The genetic history of Portugal over the past 5,000 years

Abstract

Background: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have presented very limited data for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we present the most comprehensive collection of Portuguese ancient genome-wide data, from 67 individuals spanning 5000 years of human history, from the Neolithic to the nineteenth century.

Results: We identify early admixture between local hunter-gatherers and Anatolian-related farmers in Neolithic Portugal, with a northeastern-southwestern gradient of increasing Magdalenian-associated ancestry persistence in Iberia. This profile continues into the Chalcolithic, though Bell Beaker-associated sites reveal Portugal's first evidence of Steppe-related ancestry. Such ancestry has a broader demographic impact during the Bronze Age, despite continuity of local Chalcolithic genetic ancestry and limited Mediterranean connections. The village of Idanha-a-Velha emerges in the Roman period as a site of significant migration and interaction, presenting a notably diverse genetic profile that includes North African and Eastern Mediterranean ancestries. The Early Medieval period is marked by the arrival of Central European genetic diversity, likely linked to migrations of Germanic tribes, adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant additional African admixture in the south. The latter remains stable during the post-Islamic period, suggesting enduring African influences.

Conclusions: We reveal dynamic patterns of migration in line with cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archeological data, enhancing our understanding of Iberia's biological and cultural heritage.

Keywords: Ancient DNA; Archaeology; Iberia; Molecular anthropology; Paleogenomics; Population genetics; Portuguese populations.

Fig. 1

A Geographic and B chronological distribution of newly generated paleogenomic datasets (n = 67; circles) and previously reported paleogenomic datasets (crosses) along a north–south (top to bottom) gradient. Pie charts indicate the archeological sites analyzed in this study, with colors corresponding to different temporal periods. Random jitter has been applied to other sites for clarity

Fig. 2

PCA of present-day West Eurasians and North Africans (gray points; overlaid colored polygons represent geographical clusters) with ancient individuals from Iberia and other regions projected onto the first two principal components. Colors indicate different temporal periods as shown in 1B, with a focus on A the Neolithic and B the Chalcolithic. C Ancestry proportions for Cova_das_Lapas_N/C and Torre_Velha_C (y-axis) using different admixture modeling frameworks (x-axis), p-values are provided inside each column and error bars indicate 1-SD. D Latitudinal distribution of Magdalenian-associated ancestry in Neolithic and Chalcolithic Iberia. The scatter plot shows the mean proportion of Goyet_Q2 ancestry ± 1-SE for Iberian archeological sites (x-axis) plotted against their latitude (y-axis). Ancestry proportions derive from qpAdm models where Goyet_Q2 was either required as a third source alongside Anatolia_N and WHG or significantly improved model fit. Sites adequately modeled without Goyet_Q2 were excluded from the analysis

Fig. 3

A PCA of present-day West Eurasians and North Africans (overlaid colored polygons represent geographical clusters) focusing on the Bronze Age. The ancient individuals from Iberia and other regions were projected onto the first two principal components. Colors correspond to different temporal periods, as shown in 1B. B f₄-statistics of the form f₄ (Spain_N, Test; Russia_Samara_EBA_Yamnaya, Mbuti), where Test includes Portuguese individuals from the Neolithic (N), Chalcolithic (C), Chalcolithic Bell Beaker culture (BB), and Bronze Age (BA). Bold labels in the x-axis represent individuals from the present study. The y-axis shows the f₄-statistic values, with results displayed as the mean ± 1-SD. Markers represent the genetic sex, colors indicate Y-chromosome haplogroup lineages, and the black strokes denote Z-scores > 2. C Ancestry proportions (y-axis) for Monte_da_Cabida_BA, Outeiro_Alto_BA, Torre_Velha_BA and Torre_Velha_BA_o based on different admixture modeling frameworks (x-axis), p-values are provided inside each column and error bars indicate 1-SD. D qpAdm Z scores between autosomes and the X chromosome showing no signal for Steppe-related ancestry male bias. If sex bias existed in any of the modeled ancestry sources, we would expect higher (female bias) or lower (male bias) proportions of this ancestry on the X chromosome compared to the autosomes, as the paternal contribution to the X chromosome is only one-third that of the autosomes (fathers contribute an X chromosome exclusively to their daughters). A significantly higher proportion of ancestry on the autosomes would indicate a male-driven contribution

Fig. 4

PCA of present-day West Eurasians and North Africans (overlaid colored polygons represent geographical clusters). The ancient individuals from Iberia and other regions were projected onto the first two principal components. Colors indicate different temporal periods as shown in 1B, with a focus on A the Roman and B Early Medieval periods. C Ancestry proportions using different admixture modeling frameworks for Idanha_a_Velha_Roman and Early Medieval archeological sites; p-values are provided inside each column and error bars indicate 1-SD. D f₄-statistics of the form f₄(Idanha_a_Velha_Roman, Iberia_Roman_oLocal; Test, Chimp) with Test including ancient and present-day African populations as proxies for the individuals clustering with present-day Africans in PCA (ID_25538 and PT_24182). The x-axis shows the f₄-statistic values, with results displayed as the mean ± 1-SD

Fig. 5

PCA of present-day West Eurasians and North Africans (overlaid colored polygons represent geographical clusters) with ancient individuals from Iberia and other regions projected onto the first two principal components. Colors indicate different temporal periods as shown in 1B, with a focus on the A Late Medieval period with Islamic and Christian associated sites, and B thirteenth to nineteenth century Portugal. C ROH analysis for PT_24170 from Santarém_Islamic, exhibiting cumulative ROH lengths exceeding 4 cM. D Ancestry proportions for Portuguese individuals from the Islamic and Christian Late Medieval period, thirteenth century, eighteenth century, and nineteenth century, p-values are provided inside each column and error bars indicate 1-SD