Notes: Early Siberian human strata, human interactions and influences upon Eurasian and European cultures

The following paper is of significance on the issue of evolution of the Upper Paleolithic in Eurasia:

a. it is the oldest full genome of a modern human published for Eurasia, and the authors estimate the age of the Ust’-Ishim bone artifacts to be 49,000 years BP (95% highest posterior den-sity: 31,000–66,000 years BP), consistent with the radiocarbon date

b. the Ust’-Ishim individual represents a population derived from the population involved in the dispersal of modern humans out of Africa

c. “The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today while on the mtDNA side:

“The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia (Supplementary Information section 8).”

d. “he finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000-to 24,000-year-old individuals from western Eurasia”

Qiaomei Fuet al. Genome sequence of a 45,000-year-old modern human from western Siberia Genome sequence of a 45,000-year-old modern human from western Siberia, Nature 514, 445–449 (23 October 2014) doi:10.1038/nature13810 29 August 2014  Published online 22 October 2014

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone…

 

Population relationships

About 7.7 positions per 10,000 are heterozygous in the Ust’-Ishimgenome, whereas between 9.6 and 10.5 positions are heterozygous inpresent-dayAfricans and 5.5 and 7.7 in present-day non-Africans (SupplementaryInformation section 12). Thus, with respect to genetic diversity,the population to which the Ust’-Ishim individual belonged wasmore similar to present-day Eurasians than to present-day Africans,which probably reflects the out-of-Africa bottleneck shared by nonAfricanpopulations. The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’)# see Kivisild below, which occurs today across Eurasia (Supplementary Information section 8). The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT))that occurs across Eurasia today6(Supplementary Information section 9). As expected, the number of mutations inferred to have occurred on the branch leading to the Ust’-Ishim mtDNA is lower than the numbers inferred to have occurred on the branches leading to related presentday mtDNAs (Supplementary Fig. 8.1). Using this observation and nine directly carbon-dated ancient modern human mtDNAs as calibrationpoints5,7 in a relaxed molecular clock model, we estimate the age of theUst’-Ishim bone to be ,49,000 years BP (95% highest posterior density:31,000–66,000 years BP), consistent with the radiocarbon date.In a principal component analysis of the Ust’-Ishim autosomal genomealong with genotyping data from 922 present-day individualsfrom 53 populations8(Fig. 2a), the Ust’-Ishim individual clusters withnon-Africans rather than Africans. When only non-African populationsare analysed (Fig. 2b), the Ust’-Ishim individual falls close to zeroon the twofirst principal component axes, suggesting thatit does not sharemuch more ancestry with any particular group of present-day humans.To determine how the Ust’-Ishim genome is related to the genomes of present-day humans, we tested, using D statistics8,whether it shares more derived alleles with one modern human than with another modern human using pairs of human genomes from different parts of the world (Fig. 3).Based on genotyping data for 87 African and 108 non-African individuals(Supplementary Information section 11), the Ust’-Ishim genome shares more alleles with non-Africans than with sub-Saharan Africans(jZj 5 41–89), consistent with the principal component analysis,mtDNA and Y chromosome results. Thus, the Ust’-Ishim individual represents a population derived from, or related to, the population involved in the dispersal of modern humans out of Africa. Among the non-Africans  the Ust’-Ishim genome shares more derived alleles with present-day people from EastAsia than with present-day Europeans (jZj 5 2.1–6.4). However, when an 8,000-year-old genome from western Europe (LaBran˜a)9  or a 24,000-year-old genome from Siberia (Mal’ta 1)10 were analysed, there is no evidence that the Ust’-Ishim genome shares more derived alleles with present-day East Asians than with these prehistoric individuals (jZj , 2). This suggests that the population to which the Ust’-Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other. The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000-to 24,000-year-old individuals from western Eurasia, but not to presentday Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia11.

Figure 2: Principal Components (PC) analysis exploring the relationship of Ust’-Ishim to present-day humans.close

Principal Components (PC) analysis exploring the relationship of Ust/'-Ishim to present-day humans.

a, PC analysis using 922 present-day individuals from 53 populations and the Ust’-Ishim individual. b, PC analysis using Eurasian individuals and the Ust’-Ishim individual.

We also estimated a phylogeny relating the non-recombining part of the Ust’-Ishim Y chromosome to those of 23 present-day males. Using this phylogeny, we measured the number of ‘missing’ mutations in the Ust’-Ishim Y chromosomal lineage relative to the most closely related present-day Y chromosome analysed. This results in an estimate of the Y chromosome mutation rate of 0.76 3 1029 per site per year (95% CI 0.67 3 1029 to 0.86 3 1029 ) (Supplementary Information section 9), significantly higher than the autosomal mutation rate, consistent with mutation rates in males being higher than in females18–20. Finally, using the radiocarbon date of the Ust’-Ishim femur together with the mtDNAs of 311 present-day humans,we estimated the mutation rate of the complete mtDNA to be 2.53 3 1028 substitutions per site per year (95% highest posterior density: 1.76 3 1028 to 3.23 3 1028 ) (Supplementary Information section 8) for mtDNA, in agreement with a previous study5
Neanderthal admixture The time of admixture between modern humans and Neanderthals has previously been estimated to 37,000–86,000 years BP based on the size of the DNA segments contributed by Neanderthals to present-day nonAfricans21.
Thus, the Ust’-Ishim individual could pre-date the Neanderthal admixture. From the extent of sharing of derived alleles between the Neanderthal and the Ust’-Ishim genomes we estimate the proportion of Neanderthal admixture in the Ust’-Ishim individual to be 2.3 6 0.3% (Supplementary Information section 16), similar to present-day east Asians (1.7–2.1%) and present-day Europeans (1.6–1.8%). Thus, admixture with Neanderthals had already occurred by 45,000 years ago. In contrast, we fail to detect any contribution from Denisovans, although such a contribution exists in present-day people not only in Oceania22,23, but to a lesser extent also in mainland east Asia12,24 (Supplementary Information section 17).
The DNA segments contributed by Neanderthals to the Ust’-Ishim individual are expected to be longer than such segments in presentday people as the Ust’-Ishim individual lived closer in time to when the admixture occurred, so there was less time for the segments to be fragmented by recombination. To test if this is indeed the case, we identified putative Neanderthal DNA segments in the Ust’-Ishim and presentday genomes based on derived alleles shared with the Neanderthal genome at positions where Africans are fixed for ancestral alleles. Figure 5 shows that fragments of putative Neanderthal origin in the Ust’-Ishim individual are substantially longer than those in present-day humans.
We use the covariance in such derived alleles of putative Neanderthal origin across the Ust’-Ishim genome to infer that mean fragment sizes in the Ust’-Ishim genome are in the order of 1.8–4.2 times longer than in present-day genomes and that the Neanderthal gene flow occurred 232–430 generations before the Ust’-Ishim individual lived (Supplementary Information section 18; Fig. 6). Under the simplifying assumption that the geneflow occurred as a single event, and assuming a generation time of 29 years16,25, we estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East. However, we also note that the presence of some longerfragments (Fig. 5) may indicate that additional admixture occurred even later. Nevertheless, these results suggest that the bulk of the Neanderthal contribution to present-day people outside Africa does not go back to mixture between Neanderthals and the anatomically modern humans who lived in the Middle East at earlier times; for example, the modern humans whose remains have been found at Skhul and Qafzeh…
An Initial Upper Paleolithic individual?
A common mode lfor themodern human colonization of Asia23,28 assumes that an early coastal migration gave rise to the present-day people of Oceania, while a later more northern migration gave rise to Europeans and mainland Asians. The fact that the 45,000-year-old individual from Siberia is not more closely related to the Onge from the Andaman Islands (putative descendants of an early coastal migration) than he is to present-day East Asians or Native Americans (putative descendants of a northern migration) (Fig. 3) shows that at least one other group to which the ancestors of the Ust’-Ishim individual belonged colonized Asia before 45,000 years ago. Interestingly, the Ust’-Ishim individual probably lived during a warm period (Greenland Interstadial 12) that has been proposed to be a time of expansion of modern humans into Europe29,30. However, the latter hypothesis is based only on the appearance of the so-called ‘Initial Upper Paleolithic’ industries (Supplementary Information section 5), and not on the identification of modern human remains31,32. It is possible that the Ust’-Ishim individual was associated with the Asian variant of Initial Upper Paleolithic industry, documented at sites such as Kara-Bom in the Altai Mountains at about 47,000 years BP. This individual would then represent an early modern human radiation into Europe and Central Asia that may have failed to leave descendants among present-day populations29.

 

# The major branches of the Asian mtDNA tree displaying the East Asian–specific haplogroups. The tree is rooted in haplogroup L3. You can see the root of ancestral R haplogroup branching off.   Each haplogroup is indicated by its ancestral haplotype. Informal distinction between the trunks (black), limbs (dark gray), boughs (gray), and twigs (white background boxes) is according to the main text Source: Fig. 2 Toomas Kivisild, et al., The Emerging Limbs and Twigs of the East Asian mtDNA Tree

 

High coverage genome from 45,000-year old Siberian (Ust’-Ishim) and Ust’-Ishim & the Old Race and Eurogenes Blog: Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans

See also:

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans by Maanasa Raghavan and the commentary on it… Mal’ta boy had autosomal genes present in populations with Y-haplogroups M, P, Q & R

Two weeks ago, Raghavan et al. published a paper on the genome of an Upper Palaeolithic Siberian individual, known as the Mal’ta boy. It is by far the oldest human genome tested to date.

The authors reported that the autosomal admixture of that 24,000-year-old individual was a blend of European, South Asian, Amerindian with a little bit of Papuan. I don’t know if anybody mentioned this before, but it strikes me that this particular admixture could in fact be the original source DNA representing descendants of haplogroup MP. What links Europeans and South Asian is essentially haplogroup R. Amerindians are Q and Papuans belong too M.

It has recently been found that haplogroup M fits in between NO and P in the Y-chromosomal phylogeny. In other words, there was once a haplogroup MP, which split into M and P, then P split into Q and R.

Since the Mal’ta boy belongs to R*, it makes sense that his autosomal genes should be closest to the populations with the highest percentages of haplogroup R today, namely (North) Europeans and South Asians. And indeed his genome resembles at 71% that of Europeans and South Asians. The second closest group is Q, which is mostly Amerindians. 26% of his genome matches that of Amerindian. Surely this is something inherited from the common roots of Q and R, which had split from each others only a few millennia before the Mal’ta boy’s lifetime.

The Mal’ta boy also shared 4% of similarity with modern Papuans, which may come as a surprise at first, until one realises the close phylogenetic relationship between the dominant Papuan paternal lineage (M) with Q and R. However since the split happened longer ago, the genetic similarity is more limited than with Q. Besides, there is a good chance that modern Papuans only have a small percentage of Eurasian genes themselves, and that the original carriers of Y-haplogroup M intermingled with a lot of other populations on their long journey from Central/North Asia to Papua. It is possible that only a small group of men belonging to haplogroup M came to replace the older native paternal lineages of New Guinea (C-RPS4Y711 and C-P55), just as O replaced them in East Asia and R in South Asia and Europe. Even Q might represent the post-Clovis migration that replaced older lineages (C3 ?) among Amerindians.

So we shouldn’t see the Mal’ta boy as a multi-hybrid of European, South Asian and Siberian/Amerindian ethnicities, but rather as an example of the source population which invaded those geographic regions and hybridised with the natives there. It would be interesting to use the Mal’ta boy’s genome as a reference population and see how much of modern populations inherited from the original PQR people, instead of looking at it the other way round. There might be a correlation between the percentage of similarity with his autosomal genes and the frequency of haplogroups Q and R in modern populations. Nonetheless I would expect that autosomal DNA got progressively diluted along the way as R people moved into Europe and South Asia, so the maximum percentage of similarity would probably lie between Bactria and Northwest India and in Eastern Europe.

A priori Y chromosome phylogeny from sequencing data

 The most important new piece of evidence is the joining together of haplogroup M (Papuans) with P in a new MP internal node. Your guess is as good as mine as to whether this MP may have come from, as his descendants are presently spread from the Atlantic via Siberia to the Amazon and all the way to New Guinea. The Mal’ta boy belonged to haplogroup R.
The other interesting discovery is of one Telugu man from India who shares mutations with haplogroups N and O but belongs to neither N nor O, so this defines a new “X” clade in the phylogeny. I am wondering if this could perhaps be called NO0 instead, similar to the way that more basal clades of the entire phylogeny were called A0, A00, and so on? Terminology is tricky…

I am aware of a few commercial ventures to resequence Y chromosomes, and I’m pretty sure that citizen scientists will soon not only be able to re-analyze data such as those from the 1000 Genomes Project, but will be able to generate data of their own.

bioRxiv doi: 10.1101/000802

Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data

Gregory R Magoon et al.

An approach for generating high-resolution a priori maximum parsimony Y-chromosome (“chrY”) phylogenies based on SNP and small INDEL variant data from massively-parallel short-read (“next-generation”) sequencing data is described; the tree-generation methodology produces annotations localizing mutations to individual branches of the tree, along with indications of mutation placement uncertainty in cases for which “no-calls” (through lack of mapped reads or otherwise) at particular site precludes a precise placement of the mutation. The approach leverages careful variant site filtering and a novel iterative reweighting procedure to generate high-accuracy trees while considering variants in regions of chrY that had previously been excluded from analyses based on short-read sequencing data. It is argued that the proposed approach is also superior to previous region-based filtering approaches in that it adapts to the quality of the underlying data and will automatically allow the scope of sites considered to expand as the underlying data quality (e.g. through longer read lengths) improves. Key related issues, including calling of genotypes for the hemizygous chrY, reliability of variant results, read mismappings and “heterozygous” genotype calls, and the mutational stability of different variants are discussed and taken into account. The methodology is demonstrated through application to a dataset consisting of 1292 male samples from diverse populations and haplogroups, with the majority coming from low-coverage sequencing by the 1000 Genomes Project. Application of the tree-generation approach to these data produces a tree involving over 120,000 chrY variant sites (about 45,000 sites if “singletons” are excluded). The utility of this approach in refining the Y-chromosome phylogenetic tree is demonstrated by examining results for several haplogroups. The results indicate a number of new branches on the Y-chromosome phylogenetic tree, many of them subdividing known branches, but also including some that inform the presence of additional levels along the “trunk” of the tree. Finally, opportunities for extensions of this phylogenetic analysis approach to other types of genetic data are examined.  Link

Kostenski site: see  Genomic structure in Europeans dating back at least 36,200 years by Andaine Seguin-Orlando  Science / http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114.abstract

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