Paleogenetics of Northern Iberian from Neolithic to Chalcolithic Time

Dynamics of the Neolithic transition across Europe using ancient DNA datasets have established that Neolithic European populations received a limited amount of admixture from resident hunter-gatherers. However, the genetic diversity of Neolithic and Chalcolithic human populations was shaped predominantly by local processes. In the Iberian Peninsula, the Cantabrian fringe showed different proportions of local hunter-gatherers’ ancestry through time. The objective of this chapter is to analyze the mitochondrial variation of populations from the northern Iberian Peninsula from Neolithic to Chalcolithic time using new data from El Aramo mine (Asturias), in the context of the debate about the origin and dispersion of the Beaker culture in Europe

A Customized Pigmentation SNP Array Identifies a Novel SNP Associated with Melanoma Predisposition in the SLC45A2 Gene

As the incidence of Malignant Melanoma (MM) reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2) and rs2069398 (SILV/CKD2), were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls). A novel SNP located on the SLC45A2 gene (rs35414) was found to be significantly associated with melanoma in both phase I and phase II (P<0.0001). None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively) had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls). Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date

Direct U-series analysis of the Lezetxiki humerus reveals a Middle Pleistocene age for human remains in the Basque Country (northern Iberia)

In 1964, a human humerus was found in a sedimentary deposit in Lezetxiki Cave (Basque Country, northern Iberia). The first studies on the stratigraphy, associated mammal faunal remains and lithic implements placed the deposits containing the humerus into the Riss glacial stage. Direct chronometric evidence has so far been missing, and the previous chronostratigraphic framework and faunal dating gave inconsistent results. Here we report laser ablation U-series analyses on the humerus yielding a minimum age of 164 ± 9 ka, corresponding to MIS 6. This is the only direct dating analysis of the Lezetxiki humerus and confirms a Middle Pleistocene age for this hominin fossil. Morphometric analyses suggest that the Lezetxiki humerus has close affinities to other Middle Pleistocene archaic hominins, such as those from La Sima de los Huesos at Atapuerca. This emphasizes the significance of the Lezetxiki fossil within the populations that predate the Neanderthals in south-western Europe. It is thus an important key fossil for the understanding of human evolution in Europe during the Middle Pleistocene, a time period when a great morphological diversity is observed but whose phylogenetic meaning is not yet fully understood

Ancient DNA from South-East Europe reveals different events during Early and Middle Neolithic influencing the European genetic heritage

The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations

Genome of Pesxtera Muierii skull shows high diversity and low mutational load in pre-glacial Europe

Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Pesxtera Muierii,"Romania who lived similar to 34,000 years ago to 13.5x coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (similar to 3.1%) to most EUP humans but only half compared to the similar to 40,000-year-old Pesxtera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans

Geographic location of ten Romanian sites analyzed in the present study.

<p>(The figure has been provided by M. Rotea and T. Károly).</p

Principal Component Analysis (47% of the total variance) performed considering mtDNA haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink Hunter-Gatherer groups (HG), in yellow ancient and present-day Romania groups, present-day European population in blue and present-day Near East population in orange. Interpretation based on the haplogroup frequency has been written on both PC (Absence of haplogroups D, M, C and N on one side of the first component and absence of haplogroup H on the top of the second component). PC1 represents 30% of variance and PC2 represents 17% of variance.</p

Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.

<p>Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.</p

Multidimensional Scaling Analysis performed by haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink hunter-gatherer groups and in yellow ancient and present-day Romanian groups, present-day European population in blue and present-day Near East population in orange. Stress: 0.07553 and RSQ: 0.99071.</p

Low prevalence of lactase persistence in Neolithic South-West Europe.

Item does not contain fulltextThe ability of humans to digest the milk component lactose after weaning requires persistent production of the lactose-converting enzyme lactase. Genetic variation in the promoter of the lactase gene (LCT) is known to be associated with lactase production and is therefore a genetic determinant for either lactase deficiency or lactase persistence during adulthood. Large differences in this genetic trait exist between populations in Africa and the Middle-East on the one hand, and European populations on the other; this is thought to be due to evolutionary pressures exerted by consumption of dairy products in Neolithic populations in Europe. In this study, we have investigated lactase persistence of 26 out of 46 individuals from Late Neolithic through analysis of ancient South-West European DNA samples, obtained from two burials in the Basque Country originating from 5000 to 4500 YBP. This investigation revealed that these populations had an average frequency of lactase persistence of 27%, much lower than in the modern Basque population, which is compatible with the concept that Neolithic and post-Neolithic evolutionary pressures by cattle domestication and consumption of dairy products led to high lactase persistence in Southern European populations. Given the heterogeneity in the frequency of the lactase persistence allele in ancient Europe, we suggest that in Southern Europe the selective advantage of lactose assimilation in adulthood most likely took place from standing population variation, after cattle domestication, at a post-Neolithic time when fresh milk consumption was already fully adopted as a consequence of a cultural influence.1 juli 201