The contributions of admixture and genetic drift to diversity among post-contact populations in the Americas

Craniometric variation and the ancestry of modern humans

OBJECTIVES

Ancient and contemporary DNA provide information about geographic variation in the ancestry of present-day humans. All living populations have ancestry from early Homo sapiens originating in sub-Saharan Africa. Populations of Eurasian descent also have a small amount of Neandertal ancestry. This study examines whether craniometric distances between recent modern human samples reflect this geographic variation in ancestry. Among recent modern humans, Eurasians are expected to be more similar to Neandertals, whereas both sub-Saharan Africans and Eurasians are expected to be equidistant from early H. sapiens.

MATERIALS AND METHODS

Data on 33 craniometric traits from 2524 recent modern humans were compared with data from the literature for Neandertals and early H. sapiens. Mahalanobis distances were computed for each modern specimen to both the Neandertal and early H. sapiens means. These distances were examined for differences between recent humans from sub-Saharan Africa (N = 373) and those of Eurasian descent (N = 2151).

RESULTS

Eurasians as a group are significantly closer than sub-Saharan Africans to Neandertals. There is no significant difference between the distances of sub-Saharan Africans and Eurasians to early H. sapiens.

DISCUSSION

The differences between sub-Saharan Africans and Eurasians for both Neandertals and early H. sapiens are as expected. Although there has been geographic differentiation among recent modern humans, including differences in Neandertal admixture, these differences have not affected overall similarity of recent modern sub-Saharan Africans and Eurasians to the earliest samples of H. sapiens.

Comparative evaluation of arch form among the Nepalese population: A morphological study

Aims

The study aims to identify sexual dimorphic features in the arch patterns based on tooth arrangement patterns and the maxillary and mandibular arches using Euclidean Distance Matrix Analysis (EDMA).

Settings and Design

A total of 96 Nepalese subjects, aged 18 to 25 were assessed using casts and photographs.

Materials and Methods

Thirteen landmarks representing the most facial portions of the proximal contact areas on the maxillary and mandibular casts were digitised. Seventy-eight possible, Euclidean distances between the 13 landmarks were calculated using the Analysis ToolPak of Microsoft Excel®. The male-to-female ratios of the corresponding distances were computed and ratios were compared to evaluate the arch form for variation in the genders, among the Nepalese population.

Statistical Analysis Used

Microsoft Excel Analysis ToolPak and SPSS 20.0 (IBM Chicago) were used to perform EDMA and an independent t-test to compare the significant differences between the two genders.

Results

The maxillary arch's largest ratio (1.008179001) was discovered near the location of the right and left lateral incisors, indicating that the anterior region may have experienced the greatest change. The posterior-molar region is where the smallest ratio was discovered, suggesting less variation. At the intercanine region, female arches were wider than male ones; however, at the interpremolar and intermolar sections, they were similar in width. Females' maxillary arches were discovered to be bigger antero-posteriorly than those of males. The highest ratio (1.014336113) in the mandibular arch was discovered at the intermolar area, suggesting that males had a larger mandibular posterior arch morphology. At the intercanine area, the breadth of the arch form was greater in males and nearly the same in females at the interpremolar and intermolar regions. Female mandibular arch forms were also discovered to be longer than those of males from the anterior to the posterior.

Conclusions

The male and female arches in the Nepalese population were inferred to be different in size and shape. With references to the landmarks demonstrating such a shift, the EDMA established objectively the presence of square arch forms in Nepali males and tapering arch forms in Nepalese females.

Modelling speciation: Problems and implications

Darwin's and Wallace's 1859 explanation that novel speciation resulted from natural variants that had been subjected to selection was refined over the next 150 years as genetic inheritance and the importance of mutation-induced change were discovered, the quantitative theory of evolutionary population genetics was produced, the speed of genetic change in small populations became apparent and the ramifications of the DNA revolution became clear. This paper first discusses the modern view of speciation in its historical context. It then uses systems-biology approaches to consider the many complex processes that underpin the production of a new species; these extend in scale from genes to populations with the processes of variation, selection and speciation being affected by factors that range from mutation to climate change. Here, events at a particular scale level (e.g. protein network activity) are activated by the output of the level immediately below (i.e. gene expression) and generate a new output that activates the layer above (e.g. embryological development), with this change often being modulated by feedback from higher and lower levels. The analysis shows that activity at each level in the evolution of a new species is marked by stochastic activity, with mutation of course being the key step for variation. The paper examines events at each of these scale levels and particularly considers how the pathway by which mutation leads to phenotypic variants and the wide range of factors that drive selection can be investigated computationally. It concludes that, such is the complexity of speciation, most steps in the process are currently difficult to model and that predictions about future speciation will, apart from a few special cases, be hard to make. The corollary is that opportunities for novel variants to form are maximised.

Including diverse and admixed populations in genetic epidemiology research

The inclusion of ancestrally diverse participants in genetic studies can lead to new discoveries and is important to ensure equitable health care benefit from research advances. Here, members of the Ethical, Legal, Social, Implications (ELSI) committee of the International Genetic Epidemiology Society (IGES) offer perspectives on methods and analysis tools for the conduct of inclusive genetic epidemiology research, with a focus on admixed and ancestrally diverse populations in support of reproducible research practices. We emphasize the importance of distinguishing socially defined population categorizations from genetic ancestry in the design, analysis, reporting, and interpretation of genetic epidemiology research findings. Finally, we discuss the current state of genomic resources used in genetic association studies, functional interpretation, and clinical and public health translation of genomic findings with respect to diverse populations.

Ancestry and admixture of a southernmost Chilean population: The reflection of a migratory history

OBJECTIVES

Punta Arenas is a Chilean city situated on ancestral Aönikenk territory. The city was founded by 19th- and 20th-century colonists from Chile (Chiloé) and Europe (Croatia). This work uses uniparental and ancestry-informative markers (AIMs) to explore the effects of historic migratory and admixture patterns on the current genetic composition of Punta Arenas.

METHODS

We analyzed mitochondrial DNA (mtDNA), Y-chromosome single-nucleotide polymorphisms (SNPs), and 141 AIMs obtained from 129 DNA samples from male residents with regional ancestry. After characterizing uniparental lineages and ancestry proportions, multivariate analysis was used to explore relationships among the various types of data.

RESULTS

Punta Arenas has an admixed population with three main genetic components: European (56.5%), northern Native (11.3%), and south-central Native (28.6%). The Native component is preponderant in the mtDNA (83.76%), while the foreign component predominates in the Y-chromosome (92.25%). Non-Native mtDNA lineages are associated with European genetic ancestry, and Native mtDNA lineages originated mainly in the southern and southernmost regions of Chile. Most non-Native Y-chromosome SNPs originated in Spain, and secondly, in Croatia.

CONCLUSIONS

The population of Punta Arenas is mainly of Chilote origin with south-central Native and Spanish ancestral components, as well as some Croatian components. The persistence of local Native lineages is notable, suggesting continuity with the ancestral populations of the region such as the Kawésqar, Aönikenk, Yámana, or Selknam peoples. This study contributes to our knowledge of local history and its links to national and global developments in genetic ancestry.

Geographic and temporal diversity in dental morphology reflects a history of admixture, isolation, and drift in African Americans

OBJECTIVES

While genetic studies have documented variation in admixture proportions in contemporary African Americans across the US, relatively little is known about the socio-historical roots of this variation. Our goal in this study is to use dental morphology to explore the socio-historical correlates of admixture, localized gene flow, and drift in African Americans.

METHODS

Our data are ordinally-graded dental morphological traits scored in 196 Africans, 335 Europeans and European Americans, 291 pre-Spanish-contact Native Americans, and 722 African Americans. The African American data derived from contemporary and historic samples. We eliminated from analysis individuals and traits with greater than 20% missing data. We summarized the major axes of trait variation using principal component analysis (PCA), estimated biological distance, constructed multidimensional scaling (MDS) plots of the distances, and measured the correlation between geographic and biological distance.

RESULTS

In the PCA, African American groups clustered between Africans and Europeans on PC 1, reflecting admixture between the groups. PC 2 separated African American samples, possibly reflecting movement, isolation, and drift. MDS analyses confirmed the existence of sizable biological distances between African American samples, especially between contemporary and past African American samples. We found no relationship between biological and geographic distances.

DISCUSSION

We demonstrate that admixture and drift can be inferred from multi-variable analyses of patterns of dental morphology in admixed populations. Localized gene flow has not affected patterns of trait variation in African Americans, but long-range movement, isolation, and drift have. We connect patterns of dental trait variation to efforts to flee oppression during the Great Migration, and the repeal of anti-miscegenation laws.

Colonialism and the co-evolution of ethnic and genetic structure in New Mexico

OBJECTIVE

Socially constructed ethnic identities are frequently rooted in beliefs about common descent that form when people with disparate cultures, languages, and biology come into contact. This study explores connections between beliefs about common descent, as represented by ethnic nomenclatures, and histories of migration and isolation ascertained from genomic data in New Mexicans of Spanish-speaking descent (NMS).

MATERIALS AND METHODS

We interviewed 507 NMS who further identified using one of seven ethnic terms that they associated with beliefs about connections to past ancestors. For groups of individuals who identified using each term, we estimated biogeographic ancestry, fit admixture models to ancestry distributions, and partitioned genetic distance into admixture and drift components.

RESULTS

Regardless of which ethnic term they used, all NMS had appreciable Native American (avg. 27%) and European ancestry (avg.71%). However, individuals who identified using terms associated with beliefs connecting them to colonial-period Spanish ancestors had significantly higher European ancestry than individuals who identified using terms associated with ancestral connections to post-colonial-period migrants from Mexico. Model-fitting analyses show that this ancestry difference reflects post-colonial gene flow with non-NMS European Americans, not colonial-period gene flow with Spaniards. Drift, not admixture, accounted for most of the genetic distance between NMS who expressed connections to Mexican versus Spanish ancestors, reflecting relative isolation of New Mexico and Mexico through the 19th century.

DISCUSSION

Patterns of genomic diversity in NMS are consistent with beliefs about common descent in showing that New Mexico was isolated for generations following initial colonization. They are inconsistent with these beliefs in showing that all NMS have substantial European and Native American ancestry, and in showing that a proportion of European ancestry derives from post-colonial-period admixture with non-NMS European Americans. Our findings provide insights into the construction of ethnic identity in contexts of migration and isolation in New Mexico and, potentially, throughout human prehistory.

Exploring insertions and deletions (indels) of MSRB3 gene and their association with growth traits in four Chinese indigenous cattle breeds

Methionine sulfoxide reductase B3 (MSRB3) is instrumental in ossification and fat deposition, which regulate the growth and development of cattle directly. The purpose of this study was aimed to explore insertions and deletions (indels) in MSRB3 gene and investigate their association with growth traits in four indigenous cattle breeds (Luxi cattle, Qinchuan cattle, Nanyang cattle, and Jiaxian Red cattle). Four indels were identified by sequencing with DNA pool. Association analysis showed that three of them were associated with growth traits (P<0.05). For P1, the DD (deletion and deletion) genotype was significantly associated with body length of Nanyang cattle; for P6, II (insertion and insertion) and/or DD genotypes were significantly associated with enhanced growth traits of Qinchuan cattle; for P7, II genotype was significantly associated with hucklebone width of Luxi cattle. Our results demonstrated that the polymorphisms in bovine MSRB3 gene were significantly associated with growth traits, which could be candidate loci for marker-assisted selection (MAS) in cattle breeding.

Body shape: Implications in the study of obesity and related traits

OBJECTIVES

The diagnosis and treatment of obesity are usually based on traditional anthropometric variables including weight, height, and several body perimeters. Here we present a three-dimensional (3D) image-based computational approach aimed to capture the distribution of abdominal adipose tissue as an aspect of shape rather than a relationship among classical anthropometric measures.

METHODS

A morphometric approach based on landmarks and semilandmarks placed upon the 3D torso surface was performed in order to quantify abdominal adiposity shape variation and its relation to classical indices. Specifically, we analyzed sets of body cross-sectional circumferences, collectively defining each, along with anthropometric data taken on 112 volunteers. Principal Component Analysis (PCA) was performed on 250 circumferences located along the abdominal region of each volunteer. An analysis of covariance model was used to compare shape variables (PCs) against anthropometric data (weight, height, and waist and hip circumferences).

RESULTS

The observed shape patterns were mainly related to nutritional status, followed by sexual dimorphism. PC1 (12.5%) and PC2 (7.5%) represented 20% of the total variation. In PCAs calculated independently by sex, linear regression analyses provide statistically significant associations between PC1 and the three classical indexes: body mass index, waist-to-height ratio, and waist-hip ratio.

CONCLUSION

Shape indicators predict well the behavior of classical markers, but also evaluate 3D and geometric features with more accuracy as related to the body shape under study. This approach also facilitates diagnosis and follow-up of therapies by using accessible 3D technology.

High-resolution HLA allele and haplotype frequencies in majority and minority populations of Costa Rica and Nicaragua: Differential admixture proportions in neighboring countries

The HLA system shows the most extensive polymorphism in the human genome. Allelic and haplotypic frequencies of HLA genes vary dramatically across human populations. Due to a complex history of migration, populations in Latin America show a broad variety of admixture proportions, usually varying not only between countries, but also within countries. Knowledge of HLA allele and haplotype frequencies is essential for medical fields such as transplantation, but also serves as a means to assess genetic diversity and ancestry in human populations. Here, we have determined high-resolution HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a sample of 713 healthy subjects from three Mestizo populations, one population of African descent, and Amerindians of five different groups from Costa Rica and Nicaragua and compared their profiles to a large set of indigenous populations from Iberia, Sub-Saharan Africa, and the Americas. Our results show a great degree of allelic and haplotypic diversity within and across these populations, with most extended haplotypes being private. Mestizo populations show alleles and haplotypes of putative European, Amerindian, and Sub-Saharan African origin, albeit with differential proportions. Despite some degree of gene flow, Amerindians and Afro-descendants show great similarity to other Amerindian and West African populations, respectively. This is the first comprehensive study reporting high-resolution HLA diversity in Central America, and its results will shed light into the genetic history of this region while also supporting the development of medical programs for organ and stem cell transplantation.