Structure of Y-haplogroup N

arXiv:1504.06463 [q-bio.PE]

The dichotomy structure of Y chromosome Haplogroup N

Kang Hu et al.

Haplogroup N-M231 of human Y chromosome is a common clade from Eastern Asia to Northern Europe, being one of the most frequent haplogroups in Altaic and Uralic-speaking populations. Using newly discovered bi-allelic markers from high-throughput DNA sequencing, we largely improved the phylogeny of Haplogroup N, in which 16 subclades could be identified by 33 SNPs. More than 400 males belonging to Haplogroup N in 34 populations in China were successfully genotyped, and populations in Northern Asia and Eastern Europe were also compared together. We found that all the N samples were typed as inside either clade N1-F1206 (including former N1a-M128, N1b-P43 and N1c-M46 clades), most of which were found in Altaic, Uralic, Russian and Chinese-speaking populations, or N2-F2930, common in Tibeto-Burman and Chinese-speaking populations. Our detailed results suggest that Haplogroup N developed in the region of China since the final stage of late Paleolithic Era.

Link

Origins and dispersals of Y-chromosome haplogroup N

I will simply note that the authors use the effective mutation rate that is ~1/3 the genealogical mutation rate and hence their age estimates are inflated by ~3x. I have expressed reservations about using Y-STR based age estimates in general, but these concerns become more important for older lineages.

In particular, I would be very surprised if Y-haplogroup N turns up in Europe 8-10 thousand years ago, and I expect to see it make its first appearance in the 3rd millennium BC or thereabouts, perhaps together with the Seima-Turbino expansion across northern Eurasia. Thanks to the ancient DNA -preserving boreal cold, it may be possible to find out.

Irrespective of my disagreement on the mutation rate issue, I have to applaud the comprehensive survey carried out by these Chinese scientists: numbers invariably pay off.

PLoS ONE 8(6): e66102. doi:10.1371/journal.pone.0066102

Genetic Evidence of an East Asian Origin and Paleolithic Northward Migration of Y-chromosome Haplogroup N

Hong Shi et al.

The Y-chromosome haplogroup N-M231 (Hg N) is distributed widely in eastern and central Asia, Siberia, as well as in eastern and northern Europe. Previous studies suggested a counterclockwise prehistoric migration of Hg N from eastern Asia to eastern and northern Europe. However, the root of this Y chromosome lineage and its detailed dispersal pattern across eastern Asia are still unclear. We analyzed haplogroup profiles and phylogeographic patterns of 1,570 Hg N individuals from 20,826 males in 359 populations across Eurasia. We first genotyped 6,371 males from 169 populations in China and Cambodia, and generated data of 360 Hg N individuals, and then combined published data on 1,210 Hg N individuals from Japanese, Southeast Asian, Siberian, European and Central Asian populations. The results showed that the sub-haplogroups of Hg N have a distinct geographical distribution. The highest Y-STR diversity of the ancestral Hg N sub-haplogroups was observed in the southern part of mainland East Asia, and further phylogeographic analyses supports an origin of Hg N in southern China. Combined with previous data, we propose that the early northward dispersal of Hg N started from southern China about 21 thousand years ago (kya), expanding into northern China 12–18 kya, and reaching further north to Siberia about 12–14 kya before a population expansion and westward migration into Central Asia and eastern/northern Europe around 8.0–10.0 kya. This northward migration of Hg N likewise coincides with retreating ice sheets after the Last Glacial Maximum (22–18 kya) in mainland East Asia.

Link

Thesis of Oleg Balonovsky

is available here as pdf. Lots of interesting information, and a few striking maps. Hopefully, the fact that it's all in Russian won't be much of a problem in this day and age.

I will highlight a few pieces of information. First, a distribution of Y-chromosome haplogroups in Russian groups:

Notice:

• N1c-Tat is a general feature of the Russians, but N1b-P43 is only really found at any significant frequency in the northern groups.
• A strong contrast of E-M78 between central (present) and northern (absent) groups, consistent with a late introduction of this haplogroup in easternmost Europe.
• South-Central-North decreasing frequency of R1a; now, it's not clear how R1a came to be in Russians: some of it may be legacy of its initial entry into Europe from the east, other could be of historical import, and may have even arrived during the Slavic expansion from Central Europe. The pattern probably is the reverse of the high frequency of N1, indicating increasing importance of Finno-Ugric substratum in the north.
• Fairly interesting that of the two likely "Balkan" haplogroups E-M78 and I-P37, the former is modal in central region, the latter in southern one. The absence of both in "deep Asia" suggests a late introduction, as mentioned before, but when?

Also of interest a haplotype analysis within R1a1a-M198:

My most immediate observation is the set of mainly Indian highly divergent haplotypes on the left. There has been (well-deserved) excitement about recent Y-SNP progress within this haplogroup, but we should not neglect the occurrence of outliers/relics in our reconstruction of a haplogroup's history. I'd love to see those few Indian haplotypes SNP-tested using the currently available SNPs, or even used to develop new SNPs for this important Eurasian haplogroup.

Y chromosome and mtDNA of Louis XVI of France (?)

From the paper:

After the execution of Louis XVI in January 21st, 1793, eyewitnesses stated that many people from the crowd dipped their handkerchiefs in the king’s blood and kept these objects as mementos [8]. An Italian family has owned for more than a hundred years – as demonstrated by a letter addressed to the director of the Muse/ e Carnavalet in Paris, January 31st, 1900 – a dessicated gourd that presumably contained one of these handkerchiefs.

The mtDNA results:

the majority of the cloned sequences (87%) showed a rare N1b haplotype, with the substitutions 16093C-16145A-16176(G)-16223T. The same results were found in Bologna by direct sequencing, along with another substitution (16390G), not included in the amplicon generated in Barcelona. The haplotype found at the mtDNA HVR2(73G, 151T, 152C, 189G, 194T, 195C, 263G and 315.1C), is consistent with the N1b haplotype from the HVR1, although the substitutions 151T, 189G and 194T are not described in the current N1b dataset lineages. We interpret these three substitutions as additional, undescribed modifications of a N1b haplotype.

The Y-chromosome STR markers:

A ysearch query reveals a handful of distant (3 off in 9 markers) matches ranging from Anatolia to Scotland. Likewise yhrd turns up no matches using either the full or restricted panel, but a 1-off match with DYS389II-29 in the restricted panel in Marche, Italy.

Wikipedia tells me that Louis XVI's patrilineage goes all the way to Robert the Strong, and his matrilineage to Catherine of Mayenne.

One would think that a 1,000-year long line of kings and nobles would have left enough side branches and bastards along the way to register a few hits on the European map. Perhaps, that's a reason to stress the "presumed" in the paper's title. On the other hand, I find it interesting that the presumptive haplogroup of Louis XVI was G2a, the same as 2 of 5 warriors from Merovingian Bavaria (7th c. AD).

There is a way to authenticate the results, as the authors note:

At present it is not possible to prove genetically that the sample really belongs to the king Louis XVI. One possibility would be to extract a new sample from the dry heart attributed to the Dauphin Louis XVII, son of Louis XVI, preserved at the Basilique Saint-Denis in Paris, and compare both Y-chromosome profiles. Owing to the fact that the Y-chromosome profile found is not present in our current genetic databases such as YHRD, a potential match would directly authenticate the studied blood sample.

Forensic Sci Int Genet. 2010 Oct 10. [Epub ahead of print]

Genetic analysis of the presumptive blood from Louis XVI, king of France.

Lalueza-Fox C, Gigli E, Bini C, Calafell F, Luiselli D, Pelotti S, Pettener D.

Institut de Biologia Evolutiva, CSIC-UPF, Dr. Aiguader 88, 08003 Barcelona, Spain.

Abstract
A text on a pyrographically decorated gourd dated to 1793 explains that it contains a handkerchief dipped with the blood of Louis XVI, king of France, after his execution. Biochemical analyses confirmed that the material contained within the gourd was blood. The mitochondrial DNA (mtDNA) hypervariable region 1 (HVR1) and 2 (HVR2), the Y-chromosome STR profile, some autosomal STR markers and a SNP in HERC2 gene associated to blue eyes, were retrieved, and some results independently replicated in two different laboratories. The uncommon mtDNA sequence retrieved can be attributed to a N1b haplotype, while the novel Y-chromosome haplotype belongs to haplogroup G2a. The HERC2 gene showed that the subject analyzed was a heterozygote, which is compatible with a blue-eyed person, as king Louis XVI was. To confirm the identity of the subject, an analysis of the dried heart of his son, Louis XVII, could be undertaken.

Link