The Genetic History of Portugal: Five Millennia at Europe’s Atlantic Edge

Ancient DNA now traces Portugal’s population history from Mesolithic foragers through the Neolithic transition, the Beaker/Bronze Age steppe pulse, Roman and Islamic-period mobility, to the subtle regional structure seen today.

From hunter-gatherers to early farmers (Mesolithic → Neolithic)

Genome-wide transects across Iberia show that by the Neolithic (from ~5500 BCE) Anatolian-related farmers moved into the peninsula and mixed with local Western Hunter-Gatherers (WHG). This farmer–forager blend persisted into the Chalcolithic, with a north-east to south-west gradient in the persistence of WHG-associated ancestry recorded in new Portuguese ancient genomes.

The Bronze Age transformation: Steppe ancestry and DF27

Like elsewhere in Western Europe, Steppe-derived ancestry arrived in Iberia during the 3rd–2nd millennium BCE, much of it via Bell Beaker networks. In Iberia this brought major autosomal change and, strikingly, near-complete turnover of Y-chromosomes to R1b-M269, with the Iberia-focused branch R1b-P312→DF27 later exploding in frequency (today peaking in Spain and Portugal). High-resolution Y-capture work refines DF27’s internal tree and highlights its rapid Bronze-Age radiation and Atlantic vs. Mediterranean substructure.

Iron Age and Roman Iberia: mobility without erasing locals

Across Iron Age Iberia, continuity from Late Bronze Age populations is common, but Mediterranean connectivity (Phoenician, Greek, Roman) layered in additional ancestry streams. A peninsula-wide transect shows sustained local ancestry with episodic inputs from the Mediterranean world during the Roman period. Portugal-focused genomes pinpoint sites such as Idanha-a-Velha as Roman-era hubs drawing North-African and Eastern-Mediterranean ancestries, embedded within a mainly local background.

The Early Medieval centuries: Central-European lineages reach the northwest

The Migration Period left a genetic footprint more clearly in the north than in the south. In Portuguese series, Central-European–associated ancestry appears in the Early Medieval north (consistent with Suebi/Visigoth horizons), while the south shows stronger continuity with earlier locals.

Al-Andalus and the south’s African bridge

By the Islamic centuries, Portugal’s south (Algarve, Alentejo) shows measurable North-African and Levantine-related ancestry, reflecting Umayyad and later Almoravid/Almohad connections. This admixture did not homogenize the entire country, creating a subtle north–south cline that is still visible in genome-wide analyses today.

Early Modern Portugal and Atlantic links

By the 15th–18th centuries, Portugal was deeply tied to the Atlantic. Early Modern genomes already cluster tightly with present-day Portuguese, but case studies detect traces of Atlantic slavery and colonial-era contacts (West Africa, Brazil, Atlantic Islands), mostly in urban or southern contexts.

Continuity into the present

Overall, the Portuguese population today represents a deeply local base laid down since the Bronze Age, layered with southern Mediterranean and North-African inputs in the south, and modest Central-European ones in the north. Ancient DNA from multiple time slices (Mesolithic, Neolithic, Bronze Age, Medieval, Modern) now clarifies this trajectory, showing how Portugal became one of Europe’s most distinctive yet internally diverse genetic landscapes.

G25 Coordinates

For those interested in further analysis or visualization, here are the G25 coordinates of the sample:

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Portugal_Centro_EarlyMedieval:PT_24169__AD_850__Cov_11.45%,0.060326,0.148267,0.016216,-0.034238,0.030159,-0.014223,-0.007285,0.011769,0.041314,0.030616,-0.00747,-0.007343,0.008771,-0.005367,0.014929,-0.005171,0.026207,-0.009502,-0.02162,0.008129,0.006364,-0.006801,0.003944,0.013255,0.003712
Portugal_Centro_EarlyMedieval:PT_24170__AD_850__Cov_69.14%,0.063741,0.141159,0.007165,-0.031331,0.022158,-0.011992,-0.008695,0.002308,0.027815,0.026789,-0.001624,-0.001349,0.002825,-0.007844,0.013301,-0.006099,-0.000782,-0.009248,-0.01433,0.007379,-0.00836,-0.00507,0.004437,-0.004458,0.004311
Portugal_Centro_EarlyMedieval:PT_24173__AD_850__Cov_34.27%,0.078538,0.145221,0.011691,-0.036822,0.027082,-0.014223,-0.01081,0.005538,0.030065,0.035536,0.00682,-0.003297,-0.011001,-0.01156,0.0076,-0.016574,-0.010822,-0.00266,-0.017095,-0.009004,-0.004742,-0.006925,0.001725,-0.005181,-0.002155
Portugal_Norte_Medieval:PT_22989__AD_1100__Cov_32.06%,0.121791,0.137096,0.039598,0.021318,0.033237,-0.001673,0.00235,0.005077,0.019839,0.027153,0.003248,0.006894,-0.012933,-0.009221,0.014115,0.003447,-0.00013,0.005194,0.007919,-0.004877,-0.002121,0.006554,-0.00037,-0.001325,-0.000359
Portugal_Norte_Medieval:PT_22992__AD_1100__Cov_57.51%,0.113823,0.142174,0.037712,-0.005168,0.044316,-0.005299,-0.003995,0.007615,0.029451,0.02934,-0.002598,0.01139,-0.016353,-0.012524,0.002307,0.002784,-0.00339,-0.003927,-0.006536,0.003502,0.000499,0.000866,-0.002958,0.002892,-0.000359
Portugal_Norte_Medieval:PT_22994__AD_1100__Cov_68.20%,0.105855,0.140143,0.039221,-0.008721,0.042469,-0.005578,-0.00517,0.008077,0.026793,0.028429,0.005521,0.006744,-0.019029,-0.009083,0.014115,-0.005967,-0.001565,0.005954,0.00176,0.000625,0.012852,-0.010881,0.001602,-0.009399,-0.010059
Portugal_Algarve_Medieval:PT_24175__AD_1150__Cov_55.77%,0.085367,0.144205,0.02225,-0.028747,0.043085,0.000558,-0.012221,0.006692,0.031292,0.037541,-0.001299,0.007194,-0.010406,-0.025047,0.007872,0.009812,0.0103,-0.00266,-0.006285,0.004877,-0.000998,-0.008408,0.00419,-0.003735,-0.000838
Portugal_Algarve_Medieval:PT_24176__AD_1200__Cov_9.80%,0.071709,0.147252,0.021873,-0.020672,0.03416,-0.025658,-0.017391,-0.002308,0.04295,0.047746,0.02111,-0.000599,-0.022894,-0.03413,0.002579,-0.007558,-0.011735,-0.003041,-0.012193,0.001876,-0.005615,-0.00136,0.007025,0.005543,-0.002155
Portugal_Algarve_Medieval:PT_24178__AD_1200__Cov_15.68%,0.066017,0.139128,0.029793,-0.01938,0.036314,-0.014781,-0.01034,-0.003231,0.044382,0.044466,0.003735,-0.0003,0.008176,-0.009221,0.007872,0.012994,0.015385,-0.01913,-0.000754,0.01063,0.022086,-0.011871,0.014173,-0.007712,-0.010418
Portugal_Algarve_Medieval:PT_24179__AD_1250__Cov_68.52%,-0.14797,0.116786,0.021119,-0.021641,0.020004,-0.01506,-0.022561,0.020538,0.022907,0.028611,0.000974,0.00045,0.016204,-0.01913,0.00665,0.005038,0.010822,-0.007855,-0.006159,-0.002251,0.000998,-0.019537,0.012448,0.00494,0.008023
Portugal_Algarve_LateMedieval:PT_24180__AD_1300__Cov_15.60%,0.081953,0.147252,0.033941,-0.024548,0.03693,-0.015897,-0.023736,0.007154,0.032315,0.026606,0.012991,0.005095,-0.001487,-0.014038,0.022665,0.006762,-0.014473,-0.004561,-0.011816,0.010755,0.001248,0.002597,0.008751,-0.005181,-0.002036
Portugal_Centro_LateMedieval:PT_22218__AD_1300__Cov_67.87%,0.114961,0.148267,0.041483,-0.007752,0.048932,-0.006136,-0.00611,0.002077,0.026793,0.031891,-0.002923,0.009442,-0.001189,-0.012248,0.008822,-0.019358,-0.006258,-0.004941,-0.004525,-0.000625,0.00262,-0.002597,-0.004807,-0.010242,0.005748
Portugal_Centro_LateMedieval:PT_22219-23224__AD_1300__Cov_67.58%,0.1161,0.142174,0.040729,-0.002584,0.048624,-0.000837,-0.001175,0.005769,0.027202,0.030433,-0.005846,0.005095,-0.015015,-0.02491,0.007465,0.001591,0.003651,0.004814,0.001885,-0.001751,0.005241,-0.005688,-0.012571,0.006025,0.005389
Portugal_Centro_LateMedieval:PT_22220__AD_1300__Cov_16.42%,0.118376,0.148267,0.038466,-0.000969,0.050471,-0.011992,-0.011986,-0.007846,0.025565,0.035901,0.004709,0.004196,-0.005054,-0.003853,0.01045,-0.003845,0.012126,-0.011655,-0.003268,0.009379,0.00025,0.000618,0.011709,0.001446,0.000479
Portugal_Centro_LateMedieval:PT_23221__AD_1300__Cov_14.63%,0.112685,0.152329,0.042238,-0.005814,0.035083,-0.00251,0.0047,0.009923,0.030474,0.0277,-0.012017,0.006744,-0.010555,-0.007569,0.005293,0.007292,-0.007562,-0.006588,-0.006913,-0.000625,0.001373,-0.005564,0.013064,-0.001928,-0.008861
Portugal_Centro_LateMedieval:PT_23223__AD_1300__Cov_63.61%,0.106994,0.148267,0.029415,-0.003553,0.044008,-0.001394,-0.008695,-0.002308,0.016157,0.023326,0.004872,0.003297,-0.005946,-0.012248,0.001629,0.009944,0.014864,0,-0.011564,0.004877,0.000998,-0.004328,0,0.004338,0.004191
Portugal_Centro_LateMedieval:PT_23226__AD_1300__Cov_81.28%,0.106994,0.135065,0.035826,-0.006783,0.038161,-0.000837,-0.005405,0,0.025975,0.024237,0.005684,0.006744,-0.016353,-0.010872,0.013843,-0.001061,-0.018515,-0.006714,-0.004274,0.00075,0.003993,-0.000866,0.001972,-0.002169,0.002036
Portugal_Centro_LateMedieval:PT_23227__AD_1300__Cov_50.82%,0.100164,0.145221,0.030547,-0.005168,0.029544,0.001116,-0.009165,0.001154,0.023316,0.030798,0.001461,0.008243,-0.018731,-0.007019,0.013979,0.00305,-0.001173,-0.00228,-0.003394,0.004752,-0.002371,-0.004699,0.000246,-0.007109,-0.00467
Portugal_Centro_LateMedieval:PT_23229__AD_1300__Cov_57.82%,0.097888,0.141159,0.044877,0.00323,0.045547,-0.001952,-0.015511,0.007846,0.033133,0.020593,-0.00065,0.005995,-0.006392,-0.014588,0.011401,0.002387,-0.004042,0.00076,-0.001131,-0.005503,-0.000499,-0.004204,-0.001602,-0.002771,0.002155
Portugal_Centro_LateMedieval:PT_23230__AD_1300__Cov_48.10%,0.103579,0.139128,0.043369,0.000969,0.037545,0.001952,0,0.013846,0.029247,0.031527,-0.002761,0.007343,-0.01665,-0.007156,0.010858,0.006099,0.000913,0.000887,-0.000628,0.001126,0.002121,-0.000247,0.001849,-0.000241,-0.001317
Portugal_Lisboa_LateMedieval:PT_24163__AD_1300__Cov_58.29%,0.099026,0.14319,0.034695,-0.015827,0.041546,-0.00753,-0.00846,0.004384,0.031292,0.025331,0.004547,0.002847,-0.01219,-0.01101,0.015201,-0.00716,-0.011343,-0.004561,-0.010559,-0.015382,0.000499,-0.008656,0.009983,0.000482,-0.001197
Portugal_Lisboa_LateMedieval:PT_24164__AD_1300__Cov_53.16%,0.099026,0.142174,0.035826,0.000323,0.035391,0.003068,0.00188,0.008307,0.029247,0.028429,0.003897,0.004646,-0.013528,-0.013487,0.015744,0.007425,0.011343,-0.00228,-0.009176,0.001376,0.003619,-0.013231,0.006532,0.00241,-0.005748
Portugal_Lisboa_LateMedieval:PT_24165__AD_1300__Cov_27.26%,0.097888,0.149283,0.037335,-0.001292,0.033237,-0.014223,0.001645,0.002538,0.02168,0.031709,0.000812,-0.002847,-0.004757,-0.004404,0.014522,-0.01432,-0.015255,0.006968,0.008296,-0.004252,0.002496,-0.011252,0.003204,-0.002169,-0.007784
Portugal_Lisboa_LateMedieval:PT_24166__AD_1300__Cov_12.42%,0.086506,0.152329,0.036958,0.003876,0.048932,0.000279,-0.016686,0.002538,0.027611,0.015672,-0.00341,0.010041,-0.009068,-0.009771,0.009772,-0.013126,-0.023339,-0.005954,-0.007039,-0.001751,-0.00025,-0.011871,-0.001356,-0.020846,-0.000599
Portugal_Lisboa_LateMedieval:PT_24167__AD_1300__Cov_54.30%,0.097888,0.140143,0.036204,0.010013,0.041854,-0.004741,-0.00282,0.003461,0.023725,0.021322,-0.008444,0.002548,-0.011893,-0.016239,0.006786,0.003713,-0.005867,0.003041,-0.006536,-0.005378,0.002371,-0.012736,-0.009737,0.002289,0.002395
Portugal_Algarve_LateMedieval:PT_24181__AD_1350__Cov_22.88%,0.086506,0.141159,0.01961,-0.026486,0.033237,0.006693,0.000705,0.008769,0.021066,0.031345,0.011205,0.003597,0.001635,-0.024084,0.003257,0.001724,0.022165,-0.002154,-0.010684,0.00075,-0.001373,0.001484,0.011339,0.00241,-0.00479
Portugal_Centro_EarlyModern:PT_23214__AD_1750__Cov_60.96%,0.101303,0.14319,0.034695,-0.001615,0.030467,0.003068,-0.00517,0.001846,0.023929,0.024055,0.00406,0.007493,-0.00773,-0.006055,0.009365,-0.00053,-0.01695,0.0019,-0.008045,-0.005878,0.007112,-0.004328,0.003081,-0.009519,0.004431
Portugal_Centro_EarlyModern:PT_23215__AD_1750__Cov_89.43%,0.106994,0.140143,0.033187,-0.000969,0.046778,-0.003068,-0.006815,0.002769,0.027611,0.030069,-0.009094,0.004796,-0.008474,-0.013074,0.011808,-0.002254,0.007171,0.00228,0.000126,0.001501,0.000624,-0.003462,-0.000863,-0.008073,0.003952
Portugal_Centro_EarlyModern:PT_23216__AD_1750__Cov_70.13%,0.103579,0.145221,0.04186,-0.002584,0.045855,-0.003904,0,0.008307,0.024338,0.022597,-0.001949,0.007194,-0.009366,-0.022983,0.013843,0.011535,0.017993,0.001647,-0.00088,0,0.00025,-0.000371,0.003821,-0.003374,0.000599
Portugal_Centro_EarlyModern:PT_23217__AD_1750__Cov_45.93%,0.099026,0.147252,0.04714,-0.006783,0.042469,-0.008367,-0.004935,0.002769,0.022702,0.033896,-0.001461,0.005695,0.001041,-0.012937,0.009093,-0.008088,-0.015776,0,-0.00993,0.000625,0.005865,0.00779,0.004314,-0.007712,0.003113
Portugal_Centro_EarlyModern:PT_23241__AD_1750__Cov_64.43%,0.108132,0.138112,0.033564,-0.007106,0.041546,-0.005578,-0.007285,0.001846,0.026588,0.030616,-0.008282,0.004196,-0.013379,-0.007019,0.007465,0.001458,-0.000391,-0.007601,-0.008045,-0.002626,0.002371,-0.005441,-0.006039,-0.006507,-0.001676
Portugal_Centro_EarlyModern:PT_23242__AD_1750__Cov_36.58%,0.101303,0.133034,0.039221,-0.003553,0.028621,-0.006972,-0.00611,0.002077,0.02352,0.029887,-0.000325,0.012439,-0.020664,-0.018992,0.016422,0.005038,-0.001695,-0.003927,-0.01257,0.008004,-0.001622,-0.003091,0.001602,-0.011929,-0.006347
Portugal_Norte_EarlyModern:PT_22190__AD_1750__Cov_38.38%,0.104717,0.144205,0.032055,-0.014212,0.042777,0.001394,-0.002115,-0.001615,0.025975,0.030069,0.006658,0.004496,-0.011447,0.000138,0.010586,-0.008884,-0.015907,-0.000507,-0.002514,-0.017258,-0.003743,-0.004822,-0.000493,-0.002651,0.006826
Portugal_Centro_Modern:PT_22179__AD_1850__Cov_84.72%,0.125205,0.135065,0.054682,0.034561,0.048317,0.015897,0.00282,0,0.0045,0.00328,-0.003735,0.00015,-0.013379,-0.004266,0.016151,-0.001061,-0.008736,-0.001774,0.004525,-0.001501,0.005116,0.009274,0.007148,0.018918,-0.004071
Portugal_Centro_Modern:PT_22183__AD_1850__Cov_85.59%,0.102441,0.149283,0.042615,-0.004199,0.043085,-0.000279,-0.005875,0.007615,0.026793,0.024055,-0.000487,0.006594,-0.010258,-0.020231,0.016422,0.000796,-0.001565,-0.003927,0.000628,0.000625,0.009733,-0.002844,-0.000739,0.011447,-0.002155

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