The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods.

Rui Martiniano,Rui Martiniano,Russell Mclaughlin,Joachim Burger,Daniel Fidalgo,Nuno M Silva,Ana M Silva,Ana M Silva,Lara M Cassidy,Daniel G Bradley,Ros Ó'Maoldúin,Ros Ó'Maoldúin,Ros Ó'Maoldúin,Elena Moran,Eduardo Porfirio,Maria J Coelho,Antonio C Valera,Licinio Manco,Miguel Serra,Rui Parreira,Tania Pereira,Rui Boaventura

doi:10.1371/journal.pgen.1006852

Abstract

We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature.

Highlights

Ancient genomics, through direct sampling of the past, has allowed an unprecedented parsing of the threads of European ancestry
In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, the genetic impact associated with this cultural transformation has not yet been estimated
We revealed subtle genetic differentiation between the Portuguese Neolithic and Bronze Age samples suggesting a markedly reduced influx in Iberia compared to other European regions

Summary

Introduction

Through direct sampling of the past, has allowed an unprecedented parsing of the threads of European ancestry. Longitudinal studies of genomewide variation have revealed that two major technological innovations in prehistory, agriculture and metallurgy, were associated with profound population change [1,2,3,4,5] These findings firmly address the longstanding archaeological controversy over the respective roles of migration, acculturation and independent innovation at such horizons; migration clearly played a key role. This may not be universal and genomes from several important European regions and time periods remain unexamined. Whereas dating and similarity of the Portuguese Neolithic sites to other Mediterranean regions point to a rapid spread of agriculture at around 5500 BC [6], local Mesolithic communities were sedentary, dense and innovative; they appear to have persisted for at least 500 years after the onset of the Neolithic [7] and, along with those Brittany, may have had a role in the subsequent emergence of the earliest Megalithic tradition [8]

Methods

Results

Discussion

Conclusion