Stress is known to affect health throughout life and into future generations, but the underlying molecular mechanisms are unknown. We tested the hypothesis that maternal psychosocial stress influences DNA methylation (DNAm), which in turn impacts newborn health outcomes. Specifically, we analyzed DNAm at individual, regional, and genome-wide levels to test for associations with maternal stress and newborn birth weight. Maternal venous blood and newborn cord blood (n = 24 and 22, respectively) were assayed for methylation at ∼450,000 CpG sites. Methylation was analyzed by examining CpG sites individually in an epigenome-wide association study (EWAS), as regional groups using variably methylated region (VMR) analysis in maternal blood only, and through the epigenome-wide measures using genome-wide mean methylation (GMM), Horvath's epigenetic clock, and mitotic age. These methylation measures were tested for association with three measures of maternal stress (maternal war trauma, chronic stress, and experience of sexual violence) and one health outcome (newborn birth weight). We observed that maternal experiences of war trauma, chronic stress, and sexual assault were each associated with decreased newborn birth weight (p < 1.95 × 10-7 in all cases). Testing individual CpG sites using EWAS, we observed no associations between DNAm and any measure of maternal stress or newborn birth weight in either maternal or cord blood, after Bonferroni multiple testing correction. However, the top-ranked CpG site in maternal blood that associated with maternal chronic stress and sexual violence before multiple testing correction is located near the SPON1 gene. Testing at a regional level, we found increased methylation of a VMR in maternal blood near SPON1 that was associated with chronic stress and sexual violence after Bonferroni multiple testing correction (p = 1.95 × 10-7 and 8.3 × 10-6, respectively). At the epigenomic level, cord blood GMM was associated with significantly higher levels of war trauma (p = 0.025) and was suggestively associated with sexual violence (p = 0.053). The other two epigenome-wide measures were not associated with maternal stress or newborn birth weight in either tissue type. Despite our small sample size, we identified associations even after conservative multiple testing correction. Specifically, we found associations between DNAm and the three measures of maternal stress across both tissues; specifically, a VMR in maternal blood and GMM in cord blood were both associated with different measures of maternal stress. The association of cord blood GMM, but not maternal blood GMM, with maternal stress may suggest different responses to stress in mother and newborn. It is noteworthy that we found associations only when CpG sites were analyzed in aggregate, either as VMRs or as a broad summary measure of GMM.
The genetic composition of Amerindian descendants from Patagonia has long been a focus of interest, although the information available is still scarce for many geographic areas. Here, we report the first analysis of the variation in the mitochondrial DNA (mtDNA) control region for an area of northwestern Patagonia, the North of Neuquén, with the aim of studying the processes and historical events that modeled the evolutionary history of these human groups. We analyzed 113 individuals from two localities of northern Neuquén, along with 6 from southern Neuquén and 223 previously published mtDNA sequences from neighboring areas in Argentina and Chile. We estimated the haplotypic variation and spatial structure of molecular variability. Amerindian subhaplogroups predominate in the two samples from northern Neuquén (n = 70), with D1g and C1b13 the most represented, although in different proportions. These samples exhibit Amerindian mtDNA haplotypes similar to the variants from neighboring areas. Most of haplotype variability was within group; variation among groups was relatively low and scarcely associated with geographical space. The most frequent subhaplogroups in northern Neuquén are characteristic of native populations from Patagonia and Chilean Araucanía, and probably originated in the region during the Late Pleistocene or Early Holocene. However, the spatial variation of mtDNA haplotypes departs from a latitudinal pattern and suggests differential levels of gene flow among areas during the Late Holocene, with moderate levels across the North of Neuquén as well as between this area and neighboring populations from Chile, the South of Neuquén, and Río Negro.
Isolation-by-distance models are part of the institutional creed of antiracialism used to critique claims of biological race concepts (BRCs). Proponents of antiracialism appeal to isolation-by-distance models to describe patterns of human genetic differences among and between groups as a function of distance. Isolation by distance has been referred to as the pattern that human genetic variation fits, distributing the differences we see as race throughout geographic space as a series of Gaussian gradients. Contemporary scientific critiques of BRCs fuse social constructionist race concepts with a description of the distribution of proportions of human genetic variation in geographic space as a function of distance. These two points are often followed by statements noting that there is only one human race. How these two concepts connect to each other, and whether or not they connect at all, is unclear in both academic and nonacademic spaces. Consequently, scientists and the public lack an understanding of human population structure and its relationships to varying systems of human interactions. This article reviews isolation-by-distance models in population genetics and the use of these models in the modern problem of human difference. The article presents a historical and conceptual review of isolation-by-distance models and contemporary scientific critiques of BRCs, followed by examples of the use of isolation-by-distance models in studies of human genetic variation. To address the shortcomings in the scientific critique of race, the author proposes combining Du Boisian demography with Darwinian evolutionary biology. From a Du Boisian demographic perspective, race is a product of racism, or race/ism, and is a heredity and inheritance system based on rules of partus sequitur ventrem and hypodescent. Race marks individuals and groups them to reproduce unequal relationships into which Europeans co-opted them. This synthesis propounds a new racial formation theory to understand the more general consequences of racism on genes and health outcomes.
The Tlingit from Southeast Alaska belong to the Northwest Coast cultural tradition, which is defined by regionally shared sociocultural practices. A distinctive feature of Tlingit social organization is the matrilineal exogamous marriage system among clans from two opposite moieties: the Raven/Crow and Eagle/Wolf. Clan and moiety membership are determined by matrilineal descent, and previous genetic studies of Northwest Coast populations have shown a relationship between clan membership and genetic variation of matrilines and patrilines. To further understand this association, in this study mitochondrial DNA sequences from the Tlingit (n = 154) were examined. By comparing mitochondrial DNA with moiety membership information, the authors explore the impact of marriage traditions among the Tlingit with their observable genetic variation. At the genetic level, the results support cultural persistence of Tlingit maternal moiety identity despite the negative impacts of European colonization. This study additionally illustrates the relevance of data derived from Tlingit oral traditions to test hypotheses about population history on the Northwest Coast.
We have previously hypothesized that relatively small and isolated rural communities may experience founder effects, defined as the genetic ramifications of small population sizes at the time of a community's establishment. To explore this, we used an Illumina Infinium Omni2.5Exome-8 chip to collect data from 157 individuals from four Illinois communities, three rural and one urban. Genetic diversity estimates of 999,259 autosomal markers suggested that the reduction in heterozygosity due to shared ancestry was approximately 0, indicating a randomly mating population. An eigenanalysis, which is similar to a principal component analysis but run on a genetic coancestry matrix, conducted in the SNPRelate R package revealed that most of these individuals formed one cluster, with a few putative outliers obscuring population variation. An additional eigenanalysis on the same markers in a combined data set including the 2,504 individuals in the 1000 Genomes database found that most of the 157 Illinois individuals clustered into one group in close proximity to individuals of European descent. A final eigenanalysis of the Illinois individuals with the 503 individuals of European descent (within the 1000 Genomes Project) revealed two clusters of individuals and likely two source populations; one British and one consisting of multiple European subpopulations. We therefore demonstrate the feasibility of examining genetic relatedness across Illinois populations and assessing the number of source populations using publicly available databases. When assessed, population structure information can contribute to the understanding of genetic history in rural populations.
In northeast Argentina, different Amerindian communities share territory and history with settlers, mainly Europeans. Due to miscegenation, the current Argentinean population has a particular structure that can be described through X chromosome variation. The objectives of this study were to describe the variation of 10 X-chromosome short tandem repeats (X-STRs) in urban populations of the Argentinean regions known as Gran Chaco and Mesopotamia, report the forensic parameters of these STRs, and estimate the European and indigenous genetic components in these regions. Population and forensic parameters were estimated for 419 individuals from the analyzed populations, including two indigenous groups, Wichí and Mocoví, previously reported. Population structure was estimated through FST and RST distances and analysis of molecular variance. The indigenous American and European components were assessed with STRUCTURE. X-STRs showed a high level of genetic variability in urban and indigenous populations. Indigenous people of the Gran Chaco region showed significant differentiation from the urban samples (FST = 5.5%) and among themselves (FST = 5.3%). Genetic differentiation among urban groups was almost negligible, except that the population from Misión Nueva Pompeya differed from the rest of the city populations. Forensic parameters indicate that these X-STRs are useful as a complement to paternity tests. The set of 10 STRs could be a good tool for examining population differences.
Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size.
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