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Semitic Duwa
2018-03-12, 20:31
Four millennia of Iberian biomolecular prehistory
illustrate the impact of prehistoric migrations at the far end of Eurasia (http://www.pnas.org/content/early/2018/03/06/1717762115)


http://www.pnas.org/content/pnas/early/2018/03/06/1717762115/F1.large.jpg?width=800&height=600&carousel=1
http://www.pnas.org/content/pnas/early/2018/03/06/1717762115/F2.large.jpg?width=800&height=600&carousel=1


Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.


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Nine of the 13 ancient Iberian individuals were found to carry mitochondrial haplogroups associated with European early farmers, namely K, J, N, and X (SI Appendix, Table S4.1), distributed throughout the Early Neolithic to the Bronze Age (6, 45). Two individuals have haplogroups HV0 and H, known in both European early farmers and hunter-gatherers (25, 45) and are present during the LNCA. Further, haplogroup U5, characteristic of hunter-gatherers (46, 47), is found in a Late Copper Age individual. Consistent with the mitochondrial haplogroup composition of the ancient Iberians, the Y chromosome composition (Dataset S1) displays a mix of haplogroups associated with both European farmers and hunter-gatherers. Among the Early Neolithic individuals, we find the European farmer-associated haplogroup G2a2 (9) and the European farmer-associated haplogroup H2 (1, 6), while in the LNCA we observe haplogroup I2, previously found in both hunter-gatherers and farmers (SI Appendix, Table S4.1) (1, 6). Both Bronze Age males carried haplogroup R1b-M269 (SI Appendix, Table S4.1), which is frequent among Late Neolithic and Bronze Age samples from other parts of Europe (4, 6). This uniparental marker composition is in agreement with the well-known admixture between resident hunter-gatherers and incoming farmers.

To obtain an overview of the genetic variation within prehistoric Iberia, we performed principal component analysis (PCA) on a reference panel of 26 modern-day populations from western Eurasia (1) on which we projected our 13 ancient individuals, together with relevant Mesolithic (n = 17), Neolithic/Chalcolithic (n = 98), and Late Neolithic/Bronze Age (n = 78) genomes from Europe and Anatolia (Fig. 1B and Dataset S2). This PCA replicates previous findings: (i) a clear genetic distinction between early farmers and resident hunter-gatherers, (ii) affinity of the former with the southwestern modern-day European variation, and (iii) an increased affinity of prehistoric farmers to western hunter-gatherers over time due to increased admixture between the two populations (1⇓–3, 11, 25, 26). Despite the geographic proximity of southern Iberia to northern Africa, we do not see substantial affinities of any individual to modern-day African populations, but the lack of ancient North African genomes limits our abilities to test these connections (SI Appendix, Fig. S5.1).

Zooming into the genetic variation within prehistoric Iberia, we do not find a geographic stratification pattern between North and South Iberian populations; instead, we observe stratification directly associated with chronology. Three clusters are identified among the Iberian farmers on the PCA. The first cluster comprises the early Neolithic Iberians (Fig. 1B, yellow triangles) that falls within the modern-day Sardinian genomic variation showing the highest affinity to Sardinians among all early European farmers. The second group includes the Middle Neolithic (Fig. 1B, blue triangles and squares) and LNCA (Fig. 1B, red triangles and squares) populations falling within the modern-day southern European variation but differentiating from the early Neolithic Iberians, a pattern which can be explained by the subsequent admixture with local hunter-gatherers (6, 11, 24). These Iberian farmers were likely the group that later developed Bell Beaker pottery (widely found in Western Europe during the third millennium BC), which then spread without major migrations toward central and northwestern Europe (48). The third cluster encompasses the Bronze Age individuals (Fig. 1B, turquoise triangles and squares) and is differentiated from the other two groups, showing the highest affinity to modern-day Iberians. There is a strong genetic difference among Iberian populations dating to the Mesolithic, early and middle Neolithic, LNCA, and Bronze Age; this genetic pattern is likely the result of numerous migrations and admixture events over time.

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To formally test this separation, we calculated f4 statistics to investigate if Iberian farmers form a clade to the exclusion of central European farmers. The statistic of the form f4(Chimp, X; Central_LBK_EN and Iberia_EN) measures whether an individual X shares more genetic drift with early Neolithic central Europeans (if the value is negative) or early Neolithic Iberians (if the value is positive). For this analysis, we only used SNP-captured individuals for the reference populations (Central LBK_EN and Iberia_EN) to avoid spurious affinities between references and X due to technological artifacts (49, 50). In contrast to prehistoric populations from central Europe, this statistic is consistently shifted toward positive values for prehistoric Iberian groups from different chronologies (Fig. 2A) and is qualitatively similar when using other individuals as reference (Dataset S4). This pattern does not seem to be driven by hunter-gatherer–related admixture into the farming populations (Dataset S5). This observation suggests that all Neolithic Iberians trace most of their ancestry to the first Neolithic migrants arriving in the peninsula and that later contributions from contemporary central Europeans were only minor. The overall pattern is consistent with two independent Neolithic migrations of genetically slightly different populations that spread farming practices across Europe. The Mediterranean route migrants show a strong connection with modern-day population isolates in southwestern Europe. Modern-day Sardinians have been suggested to be relatively direct descendants of the early Neolithic individuals (27, 51), and modern-day Basques also trace a high proportion of their ancestry to the first Mediterranean farmers with only minor additional admixture since the Neolithic (11).

A large migration of Pontic-Caspian steppe herders (the Yamnaya culture) during the Late Neolithic/Early Bronze Age has been found to have a substantial impact on the gene pool of central and northern European populations (4, 6⇓–8), but the impact of this migration on contemporary southern and western Europeans has been unclear. To estimate the genetic contributions of different prehistoric groups (hunter-gatherers, early Anatolian farmers, and Steppe herders) to other ancient populations, we inferred admixture fractions using both unsupervised (ADMIXTURE, ref. 52) (Dataset S3) and supervised approaches (qpAdm and ADMIXTURE, refs. 6 and 52). Neolithic European populations share different proportions of hunter-gatherer and Neolithic farmer genetic material, with a tendency toward more hunter-gatherer–related ancestry in later groups (Fig. 2B) (11). Late Neolithic and Bronze Age north-central Europeans display substantial fractions of Pontic Steppe ancestry (up to 71% estimated with qpAdm; 93% based on supervised ADMIXTURE) (SI Appendix, Fig. S5.3) at the onset of the Bronze Age. However, steppe ancestry in Bronze Age individuals from Iberia (13%; 18%) and Hungary (21%; 38%) is lower than in their north-central European counterparts (Fig. 2B), a pattern previously suggested but not directly quantified (24). The estimates for Bronze Age Iberians are close to the 15% steppe ancestry estimated for the modern Spanish population (Fig. 2B). Consistently, Bronze Age populations from Greece and Anatolia also show a limited increase in steppe ancestry compared with their Neolithic ancestors (15). This reduced impact of Steppe herders on these populations could reflect a decrease in the number of migrants or a dilution of Steppe ancestry during this process. In contrast to the events in north-central Europe, the arrival of most of the Yamnaya-related ancestry in Iberia postdates the onset of Bell Beaker pottery in Iberia, suggesting that the Bell Beaker culture spread culturally (48), while steppe ancestry was brought into Iberia through later migrations. Notably, both male Bronze Age Iberian individuals in this study as well as all three Iberian Bronze Age males in ref. 24 carried R1b-M269 Y chromosomes (SI Appendix, Table S4.1) also found with high frequency in individuals associated with the Yamnaya culture, the source population of steppe ancestry (4, 6), indicating a continuing male-driven migration from central Europe into southwestern Europe (8, 24, 53).

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We present a comprehensive biomolecular dataset spanning four millennia of prehistory across the whole Iberian Peninsula. Our results highlight the power of archaeogenomic studies focusing on specific regions and covering a temporal transect. The 4,000 y of prehistory in Iberia were shaped by major chronological changes but with little geographic substructure within the Peninsula. The subtle but clear genetic differences between early Neolithic Iberian farmers and early Neolithic central European farmers point toward two independent migrations, potentially originating from two slightly different source populations. These populations followed different routes, one along the Mediterranean coast, giving rise to early Neolithic Iberian farmers, and one via mainland Europe forming early Neolithic central European farmers. This directly links all Neolithic Iberians with the first migrants that arrived with the initial Mediterranean Neolithic wave of expansion. These Iberians mixed with local hunter-gatherers (but maintained farming/pastoral subsistence strategies, i.e., diet), leading to a recovery from the loss of genetic diversity emerging from the initial migration founder bottleneck. Only after the spread of Bell Beaker pottery did steppe-related ancestry arrive in Iberia, where it had smaller contributions to the population compared with the impact that it had in central Europe. This implies that the two prehistoric migrations causing major population turnovers in central Europe had differential effects at the southwestern edge of their distribution: The Neolithic migrations caused substantial changes in the Iberian gene pool (the introduction of agriculture by farmers) (6, 9, 11, 13, 24), whereas the impact of Bronze Age migrations (Yamnaya) was significantly smaller in Iberia than in north-central Europe (24). The post-Neolithic prehistory of Iberia is generally characterized by interactions between residents rather than by migrations from other parts of Europe, resulting in relative genetic continuity, while most other regions were subject to major genetic turnovers after the Neolithic (4, 6, 7, 9, 25, 48). Although Iberian populations represent the furthest wave of Neolithic expansion in the westernmost Mediterranean, the subsequent populations maintain a surprisingly high genetic legacy of the original pioneer farming migrants from the east compared with their central European counterparts. This counterintuitive result emphasizes the importance of in-depth diachronic studies in all parts of the continent.

Litvin
2018-03-12, 22:33
There were still many Non-IE speaking tribes in Iberia by the time when the Romans invaded it, despite the introduction of Steppe ancestry already during the Bronze Age. I wonder if they were linguistic survivors of Iberia_LNCA or the result of post-BA re-introduction of Non-IE languages.

Semitic Duwa
2018-03-12, 23:24
One of the two Bronze Age samples (esp005/IberiaNorth_BA) is DF27:

http://pichoster.net/images/2018/03/13/6d87453fca9dbe4f00a969839b789313.png

S1.5 Cueva de los Lagos
The Cueva de los Lagos is located in Aguilar del río Alhama, La Rioja, in northern Spain on the
south bank of the Ebro River. The abundance of permeable and soluble limestone in the local
geology promotes the formation of a series of wells and cavities inside the cave. Several of these
interconnected cavities are responsible for the formation of lakes, in one of which the burial of
the individual analysed in this study (ESP005) was found. It is possible that more than one burial
occurred here, as a fragment of skull belonging to a second individual was also found. Although
the human remains recovered from the interior of the cave come from uncontrolled excavation
and thus lacks context, both the settlement and the burial are associated to the Cogotas culture of
the Late Bronze Age, whose most characteristic element is the type of ceramic decoration termed
Boquique (Fig. S1.5A&B). This type of decoration is found in a vast number of the ceramics
found(14, 15).

Litvin
2018-03-12, 23:33
What a shame that they failed to C14 radiocarbon date this sample.

I'm DF27 and I wonder if my subclade's TMRCA is older or younger. :)

Semitic Duwa
2018-03-12, 23:50
What a shame that they failed to C14 radiocarbon date this sample.

I'm DF27 and I wonder if my subclade's TMRCA is older or younger. :)

Does your subclade's TMRCA predate the Late Bronze Age? Because the authors' assessment is that "both the settlement and the burial are associated to the Cogotas culture of the Late Bronze Age":

https://www.researchgate.net/profile/Antonio_Blanco-Gonzalez/publication/276167580/figure/fig2/AS:[email protected]/Colour-online-Spatial-representation-of-Cogotas-I-and-El-Argar-cultures-in-Iberia-as.jpg

http://pichoster.net/images/2018/03/13/66df63d20f44abd61f5809eed833a107.png

http://pichoster.net/images/2018/03/13/952d9406079cbe5152bfc8b2d579e340.png

https://d8v5jhqx5tv4l.cloudfront.net/wp-content/uploads/2017/09/bronze_age_late.jpg

Litvin
2018-03-13, 00:02
My subclade's TMRCA is probably 2000-1400 BCE, so I guess it is older.

Power77
2018-03-13, 02:05
I wonder if those I2, G2a2 and H2 samples belonged to Vasconic speakers.