Self-Reported Ancestry and Craniofacial SNPs

Genotype-phenotype studies increasingly link single nucleotide polymorphism (SNPs) to the dimensions of the face for presumed homogeneous populations. To appreciate the significance of these findings, it is essential to investigate how these results differ between the genetic and phenotypic profiles of individuals. In prior work, we investigated the connection between SNPs previously identified as informative of soft tissue expression and measurements of the craniofacial skeleton. Using matched genetic and skeletal information on 17 individuals who self-identified as White with presumed common continental ancestry (European), we obtained significant Spearman correlations for 11 SNPs. In the present study, we looked at self-identified ancestry to understand the intersectional background of the individual’s phenotype and genotype. We integrated our samples within a diverse dataset of 2,242 modern Americans and applied an unsupervised model-based clustering routine to 13 craniometrics. We generated a mean estimate of 69.65% (±SD = 18%) European ancestry for the White sample under an unsupervised cluster model. We estimated higher quantities of European ancestry, 88.5%–93%, for our subset of 17 individuals. These elevated estimates were of interest with respect to the distribution of population-informative SNPs; we found, for example, that one of our sampled self-identified White individuals displayed SNPs commonly associated with Latin American populations. These results underscore the complex interrelationship between environment and genetics, and the need for continued research into connections between population affinity, social identity, and morphogenetic expression.

Craniometric Variation in a Regional Sample from Antioquia, Medellín, Colombia

Population affinity estimation is frequently assessed from measurements of the cranium. Traditional models place individuals into discrete groups―such as Hispanic―that often encompass very diverse populations. Current research, including this study, challenges these assumptions using more refined population affinity estimation analyses. We examine craniometric data for a sample of individuals from different regions in Antioquia, Colombia. We first assessed the sample to understand intraregional variation in cranial shape as a function of birthplace or a culturally constructed social group label. Then, pooling the Colombian data, we compare cranial variation with global contemporary and prehistoric groups. Results did not indicate significant intraregional variation in Antioquia; classification models performed poorly (28.6% for birthplace and 36.6% for social group). When compared to other groups (American Black, American White, Asian, modern Hispanic, and prehistoric Native American), our model correctly classified 75.5% of the samples. We further refined the model by separating the pooled Hispanic sample into Mexican and Guatemalan samples, which produced a correct classification rate of 74.4%. These results indicate significant differences in cranial form among groups commonly united under the classification “Hispanic” and bolster the addition of a refined approach to population affinity estimation using craniometric data.

Assumed Differences; Unquestioned Typologies

Forensic anthropologists traditionally estimate “race” or “ancestry” as part of the biological profile. While practitioners may have changed the terms used to describe regionally patterned human skeletal variation, the degree to which they have altered their typological approaches remains unclear. This study analyzed 119 peer-reviewed forensic anthropology articles published in four relevant journals (1966–2020) by matching combination(s) of the key words “race,” “ancestry,” “ethnicity,” and/or “population affinity.” Results indicated that while “ancestry” has supplanted “race,” this change has not brought concurrent modifications in approach, nor deeper scrutiny of underlying concepts. “Race” and “ancestry” were infrequently defined in 13% and 12% of sampled articles, respectively, and a plethora of social, geographic, and pseudoscientific terms persisted. Forensic anthropologists increasingly engaged with questions addressing the forces patterning human biological variation: 65% of studies postdating 1999 discussed population histories/structures and microevolution; 38% between 1966–1999. Fewer studies contextualized or critiqued approaches to analyzing population variation (32% of studies postdating 1999; 4% from 1966–1999), and virtually no studies considered the possibility that skeletal variation reflected embodied social inequity (5% of studies postdating 1999; 0% from 1966–1999). This lack of interrogation and clarity contributes to the faulty notion that all forensic anthropologists share similar definitions and leads to an oversimplification of complex biocultural processes. While the lack ofdefinitions and biocultural engagement may be partly due to editorial and peer-review pressures, it is likely that many forensic anthropologists have not interrogated their own perspectives. This article holds that it is essential for us to do so.

Population affinity and variation of sexual dimorphism in three-dimensional facial forms: comparisons between Turkish and Japanese populations

Examining the extent to which sex differences in three-dimensional (3D) facial soft tissue configurations are similar across diverse populations could suggest the source of the indirect evolutionary benefits of facial sexual dimorphism traits. To explore this idea, we selected two geographically distinct populations. Three-dimensional model faces were derived from 272 Turkish and Japanese men and women; their facial morphologies were evaluated using landmark and surface-based analyses. We found four common facial features related to sexual dimorphism. Both Turkish and Japanese females had a shorter lower face height, a flatter forehead, greater sagittal cheek protrusion in the infraorbital region but less prominence of the cheek in the parotid-masseteric region, and an antero-posteriorly smaller nose when compared with their male counterparts. The results indicated the possible phylogenetic contribution of the masticatory organ function and morphogenesis on sexual dimorphism of the human face in addition to previously reported biological and psychological characteristics, including sexual maturity, reproductive potential, mating success, general health, immune response, age, and personality.

The Y chromosome ancestry marker R1b1b2: a surrogate of the SARS-CoV-2 population affinity

Individual and population susceptibilities to disease remain a murky area of investigation, clouded by past bias based on ideological differences and wars. The current SARS-CoV-2 pandemic, the largest in living memory, brought this matter to forefront as the disparity in disease burden became apparent. A timeline analysis of the pandemic revealed the presence of country clusters that display a marked preponderance of disease among populations carrying the ancestry marker R1b1b2, notably associated with both infection and mortality. This marker is a relic of past human expansions from western Asia and subsequently Europe and the rest of the world, which may have been accompanied by peculiar biological events rendering these populations vulnerable to SARS-CoV-2.

Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers

Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis and gives insight on the mechanisms through which antigen availability controls the rate of maturation and the expansion of the antibody population. It is also capable, upon maximum-likelihood inference of the parameters, to reproduce accurately the distributions of affinities of IgG-secreting cells we measure in mice immunized against Tetanus Toxoid under largely varying conditions (antigen dosage, delay between injections). Both model and experiments show that the average population affinity depends non-monotonically on the antigen dosage. We show that combining quantitative modeling and statistical inference is a concrete way to investigate biological processes underlying affinity maturation (such as selection permissiveness), hardly accessible through measurements.

Quantitative modeling of the effect of antigen dosage on B-cell affinity distributions in maturating germinal centers

Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis, and gives insight on the mechanisms through which antigen availability controls the rate of maturation and the expansion of the antibody population. It is also capable, upon maximum-likelihood inference of the parameters, to reproduce accurately the distributions of affinities of IgG-secreting cells we measure in mice immunized against Tetanus Toxoid under largely varying conditions (antigen dosage, delay between injections). Both model and experiments show that the average population affinity depends non-monotonically on the antigen dosage. We show that combining quantitative modelling and statistical inference is a concrete way to investigate biological processes underlying affinity maturation (such as selection permissiveness), hardly accessible through measurements.

Testing the utility of dental morphological trait combinations for inferring human neutral genetic variation

Researchers commonly rely on human dental morphological features in order to reconstruct genetic affinities among past individuals and populations, particularly since teeth are often the best preserved part of a human skeleton. Tooth form is considered to be highly heritable and selectively neutral and, therefore, to be an excellent proxy for DNA when none is available. However, until today, it remains poorly understood whether certain dental traits or trait combinations preserve neutral genomic signatures to a greater degree than others. Here, we address this long-standing research gap by systematically testing the utility of 27 common dental traits and >134 million possible trait combinations in reflecting neutral genomic variation in a worldwide sample of modern human populations. Our analyses reveal that not all traits are equally well-suited for reconstructing population affinities. Whereas some traits largely reflect neutral variation and therefore evolved primarily as a result of genetic drift, others can be linked to nonstochastic processes such as natural selection or hominin admixture. We also demonstrate that reconstructions of population affinity based on many traits are not necessarily more reliable than those based on only a few traits. Importantly, we find a set of highly diagnostic trait combinations that preserve neutral genetic signals best (up to x∼r = 0.580; 95% r range = 0.293 to 0.758; P = 0.001). We propose that these trait combinations should be prioritized in future research, as they allow for more accurate inferences about past human population dynamics when using dental morphology as a proxy for DNA.