View Full Version : Ancient mtDNA paper involving the Baikal region (the likely homeland of Proto-Turks)

Onur Dincer
06-12-2018, 11:03 PM

Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene."

From the main text:

"Recent ancient DNA studies have contributed to four major discoveries about the Holocene human population history in Eurasia: i. Gene flow from Near East through Europe during the Neolithization1,2,3,4,5,6,7, ii. Genetic continuity between pre-Neolithic and Neolithic populations of Near East8,9,10, iii. Increased mobility in West Eurasia during Bronze Age11,12, and iv. Genetic continuity in East Asia during the Holocene13. In contrast, the population history in North Asia has remained largely unknown with a limited number of published ancient genomes14,15. Here we fill this archaeogenetic gap by examining complete mitochondrial genome sequences and presenting radiocarbon dates of 41 serially sampled ancient individuals from North Asia, corresponding to the three major administrative regions of the Russian Federation including Cis-Baikal (Irkutsk Oblast), Trans-Baikal (Republic of Buryatia and Zabaykalsky Krai) and Yakutia (Sakha Republic) (Fig. 1 and Supplementary Table S1)."

"We identified 25 different mtDNA haplogroups across all individuals (Supplementary Tables S4 and S5), belonging to the macro-haplogroups M, N, or R. These three non-African macro-haplogroups have been reported to have diverged around 60–65 kya, and being carried to Southeast Asia by the first modern humans37. Specifically, 38 individuals carried the East Eurasian mitochondrial haplogroups of A, C, D, F, G and their sub-haplogroups. A Palaeolithic individual from Yakutia and a Bronze Age individual from Cis-Baikal carried the mitochondrial haplogroups R1 and R1b, respectively (Supplementary Table S4); which are sub-clades of the common West Eurasian macro-haplogroup R that was also observed in the Upper Paleolithic Ust’-Ishim14. As the Ust’ Ishim is from West Siberia, our result raises the possibility that the R haplogroup may have been distributed throughout North Asia."

"To assess the maternal genetic relationship with other ancient and present-day populations, we compiled two haplogroup frequency datasets by merging 41 ancient individuals with ancient and present-day individuals i. comprising full mitochondrial sequences (n = 291), and ii. comprising full mitochondrial sequences, mitochondrial HVRI (16059–16365) sequences and haplogroup data (n = 1,780) (Supplementary Tables S6–S8). Haplogroup frequencies were calculated by grouping ancient North Asians into (a) a single group, (b) three spatial groups (Cis-Baikal (CISB, n = 23), Trans-Baikal (TRAB, n = 7), and Yakutia (YAK, n = 9)) and (c) three temporal groups (Early (n = 11, mean = 7,000 BP), Middle (n = 16, mean = 4,800 BP), and Late (n = 11, mean = 3,000 BP)) (Supplementary Tables S9–S11). This analysis revealed that the haplogroup distribution in ancient North Asians is similar to that of present-day populations of the same region (Fig. 2a). Principal component analysis (PCA) of the haplogroup frequency data based on full mitochondrial genome sequence dataset revealed that ancient individuals grouped as a single unit clustered with present-day populations of the same region, to the exclusion of other ancient groups (Fig. 2b). This was also observed when more population groups were included in the analysis (Fig. S3a in Supplementary Information) and when ancient individuals were spatially (Fig. 2c) or temporally (Fig. S3b in Supplementary Information) grouped. This lack of distinction between ancient and present-day groups could, however, be resulted from relative homogeneity of the haplogroup variation amongst North Asian groups38."

"Since the haplogroup frequency based analysis might be affected by relatively low sample size of some populations, we further evaluated the genetic affinities between ancient North Asians and other populations based on the mitochondrial sequences. We calculated Slatkin’s linearized pairwise F ST on two datasets including ancient and present-day individuals i. with full mitochondrial sequences (n = 355) and ii. with HVRI sequences (n = 1,140) both merged with presented ancient individuals from North Asia (Supplementary Tables S12 and S13). We observed low F ST between ancient and modern North Asian populations including Evenk, Nganasan and Tubalar (Fst ≤ 0.05) (Fig. S3c and d in Supplementary Information, Supplementary Table S14). MDS analysis based on F ST showed that the first dimension differentiated both the present-day and the ancient North Asians from other ancient groups (Fig. 3a). We observed consistent results even when more population groups were included in the analysis and when the ancient North Asian individuals were grouped into three different spatial populations (Fig. 3b and Supplementary Table S14)."

F ST (Fst) is a measure of genetic distance, so low F ST means low genetic distance.



06-12-2018, 11:32 PM
As expected, lots of A and D.

06-13-2018, 05:40 AM
I find this paragraph interesting as well:
"Examination of the mitochondrial genomes led to the discovery of the West Eurasian R1 haplogroup in two individuals. This finding raised the possibility of a common distribution of this haplogroup during the Holocene in a large region of Asia. This was supported also by the presence of the mitochondrial haplogroup F1b (descending from R9) in Mesolithic and Early Neolithic Cis-Baikal individuals. The mitochondrial haplogroups F and R are widespread amongst modern southern and eastern Asian groups and the presence of R in Asia has been considered a remnant of the earliest human expansions in the continent. Presence of the R1 haplogroup in the Palaeolithic individual from Yakutia supported the archaeological records pointing to the West Eurasian origin of the first humans in the region. Furthermore, presence of East Eurasian mitochondrial haplogroups amongst the Neolithic individuals supported the eastern origin of pottery in the region."

However, I would like to add that the oldest R haplogroups are to my knowledge in India (R6, R30, R31) and in Sahul (P). The earliest genomes in northern areas have all been R: Ust Ishim R (preB?), Tianyuan (B-8281-9d), Malta (U). In Upper Palaeolithic Europe there is U8, U2 and U5.

My hunch is that the cradle of mtDNAs A and D is in the Okhotsk area, Amur and Primorskij kraj, and that explains why they spread to America early.

This is what the supplementary material tells us about Neolithic in Northeast Asia as well as pottery:
The Neolithic in North Asia is defined by the appearance and dispersal of new stone (tool) technologies (nephrite) and the use of different manufacturing methods. Important features of the period are several categories of tools, which include the bow, early pottery and fishing equipment of great variety: fishing hooks (often of composite types) and harpoons. The earliest known pottery in Eurasia is found in South-East China 20,000-16,000 BP. In North Asia the oldest ceramic dates are from 14,000–10,000 BP and are found in the Transbaikal region, the lower Amur river, in Primorsky Krai and in Japan. Early pottery has also been discovered in the Cis-Baikal area but the remains a rare type of archaeological artefact. Pottery has been found on a number of sites examined in the present study. For instance, remains of pottery were found in Popovskij Lug Popovskij Lug in layers dated to the Early Neolithic around 8,000-7,000 BP and in Makarovo 1 in layers dating to Late Neolithic layers. The Cis-Baikal pottery has similar traits as the earliest pottery in North Asia, and is argued to have a south-east origin.