New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0

BACKGROUND: R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (approximately 40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies. METHODOLOGY/PRINCIPAL FINDINGS: We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (approximately 57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6+/-8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM). CONCLUSIONS/SIGNIFICANCE: In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days

Paleogenetic evidence of a Pyrenean Neolithic family: Kinship, physical appearance and biogeography multidisciplinary analysis

One of the most important Neolithic necropolises in the north-east of the Iberian Peninsula is La Feixa del Moro (3975-3790 cal. BC), located at 1335 mamsl in the Pyrenees (Juberri, Sant Julia de Lòria, Andorra). Within the scarcity of multiple simultaneous Neolithic burials, the main importance of La Feixa del Moro lies in the fact that it is one of the very few cases to suggest a biological family burial, comprising two adults and a newborn baby. Accordingly, the purpose of the present work was the multidisciplinary interpretation of the necropolis in the Neolithic context of the Pyrenees, on a potential route between the Iberian Peninsula and Europe. Therefore, kinship and biogeographic analyses were performed, as well as external visible characteristics phenotyping. Our results suggest the possibility of a traditional nuclear family, pointing to a very probable relation between the newborn and both adults. First, two mitochondrial haplotypes and two lineages were determined: H1, for the presumable mother and newborn, and U5, for the presumed father. Second, regarding their physical appearance, they all had brown eyes, the adult female and the neonate had dark brown hair, while the adult male's hair was dark red-brown. Finally, it was possible to confirm the sex of two of the individuals, as the newborn baby gender was also confirmed by the High Troughoutput Sequencing analysis. The multidisciplinary analysis of the La Feixa del Moro burial place envisions a very probable familial burial. Not only does the genetic evidence point to biological kinship, but also the archaeological record indicates a habitational area surrounding the burial site. The similar artefacts and the care shown during the funerary ritual suggest a probable biological Neolithic family.This work was supported by the research project (Santander-Universidad Complutense de Madrid, Spain, https://www.bancosantander.es/es/universidades) [G/6401400/8000] for C.G; by the [HAR2015-67323-C2-2-P] project, funded by the Ministerio de Ciencia, Innovación y Universidades of the Spanish Government (MICINNhttp://www.ciencia.gob.es/portal/site/MICINN/) and the BES2010-035322, and by [PR41/17–21018] project, funded by Banco Santander-Universidad Complutense de Madrid, Spain (https://www.bancosantander.es/es/universidades). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects