Structure Of Human Populations Research Articles

Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji.

Dengue is a major health burden, but it can be challenging to examine transmission and evaluate control measures because outbreaks depend on multiple factors, including human population structure, prior immunity and climate. We combined population-representative paired sera collected before and after the 2013/14 dengue-3 outbreak in Fiji with surveillance data to determine how such factors influence transmission and control in island settings. Our results suggested the 10-19 year-old age group had the highest risk of infection, but we did not find strong evidence that other demographic or environmental risk factors were linked to seroconversion. A mathematical model jointly fitted to surveillance and serological data suggested that herd immunity and seasonally varying transmission could not explain observed dynamics. However, the model showed evidence of an additional reduction in transmission coinciding with a vector clean-up campaign, which may have contributed to the decline in cases in the later stages of the outbreak.

Complete Anopheles funestus mitogenomes reveal an ancient history of mitochondrial lineages and their distribution in southern and central Africa

Anopheles funestus s.s. is a primary vector of malaria in sub-Saharan Africa. Despite its important role in human Plasmodium transmission, evolutionary history, genetic diversity, and population structure of An. funestus in southern and central Africa remains understudied. We deep sequenced, assembled, and annotated the complete mitochondrial genome of An. funestus s.s. for the first time, providing a foundation for further genetic research of this important malaria vector species. We further analyzed the complete mitochondrial genomes of 43 An. funestus s.s. from three sites in Zambia, Democratic Republic of the Congo, and Tanzania. From these 43 mitogenomes we identified 41 unique haplotypes that comprised 567 polymorphic sites. Bayesian phylogenetic reconstruction confirmed the co-existence of two highly divergent An. funestus maternal lineages, herein defined as lineages I and II, in Zambia and Tanzania. The estimated coalescence time of these two mitochondrial lineages is ~500,000 years ago (95% HPD 426,000–594,000 years ago) with subsequent independent diversification. Haplotype network and phylogenetic analysis revealed two major clusters within lineage I, and genetic relatedness of samples with deep branching in lineage II. At this time, data suggest that the lineages are partially sympatric. This study illustrates that accurate retrieval of full mitogenomes of Anopheles vectors enables fine-resolution studies of intraspecies genetic relationships, population differentiation, and demographic history. Further investigations on whether An. funestus mitochondrial lineages represent biologically meaningful populations and their potential implications for malaria vector control are warranted.

Testing Modern Human Out-of-Africa Dispersal Models Using Dental Nonmetric Data

The mode and timing of the dispersal of modern humans out of Africa and into Eurasia has important implications for the genetic and phenotypic structure of extant human populations. However, no consensus exists on the number, geographic route, and chronology of dispersal events. In this paper, we review competing dispersal models and evaluate their spatial and temporal predictions against geographical distances between population samples and measures of population differentiation derived from nonmetric dental data. The implications of our results for the modern human expansion into Asia are discussed.

Testing Modern Human Out-of-Africa Dispersal Models Using Dental Nonmetric Data

The mode and timing of the dispersal of modern humans out of Africa and into Eurasia has important implications for the genetic and phenotypic structure of extant human populations. However, no consensus exists on the number, geographic route, and chronology of dispersal events. In this paper, we review competing dispersal models and evaluate their spatial and temporal predictions against geographical distances between population samples and measures of population differentiation derived from nonmetric dental data. The implications of our results for the modern human expansion into Asia are discussed.

AB007. Search of signals for cold adaptation in native populations of Siberia by whole exome sequencing

Background: Adaptation to cold climate, mediated by natural selection has played the substantial role in shaping the genetic and phenotypic structure of human populations settled in Siberia and North Asia. Goal of this work was to characterize the portion of genetic diversity in coding regions of the genome in native Siberian and North Asian populations, potentially adaptive for cold climate conditions.

Genomic landscape of human diversity across Madagascar

Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

Are Clusters Races? A Discussion of the Rhetorical Appropriation of Rosenberg et al.’s “Genetic Structure of Human Populations”

Noah Rosenberg et al.'s 2002 article “Genetic Structure of Human Populations” reported that multivariate genomic analysis of a large cell line panel yielded reproducible groupings (clusters) suggestive of individuals' geographical origins. The paper has been repeatedly cited as evidence that traditional notions of race have a biological basis, a claim its authors do not make. Critics of this misinterpretation have often suggested that it follows from interpreters' personal biases skewing the reception of an objective piece of scientific writing. I contend, however, that the article itself to some degree facilitates this misrepresentation. I analyze in detail several verbal and visual features of the original article that may predispose aspects of its racial interpretation; and, tracing the arguments of one philosopher and one popular science writer, I show how these features are absorbed, transformed into arguments for a biological basis of race, and re-attributed to the original. The essay demonstrates how even slight ambiguities can enable the misappropriation of scientific writing, unintentionally undermining the authors' stated circumspection on the relationship between cluster and race.

Assessing footprints of natural selection through PCA analysis in cattle

Assessing footprints of natural selection through PCA analysis in cattle

Human ancestry correlates with language and reveals that race is not an objective genomic classifier

Genetic and archaeological studies have established a sub-Saharan African origin for anatomically modern humans with subsequent migrations out of Africa. Using the largest multi-locus data set known to date, we investigated genetic differentiation of early modern humans, human admixture and migration events, and relationships among ancestries and language groups. We compiled publicly available genome-wide genotype data on 5,966 individuals from 282 global samples, representing 30 primary language families. The best evidence supports 21 ancestries that delineate genetic structure of present-day human populations. Independent of self-identified ethno-linguistic labels, the vast majority (97.3%) of individuals have mixed ancestry, with evidence of multiple ancestries in 96.8% of samples and on all continents. The data indicate that continents, ethno-linguistic groups, races, ethnicities, and individuals all show substantial ancestral heterogeneity. We estimated correlation coefficients ranging from 0.522 to 0.962 between ancestries and language families or branches. Ancestry data support the grouping of Kwadi-Khoe, Kx’a, and Tuu languages, support the exclusion of Omotic languages from the Afroasiatic language family, and do not support the proposed Dené-Yeniseian language family as a genetically valid grouping. Ancestry data yield insight into a deeper past than linguistic data can, while linguistic data provide clarity to ancestry data.

A longitudinal cline characterizes the genetic structure of human populations in the Tibetan plateau.

Indigenous populations of the Tibetan plateau have attracted much attention for their good performance at extreme high altitude. Most genetic studies of Tibetan adaptations have used genetic variation data at the genome scale, while genetic inferences about their demography and population structure are largely based on uniparental markers. To provide genome-wide information on population structure, we analyzed new and published data of 338 individuals from indigenous populations across the plateau in conjunction with worldwide genetic variation data. We found a clear signal of genetic stratification across the east-west axis within Tibetan samples. Samples from more eastern locations tend to have higher genetic affinity with lowland East Asians, which can be explained by more gene flow from lowland East Asia onto the plateau. Our findings corroborate a previous report of admixture signals in Tibetans, which were based on a subset of the samples analyzed here, but add evidence for isolation by distance in a broader geospatial context.

Risky business: The impact of climate and climate variability on human population dynamics in Western Europe during the Last Glacial Maximum

The extent to which climate change has affected the course of human evolution is an enduring question. The ability to maintain spatially extensive social networks and a fluid social structure allows human foragers to “map onto” the landscape, mitigating the impact of ecological risk and conferring resilience. But what are the limits of resilience and to which environmental variables are foraging populations sensitive? We address this question by testing the impact of a suite of environmental variables, including climate variability, on the distribution of human populations in Western Europe during the Last Glacial Maximum (LGM). Climate variability affects the distribution of plant and animal resources unpredictably, creating an element of risk for foragers for whom mobility comes at a cost. We produce a model of habitat suitability that allows us to generate predictions about the probable distribution of human populations and discuss the implications of these predictions for the structure of human populations and their social and cultural evolution during the LGM.

Molecular polymorphisms of the ABO locus as informative markers of ancestry in Central Argentina.

The aim of this study was to investigate the distribution of molecular polymorphisms of the ABO gene in four population samples from the province of Córdoba, in Central Argentina, and to compare them with other worldwide populations. A total of 110 buccal swab samples from autochthonous individuals of Córdoba were typified. Molecular characterization of the allelic variants was performed by the analysis of exons 6 and 7 of the ABO gene using PCR-RFLP analysis. Additionally, the Native American AIM O1v542 was characterized by direct sequencing. The four Córdoba populations did not show significant geographic structure, although the frequency of the O1v542 haplotype, detected in all the populations studied, ranged from 0.019 to 0.222. The principal component analysis based on O allele distribution showed that the populations from Córdoba clustered close to the admixed populations of Santiago and Mexico City, and at intermediate distances between European and Native American populations, while being distant from the African population. The results demonstrate that the analysis of the ABO system constitutes a useful tool for the study of the genetic structure and evolutionary history of human populations, reflecting accurately the relative contribution of parental continental contribution to the gene pool of admixed populations.

MATHEMATICAL MODELING OF EPIDEMIOLOGICAL AND BIOLOGICAL HIV INFECTION PROCESSES

In this paper analyzed the publications of international databases HighWire, PubMed, Google Scholar in the period 1981–2016 years. Proposed an original classification models. All the basic mathematical models developed for the human immunodeficiency virus are categorized into 2 levels: organism and population. The organism level is divided into models of virus and human interaction (HIV replication, study of the kinetics of viral population in the development of the disease, the molecular mechanisms of inte- raction with immune cells) and models of the inhibitory effect of anti-retroviral drugs (simulations of different therapeutic schemes, the development of resistance mutations HIV in cell reservoirs, treatment as a preventive measure). The population level can be divided into models of spread of HIV in a population (the circulation of different genotypes of HIV, the analysis of human population structure by age, sex and risk of contingent and trends in different geographical areas, the study of factors contributing to the spread of HIV infection) and management models, making the most effective use of health care system resources for the counteract the epidemic (preventive work analysis, evaluation of the economic costs of screening, therapeutic activities, forecasting the socio-eco- nomic impact). The authors consider the most significant achievements of each of these groups, and highlight unresolved problems

Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations.

The genetic structure of human populations is often characterized by aggregating measures of ancestry across the autosomal chromosomes. While it may be reasonable to assume that population structure patterns are similar genome-wide in relatively homogeneous populations, this assumption may not be appropriate for admixed populations, such as Hispanics and African-Americans, with recent ancestry from two or more continents. Recent studies have suggested that systematic ancestry differences can arise at genomic locations in admixed populations as a result of selection and nonrandom mating. Here, we propose a method, which we refer to as the chromosomal ancestry differences (CAnD) test, for detecting heterogeneity in population structure across the genome. CAnD can incorporate either local or chromosome-wide ancestry inferred from SNP genotype data to identify chromosomes harboring genomic regions with ancestry contributions that are significantly different than expected. In simulation studies with real genotype data from phase III of the HapMap Project, we demonstrate the validity and power of CAnD. We apply CAnD to the HapMap Mexican-American (MXL) and African-American (ASW) population samples; in this analysis the software RFMix is used to infer local ancestry at genomic regions, assuming admixing from Europeans, West Africans, and Native Americans. The CAnD test provides strong evidence of heterogeneity in population structure across the genome in the MXL sample ([Formula: see text]), which is largely driven by elevated Native American ancestry and deficit of European ancestry on the X chromosomes. Among the ASW, all chromosomes are largely African derived and no heterogeneity in population structure is detected in this sample.

Genetic structure of human populations based on 5 gene loci: A preliminary report from Northern India

The genetics of human populations reveals the evolutionary causes of population structure, population history, human diversity, racial divergence, adaptation, cultural and social behaviors and understanding human adaptation to local environmental constraints. The study aimed to determine the genetic relationship among six human population of Jammu and Kashmir, Northern India. This preliminary effort involved five gene loci of genetic traits, viz. ABO and Rh blood type, phenylthiocarbamide, color blindness and sickle cell trait. A total of 3679 healthy subjects were selected from six Muslim populations viz., Gujjar and Bakarwal (n=762), Mughal (n=560), Khan (n=642), Malik (n=564), Mir (579) and Syed (n=572). The allele frequencies and heterozygosity levels show significant differences among six populations (p<0.05). The phylogentic tree revealed that Mughal and Gujjar and Bakarwal (tribal population) are close to each other and differ from other four populations (Malik, Mir, Khan and Syed). Further studies in context genomic diversity, history and origin of these populations will be undertaken in future to get more conclusive proof.

Pong: fast analysis and visualization of latent clusters in population genetic data.

Motivation: A series of methods in population genetics use multilocus genotype data to assign individuals membership in latent clusters. These methods belong to a broad class of mixed-membership models, such as latent Dirichlet allocation used to analyze text corpora. Inference from mixed-membership models can produce different output matrices when repeatedly applied to the same inputs, and the number of latent clusters is a parameter that is often varied in the analysis pipeline. For these reasons, quantifying, visualizing, and annotating the output from mixed-membership models are bottlenecks for investigators across multiple disciplines from ecology to text data mining. Results: We introduce pong, a network-graphical approach for analyzing and visualizing membership in latent clusters with a native interactive D3.js visualization. pong leverages efficient algorithms for solving the Assignment Problem to dramatically reduce runtime while increasing accuracy compared with other methods that process output from mixed-membership models. We apply pong to 225 705 unlinked genome-wide single-nucleotide variants from 2426 unrelated individuals in the 1000 Genomes Project, and identify previously overlooked aspects of global human population structure. We show that pong outpaces current solutions by more than an order of magnitude in runtime while providing a customizable and interactive visualization of population structure that is more accurate than those produced by current tools.Availability and Implementation: pong is freely available and can be installed using the Python package management system pip. pong’s source code is available at https://github.com/abehr/pong.Contact: aaron_behr@alumni.brown.edu or sramachandran@brown.eduSupplementary Information: Supplementary data are available at Bioinformatics online.

Do Landscape Structure and Socio-Economic Variables Explain the Solidago Invasion?

Biological invasions are considered a major threat to biodiversity on a global scale. In this study, we examined the effect of landscape structure and socio-economic variables on the invasion pattern of alien Solidago species. Field data were collected in a set of 309 sampling plots, regularly placed on the intersecting lines of a 10 × 10-km grid, in south-western Poland (Silesia, Central Europe). Landscape characteristics and average values of socio-economic variables, such as human population density and total income per capita, were calculated. To examine the effect of landscape structure across different spatial extents, the landscape characteristics were analysed for three different buffers (radius: 500 m, 2 km and 5 km). A model explaining the pattern of the invasion was developed using a univariate, binary classification (decision) tree. The results show that both landscape structure and density of human population explain the spatial pattern of the invasion by alien Solidago species. The pattern was mostly shaped by the presence of unsuitable (forests) and suitable (roadsides) habitats for Solidago. The influence of percentage forest cover and road length was the strongest at the small spatial extent (radius = 500 m). The sum of linear elements length, percentage of urban areas and human population density calculated at the large extent (radius = 5 km) significantly improved the model. However, the predictive ability of these variables was less accurate. The model can be used by local authorities and land managers for modelling/predicting the hazards of invasion and elaborating a landscape-level system of Solidago control.

Characterization of the biological processes shaping the genetic structure of the Italian population.

BackgroundThe genetic structure of human populations is the outcome of the combined action of different processes such as demographic dynamics and natural selection. Several efforts toward the characterization of population genetic architectures and the identification of adaptation signatures were recently made. In this study, we provide a genome-wide depiction of the Italian population structure and the analysis of the major determinants of the current existing genetic variation.ResultsWe defined and characterized 210 genomic loci associated with the first Principal Component calculated on the Italian genotypic data and correlated to the North–south genetic gradient. Using a gene-enrichment approach we identified the immune function as primarily involved in the Italian population differentiation and we described a locus on chromosome 13 showing combined evidence of North–south diversification in allele frequencies and signs of recent positive selection. In this region our bioinformatics analysis pinpointed an uncharacterized long intergenic non-coding (lincRNA), whose expression appeared specific for immune-related tissues suggesting its relevance for the immune function.ConclusionsOur study, combining population genetic analyses with biological insights provides a description of the Italian genetic structure that in future could contribute to the evaluation of complex diseases risk in the population context.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0293-x) contains supplementary material, which is available to authorized users.

Economic inequality caused by feedbacks between poverty and the dynamics of a rare tropical disease: the case of Buruli ulcer in sub-Saharan Africa

Neglected tropical diseases (NTDs) have received increasing attention in recent years by the global heath community, as they cumulatively constitute substantial burdens of disease as well as barriers for economic development. A number of common tropical diseases such as malaria, hookworm or schistosomiasis have well-documented economic impacts. However, much less is known about the population-level impacts of diseases that are rare but associated with high disability burden, which represent a great number of tropical diseases. Using an individual-based model of Buruli ulcer (BU), we demonstrate that, through feedbacks between health and economic status, such NTDs can have a significant impact on the economic structure of human populations even at low incidence levels. While average wealth is only marginally affected by BU, the economic conditions of certain subpopulations are impacted sufficiently to create changes in measurable population-level inequality. A reduction of the disability burden caused by BU can thus maximize the economic growth of the poorest subpopulations and reduce significantly the economic inequalities introduced by the disease in endemic regions.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

BackgroundAn understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution.ResultsWe compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure.ConclusionsWGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1854-0) contains supplementary material, which is available to authorized users.