methods showed significant genetic homogeneity between these two populations, suggesting a common biological ancestry. After Islamization in this region during the fourteenth century AD, gradual albeit nonstatistically significant genetic changes occurred within these two populations. Cultural barriers possibly influenced these genetic changes. MUS have closer admixture to Malaysian-Malay Muslims than BUD countrywide. Admixture proportions also support certain degree of genetic dissimilarity between the two studied populations, as shown by the unequal genetic contribution from Malaysian-Malay Muslims. Cultural transformation and recent minor genetic admixture are the likely processes that shaped the genetic structure of both MUS and BUD.

On Racial Speculation and Racial Science

In June 2012, Sociological Theory published “The Genomic Challenge to the Social Construction of Race” by Jiannbin Lee Shiao, Thomas Bode, Amber Beyer, and Daniel Selvig. The article argues that “recent research on the human genome challenges the basic assumption that human races have no biological basis” (p. 68). The authors advance a “bounded nature” account of race to suggest that “biological ancestry” might lead to “different frequencies of personality and cognitive characteristics” by race (p. 83). In this response I investigate three propositions central to Shiao et al.’s argument: (1) the contention that contemporary genetics research has documented a biological basis to race, (2) the assertion that such research warrants inquiries into the way “biological ancestry” might “contribute to average group differences” by race (p. 83), and (3) the claim that there is no “essential characteristic” of their findings that might be complicit with biological racism.

Molar size and shape in the estimation of biological ancestry: A comparison of relative cusp location using geometric morphometrics and interlandmark distances

Human molars exhibit varying shapes when viewed from the occlusal surface. Available methods for quantifying molar occlusal shape have historically been confined to qualitative descriptions. The present study utilized geometric morphometric analyses to capture molar shape as defined through relative cusp locations. Cusp apices of maxillary and mandibular first and second molars were digitized from 190 American Blacks and Whites to estimate biological affinity through the shape of relative cusp locations. The coordinate data were subjected to a Generalized Procrustes Analysis to generate Procrustes coordinates and calculate centroid sizes. Procrustes coordinates were then subjected to a principal component analysis to examine the direction and magnitude of shape change inherent in the sample. Centroid size and major shape component group means were compared with t-tests. Interlandmark distances were then calculated from the raw coordinate information and also subjected to a principal components analysis. Procrustes coordinates and the principal components derived from them with and without centroid size, along with the interlandmark distances and the principal components derived from them, were each subjected to a discriminant function analysis to examine which methods yielded the highest correct classification between population groups. Total correct classifications ranged from 62.7% to 87.9% depending on the variables forward stepwise selected for each analysis. Using a combination of the second maxillary molar and first mandibular molar yielded the most optimistic results and corroborates theoretical models of molar development.