Ancient genomes from present-day France unveil 7,000 years of its demographic history

[dududud]

Link: https://cvws.icloud-content.com/B/Aa...Ar8HMgLgM&cd=i

[dududud]

Results and Discussion
All analyzed individuals belong to well-defined archaeological
contexts from the Mesolithic Period to the Iron Age and 40 were directly radiocarbon-dated for this study (Dataset S2). We built sequencing libraries for 243 individuals and enriched them for mitochondrial genomes and a panel of 120 selected SNPs across the nuclear genome (Dataset S1). Along with complete mitochondrial genomes of 223 individuals and Y-chromosome haplogroups of 62 male individuals, we report 58 ∼0.05 to 0.5× genomes sequenced from uracil-DNA glycosylase (UDG)-treated libraries. We combined our genotype data with either complete genomes or 1,240k genome-wide polymorphisms in ancient individuals and genotypes of modern individuals from Europe, the Caucasus, and the Near East genotyped on the Affymetrix Human Origins array (3, 5, 9, 10, 12, 13, 21, 22). Complete mitochondrial genomes were retrieved from this ancient dataset and were grouped based on temporal and geographic proximity, often translating into cultural classifications (SI Appendix, Fig. S3-1). Contamination estimates derived from X-chromosome polymorphisms in male individuals were consistently low (between 0.68 ± 1.26 and 3.55 ± 0.62% depending on the method considered), with only one individual displaying more than 5% X-chromosome contamination (PIR3037AB) (Dataset S1).


The French Mesolithic Substrate.
We generated genomic data for five Mesolithic individuals from Les Perrats cave (Agris, Charente) dated from 7177 to 7057 calibrated years BCE (calBCE) including low-coverage shotgun sequencing for three of them
(0.111 to 0.134×). All possess haplogroup U5b, demonstrating in the territory of present-day France the presence of a Mesolithic substrate akin to that described elsewhere, where it was characterized by haplogroups U5b (85%) and, to a lesser extent, U5a (15%) (3, 23). Mesolithic hunter-gatherers (HGs) discovered in France are located near the edge of a principal-component analysis (PCA) plot obtained from genome-wide genotypes, falling near the Mesolithic individuals from western Europe (5, 6, 9) (Fig. 1B and SI Appendix, Fig. S4-3). While the ancestry from an ∼14,000-y-old individual from Villabruna in Italy was found to be dominant in Holocene HGs across western and central Europe (3), recently published studies conducted on ancient Iberians highlighted the survival of Magdalenian-associated ancestry (11).
This dual ancestry is found in all Iberian HGs (ranging from 23.7 to 75.3%), while in most other regions only the Villabrunaassociated ancestry remained. In order to investigate the proportions of ancestry in French HGs derived from these two Late Pleistocene lineages, we used qpAdm to model it as a mixture of two sources: ∼15,000-y-old GoyetQ2 from Belgium, the leastadmixed individual associated with the Magdalenian complex in Europe sequenced so far (11), and Villabruna. We found that French HGs from Les Perrats harbored relatively high proportions of GoyetQ2 ancestry ranging from 31.3 to 45.6% (Fig. 1C), comparable to proportions described in the La Braña or Canes1 Mesolithic individuals from Spain, suggesting a late survival of Magdalenian-associated ancestry in HGs outside the Iberian Peninsula.


Successive Waves of Migration and Admixture over the Course of the Neolithic in France.

The arrival of an Anatolian Neolithicassociated ancestry component at the onset of the Neolithic is clearly visible in our dataset from both uniparentally inherited markers and at the genome-wide level. Maternal lineages from Neolithic farmers in France (from ∼5300 BCE onward) are more diverse than those from HGs, and display variable frequencies across the time transect (SI Appendix, Fig. S3-2). Early and Middle Neolithic individuals share more affinity with present-day
southern Europeans (SI Appendix, Fig. S4-2), and their genetic variation is encompassed within that of contemporaneous European populations (Fig. 1B). Three of our individuals associated with the LBK culture, which stems from the Danubian Neolithic current, cluster genetically with other central European Early Neolithic (EN) individuals and share drift with other early farmers associated with the LBK cultural complex (SI Appendix, Fig. S4-6). Values of D (Mbuti, France_EN; western huntergatherers [WHGs], Anatolia_Neolithic) are consistent with those observed in LBK-associated individuals, with the exception of Mor6 (∼7,100 calB.P.) in northeastern France (Fig. 2B).Despite a consistent dating and cultural assignment to the LBK, this individual falls within the genetic diversity of Iberian_EN individuals and harbors the highest proportion of shared alleles with WHGs. After testing the potential origin of this ancestry with qpAdm, we found the best fit to be with a two-source ancestry model between Anatolia_Neolithic and GoyetQ2 (P =0.0911155), a situation so far only described in Early Neolithic individuals from the Iberian Peninsula. This is the northern-most description of such ancestry. To date, the distribution of the Magdalenian-associated ancestry in the HG population in western Europe that admixed with the Neolithic farmers in Europe is not clear because of the scarcity of genetic data from Mesolithic HGs. The observation of this ancestry in the Iberian Peninsula has been interpreted as a feature distinguishing the Cardial from the LBK Neolithic migrants (12).
The observation that the ancestry of GoyetQ2 was found alongside Villabruna ancestry in HGs from Les Perrats in western France (∼9,100 calB.P.), as well as in HGs from Rigney1 (central-eastern France; ∼15,500 calB.P.) and from two caves in
southwestern Germany, Hohlefels (∼15,000 calB.P.) and Burkhardtshöhle (∼14,600 calB.P.), rather indicates that this mixed
ancestry is characteristic of western European HGs (11). Thus, the admixture between HGs with GoyetQ2 ancestry and Neolithic migrants is not necessarily characteristic of the Cardial Neolithic migration wave, as it seems to have occurred as well in more northern locations in western Europe. While the only male Mesolithic individual from our dataset
was assigned to Y-haplogroup I, LBK individuals from France showed relative diversity, belonging to Y-haplogroups C1a2,
G2a, and H2. G2a and H2 have been described in various European Early Neolithic contexts in both central Europe and
Iberia (3, 6, 24). I2 haplogroups are likely to have been introduced into the Neolithic pool through admixture with huntergatherers.

In eastern France, the transition into the Middle Neolithic is represented by individuals from the Grossgartach culture, that derives from the Danubian sphere (∼4700 to 4500 BCE; SI Appendix, Fig. S1-1). Their proximity to central European contemporaneous individuals on PCA plots generated from both mitochondrial haplogroup frequencies and genome-wide markers suggests genetic homogeneity within the Danubian current (Fig. 1B and SI Appendix, Fig. S3-3). Interestingly, the BUCH2 individual harbors mixed GoyetQ2 and Villabruna HG ancestry (Fig. 1C), suggesting again that the GoyetQ2 ancestry is not a specific signature of southwestern Europe. However, we can observe a subtle shift away from LBK individuals and toward WHGs, reflecting an increase in shared alleles with the latter. This echoes observations from other ancient populations across Europe (Figs. 1C and 2A), yet with a higher proportion. This phenomenon seems to appear in France very early and becomes stronger as the Neolithic progresses, since individuals from French Middle Neolithic sites share a higher proportion of ancestry with HGs (Fig. 2A) and display Mesolithic signature haplogroups (e.g., U5b) at variable frequencies across the territory (SI Appendix, Fig. S3-2). Predominant in the Champagne region of northeastern France, these haplogroups suggest variable proportions of admixture between autochthonous hunter-gatherers and farmers. During the second half of the Middle Neolithic (MN2, ∼4500 BCE), individuals from northern and southern France are poorly distinguished on the PCA plot (Fig. 1B). Unlike in Iberia, the migration wave from which the Neolithic ancestry in ancient populations from France originated could not clearly be established using D statistics comparing the ancestry proportion between Iberia_EN and LBK_EN, as most individuals display nonsignificant values (SI Appendix, Fig. S4-6) (12). Using qpAdm, we investigated the ancestral source of the HG ancestry in individuals from French MN2 sites. Only individuals from southern France harbor varying levels of GoyetQ2-like ancestry, suggesting admixture with different populations of hunter-gatherers (Fig. 1C).

[XenophobicPrussian]

Told you mothercluckers, not a single one of the southern shifted IA Gauls was actually from the south. They're all from Alsace and Paris area, including the Iberian clustering ones.

Rhaetians?

muh genetic continuity

[Aren]

Holy, a fully Yamnaya scoring individual from Bronze Age France(!). And he's R1b, anyone know his final subclade? The link doesn't work btw anymore.

[dududud]

Told you petit coquin, not a single one of the southern shifted IA Gauls was actually from the south. They're all from Alsace and Paris area, including the Iberian clustering ones.

Rhaetians?

muh genetic continuity

There are samples from the South. You seem blind and stupid.

[Lucas]

Only two IA are from Hauts de France
Probably only this (Att226) is in G25.

[Lucas]

The link doesn't work btw anymore.

https://sci-hub.ren/https://doi.org/...nas.1918034117

[Lucas]

Suplemental https://www.pnas.org/content/pnas/su...34117.sapp.pdf

Bronze and Iron Age France share a common space in thePCA plot, both shifted toward modern central Europe and falling within the genetic diversity of Bronze Age Britain and central Europe (Fig. 1B), with a homogenization of the steppe component (Figs. 1Cand 2C). In contrast to what was described for central Europe (9), there is no further shift toward eastern Eurasian genotypes during the Iron Age (9). Instead, the steppe component, heterogeneously distributed between individuals during the Bronze Age (ranging from 30 to 70%), becomes homogeneous (Figs. 1Cand 2C), and individuals from the Hallstatt and La Tène culture in the French territory display similar affinities toward both modern and ancient populations. This could indicate that the transition from the Bronze Age to the Iron Age in France was mostly driven by cultural diffusion, without major gene flow from an external population. This would be consistent with an archeological and linguistic hypothesis proposing that the Celts from the second Iron Age descended from populations already established in western Europe, within the boundaries of the Bell Beaker cultural complex (26–29). It is important to mention, however, that due to the relative genetic homogeneity among European populations by the Bronze Age, subsequent migrations between different parts of Europe could easily remain unnoticed at this level of coverage.

[XenophobicPrussian]

There are samples from the South. You seem blind and stupid.

Don't bother me with your English second language or coping mechanisms right now Frenchie(or should I say Germanic+Celt+Roman+native Beaker).

COL153i, ERS88, Jeb8, NOR2B6, NOR3-15, NOR4, all the southern shifted(SW/S French or Iberian clustering) samples that were out already, are all in Alsace or Paris area France, not a single one in southern France, according to the image.

Game over.

[Lucas]

OK New averages comparing to modern pops.

Target: FRA_IA_north (no big difference than today)
Distance: 2.7289% / 0.02728949 | ADC: 1x
86.2 Belgian
8.4 French_Paris
5.4 French_Brittany

Target: FRA_IA_central (southern shifted central French)
Distance: 1.3569% / 0.01356942 | ADC: 1x
63.2 French_Occitanie
36.8 French_Nord

Target: FRA_IA_south YES
Distance: 2.8076% / 0.02807648 | ADC: 1x
68.2 French_Brittany
24.2 Orcadian
7.6 French_Seine-Maritime

north

FRA_IA:ATT26,0.1161,0.132019,0.044877,0.039083,0.038776,0.013108,-0.006815,0.011999,0.014112,0.020957,-0.001299,0.007793,-0.024678,-0.011836,0.007872,0.007027,0.006128,0.008361,0.010307,-0.013632,0.003993,0.00779,0.020706,0.000482,0.008742
FRA_IA:BFM265,0.122929,0.148267,0.05242,0.037468,0.047086,0.018128,-0.00235,-0.000231,0.008795,0.012392,-0.007957,0.005695,-0.015312,-0.007844,0.020765,-0.003182,-0.016428,0.009122,0.006034,0.007504,-0.002246,0.000124,0.001109,-0.00012,0.002036
average,0.1195145,0.140143,0.0486485,0.0382755,0.042931,0.015618,-0.0045825,0.005884,0.0114535,0.0166745,-0.004628,0.006744,-0.019995,-0.00984,0.0143185,0.0019225,-0.00515,0.0087415,0.0081705,-0.003064,0.0008735,0.003957,0.0109075,0.000181,0.005389


central
FRA_IA:COL11,0.122929,0.13405,0.058454,0.064923,0.037238,0.020917,-0.008225,0.01223,0.008795,0.011116,-0.002273,0.002548,-0.016353,-0.003991,0.017508,-0.008221,-0.014603,-0.005954,0.006662,0.005378,0.006489,0.008161,0.010106,-0.001446,0.000599
FRA_IA:COL153A,0.130897,0.158423,0.045254,0.02584,0.036622,0.012271,0.006815,0.008538,0.003272,0.015126,0.009419,-0.007194,0.001189,-0.000963,0.005022,0.003182,-0.013038,0.00038,0.016592,0.001,-0.015847,0.007543,0.000863,-0.018798,0.005389
FRA_IA:COL153i,0.120652,0.127957,0.046763,0.024548,0.045239,-0.006136,0.015276,0.004154,0.015748,0.034078,-0.00341,0.017235,-0.022448,-0.010459,0.012622,-0.026518,0.005476,0.008868,-0.001131,0.015883,-0.000749,-0.000742,-0.010476,0.003253,0.008143
FRA_IA:ERS86,0.122929,0.161469,0.040729,0.030039,0.040623,0.008646,-0.010105,0.005077,0.006954,0.007289,-0.00065,0.005845,-0.010852,-0.002752,0.005157,0.021745,-0.004172,0.009755,0.011313,-0.005753,0.000624,0.012365,-0.004683,-0.012893,0.00012
FRA_IA:ERS88,0.130897,0.155376,0.044123,0.005168,0.033237,0.000837,-0.004935,-0.005769,0.011249,0.02442,-0.004872,-0.001499,-0.023042,-0.016239,0.012079,-0.017104,-0.014603,-0.006461,-0.014204,-0.002251,-0.002496,0.000742,0.001356,0,0.000239
FRA_IA:ERS1164,0.124067,0.121864,0.052797,0.030039,0.033237,0.010877,0.011516,0.00923,0,0.019135,-0.002598,-0.01154,-0.01115,-0.012799,0.009908,0.006364,-0.002738,0.00038,0.001257,-0.004627,-0.007487,0.003957,0.002218,-0.011809,0.005389
FRA_IA:Jeb8,0.118376,0.138112,0.05506,0.027132,0.045239,-0.008367,-0.00329,0.003461,0.012271,0.010023,-0.00341,0.007194,-0.020812,-0.010046,0.016694,0.007425,-0.000391,-0.001647,0.000377,0.005378,-0.003868,-0.00136,-0.009983,-0.003615,0.007065
FRA_IA:NOR2B6,0.120652,0.147252,0.044877,0.005814,0.0397,0.003347,-0.010105,0.007384,0.016975,0.014943,0.010718,0.01109,-0.008771,-0.004542,0.012215,0.018165,0.027772,0.004941,0.005405,0.002876,0.006364,-0.007543,-0.001109,-0.00253,-0.007784
FRA_IA:NOR3-6,0.133173,0.146236,0.050157,0.046189,0.029852,0.017291,-0.007755,0.005077,0.012885,0.001276,-0.002598,0.015137,-0.022745,-0.013212,0.020087,-0.007823,-0.021383,0.007095,-0.001006,0.006753,0.004866,0.005193,-0.002835,-0.007953,-0.000239
FRA_IA:NOR3-15,0.117238,0.149283,0.061471,0.022287,0.043393,-0.005299,0.005405,-0.001615,0.013703,0.018224,-0.005196,0.00045,-0.014569,-0.012111,0.022394,-0.005171,-0.019558,-0.006841,-0.004902,0.013381,-0.002121,-0.002844,-0.015652,-0.003615,0.002395
FRA_IA:NOR4,0.12862,0.151314,0.058454,0.001615,0.046778,-0.006136,-0.000705,0.014538,0.023929,0.031345,-0.013153,0.006594,-0.022448,-0.016377,-0.016965,0.004773,0.005737,-0.010135,0.011941,0.005503,0.006239,0.006183,-0.011462,0.007471,-0.002994
average,0.1245845455,0.1446669091,0.0507399091,0.0257812727,0.0391961818,0.0043861818,-0.0005552727,0.0056640909,0.0114346364,0.0169977273,-0.0016384545,0.0041690909,-0.0156364545,-0.0094082727,0.010611,-0.0002893636,-0.0046819091,3.46363636363638E-005,0.0029367273,0.0039564545,-0.000726,0.0028777273,-0.003787,-0.0047213636,0.0016656364

south
FRA_IA:PEY53,0.133173,0.139128,0.050534,0.039083,0.050163,0.010598,-0.006345,-0.000692,0.008181,0.005103,-0.001624,0.016935,-0.019326,-0.007844,0.029451,-0.001724,-0.008996,0.003674,0.005028,-0.007128,0.010606,0.005193,-0.01861,-0.006507,0.008023
FRA_IA:BES1248,0.12862,0.127957,0.064488,0.042636,0.043085,0.027052,0.007755,-0.003461,0.001636,0.007836,0.010718,0.011839,-0.00892,-0.007569,0.016015,-0.000663,-0.001434,0.004687,-0.015461,0.004002,0.01984,-0.002597,-0.009367,0.008555,-0.016765
average,0.1308965,0.1335425,0.057511,0.0408595,0.046624,0.018825,0.000705,-0.0020765,0.0049085,0.0064695,0.004547,0.014387,-0.014123,-0.0077065,0.022733,-0.0011935,-0.005215,0.0041805,-0.0052165,-0.001563,0.015223,0.001298,-0.0139885,0.001024,-0.004371