Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers

Abstract

The genetic background of the European Mesolithic and the extent of population replacement during the Neolithic is poorly understood, both due to the scarcity of human remains from that period and the inherent methodological difficulties of ancient DNA research. However, advances in sequencing technologies are both increasing data yields and providing supporting evidence for data authenticity, such as nucleotide misincorporation patterns. We use these methods to characterize both the mitochondrial DNA genome and generate shotgun genomic data from two exceptionally well-preserved 7,000-year-old Mesolithic individuals from La Braña-Arintero site in León (Northwestern Spain). The mitochondria of both individuals are assigned to U5b2c1, a haplotype common among the small number of other previously studied Mesolithic individuals from Northern and Central Europe. This suggests a remarkable genetic uniformity and little phylogeographic structure over a large geographic area of the pre-Neolithic populations. Using Approximate Bayesian Computation, a model of genetic continuity from Mesolithic to Neolithic populations is poorly supported. Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

Ancient mitochondrial lineages support the prehistoric maternal root of Basques in Northern Iberian Peninsula

“…13,14 The samples selected for this analysis were those belonging to the phylogenetic branch of haplogroup U5, since it is the most represented on pre-Neolithic period and some of its subhaplogroups are highly frequent in current Basque population, what has been seen as a sign of genetic continuity in this region. 16,41,45 The estimated time between the selected different ancestors and their respective descendents is close to the time elapsed between these dated individuals (Supplementary Figure S4), supporting the possible genetic link among ancient and current populations (Supplementary Appendix).…”

“…On the other hand, Mesolithic sample from Santimamiñe, S.12N, was joined to previously studied pre-Neolithic/hunter-gatherer remains from the northern Iberian Peninsula (HGNI). 13,14 A PCA was performed with haplogroup frequencies of European populations from different prehistoric periods (Figure 3, Supplementary Dataset S3).…”

“…In contrast with several studies focused on the analysis of the current autochthonous population, there are only a few reports on pre-Neolithic samples from the Franco-Cantabrian region. 13,14 These studies are grounded in the supposedly genetic continuity between the Palaeolithic huntergatherers and the autochthonous Basque population. 15,16 Herein we report a study on ancient maternal lineages of the Franco-Cantabrian region and their persistence in modern populations.…”

Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process

“…From Europe, data are available from nine Neolithic farmers [23,29,30], six Neolithic PWC hunter-gatherers [23,30], four Mesolithic hunter-gatherers [29][30][31] and the Tyrolean Iceman, a mummified body dated to the transition from the Neolithic to the Copper Age [32]. These techniques have also rendered possible the recovery of nuclear DNA data, from a range of archaeological materials [33][34][35].…”

“…We deep-sequenced the mtDNA d-loop from Neolithic samples using a genome sequencer (GS) FLX platform, and used postmortem DNA damage patterns to authenticate clone sequences from 13 PWC hunter-gatherers and from seven farmers (six associated with TRB and one with BAC). This data were merged with 124 previously published mtDNA sequences from Neolithic farmers and Mesolithic and Neolithic hunter-gatherers, from three geographical locations (Scandinavia: [22], Central Europe: [21,27] and Iberia: [24][25][26]31]), and we investigated the genetic diversity between and within groups, as well as possible continuity between either of the Neolithic Scandinavian groups and extant Scandinavians [40].…”