Genetic ancestry changes in Stone to Bronze Age transition in the East European plain
Abstract
INTRODUCTION
RESULTS
Samples and archaeological background
Individual | Site | Location | Group | Date (cal BCE) | Morph. sex | Gen. sex | MT hg | Y hg | Av. cov. |
---|---|---|---|---|---|---|---|---|---|
BER001 | Berendeyevo | Yaroslavl, RUS | WeRuHG | 4447–4259 | Male | XY | K1 | Q1 | 0.13 |
KAR001 | Karavaikha 1 | Vologda, RUS | WeRuHG | 6457–6258 | Female? | XX | T2a1 | – | 0.19 |
PES001 | Peschanitsa | Arkhangelsk, RUS | WeRuHG | 10785–10626 | Male | XY | U4a1 | R1a5 | 5.03 |
BOL001 | Bolshnevo 3 | Tver, RUS | Fatyanovo | 2829–2460 | Male | XY | H1b | R1a | 0.11 |
BOL002 | Bolshnevo 3 | Tver, RUS | Fatyanovo | 2468–2211 | Female | XX | J1c1 | – | 0.12 |
BOL003 | Bolshnevo 3 | Tver, RUS | Fatyanovo | 2571–2345 | Male | XY | H41a | R1a2 | 1.13 |
GOL001 | Goluzinovo | Yaroslavl, RUS | Fatyanovo | 2575–2349 | Male | XY | T2b | R1a | 0.12 |
HAL001 | Khaldeevo | Yaroslavl, RUS | Fatyanovo | 2832–2473 | Male | XY | N1a1 | R1a2 | 1.35 |
HAN002 | Khanevo | Moscow, RUS | Fatyanovo | 2859–2495 | Male | XY | U5a1 | R1a2 | 1.28 |
HAN004 | Khanevo | Moscow, RUS | Fatyanovo | 2835–2471 | Male | XY | H6a1 | R1a2 | 1.25 |
IVA001 | Ivanovogorsky | Moscow, RUS | Fatyanovo | 2864–2496 | Female | XX | U4a1 | – | 1.29 |
MIL001 | Miloslavka | Ivanovo, RUS | Fatyanovo | 2624–2474 | Female | XX | U5b2 | – | 0.17 |
MIL002 | Miloslavka | Ivanovo, RUS | Fatyanovo | 2287–2047 | Female | XX | H | – | 0.11 |
NAU001 | Naumovskoye | Yaroslavl, RUS | Fatyanovo | 2836–2573 | Male | XY | T2a1 | R1a2 | 1.58 |
NAU002 | Naumovskoye | Yaroslavl, RUS | Fatyanovo | 2836–2469 | Male | XY | U5b2 | R1a2 | 1.14 |
NIK002 | Nikultsino | Yaroslavl, RUS | Fatyanovo | 2865–2500 | Male | XY | U5a1 | R1a | 0.12 |
NIK003 | Nikultsino | Yaroslavl, RUS | Fatyanovo | 2522–2298 | Male | XY | H15a1 | R1a | 0.12 |
NIK004 | Nikultsino | Yaroslavl, RUS | Fatyanovo | 2876–2620 | Male | XX | T2a1 | – | 0.18 |
NIK005 | Nikultsino | Yaroslavl, RUS | Fatyanovo | 2881–2581 | Female | XX | J1c1 | – | 0.12 |
NIK007 | Nikultsino | Yaroslavl, RUS | Fatyanovo | 2862–2466 | Female | XX | U5a1 | – | 0.12 |
NIK008AB | Nikultsino | Yaroslavl, RUS | Fatyanovo | 2834–2472 | Male | XY | H5b | R1a | 1.34 |
RDT002 | Nikolo-Perevoz | Moscow, RUS | Fatyanovo | 2562–2299 | NA | XX | T2b | – | 0.02 |
TIM001 | Timofeyevka | Ivanovo, RUS | Fatyanovo | NA | Male | XY | K1b1 | R1a | 0.02 |
TIM006 | Timofeyevka | Ivanovo, RUS | Fatyanovo | 2833–2470 | Female | XX | W6 | – | 0.12 |
TIM008 | Timofeyevka | Ivanovo, RUS | Fatyanovo | 2832–2473 | Male | XY | K1c1 | R1a | 0.12 |
VOD001 | Volosovo-Danilovsky | Yaroslavl, RUS | Fatyanovo | 2570–2299 | Female | XX | J1c1 | – | 0.24 |
VOR003 | Voronkovo | Yaroslavl, RUS | Fatyanovo | 2573–2466 | Male | XY | H6a1 | R1a | 0.12 |
VOR004 | Voronkovo | Yaroslavl, RUS | Fatyanovo | 2878–2627 | Female | XX | W6 | – | 1.38 |
VOR005 | Voronkovo | Yaroslavl, RUS | Fatyanovo | 2840–2343 | Male | XY | K2a5 | R1a | 0.12 |
SOP002 | Sope | Ida-Viru, EST | EstCWC | 2864–2495 | Female | XX | R1b1 | – | 0.12 |
Affinities of Western Russian HGs
EF ancestry in Fatyanovo Culture individuals
Phenotype-informative allele frequency changes in western Russia
Proportion in period | |||||||
---|---|---|---|---|---|---|---|
Western Russian HGs |
Latvian HGs | Estonian and Latvian Corded Ware complex farmers |
Fatyanovo | Estonian Late Bronze Age |
Estonian/ Ingrian Iron Age |
Estonian Middle Age |
|
Phenotype | N = 3 | N = 5 | N = 7 | N = 24 | N = 10 | N = 9 | N = 4 |
Blue eyes | 0.00 | 0.60 | 0.29 | 0.21 | 0.70 | 1.00 | 1.00 |
Brown eyes | 1.00 | 0.40 | 0.71 | 0.79 | 0.30 | 0.00 | 0.00 |
Blond + dark blond hair | 0.00 | 0.20 | 0.00 | 0.04 | 0.10 | 0.78 | 0.75 |
Red hair | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 |
Brown/dark brown hair | 0.00 | 0.00 | 0.14 | 0.21 | 0.30 | 0.11 | 0.00 |
Dark brown + black hair | 1.00 | 0.80 | 0.86 | 0.75 | 0.60 | 0.11 | 0.00 |
Very pale + pale skin | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.00 | 0.00 |
Mixed/unpredictable very pale-pale- intermediate skin |
0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.22 | 0.50 |
Intermediate skin | 0.33 | 0.60 | 0.57 | 0.58 | 0.80 | 0.67 | 0.50 |
Mixed/unpredictable intermediate-dark + dark + black skin |
0.67 | 0.40 | 0.43 | 0.42 | 0.00 | 0.11 | 0.00 |
Lactase persistence (rs4988235) |
0.00 | 0.00 | 0.07 | 0.17 | 0.40 | 0.50 | 0.75 |
High cholesterol (rs174546) |
1.00 | 0.90 | 0.57 | 0.83 | 0.45 | 0.56 | 0.13 |
DISCUSSION
MATERIALS AND METHODS
Experimental design
Laboratory methods
DNA extraction
Library preparation
DNA sequencing
Statistical analysis
Mapping
aDNA authentication
Kinship analysis
Calculating general statistics and determining genetic sex
Determining mtDNA hgs
chrY variant calling and hg determination
Genome-wide variant calling
Preparing the datasets for autosomal analyses
Principal components analysis
Admixture analysis
Outgroup f3 statistics
D statistics
FST
qpAdm
ChromoPainter/NNLS
DATES
Phenotyping
Acknowledgments
Supplementary Material
REFERENCES AND NOTES
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