Rivollat et al, Neolithic kinship at Gurgy, France

[teepean47]

Extensive pedigrees reveal the social organisation of a Neolithic community

Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations. However, for prehistoric societies these systems can only be studied indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local vs. non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which allows for the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here, we report ancient DNA, strontium isotope and contextual data from >100 individuals from the site Gurgy ‘les Noisats’ (France), dated to the western European Neolithic ~4850-4500 BCE. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, which were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The micro-demographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and high number of adult full siblings suggest stable health conditions and a supportive social network, facilitating high fertility and low mortality. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.

Data is available:

https://www.ebi.ac.uk/ena/browser/view/PRJEB61818

[teepean47]

A lot of individuals here but I am not sure what the difference between TF and IM as not all of them have IM.

All the males have separate Y-DNA bams with the letter YC.

[PLogan]

Haven't been able to find a paper or preprint. Does one exist? Closest was a paper in 2017.

[teepean47]

I would expect the paper will be released shortly.

[teepean47]

Yleaf with two reads.

Sample_name	Hg	Hg_marker	Total_reads	Valid_markers	QC-score	QC-1	QC-2	QC-3
GLN201_GRG001_YC	G-CTS796	PF3331	5431029	52933	1.0	1.0	1.0	1.0
GLN202_GRG002_YC	G-P303	Z765;CTS946;etc.	4358009	38346	1.0	1.0	1.0	1.0
GLN204_GRG003_YC	G-CTS796	CTS796	4750996	51126	1.0	1.0	1.0	1.0
GLN206_GRG004_YC	G-CTS796	PF3331	5239767	46198	1.0	1.0	1.0	1.0
GLN207A_GRG005_YC	G-P303	Z3243;CTS10366;etc.	4692710	44901	1.0	1.0	1.0	1.0
GLN209_GRG061_YC	G-P303	PF3329;PF3339;etc.	5398461	48676	1.0	1.0	1.0	1.0
GLN210_GRG008_YC	G-P303	CTS688;PF3329	3231148	32703	1.0	1.0	1.0	1.0
GLN211B_GRG010_YC	G-P303	PF3328;CTS7698;etc.	4204810	45708	1.0	1.0	1.0	1.0
GLN220_GRG016_YC	G-CTS796	PF3331	3713773	37354	1.0	1.0	1.0	1.0
GLN221B_GRG017_YC	G-P303	PF3329;CTS10366	1971983	11070	1.0	1.0	1.0	1.0
GLN224_GRG084_YC	G-P303	CTS10366	774061	3773	1.0	1.0	1.0	1.0
GLN226_GRG020_YC	G-P303	Z765;CTS10366;etc.	4019196	37289	0.8	1.0	0.8	1.0
GLN227_GRG021_YC	G-P303	Z765;CTS946;etc.	3288394	35630	1.0	1.0	1.0	1.0
GLN231A_GRG023_YC	G-P303	CTS946;PF3339	1406426	7110	1.0	1.0	1.0	1.0
GLN235_GRG085_YC	G-P303	Page98;CTS7698;etc.	4881131	47775	1.0	1.0	1.0	1.0
GLN236B_GRG087_YC	G-P303	Z3243;PF3339;etc.	7382036	62056	1.0	1.0	1.0	1.0
GLN237A_GRG088_YC	G-P303	CTS10366;CTS946	2704712	19329	1.0	1.0	1.0	1.0
GLN241_GRG026_YC	G-P303	PF3329;Z3243;etc.	2967226	23906	1.0	1.0	1.0	1.0
GLN243A_GRG027_YC	G-P303	PF3329;Page98;etc.	4363975	42145	1.0	1.0	1.0	1.0
GLN245A_GRG029_YC	G-P303	Z765;CTS946;etc.	4971068	48158	1.0	1.0	1.0	1.0
GLN245B_GRG030_YC	G-P303	PF3329;PF3330;etc.	5116298	39886	1.0	1.0	1.0	1.0
GLN250_GRG063_YC	G-P303	Z3243;PF3342;etc.	3616926	30672	1.0	1.0	1.0	1.0
GLN255_GRG034_YC	G-CTS796	PF3331	3944041	38534	1.0	1.0	1.0	1.0
GLN256_GRG035_YC	G-P303	Z3243;PF3342;etc.	3701926	34372	1.0	1.0	1.0	1.0
GLN257_GRG064_YC	G-CTS796	PF3331	5019922	50250	1.0	1.0	1.0	1.0
GLN258_GRG036_YC	G-P303	PF3342;CTS946;etc.	3141382	25822	1.0	1.0	1.0	1.0
GLN260_GRG037_YC	G-P303	PF3339;CTS10366;etc.	3109274	32601	1.0	1.0	1.0	1.0
GLN261_GRG065_YC	G-P303	PF3342;Z3243;etc.	5040661	47295	1.0	1.0	1.0	1.0
GLN263_GRG067_YC	G-P303	PF3329;PF3330;etc.	4158656	41485	1.0	1.0	1.0	1.0
GLN265_GRG068_YC	G-P303	PF3330;CTS946;etc.	4847786	36408	1.0	1.0	1.0	1.0
GLN266_GRG107_YC	G-P303	Z3243;CTS946	4674073	37492	1.0	1.0	1.0	1.0
GLN268B_GRG103_YC	NA		136370	388	0	0	0	0
GLN270B_GRG102_YC	NA		174880	418	0	0	0	0
GLN280_GRG043_YC	G-P303	CTS946;PF3329;etc.	5428874	45630	1.0	1.0	1.0	1.0
GLN282_GRG095_YC	G-Y18939*(xY51846)	Y50243;Y47295;etc.	3543177	37297	0.7272727272727273	1.0	0.7272727272727273	1.0
GLN285A_GRG045_YC	G-CTS796	CTS12891;PF3331	6360312	48770	1.0	1.0	1.0	1.0
GLN285B_GRG046_YC	G-Y18939*(xY51846)	Y57005;Y53430;etc.	3988950	42038	0.8181818181818182	1.0	0.8181818181818182	1.0
GLN287_GRG047_YC	G-CTS796	CTS796	4108685	25479	1.0	1.0	1.0	1.0
GLN291_GRG096_YC	G-P303	CTS946;PF3342;etc.	5132637	45180	1.0	1.0	1.0	1.0
GLN299_GRG052_YC	G-P303	Y350;Z3243;etc.	3804364	34170	1.0	1.0	1.0	1.0
GLN300_GRG097_YC	G-L30	M3224	1686975	7438	1.0	1.0	1.0	1.0
GLN302_GRG073_YC	G-Y18939*(xY51846)	Y46201;Y53430;etc.	3469330	26605	0.7142857142857143	1.0	0.7142857142857143	1.0
GLN305_GRG053_YC	G-P303	CTS946;CTS10366;etc.	2567843	23067	1.0	1.0	1.0	1.0
GLN308_GRG054_YC	G-CTS796	CTS12570	5892051	47731	1.0	1.0	1.0	1.0
GLN309_GRG055_YC	G-CTS796	CTS12891	6045752	55046	1.0	1.0	1.0	1.0
GLN310B_GRG076_YC	G-P303	CTS946;Z765;etc.	3627813	41795	1.0	1.0	1.0	1.0
GLN317_GRG057_YC	G-P303	CTS688;CTS10366;etc.	3295600	27685	1.0	1.0	1.0	1.0
GLN319_GRG078_YC	G-CTS796	CTS12570;PF3331	4861706	40223	1.0	1.0	1.0	1.0
GLN320_GRG079_YC	G-PF3346	PF3346	4588188	43338	1.0	1.0	1.0	1.0
GLN321_GRG058_YC	G-P303	CTS10366;CTS946;etc.	4328226	38141	1.0	1.0	1.0	1.0
GLN322_GRG059_YC	G-P303	Z765;PF3329;etc.	3277988	31607	1.0	1.0	1.0	1.0

[Pribislav]

A lot of samples from Gurgy ‘les Noisats’ were published in Rivollat 2020, and most of males (8 and 6, respectively) were in these two clades:

G2a2b-P303>CTS796>L140>PF3346>pre-Y18939

H2-P96>Y19966>Y21618>Y19962>Z19072>FT362000 (together with those two Neolithic samples from Ireland)

[Olymp]

Thanks

[Miqui Rumba]

I am processing all MT BAMs (I'll need a few days to complete all). It's difficult to find 2 samples with identical MT haplotype (except several H1 by HVR-I low coverage). Many samples are H1 or K1a although they belong to different subclades or show rare extra variants i.e.

GRG004 H1 extra 13327G
GRG005 J1c1 non extra
GRG061 K1a2a non extra
GRG006 K1b1a1 non extra
GRG009 K1a3 non extra
GRG010 K1a3 (3)extra 152C 9266A 13708A
GRG011 H1 non extra
GRG012 H1 (3)extra 1536G 1556Y 14766T

[Miqui Rumba]

I am very busy this week. However, I have extracted most of fasta sequences with ultra-sensitive parameters (Qual10, DP1)
therefore, many sequences may show wrong interpretations. I checked many with jameslick and it seems they agre with Rivollat thesis (many siblings with exact same haplotype but different subclades out of every family)
Please, if you are interested in advanced processing with mitomaster pr another MT software, you could download free multsample fasta file I made
https://drive.google.com/file/d/1Ayn...w?usp=drivesdk

Most of H1 samples are not reliable and GRG001 have been discarded (only a few nucleotides called)
I wish Maite Rivollat publish paper this week for checking genealogies

sorry, there are a few samples duplicated. Howver, you can download mitomaster's subclade prediction here

https://docs.google.com/spreadsheets...f=true&sd=true

N1a1a1a samples belong to a different N1a1a1a2 branch never reported yet (only G207A marker)

[Miqui Rumba]

duplicates deleted

https://docs.google.com/spreadsheets...f=true&sd=true

66 samples with MT haplogroup detected although several H1 have rare extra variants or many no calls (no reliable predictions)

H1 11 samples
H1-152C 2 samples
H3 2 samples
H3+152 4 samples
H4a1a+195 2 samples
J1c1 2 samples
J1c1b 1 sample
J1c1b1 2 samples
J2a1a1 2 samples
J2b1a 2 samples
K1a2 7 samples
K1a2a 2 samples
K1a2c 1 sample
K1a3 2 samples
K1b1a 1 sample
K1b1a1 1 sample
K2b1a 5 samples
N1a1a1a 3 samples
T2c1d+152 1 sample
U4a2f 1 sample
U5b1d1 1 sample
U5b3 2 samples
U8b1b 1 sample
V* 2 samples
X2b+226 1 sample

Many detected clades were very common in Western Europe during Neolithic. However the lack of U3a1 or W (like modern basques!) and only a few paleoeuropean U5-U4 subclades seems a strong founder effect since EEF arrival