How Mitochondrial DNA Can Write Pre-History: Kinship and Culture in Duero Basin (Spain) during Chalcolithic and Bronze Age

The chronological period from the beginning of the Chalcolithic Age to the end of the Bronze Age on the Iberian northern sub-plateau of the Iberic Peninsula involves interesting social and cultural phenomena, such as the appearance of the Bell Beaker and, later, the Cogotas I cultures. This work constructs a genetic characterisation of the maternal lineages of the human population that lived on the northern sub-plateau between 5000 and 3000 years ago through an analysis of mitochondrial DNA (mtDNA), a kind of genetic marker that is inherited through maternal lineages, unaltered from generation to generation. Population and cultural questions are investigated through mtDNA analyses. This study intends to shed light on the following questions. Were individuals who were buried together in multiple or collective burials biologically related through their maternal lineages? Were there distinct maternal human lineages in the same or different geographical areas if different material cultures (Bell Beaker and Cogotas I) were associated with the arrival of new human populations who established close biological relationships with the endogenous populations? Or could this be the result of the transmission of knowledge without human populations mixing? Another important question is whether the material cultures were related to the female populations. We analysed 91 individuals from 28 different archaeological sites of the Iberian northern sub-plateau from four different chrono-cultural periods (Pre-Bell Beaker, Bell Beaker, Proto-Cogotas I, and Cogotas I), from the end of the Chalcolithic Age up to the Bronze Age. There were two historical moments of new populations arriving: the first during the Pre-Bell Beaker period, associated with the K mtDNA haplogroup, and the second during the Proto-Cogotas I culture, with new lineages of the H, HVO, and T haplogroups. Neither of these new population flows were directly associated with the maximum development of the two main material cultures Bell Beaker and Cogotas I, so they must have occurred immediately beforehand, during the Pre-Bell Beaker and Proto-Cogotas I periods, respectively. However, we cannot discard an association between the populations and material cultures. Curiously, it has also been observed that there was also a tendency towards multiple burials, in which the individuals who were buried together belonged to the same maternal lineage, during these two periods of population change. This study has shed some light on the populational changes that occurred through these different periods in this specific geographical area of the northern sub-plateau of the Iberian Peninsula

Family History in the Iberian Peninsula during Chalcolithic and Bronze Age: An Interpretation through the Genetic Analysis of Plural Burials

Throughout history, it has been observed that human populations have buried the deceased members of their communities following different patterns. During the Copper Age and the Bronze Age-periods on which this study focuses-in the northern sub-plateau of the Iberian Peninsula, we identified different patterns of multiple or collective burial. This work analyzes a total of 58 individuals buried in different multiple or collective graves, to investigate whether the practice of these burials implies a family or biological link between individuals buried together. With this aim, STR markers of nuclear DNA were analyzed, as well as the hypervariable regions I and II of mitochondrial DNA, establishing both close kinship relationships and relationships through maternal lineage. We observed different burial patterns, detecting certain maternal lines preserved in some common burials maintained over time. Close family relationships were observed to a lesser extent, with some occasional exceptions. The results of the analysis formed the basis for a discussion on the concepts of family and community

Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization

Mitochondrial DNA genetic relationships at the ancient Neolithic site of Tell Halula

The extent of racemization of aspartic acid (Asp) -expressed as D/L ratio- has been used as a marker of biomolecular degradation in ancient remains. However, Asp racemization rate is highly variable, and depends on biochemical and geochemical factors. In this paper we aim to determine to which extent the fraction analyzed and the kind of sample used may influence the D/L Asp ratios. Other factors, such as burial site and sample preservation conditions, are also considered. D/L Asp ratios were obtained in 38 ancient human samples from 30 different individuals in which Real Time PCR quantification and amplification of short mtDNA fragments had been previously achieved. Four samples were taken from bones, 16 from whole teeth and 18 from dentine. In 7 cases whole tooth and dentine fractions from the same individual were analyzed. The samples belonged to 8 archaeological sites from Pre-pottery Neolithic B (PPNB), Cardial Neolithic and Chalcolithic time periods. Results show significant differences between the D/L Asp ratios obtained in dentine and whole tooth fractions from the same tooth and individual, as well as among dentine samples from the same archaeological site and among samples of the same age from different, though nearby, archaeological sites. Ancient DNA (aDNA) could be characterized in the majority of the samples, independently from their racemization values, which suggests that other factors, apart from the sample preservation stage, are more significantly affecting the racemization rate. A generalized use of the Asp racemization ratio as a threshold value for ancient DNA preservation needs to be questioned until further methodological standardization is considered

A matter of life and death: the Middle Neolithic population from Bom Santo Cave (Lisbon, Portugal)

The study of the Bom Santo Cave (central Portugal), a Neolithic cemetery, indicated a complex social, palaeoeconomic and population scenario. With isotope, aDNA and provenience analyses of raw materials coupled with stylistic variability of material culture items and palaeogeographical data light is shed on the territory and social organization of a population dated to 3800–3400 cal BC, i.e. the middle phase of the period. Results indicate an itinerant farming, segmentary society, where exogamic practices were the norm and patrilocality probably predominated. Its lifeway may be that of the earliest megalithic builders of the region, but further research is needed to correctly evaluate the degree of participation in such phenomenon

El papel de los estudios bioarqueológicos en las interpretaciones sobre las comunidades neolíticas del noreste peninsular

Resumen del trabajo presentado al VI Congreso del Neolítico en la Península Ibérica: "Los cambios económicos y sus implicaciones sociales durante el Neolítico de la Península Ibérica", celebrado en Granada del 22 al 26 de junio de 2016.-- et al.El marco del proyecto I+D: “Aproximación a las primeras comunidades neolíticas del NE peninsular a través de sus prácticas funerarias” (2011-2015), y su continuidad para los próximos cuatro años al haber sido renovado, tiene por objetivo conocer cada día más y mejor las comunidades de agricultores y pastores que entre finales del V e inicios del IV milenio cal BC ocuparon y enterraron a sus muertos en el noreste de la Península Ibérica. El contexto de estudio es excepcional, puesto que aquellas comunidades inhumaron sistemáticamente a sus congéneres en tumbas habitualmente individuales y ocasionalmente junto a otro individuo. En esta presentación no sólo queremos mostrar los nuevos análisis y metodologías que estamos aplicando al estudio de los restos humanos, sino también el modelo de trabajo que hemos seguido. A este respecto, tres aspectos son fundamentales: 1) las dataciones absolutas son el eje que vertebra los posteriores análisis; 2) la colaboración con los distintos investigadores/as y laboratorios debe ser estrecha (no es cuestión de solicitar los resultados de un análisis a un laboratorio sino trabajar con las personas que manipulan las muestras y conocen los pros y contras de cada una de las técnicas empleadas) y 3) los estudios y análisis a realizar confluyen para responder a las hipótesis planteadas. A este respecto, en el proyecto hemos tenido la fortuna de poder colaborar con numerosos investigadores/as cuya especialidad versa alrededor de los restos funerarios y que firman la presente comunicación: análisis isotópicos, Adn, tafonomía funeraria, estudios de stress muscular y análisis de morfología dental.Peer Reviewe

Ecophysiology of Aspergillus Section Nigri Species Potential Ochratoxin A Producers

After aflatoxins, ochratoxin A (OTA) is the most studied mycotoxin due to the toxicological significance in human and animal diets. OTA presence has been extensively reported worldwide in the last decade in several agricultural products. The main OTA producer in tropical and temperate climates is Aspergillus carbonarius followed by species belonging to A. niger aggregate. Currently, many scientists worldwide have studied the influence of water activity and temperature for growth and biosynthesis of OTA by these species on synthetic media. This article reviews ecophysiological studies of Aspergillus section Nigri strains on synthetic media and natural substrates. The results of these investigations suggest that significant amounts of OTA can be produced in only five days and that the use of different storage practices, such as aW and temperature levels below 0.930 and 15 °C, respectively, allow controlling fungal contamination and minimizing the OTA production in several products as peanuts, corn, dried grapes and derived products for human consumption

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51x, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes

Early Neolithic tombs from the interior of Iberia: new data for an updating of the empirical evidences

[EN] Together with the publication of new tombs and radiocarbon dates from the Early Neolithic, an analysis is made about the complete catalogue of graves known of this chronology in the interior of the Iberian Peninsula and the Ebro Valley: the structure of the tomb used, the nature of the burial deposition, the sex and age of the individuals, the grave offerings (presence or absence) as well as the position and orientation of the deceased inside the grave. The aim is to show a general overview of the burial evidences of the first farmers in this region.[ES] A la vez que dar a conocer tumbas y cronologías inéditas de los inicios del Neolítico en el interior peninsular, se pretende analizar con el detalle que nos permite en cada contexto la bibliografía existente, todos los casos de tumbas de esta fase en el interior peninsular y en el Valle del Ebro. Serán analizados con detalle el tipo de estructura utilizada y la naturaleza del depósito funerario, la edad y el sexo de los enterrados, el tipo de ajuar, su presencia o ausencia en cada caso, así como la posición y la orientación de los difuntos en la tumba. Todo ello con la intención de ofrecer una visión integral de las evidencias funerarias en los inicios de la economía con rendimientos diferidos.Peer reviewe

Analysis of paternal lineages in Brazilian and African populations

The present-day Brazilian population is a consequence of the admixture of various peoples of very different origins, namely, Amerindians, Europeans and Africans. The proportion of each genetic contribution is known to be very heterogeneous throughout the country. The aim of the present study was to compare the male lineages present in two distinct Brazilian populations, as well as to evaluate the African contribution to their male genetic substrate. Thus, two Brazilian population samples from Manaus (State of Amazon) and Ribeirão Preto (State of São Paulo) and three African samples from Guinea Bissau, Angola and Mozambique were typed for a set of nine Y chromosome specific STRs. The data were compared with those from African, Amerindian and European populations. By using Y-STR haplotype information, low genetic distances were found between the Manaus and Ribeirão Preto populations, as well as between these and others from Iberia. Likewise, no significant distances were observed between any of the African samples from Angola, Mozambique and Guinea Bissau. Highly significant Rst values were found between both Brazilian samples and all the African and Amerindian populations. The absence of a significant Sub-Saharan African male component resulting from the slave trade, and the low frequency in Amerindian ancestry Y-lineages in the Manaus and Ribeirão Preto population samples are in accordance with the accentuated gender asymmetry in admixture processes that has been systematically reported in colonial South American populations