Analyses of complete genomes of 10 French Late Mesolithic individuals form the sites

[teepean]

Analyses of complete genomes of 10 French Late Mesolithic individuals form the sites of Hoedic, Téviec and Champigny

Abstract

Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). These groups were eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.

https://www.ebi.ac.uk/ena/browser/view/PRJEB71770

G25 (no labels)

Code:

Scaled

various:hoe001,0.112685,0.103584,0.194971,0.200261,0.145566,0.061914,0.011751,0.039229,0.098171,0.025695,-0.015914,-0.009891,0.022745,-0.002752,0.065417,0.066825,0.0103,0.009882,-0.011313,0.054276,0.11879,0.019537,-0.05731,-0.181351,0.024788
various:hoe002,0.121791,0.111708,0.191577,0.197677,0.163415,0.051874,0.017861,0.038075,0.098785,0.016037,-0.014777,-0.010641,0.014569,-0.012524,0.065146,0.065764,0.004563,0.008361,-0.01169,0.057027,0.109557,0.016569,-0.052997,-0.177013,0.026345
various:hoe003,0.125205,0.105615,0.199497,0.198646,0.165877,0.054941,0.021621,0.039921,0.097149,0.014397,-0.0177,-0.014237,0.014717,-0.000826,0.060396,0.067621,0.005346,0.004307,-0.006536,0.061029,0.121036,0.010881,-0.058912,-0.187014,0.026465
various:hoe004,0.124067,0.119832,0.193463,0.199292,0.159414,0.058567,0.023736,0.044075,0.094081,0.020775,-0.0177,-0.015286,0.01665,0.005092,0.066232,0.047997,-0.029076,0.010008,-0.006034,0.054026,0.106687,0.020774,-0.051641,-0.174964,0.021076
various:hoe005,0.119514,0.114755,0.198365,0.192832,0.170493,0.059683,0.017156,0.047536,0.099603,0.014397,-0.014128,-0.014387,0.014866,0.001651,0.070032,0.043755,-0.026989,0.014949,-0.006662,0.054526,0.122783,0.016075,-0.051148,-0.182074,0.023351
various:stp001,0.124067,0.107646,0.193463,0.203814,0.159107,0.066934,0.018096,0.040614,0.09858,0.008018,-0.018837,-0.014837,0.015609,-0.003716,0.066503,0.048263,-0.023469,0.012289,-0.004651,0.053776,0.11068,0.009274,-0.059529,-0.178218,0.024908
various:tev001,0.117238,0.110693,0.19384,0.190894,0.160645,0.053547,0.012691,0.043844,0.103489,0.021686,-0.020461,-0.018583,0.011001,-0.010459,0.06311,0.061919,0.002738,0.007095,-0.00905,0.06178,0.114922,0.011623,-0.054475,-0.189906,0.021196
various:tev002,0.127482,0.105615,0.18592,0.201553,0.166185,0.064145,0.00752,0.027922,0.096944,0.02041,-0.019324,-0.016036,0.011596,-0.012661,0.063924,0.063113,0.002868,0.010135,-0.008422,0.064906,0.117917,0.006677,-0.057064,-0.178941,0.02371
various:tev003,0.121791,0.108662,0.1912,0.191863,0.166493,0.058009,0.015981,0.03023,0.095308,0.015308,-0.019811,-0.014687,0.018434,-0.005918,0.06786,0.067223,-0.004433,0.013682,-0.009302,0.054276,0.115671,0.011252,-0.055092,-0.183038,0.022513

Raw

various:hoe001,0.0099,0.0102,0.0517,0.062,0.0473,0.0222,0.005,0.017,0.048,0.0141,-0.0098,-0.0066,0.0153,-0.002,0.0482,0.0504,0.0079,0.0078,-0.009,0.0434,0.0952,0.0158,-0.0465,-0.1505,0.0207
various:hoe002,0.0107,0.011,0.0508,0.0612,0.0531,0.0186,0.0076,0.0165,0.0483,0.0088,-0.0091,-0.0071,0.0098,-0.0091,0.048,0.0496,0.0035,0.0066,-0.0093,0.0456,0.0878,0.0134,-0.043,-0.1469,0.022
various:hoe003,0.011,0.0104,0.0529,0.0615,0.0539,0.0197,0.0092,0.0173,0.0475,0.0079,-0.0109,-0.0095,0.0099,-0.0006,0.0445,0.051,0.0041,0.0034,-0.0052,0.0488,0.097,0.0088,-0.0478,-0.1552,0.0221
various:hoe004,0.0109,0.0118,0.0513,0.0617,0.0518,0.021,0.0101,0.0191,0.046,0.0114,-0.0109,-0.0102,0.0112,0.0037,0.0488,0.0362,-0.0223,0.0079,-0.0048,0.0432,0.0855,0.0168,-0.0419,-0.1452,0.0176
various:hoe005,0.0105,0.0113,0.0526,0.0597,0.0554,0.0214,0.0073,0.0206,0.0487,0.0079,-0.0087,-0.0096,0.01,0.0012,0.0516,0.033,-0.0207,0.0118,-0.0053,0.0436,0.0984,0.013,-0.0415,-0.1511,0.0195
various:stp001,0.0109,0.0106,0.0513,0.0631,0.0517,0.024,0.0077,0.0176,0.0482,0.0044,-0.0116,-0.0099,0.0105,-0.0027,0.049,0.0364,-0.018,0.0097,-0.0037,0.043,0.0887,0.0075,-0.0483,-0.1479,0.0208
various:tev001,0.0103,0.0109,0.0514,0.0591,0.0522,0.0192,0.0054,0.019,0.0506,0.0119,-0.0126,-0.0124,0.0074,-0.0076,0.0465,0.0467,0.0021,0.0056,-0.0072,0.0494,0.0921,0.0094,-0.0442,-0.1576,0.0177
various:tev002,0.0112,0.0104,0.0493,0.0624,0.054,0.023,0.0032,0.0121,0.0474,0.0112,-0.0119,-0.0107,0.0078,-0.0092,0.0471,0.0476,0.0022,0.008,-0.0067,0.0519,0.0945,0.0054,-0.0463,-0.1485,0.0198
various:tev003,0.0107,0.0107,0.0507,0.0594,0.0541,0.0208,0.0068,0.0131,0.0466,0.0084,-0.0122,-0.0098,0.0124,-0.0043,0.05,0.0507,-0.0034,0.0108,-0.0074,0.0434,0.0927,0.0091,-0.0447,-0.1519,0.0188

Y-DNA with Yleaf (two read minimum)

Code:

Sample_name    Hg    Hg_marker    Total_reads    Valid_markers
hoe001    NA        13227633    479
hoe002    I-Y3104*(xL621,L161)    S7721;Z2589;etc.    325651200    94608
hoe003    I-Y3104*(xL621,L161)    YP202;Y3109;etc.    2137673885    128055
hoe004    R-L52    CTS7650    402728620    14992
hoe005    R-L52    CTS7650    652343679    18903
hoe006    NA        2267412    11
stp001    I-CTS616*(xCTS10057)    CTS9139;CTS11271;etc.    1021738494    127816
tev001    I-L460*(xM436)    AM00522;Y8776    250203247    61589
tev002    A1*(xA1a)    Y9619;YP3891    21552051    1717
tev003    I-Y3104*(xL621,L161)    Z2585;YP212;etc.    2066566932    128063

[Awood]

Y-DNA with Yleaf (two read minimum)

Code:

Sample_name    Hg    Hg_marker    Total_reads    Valid_markers
hoe004    R-L52    CTS7650    402728620    14992
hoe005    R-L52    CTS7650    652343679    18903

L52 in French hunter-gatherers? This would be a first if correct.

[AimSmall]

My closest match was hoe004

Decided to look at just him more closely.

Distance to: various:hoe004
0.02987332 Ireland_Mesolithic.SG:KGH6.SG
0.03224995 France_Ranchot88:Ranchot88_noUDG
0.03755956 Ireland_Mesolithic.SG:SRA62.SG
0.04073672 Italy_Sicily_LateMesolithic:UZZ088_noUDG
0.04170999 Italy_Sicily_LateMesolithic:UZZ5054_noUDG
0.04248817 England_Mesolithic:I6767
0.04298676 Germany_Mesolithic:BDB001
0.04404056 Wales_Mesolithic:I6754
0.04481165 Italy_Tagliente_LPaleolithic:RIP001_noUDG
0.04915542 Luxembourg_Loschbour.DG:Loschbour_snpAD.DG
0.04961860 Italy_North_Villabruna_HG:Villabruna_noUDG
0.05017911 Italy_Sicily_LateMesolithic:UZZ071_noUDG
0.05032650 France_NouvelleAquitaine_Mesolithic.SGER3023.SG
0.05072355 France_NouvelleAquitaine_Mesolithic.SGER503.SG
0.05381253 Germany_Falkenstein:Falkenstein_noUDG
0.05682799 Italy_Sicily_LateMesolithic_Castelnovian:UZZ082_noUDG
0.05749546 Italy_Sicily_LateMesolithic_Castelnovian:UZZ081_noUDG
0.05806243 Italy_Mesolithic.SG:R15.SG
0.05879185 Italy_Sicily_LateMesolithic_Castelnovian:UZZ080_noUDG
0.05907663 Italy_Mesolithic.SG:R7.SG
0.05947841 Italy_Mesolithic.SG:R11.SG
0.06178238 Italy_Sicily_LateMesolithic_Castelnovian:UZZ079_noUDG
0.06279813 Croatia_Mesolithic_HG:I1875
0.06361532 France_Rochedane:Rochedane
0.06753382 Denmark_Syltholm_LM_EN:Syltholm1.SG


Target: various:hoe004
Distance: 2.2126% / 0.02212634 | ADC: 0.25x RC

49.0 Ireland_Mesolithic.SG:KGH6.SG
41.0 France_Ranchot88:Ranchot88_noUDG
  4.0 England_Mesolithic:I6767
  3.4 Italy_Sicily_LateMesolithic:UZZ5054_noUDG
  1.4 Germany_Mesolithic:BDB001
  1.2 Spain_C:I1280

[Sephesakueu]

Y-DNA with Yleaf (two read minimum)

Code:

Sample_name    Hg    Hg_marker    Total_reads    Valid_markers
hoe004    R-L52    CTS7650    402728620    14992
hoe005    R-L52    CTS7650    652343679    18903

L52 in French hunter-gatherers? This would be a first if correct.

No way that is correct.

[TanTin]

https://www.ebi.ac.uk/ena/browser/view/PRJEB71770

G25 (no labels)

Do you have the plink converted files?

[Capsian20]

Do you have info about mtDNA ?

[teepean]

https://www.ebi.ac.uk/ena/browser/view/PRJEB71770

G25 (no labels)

Do you have the plink converted files?

Sure thing.

https://drive.google.com/drive/folders/1...sp=sharing

[teepean]

Y-DNA with Yleaf (two read minimum)

Code:

Sample_name    Hg    Hg_marker    Total_reads    Valid_markers
hoe004    R-L52    CTS7650    402728620    14992
hoe005    R-L52    CTS7650    652343679    18903

L52 in French hunter-gatherers? This would be a first if correct.

No way that is correct.

That's Yleaf's interpretation and needs manual checking. Snipsa gives these results.

Code:

Hoe004:
Result (5.3% 1 -0 +18): R-FT87109
R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-PF6538 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Z258 -> R-L20 -> R-Z1909 -> R-Y6789 -> R-Y15103 -> R-BY137174 -> R-FT87109 (ISOGG: )
Extra: P279/PF5065:A FT74184/PR4337(H):G FT319138(H):G FTC60807(H):G FT129821(H):T FT195078:T FT307459(H):T FT148647:T FT184689:G Y4847/A3242:A FT45000:C Z37822:C FGC58892:T Z9083(H):T CTS5707:G CTS10207:G Z29483:T CTS12954:G

Code:

Hoe005:
Result (3.0% 4 -1 +29): R-FGC37088
R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-PF6538 -> R-L151 -> R-A8053 -> R-A8051 -> R-FGC57291 -> R-FGC37108 -> R-FGC37090 -> R-FGC37084 -> R-FGC37088 (ISOGG: )
Extra: Y172006:T FT203261:T FT97603(H):T FT100401(H):T FGC7862:T Z18652/FGC23610(H):T Y367008(H):G A22122:T FTA34303:T FTD87509/Y433063:G L687:A FT45000:C Z37822:C TY133092:A Y29212:G FTB33009:T MF93894:C TY135350/Y300104:G BY14580:A FTA18624:T Y144103:T Y151158/FGC91133:T F19771:T CTS5707:G CTS8072:T ZS2704(H):G CTS10207:G Y76781:C CTS12954:G

[Parastais]

Sooo?!
L52 in Mesolithic France? Autosomal these guys fit rest of samples.

Earliest L52 so far was found in France and none was found in Yamnaya (?). That is quite interesting.

Ok, both seem to be L151 as per teepan’s post, which is normally dated 3,500 BCE at yfull. What is happening here?

[ph2ter]

Their average on the Neolithic similarity map:

[eastara]

Sooo?!
L52 in Mesolithic France? Autosomal these guys fit rest of samples.

Earliest L52 so far was found in France and none was found in Yamnaya (?). That is quite interesting.

Ok, both seem to be L151 as per teepan’s post, which is normally dated 3,500 BCE at yfull. What is happening here?

The Mesolithic site Téviec was dated   between 6740 and 5680 years BP, so up to 3600BC, which is not that old, It was not only Chalcolithic, but even beginning of the Bronze on the Balkans, so the dates are not that far off. Maybe R1b-L52 was native to Europe after all.
https://en.wikipedia.org/wiki/T%C3%A9viec

[Codaman]

R-FGC37088 and R-FT87109 are modern Irish/British subclades which are only a thousand years old. Could these samples be female and have an extra Y-chromosome as contamination?

[ArmandoR1b]

I have extreme doubts about the validity of the Y-DNA results. I haven't had time to analyze the BAM files myself. In order for the results to be believable all of the derived and ancestral positions and reads need to be analyzed. Deamination also had to be ruled out.

[Pribislav]

I can tell just by the number of valid markers teepean posted that hoe004 and hoe005 are females, there's no need to check the BAMs.

[AimSmall]

The Snipsa results are interesting and consistent with Yleaf, but I'm drawn to the confidence values...

3% and 5.3%.... think the lack of SNPs is coming into play here.

Hoe004:
Result (5.3% 1 -0 +18): R-FT87109
Hoe005:
Result (3.0% 4 -1 +29): R-FGC37088