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

[Tautalus]

Abstract

Background: Recent ancient DNA studies uncovering large-scale demographic events in Iberia have focused primarily on Spain, with limited reports for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we introduce the largest collection of ancient Portuguese genomic datasets (n = 68) to date, spanning 5,000 years, from the Neolithic to the 19th century. Results: We found evidence of patrilocality in Neolithic Portugal, with admixture from local hunter-gatherers and Anatolian farmers, and persistence of Upper Paleolithic Magdalenian ancestry. This genetic profile persists into the Chalcolithic, reflecting diverse local hunter-gatherer contributions. During the Bronze Age, local genetic ancestry persisted, particularly in southern Iberia, despite influences from the North Pontic Steppe and early Mediterranean contacts. The Roman period highlights Idanha-a-Velha as a hub of migration and interaction, with a notably diverse genetic profile. The Early Medieval period is marked by Central European ancestry linked to Suebi/Visigoth migrations, adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant African admixture in the south, with persistent Jewish and Islamic ancestries suggesting enduring influences in the post-Islamic period. Conclusions: This study represents the first attempt to reconstruct the genetic history of Portugal from the analysis of ancient individuals. We reveal dynamic patterns of migration and cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archaeological data, enhancing our understanding of Iberia's ancient heritage.​

https://www.biorxiv.org/content/10.1101/2024.09.12.612544v1

 

[Luso]

Great post

 

[Tautalus]

From the supplementary data:

Y-Haplogroup details, sorted by chronological period.

ACAD ID	Library ID	Chronology	Haplogroup	SNP
PT_22213	LP116_15	Mid-Neolithic	I2a1a1a1a1	I-L160 (I-M26)
PT_22207	LP116_12	Mid-Neolithic	I2a1a2a	I-L161 (I-M423)
PT_22212	LP123_7	Mid-Neolithic	I2a1a2a	I-L161 (I-M423)
PT_22194	LP128_2	Mid-Neolithic	I2a1a2a1a	I-L1498 (I-M423)
PT_22200	LP128_4	Mid-Neolithic	I2a1a2a1a	I-L1498 (I-M423)
PT_22204	LP116_11	Mid-Neolithic	I2a1a2a1a	I-L1498 (I-M423)
PT_22210	LP116_13	Mid-Neolithic	I2a1a2a1a	I-L1498 (I-M423)
PT_22214	LP116_16	Mid-Neolithic	I2a1a2a1a	I-L1498 (I-M423)
PT_22197	LP128_3	Chalcolithic	I2a1a1a1a1	I-L160 (I-M26)
PT_23202	LP115_14	Bronze Age	F	F
PT_23200	LP113_10	Bronze Age	R1b1a1b	R-M269
PT_23212	LP123_14	Bronze Age	R1b1a1b1a1	R-P310
PT_23197	LP113_8	Bronze Age	R1b1a1b1a1a	R-L151
PT_23198	LP113_5 + LP123_3	Bronze Age	R1b1a1b1a1a	R-L151
PT_23207	LP111_6	Bronze Age	R1b1a1b1a1a	R-L151
PT_23210	LP112_10	Bronze Age	R1b1a1b1a1a	R-L151
PT_23219	LP123_11	Bronze Age	R1b1a1b1a1a	R-L151
PT_24182	LP115_2 + LP123_10	2nd-3rd century	R1b1a1b1a1a	R-L151
PT_23001	LP117_4	7th-8th century	R1b1a	R-L389
PT_23002	LP112_13	7th-9th century	R1b1a1b1a1a	R-L151
PT_24170	LP114_10	8th - 10th century	J1a2a1a1b	J-PF7263
PT_22994	LP117_3	11th-12th century	R1b1a1b1a1	R-P310
PT_22992	LP117_2	11th-12th century	R1b1a1b1a1a	R-L151
PT_24175	LP114_15	11th - 13th century	J2a1a1a2b2a3b1a1b1	J-Y150765 (J-M67)
PT_23234	LP116_7	12th century	R1b1a1b	R-M269
PT_24176	LP115_3	12th - 13th century	R1a1a1b2a	R-Z94
PT_24163	LP114_3	12th-15th century	J2b1b1	J-CTS5338 (J-M205)
PT_24165	LP114_5	12th-15th century	J2b1b1	J-CTS5338 (J-M205)
PT_24167	LP114_7	12th-15th century	R1b1a1b1a1	R-P310
PT_24179	LP115_5	13th -13th century	R1b1a1b1a1a	R-L151
PT_23221	LP117_10	13-14th century	E1b1b1b1a1	E-183 (E-M81)
PT_22218	LP113_1	13-14th century	E1b1b1b2b	E-CTS10880 (E-M35)
PT_23226	LP113_4	13-14th century	J2a1a1a2b1b2a1	J-M319 (J-L26)
PT_23227	LP123_6	13-14th century	Q1b1a3a1	Q-L330
PT_22219-23224	LP117_12-LP123_5	13-14th century	R1b1a1b1a1a	R-L151
PT_23223	LP117_7	13-14th century	R1b1a1b1a1a	R-L151
PT_24181	LP115_6	15th -13th century	E1b1b1b2a1a1a2	E-Y5427 (E-M34)
PT_22187	LP128_1	post-medieval	R [K2b2a2]	R
PT_23241	LP111_8	18th century	E1b1b1a1b1a10a1a3	E-Z16661 (E-V13)
PT_22190	LP116_10	18th century	E1b1b1b1a1	E-183 (E-M81)
PT_23214	LP113_9	18th century	J1a2a1a2d2b2b2c4b1	J-FGC8223
PT_22183	LP117_11	19th century (Napoleonic)	I2a1b1a1b1a1a1a	I-L812 (I-M223)
PT_22179	LP116_9	19th century (Napoleonic)	R1b1a1b1a1a1c1a	R-U106

 

[D.L.M]

Duh obviously.

 

[kingdavid]

Tautalus thanks for sharing
Interesting to see
medieval individual remain PT_22218 under e-z830>v1515
though in the e3b project there are some testers with portuguese paternal background who belongs to it

P.s
Hope the bam files will be out that experts here and in other forums could see the terminal snp below e-v1515

 

[Tautalus]

There are some y-haplogroups that are poorly understood by the study authors, at least in their geographical distribution. For example, they say, erroneously, that “PT_22183 carries a Y-chromosome haplogroup I2a1b1a1b1a1a1a which is more commonly found in Eastern and Southeastern Europe.”
And again “Additionally, PT_22183’s Y-chromosome haplogroup I2a1b1a1b1a1a1a is more commonly found in Eastern and Southeastern Europe. This haplogroup’s presence indicates possible migration or conscription of individuals from these regions into the Napoleonic forces.”
I2a1b1a1b1a1a1a is I2-L812 (ISOGG Tree 15.73), a sub-clade of I2-M223, it has a predominantly western, northern and central distribution, not an eastern or southeastern one. They should have been better informed.​

I2-L812 tested descendants in FTDNA

Country	Tested_Descendants​
United States​	11​
England​	8​
Portugal​	6​
Spain​	6​
Germany​	5​
Sweden​	5​
Wales​	5​
Mexico​	4​
Scotland​	3​
Canada​	2​
France​	2​
United Kingdom​	2​
Chile​	1​
Greece​	1​
Italy​	1​
Macedonia​	1​
Netherlands​	1​
Norway​	1​
Poland​	1​
Switzerland​	1​
Ukraine​	1​
Vietnam​	1​
Unknown Origin​	125​

 

[MOESAN]

The samples tested by all these companies are not a good representation of the genuine total relative distribution, there is the question, I think.

 

[Vitruvius]

I see a lot of continuity from the bronze age to modern day. There is a shift from the iron age as we enter the Roman period towards the Aegean and also two outliers from north Africa. It seems like the north african outliers disappear and the average is remains slightly more Aegean like (compared to iron age iberians) by the visigoth era. This would imply an slight increase in Caucasian neolithic ancestry and a slight decrease in Eastern and Western hunter gatherer ancestry. This would've been likely brought by imperial Roman colonists from Italy, probably mostly through the numerous veteran colonies established in Iberia.

The post Roman/Visigothic population seems to remain the standard genetic structure for Portugese to this day. There is a considerable shift towards proper arab populations during the Islamic era for specifically Islamic burials but similar to the roman era north african outliers, they do not last. Meanwhile the contemporary Catholic population in Iberia during this period remains still representative of the Visigothic/post roman population and genetically replaces the islamic population through expulsion and superior fertility/demography after the reconquista.

 

[Vitruvius]

We see the same phenomenon here that was seen with the Islamic period in Sicily in which over the course of 300 years, the established Islamic population absorbed most of their ancestry from the locals, creating a hybridized population which was mostly southern European, but yet still roughly 25% north african shifted. This population failed to maintain any permanancy and was expelled and replaced by locals from other parts of the Italian pensinula which lacked any north african influence.

I don't really see any notable differences between Iberia and Italy in these comparative scenarios from a genetic standpoint. It seems like the local genetic structure became the prevailing successor demography in both cases.

 

[Tautalus]

There is a significant degree of genetic continuity from the Bronze Age to the present day in Portugal. While there have been various migrations and cultural shifts, mainly from the Roman period onwards, the genetic impact of these events wasn't as significative as in previous migrations.
The genetic makeup of modern Portuguese people retains a notable proportion of ancestry from the Bronze Age populations. So, we can say that the Westen Iberia Bronze Age genetics constitutes the backbone of Portuguese genetics. This continuity is evident in the genetic markers shared between ancient BA and modern genomes, like the Y-Chromosome.
This continuity is interspersed with periods of genetic influx due to migrations and population movements. The Iron Age reinforced some elements of the Bronze Age, such as the EHG component. The period of the Roman Empire brought shifts to the Eastern Mediterranean and to a lesser extent to North Africa. The Germanic invasions had a minimal and localized impact. The Islamic period introduced a larger North African component, but due to cultural, religious or demographic reasons, this component was significantly reduced after the Reconquista.
As you said the genetics of the post Roman/Visigothic period represents the typical Portuguese genetic structure of today.​

 

[Vitruvius]

There is a significant degree of genetic continuity from the Bronze Age to the present day in Portugal. While there have been various migrations and cultural shifts, mainly from the Roman period onwards, the genetic impact of these events wasn't as significative as in previous migrations.
The genetic makeup of modern Portuguese people retains a notable proportion of ancestry from the Bronze Age populations. So, we can say that the Westen Iberia Bronze Age genetics constitutes the backbone of Portuguese genetics. This continuity is evident in the genetic markers shared between ancient BA and modern genomes, like the Y-Chromosome.
This continuity is interspersed with periods of genetic influx due to migrations and population movements. The Iron Age reinforced some elements of the Bronze Age, such as the EHG component. The period of the Roman Empire brought shifts to the Eastern Mediterranean and to a lesser extent to North Africa. The Germanic invasions had a minimal and localized impact. The Islamic period introduced a larger North African component, but due to cultural, religious or demographic reasons, this component was significantly reduced after the Reconquista.
As you said the genetics of the post Roman/Visigothic period represents the typical Portuguese genetic structure of today.​

Yes, we are on the same page here. Based off this data, in my opinion the Romans were the very last people to permanently affect the population genetics of Portugal's population and the shift itself was still not very large or drastic. The bulk of the genetic structure of modern Portugese was definitely created during the bronze age.

 

[Luso]

To be direct, I've asserted that Portugal and West Iberia form a distinct genetic cluster, a conclusion not solely attributable to Moorish rule. In fact, it seems increasingly evident that significant change during the Moorish period was minimal; however, if new evidence were to suggest otherwise, I would be open to reconsideration.

Despite the skepticism surrounding this viewpoint, it's crucial to note that numerous samples from the pre-Islamic period display contemporary North African admixture, readily accessible online. Here is an average of all those roman-period Portuguese samples encompassing Conimbriga, Monte de Nora and Mirioco:

coordinates:

Portugal_Roman_Period_n=11,0.0969566,0.1439282,0.035038,-0.0097194,0.0422735,-0.0052989,-0.0049779,0.0014055,0.0305485,0.0312286,-0.0030412,0.0062945,-0.0098385,-0.0131867,0.0105492,0.000434,-0.0005335,-0.0019117,-0.0073019,0.0012052,0.0022006,-0.0024505,0.001053,-0.0052361,0.0009253

Here is what the average of all 11 samples scores:

Target: Portugal_Roman_Period_n=11
Distance: 2.7169% / 0.02716935
53.8 TUR_Barcin_N

27.2 Yamnaya_RUS_Samara

11.4 WHG

7.6 MAR_Taforalt


These older samples reveal a range of variation from unusually low to notably unusually high levels of North African ancestry, with averages aligning closely with what contemporary Portuguese individuals exhibit today when omitting one sample that scores a crazy amount of north-african admixture. This variability is not surprising when we analyze the genetic coordinates of ethnically Portuguese individuals; even within this forum, we can observe subtle differences, with outliers and averages. Of course a sample size of 11 is quite low, but these are in-fact roman dated individuals living in Roman period. Without dating most people would assume this higher taforalt component is the result of Moors, but clearly it was not.

As the evidence continues to clarify, it becomes increasingly clear that a genetic continuum in Portugal extends back to the Bronze Age. Significant shifts did occur during the Roman period, reshaping what it today Portugal's genetic landscape.

 

[Tautalus]

Despite the skepticism surrounding this viewpoint, it's crucial to note that numerous samples from the pre-Islamic period display contemporary North African admixture, readily accessible online.

These older samples reveal a range of variation from unusually low to notably unusually high levels of North African ancestry, with averages aligning closely with what contemporary Portuguese individuals exhibit today when omitting one sample that scores a crazy amount of north-african admixture. This variability is not surprising when we analyze the genetic coordinates of ethnically Portuguese individuals; even within this forum, we can observe subtle differences, with outliers and averages. Of course a sample size of 11 is quite low, but these are in-fact roman dated individuals living in Roman period. Without dating most people would assume this higher taforalt component is the result of Moors, but clearly it was not.

Luso, to my knowledge there are no skepticism surrounding the viewpoint that the North African admixture arrived in Iberia before the Islamic conquest. And if this skepticism exists, it is because they are unaware of the most recent genetic studies on ancient Iberia.
As you said numerous samples from the roman period show that admixture. The spread of this admixture, mainly in southern Iberia, may have started even before the Romans, in the Phoenician-Punic period.
This has already been mentioned in some studies, namely in The genomic history of the Iberian Peninsula over the past 8000 years.
They said “These results demonstrate that by the Roman period, southern Iberia had experienced a major influx of North African ancestry, probably related to the well-known mobility patterns during the Roman Empire or to the earlier Phoenician-Punic presence; the latter is also supported by the observation of the Phoenician-associated Y-chromosome J2.”​

 

[Luso]

Luso, to my knowledge there are no skepticism surrounding the viewpoint that the North African admixture arrived in Iberia before the Islamic conquest. And if this skepticism exists, it is because they are unaware of the most recent genetic studies on ancient Iberia.
As you said numerous samples from the roman period show that admixture. The spread of this admixture, mainly in southern Iberia, may have started even before the Romans, in the Phoenician-Punic period.
This has already been mentioned in some studies, namely in The genomic history of the Iberian Peninsula over the past 8000 years.
They said “These results demonstrate that by the Roman period, southern Iberia had experienced a major influx of North African ancestry, probably related to the well-known mobility patterns during the Roman Empire or to the earlier Phoenician-Punic presence; the latter is also supported by the observation of the Phoenician-associated Y-chromosome J2.”​

It'll be interesting to see these new Bronze Age samples and how they score! Btw I didn't want to sound like my comment was towards you. Not at all, I should have used less assertive language. I agree that the skeptics typical neglect these recent results including Olalde's interpretations, however, those were very much a seed in the soil compared to the last 2-3 years.

 

[Tautalus]

It'll be interesting to see these new Bronze Age samples and how they score! Btw I didn't want to sound like my comment was towards you. Not at all, I should have used less assertive language. I agree that the skeptics typical neglect these recent results including Olalde's interpretations, however, those were very much a seed in the soil compared to the last 2-3 years.

No problem, I didn't interpret your comment as directed at me personally.