RT Journal Article SR Electronic T1 The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods JF bioRxiv FD Cold Spring Harbor Laboratory SP 134254 DO 10.1101/134254 A1 Rui Martiniano A1 Lara M Cassidy A1 Ros Ó’Maoldúin A1 Russell McLaughlin A1 Nuno M Silva A1 Licinio Manco A1 Daniel Fidalgo A1 Tania Pereira A1 Maria J Coelho A1 Miguel Serra A1 Joachim Burger A1 Rui Parreira A1 Elena Moran A1 Antonio C Valera A1 Eduardo Porfirio A1 Rui Boaventura A1 Ana M Silva A1 Daniel G Bradley YR 2017 UL http://biorxiv.org/content/early/2017/05/10/134254.abstract AB 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.Author Summary Recent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age. In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, however, the genetic impact associated with this cultural transformation has not yet been estimated. In order to investigate this, we sequence Neolithic and Bronze Age samples from Portugal, which we compare to other ancient and present-day individuals. Genome-wide imputation of a large dataset of ancient samples enabled sensitive methods for detecting population structure and selection in ancient samples. 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. Furthermore, we predict individual height in ancients, suggesting that stature was reduced in the Neolithic and affected by subsequent admixtures. Lastly, we examine signatures of strong selection in important traits and the timing of their origins.