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

View ORCID ProfileRui Martiniano, Lara M Cassidy, Ros Ó’Maoldúin, Russell McLaughlin, Nuno M Silva, Licinio Manco, Daniel Fidalgo, Tania Pereira, Maria J Coelho, Miguel Serra, Joachim Burger, Rui Parreira, Elena Moran, Antonio C Valera, Eduardo Porfirio, Rui Boaventura, Ana M Silva, Daniel G Bradley
doi: https://doi.org/10.1101/134254
Rui Martiniano
1Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
2Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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  • ORCID record for Rui Martiniano
  • For correspondence: dbradley@tcd.ie ruidlpm@gmail.com
Lara M Cassidy
1Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
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Ros Ó’Maoldúin
1Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
3The Irish Fieldschool of Prehistoric Archaeology, Department of Archaeology, NUI Galway, Galway, Ireland
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Russell McLaughlin
1Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
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Nuno M Silva
4Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Switzerland
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Licinio Manco
2Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Daniel Fidalgo
2Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Tania Pereira
2Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Maria J Coelho
2Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Miguel Serra
5Palimpsesto - Estudo e Preservação do PatrimÓnio Cultural Lda., Coimbra, Portugal
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Joachim Burger
6Palaeogenetics Group, Johannes Gutenberg University, Bentzelweg 7, Mainz, Germany
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Rui Parreira
7Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
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Elena Moran
7Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
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Antonio C Valera
8Nucleo de Investigação Arqueologica - ERA Arqueologia, Cruz Quebrada, Portugal
9Interdisciplinary Center for Archaeology and Evolution of Human Behavior – University of Algarve
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Eduardo Porfirio
5Palimpsesto - Estudo e Preservação do PatrimÓnio Cultural Lda., Coimbra, Portugal
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Rui Boaventura
7Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
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Ana M Silva
2Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
7Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
10Laboratory of Forensic Anthropology, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
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Daniel G Bradley
1Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
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  • For correspondence: dbradley@tcd.ie ruidlpm@gmail.com
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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.

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.

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Posted May 10, 2017.
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The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods
Rui Martiniano, Lara M Cassidy, Ros Ó’Maoldúin, Russell McLaughlin, Nuno M Silva, Licinio Manco, Daniel Fidalgo, Tania Pereira, Maria J Coelho, Miguel Serra, Joachim Burger, Rui Parreira, Elena Moran, Antonio C Valera, Eduardo Porfirio, Rui Boaventura, Ana M Silva, Daniel G Bradley
bioRxiv 134254; doi: https://doi.org/10.1101/134254
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The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods
Rui Martiniano, Lara M Cassidy, Ros Ó’Maoldúin, Russell McLaughlin, Nuno M Silva, Licinio Manco, Daniel Fidalgo, Tania Pereira, Maria J Coelho, Miguel Serra, Joachim Burger, Rui Parreira, Elena Moran, Antonio C Valera, Eduardo Porfirio, Rui Boaventura, Ana M Silva, Daniel G Bradley
bioRxiv 134254; doi: https://doi.org/10.1101/134254

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