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Figure 4
Ancestry modeling results for ROT and BOO individuals. (a) qpAdm models 306 using Eastern Siberia LNBA, Russia MLBA Sintashta, and WSHG as sources; (b) qpAdm 307 models with Eastern Siberia LNBA and Sintashta as sources; (c) qpAdm models with Eastern 308 Siberia LNBA and WSHG as sources; (d) qpAdm models with Eastern Siberia LNBA and 309 EEHG as sources. Corresponding p-values for each analysis are shown to the right of each 310 row. Models with p-values < 0.05 are grayed out, and the models with negative ancestry 311 proportions are indicated as "Not feasible". 312
Figure 6
Momi2 demographic model for BOO004 using shotgun sequencing data from 380 published ancient and modern individuals. Point estimates of the final model are shown in blue; 381 results for 100 nonparametric bootstraps are shown in gray. The sampling times of populations 382 are indicated by circles. The population sizes are indicated by the thickness of branches. The 383 y-axis is linear below 10,000 years ago, and logarithmic above it. See Supplementary Table 6 384
Ancestry modeling results for ROT and BOO individuals. (a) qpAdm models 306 using Eastern Siberia LNBA, Russia MLBA Sintashta, and WSHG as sources; (b) qpAdm 307 models with Eastern Siberia LNBA and Sintashta as sources; (c) qpAdm models with Eastern 308 Siberia LNBA and WSHG as sources; (d) qpAdm models with Eastern Siberia LNBA and 309 EEHG as sources. Corresponding p-values for each analysis are shown to the right of each 310 row. Models with p-values < 0.05 are grayed out, and the models with negative ancestry 311 proportions are indicated as "Not feasible". 312
300 We then estimated the date of the admixture event in BOO individuals between the EEHG and
Eastern_Siberia_LNBA sources using DATES v.75330 301 . The admixture date was estimated to
302 be 17.98±1.06 generations ago, or around 500 calendar years prior to the mean radiocarbon
date of BOO, assuming a generation time of 29 years31 303 (Supplementary Figure 8).
Figure 6
Momi2 demographic model for BOO004 using shotgun sequencing data from 380 published ancient and modern individuals. Point estimates of the final model are shown in blue; 381 results for 100 nonparametric bootstraps are shown in gray. The sampling times of populations 382 are indicated by circles. The population sizes are indicated by the thickness of branches. The 383 y-axis is linear below 10,000 years ago, and logarithmic above it. See Supplementary Table 6 384
362 Demographic modeling. High-coverage shotgun data from BOO004 (~30x) allowed us to
363 perform demographic modeling to investigate North Eurasian genetic ancestry and the nature
364 of the admixture of the Eastern and Western Eurasian sources found in BOO individuals using
366 a site-frequency spectrum published data from representative North Eurasian populations, both preceding and
367 contemporaneous to BOO. After an incremental build-up of our model and including three
368 admixture events, our final model indicates a recent admixture for BOO individuals (95%
369 confidence interval (CI) 3596-4429 years ago), with substantial gene flow (39.9%; 95% CI
370 34.0-44.8%) from Eastern Eurasians (represented here by Late Neolithic/Bronze Age Siberian
371 individuals), which is consistent with the results from qpAdm. The population size estimated
372 for BOO (N=190, 95% CI 6-482) from momi2 (Fig. 6, Supplementary Table 6) is smaller than
373 the estimate obtained from hapROH (2N between 400 and 800 individuals, Fig. 6). This could
374 be explained by momi2 not taking into account inbreeding via the analysis of the runs of
375 homozygosity, and thus producing a biased estimate of the true effective population size. Thus,
376 we believe that the results produced by hapROH are closer to the true value of the effective
377 population size.(SFS) modeling-based method called momi239.
387 Y-chromosome haplogroups. We performed Y-haplogroup (Y-hg) typing of the ROT males
using the YMCA method19 388 (Table 1). We identified two individuals that carried the R1a Y-hg
389 (ROT003 (R1a-M417) and ROT016 (R1a-Z645)), one of the most widely distributed Y-hgs in
Eurasia40 390 . However, both individuals could be R1a-Z645, since ROT003 does not have either
391 ancestral or derived ISOGG list SNPs after R1a-M417. The earliest evidence for Y-hg R1a
392 comes from Mesolithic EEHG individuals41,42, and it is widespread throughout Eurasia today,
393 from Scandinavia to South Asia and Siberia40. Specifically, R1a-M417 is common among
394 Corded Ware-associated individuals41,43, while the derived R1a-Z645 is common in the Baltic
395 Corded Ware44 and Fatyanovo13. Generally, due to their geographic distribution, these R1a
396 haplogroups are thought to represent the eastward movement of the Corded Ware-, and
397 Fatyanovo-associated groups.
398 ROT002, the individual with the highest proportion of north Siberian ancestry, was assigned to
399 the N1a1a1a1a (N-L392) haplogroup. This Y-hg has also been found in two published BOO
400 individuals15. The lineage N-L392 is one of the most common in present-day Uralic
401 populations, and was estimated to have split from other N-lineages around 4,995 years ago45.
402 This finding further highlights the importance of Y-hg N-L392 as being linked to the
403 dissemination of proto-Uralic, but potentially also involving the ST network.
404 One of the males (ROT004) was assigned to haplogroup Q1b (Q-M346), which is found
405 throughout Asia, including in several Turkic speaking populations, i.e. Tuvinians, Todjins,
406 Altaians, Sojots, etc., and Mongolian-speaking Kalmyk population46. Another individual
407 (ROT017) was determined to belong to the Q1b1 (Q-L53) haplogroup, which is common
408 among present-day Turkic speakers across Eurasia. The branch Q-YP4004 includes Central
409 Asian Q-L53(xL54) lineages and one ancient Native American individual from Lovelock Cave
410 in Nevada dated 1.8 ky47, and the oldest individual with this haplogroup is irk040 (Cis-Baikal
411 Neolithic, 4846 BP)28. The lineage C2a-L1373, carried by ROT011, is found at high frequency
412 in Central Asian populations, North Asia and the Americas. C2a-L1373 expanded to North Asia
413 and the Americas post-LGM, around 17,700–14,300 years ago48. Lastly, haplogroup R1b1a1a
414 (R1b-M73), a sister-clade of R1b-M269, is carried by ROT006. This lineage is common in the
415 Caucasus, Siberia, Mongolia, and Central Asia today46.
416 Overall, the Y-hg lineage diversity of male ROT individuals further highlights the
417 heterogeneous nature of the ST, which has also been proposed by archaeologists49.