Skin pigmentation and genetic variants in an admixed Brazilian population of primarily European ancestry.

Although many genes have been shown to be associated with human pigmentary traits and forensic prediction assays exist (e.g. HIrisPlex-S), the genetic knowledge about skin colour remains incomplete. The highly admixed Brazilian population is an interesting study population for investigation of the complex genotype-phenotype architecture of human skin colour because of its large variation. Here, we compared variants in 22 pigmentary genes with quantitative skin pigmentation levels on the buttock, arm, and forehead areas of 266 genetically admixed Brazilian individuals. The genetic ancestry of each individual was estimated by typing 46 AIM-InDels. The mean proportion of genetic ancestry was 68.8% European, 20.8% Sub-Saharan African, and 10.4% Native American. A high correlation (adjusted R2 = 0.65, p < 0.05) was observed between nine SNPs and quantitative skin pigmentation using multiple linear regression analysis. The correlations were notably smaller between skin pigmentation and biogeographic ancestry (adjusted R2 = 0.45, p < 0.05), or markers in the leading forensic skin colour prediction system, the HIrisPlex-S (adjusted R2 = 0.54, p < 0.05). Four of the nine SNPs, OCA2 rs1448484 (rank 2), APBA2 rs4424881 (rank 4), MFSD12 rs10424065 (rank 8), and TYRP1 1408799 (rank 9) were not investigated as part of the HIrisPlex-S selection process, and therefore not included in the HIrisPlex-S model. Our results indicate that these SNPs account for a substantial part of the skin colour variation in individuals of admixed ancestry. Hence, we suggest that these SNPs are considered when developing future skin colour prediction models.

Genetic characterization of Rio de Janeiro for different Y-STR sets.

In this work, the YfilerPlus kit was used to investigate a sample of 258 males from Rio de Janeiro. In addition, the previous database of 760 Yfiler profiles deposited in the YHRD was updated to 1610. YfilerPlus markers showed a high haplotype diversity (0.99997), with only one haplotype shared by two individuals. When only considering the Yfiler markers, the haplotype diversity was slightly lower (0.99976), with 5 haplotypes shared by two individuals and 1 haplotype shared by three individuals. Low genetic distances were found between the Rio de Janeiro and European populations as well as the European/Hispanic American samples.

Maternal ancestry and lineages diversity of the Santander population from Colombia.

Santander, located in the Andean region of Colombia, is one of the 32 departments of the country. Its population was shaped by intercontinental admixture between autochthonous native Americans, European settlers, and African slaves. To establish forensic databases of haplotype frequencies, the evaluation of population substructure is crucial to capture the genetic diversity in admixed populations. Total control region mitochondrial deoxyribonucleic acid haplotypes were determined for 204 individuals born in the seven provinces across the department. The maternal native heritage is highly preserved in Santander genetic background, with 90% of the haplotypes belonging to haplogroups inside A2, B4, C1, and D. Most native lineages are found broadly across the American continent, while some sub-branches are concentrated in Central America and north South America. Subtle European (6%) and African (4%) input was detected. In pairwise comparisons between provinces, relatively high FST values were found in some cases, although not statistically significant. Nonetheless, when provinces were grouped according to the principal component analysis results, significant differences were detected between groups. The database on mitochondrial deoxyribonucleic acid control region haplotype frequencies established here can be further used for populational and forensic purposes.

The multifaceted genomic history of Ashaninka from Amazonian Peru.

Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.

Tierra Del Fuego: What Is Left from the Precolonial Male Lineages?

Similar to other South American regions, Tierra del Fuego has an admixed population characterized by distinct ancestors: Native Americans who first occupied the continent, European settlers who arrived from the late 15th century onwards, and Sub-Saharan Africans who were brought to the Americas for slave labor. To disclose the paternal lineages in the current population from Tierra del Fuego, 196 unrelated males were genotyped for 23 Y-STRs and 52 Y-SNPs. Haplotype and haplogroup diversities were high, indicating the absence of strong founder or drift events. A high frequency of Eurasian haplogroups was detected (94.4%), followed by Native American (5.1%) and African (0.5%) ones. The haplogroup R was the most abundant (48.5%), with the sub-haplogroup R-S116* taking up a quarter of the total dataset. Comparative analyses with other Latin American populations showed similarities with other admixed populations from Argentina. Regarding Eurasian populations, Tierra del Fuego presented similarities with Italian and Iberian populations. In an in-depth analysis of the haplogroup R-M269 and its subtypes, Tierra del Fuego displayed a close proximity to the Iberian Peninsula. The results from this study are in line with the historical records and reflect the severe demographic change led mainly by male newcomers with paternal European origin.

The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture.

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

Patterns of genetic diversity in Colombia for 38 indels used in human identification.

The current population of Colombia has a genetic heterogeneity resulting from different migrations from other continents and within the country. In addition, there are small groups in their territory that have remained isolated and therefore have a different genetic pool in relation to that of the neighbouring urban populations. This population stratification must be considered in forensic analysis, being more complex for markers with marked intercontinental differentiation. In this study, population differentiation in Colombian admixed, native, and Afro-descendant populations was evaluated for a group of 38 indels described for forensic use. Allelic frequencies and parameters of forensic relevance were determined in each of the groups defined based on population differentiation analyses. In addition to the differences found between population groups, the results show that the set of 38 indels analysed could be useful in studies of individual identification in Colombia. The exclusion power presented by this set of markers suggests the need for joint use with other markers, being able to complement the STRs in paternity cases. High levels of both power of discrimination and exclusion were found when complementing the 38 HID-indels with a second multiplex, for a total of 83 indels.

Searching for the roots of the first free African American community.

San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions.

The maternal inheritance of Alto Paraná revealed by full mitogenome sequences.

Most studies on maternal lineages of South America populations are restricted to control region (CR) markers and, for some geographical regions, the number of studied samples does not adequately represent the existing diversity. This is the case of mitochondrial DNA (mtDNA) studies on Paraguay that are limited to two Native ethnic groups. To overcome this deficiency, we analysed the mitogenomes from 105 individuals living in Alto Paraná, the second most populated department of the country. Using the Precision ID mtDNA Whole Genome Panel, the molecule was sequenced on Ion S5. The majority of the haplotypes belong to the Native American lineages A, B, C and D. Analyses of maximum parsimony using mitogenome data retrieved from publications and in The 1000 Genomes Project showed a high number of new native American subclades in Paraguay. Also, none of the haplotypes found in Alto Paraná match the remaining South American samples, which include admixed populations from Colombia, Peru and Ecuador, and natives from Colombia and Ecuador. FST genetic distance analysis showed that the native genetic background of Alto Paraná has an intermediate position between the Amazonian groups and the admixed populations from Peru and Ecuador, supporting the theory about the Amazonian origin of the Tupi-Guarani and, at the same time, showing the influence of other linguistic groups.

A view of the maternal inheritance of Espírito Santo populations: The contrast between the admixed and Pomeranian descent groups.

In addition to its valuable utility in forensic investigations, mitochondrial DNA (mtDNA) analysis is a reliable tool to uncover the origins of admixed populations, such as Brazilians. The state of Espírito Santo (ES), similar to other coastal Brazilian states, has a population shaped by 3 main ancestral roots: Amerindian, African and European. Among the latter, the Pomeranian descendants stand out due to the preservation of the traditional aspects of their culture, especially the Pomeranian language. Despite the genetic data already available, there is no mtDNA database that adequately reflects the diversity, the geographic distribution, and the origins of the maternal lineages from ES. To increase the knowledge of maternal ancestry and to investigate the population's genetic stratification, a total of 291 samples were collected in the 4 macroregions (Metropolitan, South, Central and North) of ES and in the Pomeranian communities. Complete control region data were produced for the general (N=214) and Pomeranian (N=77) groups. Regarding the general population, the high values of haplotype diversity (H=99.9%) and pairwise differences (MNPD=16.9) found are in agreement with those reported for other populations in the southeast region of the country. Regarding maternal inheritance, the ES populations stood out due to the predominance of European haplogroups (49.5%), although the North macroregion had a higher African ancestry (47.1%). Among the Pomeranians, the lowest MNPD value (11.2) and the high percentage of shared haplotypes (15%) were indicative of founder events. The FST analysis showed that the Pomeranians (98.7% of European lineages) are genetically isolated from the other admixed populations in Brazil. This study demonstrated that the ES state contains singularities regarding the intrapopulational and interpopulational diversity of mtDNA. Even after 5 centuries of interethnic admixture, the present-day population of Espírito Santo harbors genetic marks that trace back to the historical aspects of its formation.

Defining mtDNA origins and population stratification in Rio de Janeiro.

The genetic composition of the Brazilian population was shaped by interethnic admixture between autochthonous Native Americans, Europeans settlers and African slaves. This structure, characteristic of most American populations, implies the need for large population forensic databases to capture the high diversity that is usually associated with admixed populations. In the present work, we sequenced the control region of mitochondrial DNA from 205 non-related individuals living in the Rio de Janeiro metropolitan region. Overall high haplotype diversity (0.9994 ±â€¯0.0006) was observed, and pairwise comparisons showed a high proportion of haplotype pairs with more than one-point differences. When ignoring homopolymeric tracts, pairwise comparisons showed no differences 0.18% of the time, and differences in a single position were found with a frequency of 0.32%. A high percentage of African mtDNA was found (42%), with lineages showing a major South West origin. For the West Eurasian and Native American haplogroups (representing 32% and 26%, respectively) it was not possible to evaluate a clear geographic or linguistic affiliation. When grouping the mtDNA lineages according to their continental origin (Native American, European and African), differences were observed for the ancestry proportions estimated with autosomal ancestry-informative markers, suggesting some level of genetic substructure. The results from this study are in accordance with historical data where admixture processes are confirmed with a strong maternal contribution of African maternal ancestry and a relevant contribution of Native American maternal ancestry. Moreover, the evidence for some degree of association between mtDNA and autosomal information should be considered when combining these types of markers in forensic analysis.

Quantification of urinary chorionic gonadotropin in spontaneous abortion of pre-clinically recognized pregnancy: method development and analytical validation.

Determination of environmental impacts on reproductive health and specifically on the incidence of early spontaneous abortion requires accurate estimates of the latter. This negative reproductive outcome can be detected by the pattern of elevation and decline of human chorionic gonadotropin (hCG) levels near and shortly beyond the expected time of implantation, requiring daily biomonitoring of hCG levels during the relevant period of the menstrual cycle. Prospective pregnancy studies to assess effects of potentially toxic exposures on human reproductive outcomes can involve up to three menstrual cycles and a huge number of samples in each, for the quantification of the inherently very low hCG levels usually can be determined only in serum. The invasive nature of blood collection, the number of samples needed for the development of prospective studies, and the lack of quantitative methods for the determination of low hCG levels in urine point to the need for collecting urine rather than blood and make it imperative to develop suitable quantitative methods for biomonitoring of very low levels of hCG in urine. This paper describes the development and validation procedures of an automated solid-phase two-site chemiluminescent immunometric assay for the quantification of urinary hCG in early pregnancy and early pregnancy loss. For the validation, both undiluted and diluted urine and control samples have been prepared. From the results, it can be concluded that the assay has a calibration range that extends to 5000 mIU/ml, with a detection limit of approximately 1.2 mIU/ml, practically identical to that found by the IMMULITE 2000 manufacturer's validation study. The intra- and inter-assay precision ranges up to a maximum of around 7%, meaning that the practical limit for functional sensitivity can be established as low as 10%. This means that the immunoassay from DPC can identify, with relatively high confidence, non-pregnant women and the typical "rise and fall" pattern of early pregnancy loss through analysis of urine samples. Results also lead to the conclusion that there is a very good agreement between expected and observed urinary hCG levels indicative of good immunoassay accuracy for the studied range of hCG concentrations. In terms of analyte stability, it can be concluded that urinary hCG is stable under the expected conditions required for ongoing investigations that include temperatures of 2-8 degrees C for up to 48 h and temperatures of around -20 degrees C for longer periods that can extend to over 3 months.

Human exposure to heavy metals in the vicinity of Portuguese solid waste incinerators--Part 2: biomonitoring of lead in maternal and umbilical cord blood.

As part of environmental health surveillance programs related to solid waste incinerators located near Lisbon and on Madeira Island, human biomonitoring projects have been implemented in Portugal, some of them focused on cross-sectional surveys of heavy metals in blood. One of the general aims of these programs is to provide Portuguese data on the extent and pattern of human exposure to the pollutants potentially released in the stack gases from the incinerators, namely heavy metals. The present investigation reports information specifically on blood lead levels of newborn-mother pairs living in the vicinity of the incinerators under study, as well as of statistically similar participants living outside the exposed area. For Lisbon, lead levels determined at the baseline period (T0), as well as three subsequent evaluations of potential specific impacts of the incinerator (T1, T2 and T3) are described in order to investigate spatial and temporal trends of human exposure to lead. Available data for Madeira, namely lead levels in blood from the study population before the incinerator started operation, is also described. For Lisbon, analyses showed a statistically significant decrease of lead concentrations in maternal (p<0.001) and umbilical cord blood (p<0.001) during the whole monitoring period. Practically "overt" transplacental exposure to lead was observed only in the Lisbon biomonitoring project and for some cross-sectional surveys. Baseline levels for Madeira were the lowest found in all observations already performed in both programs (maternal and umbilical cord mean lead levels of 0.4 microg/dl and 0.3 microg/dl, respectively). No statistical associations have been found between lead levels in blood and age neither for global populations from Lisbon and Madeira nor for specific groups included in the different observational periods.

Human exposure to heavy metals in the vicinity of Portuguese solid waste incinerators--Part 3: biomonitoring of Pb in blood of children under the age of 6 years.

As a part of environmental health surveillance programs related to Portuguese solid waste incinerators (SWI), two biomonitoring projects have been established to investigate additional exposure to lead in children under the age of 6 years living in the vicinity of those facilities. The above-mentioned programs, being the only ones in the country that integrate systematic observations on human exposure to heavy metals, have to provide systematic data from Portuguese regions on the extent and pattern of human exposure to heavy metals, namely to lead. The present paper is the third of a series of papers prepared to accomplish that objective in regards to lead exposure as evaluated by measuring lead levels in children under the age of 6 years. Altogether, 250 children from Lisbon and 247 from Madeira Island have already been involved in the investigation. The present study evaluates spatial and temporal trends of lead exposure, based on comparisons of children's blood lead levels, either stratified by living area (exposed and control groups), or by time of exposure (T0, the baseline time, and T1, after approximately 2 years of regular operation of the facilities). The results obtained correspond to a relatively reduced number of individuals. Possibly for this reason, they are not fully conclusive in relation to whether living in the vicinity of SWI represents an additional risk of higher exposure to lead. Time trends of lead exposure as evaluated by blood lead levels in children also do not show any clear pattern. These conclusions and the fact that altogether around 3% of children from the whole group have blood lead levels >or=10 microg/dl warrant further investigation in order to clarify the contribution of incinerator emissions to the levels of lead in children and to identify alternative sources for preventive purposes, taking into consideration the relevance of even low lead exposure from a public health perspective, mainly in relation to children.

Human exposure to heavy metals in the vicinity of Portuguese solid waste incinerators--Part 1: biomonitoring of Pb, Cd and Hg in blood of the general population.

Human exposure to heavy metals makes it necessary to monitor these elements in the human body if the objective is to relate heavy metal exposure to adverse health effects. In Portugal, biomonitoring projects on heavy metals are being carried out on people living in the vicinity of solid waste incinerators. The projects are being developed in the ambit of two environmental health surveillance programs related to solid waste incineration facilities, one near Lisbon and the other on Madeira Island, that have the main objective of guaranteeing the safeguard of public health in relation to the potential negative impact of incineration processes on human health. These programs are the only ones in the country that integrate a systematic observation of human exposure to heavy metals as determined by the respective body burden in several population groups. Therefore, they are the only ones that are currently able to provide systematic data from Portuguese regions on the extent and pattern of human exposure to this type of pollutants. The present paper is the first of a series of three prepared papers with the objective of presenting and discussing available data. It addresses exposure to lead, cadmium and mercury as determined by their levels in blood of general population adults. Results suggest the effectiveness of source control measures in relation to both incinerators under study, similarly to what has been concluded from previous studies addressing exposure to dioxins. They also show, in relation to the baseline situation, a general significant trend for reduction of exposure to all studied heavy metals. Individuals from Lisbon seem to have a significantly higher body burden of the studied metals than those living in Madeira and, in general, metal exposure in men is significantly higher than in women, with the most relevant exception being the case of higher mercury levels in women, at the baseline and for both communities. Compared with published reference values for similar conditions, blood levels of cadmium, lead, and mercury of the present investigation seem to be relatively higher, in median terms and for extreme values, mainly in the case of cadmium and mercury. In the case of lead the differences are not so marked.

Genetic portrait of Lisboa immigrant population from Angola with mitochondrial DNA.

Portugal has been considered a country of emigrants, nevertheless in the past decades the number of immigrants has grown throughout all the country. This migratory flux has contributed to a raise of heterogeneity at multiple levels. According to statistical data, at the end of 2012 the total number of Angolan immigrants in Portugal equalled about 20,000 individuals. A territorial predominance has been found for the metropolitan region of Lisboa. Angola is a country located in the Atlantic coast of Africa. The presence of Bantu people and the colonisation by Portuguese people on Angolan territory are considered to be the major modulators of the genetic patterns in Angola. Mitochondrial DNA is known for its features that enable an approach to the study of human origin and evolution, as well to the different migration pathways of populations. This genetic marker can also contribute to ascertaining the identity of individuals in forensic cases. The main aim of this study was to determine the genetic structure of the Angolan immigrant population living in Lisboa. Therefore, a total of 173 individuals, inhabitants in Lisboa, nonrelated and with Angolan ancestry were studied. Total control region of mitochondrial DNA was amplified from position 16,024 to position 576 using two pairs of primers - L15997/H016 and L16555/H639. The majority of the identified haplotypes belong to mtDNA lineages known to be specific of the sub-Saharan region. Our results show that this immigrant population inhabitant in Lisboa presents a genetic profile that is characteristic of African populations. This study also demonstrates the genetic diversity that this immigrant population introduces in Lisboa. This does not contradict the historical data concerning colonization of Angola, since this was made mainly by male European individuals, who did not contribute with their maternal information of mtDNA. Lisboa immigrant population from Angola can be accessed via EMPOP dataset with accession number EMPOP662.