Genome sequence of a 45,000-year-old modern human from western Siberia

[Hevo]

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.

Y DNA K-M526

mtDNA R

autosomal data



The Ust’-Ishim individual shares significantly fewer alleles with present-day Europeans
than with any other non-Africans we analyzed ... and suggest that Ust’-Ishim may not have carried any Basal Eurasian ancestry.


http://www.nature.com/nature/journal/v514/n7523/full/nature13810.html

[Kale]

This makes the whole basal thing a lot more interesting. Or more importantly why it isn't more visible. If basal is pre Ust-Ishim, and Ust-Ishim is Mtdna R, and yDna pre-K, it should make sense we'd see some groups that are more divergent in West Eurasians. However 95% of West Eurasian mtdna is downstream of R (H, V, J, T, U, K) and the y-dna is mostly descended from K (R1a, R1b), it's closest siblings (I, J), or something that branched off not significantly earlier than it (G). I mean, we do have E...but East Eurasians have D. Basal was defined as something that diverged prior to the common ancestor of Loschbur and Onge. Onge are mtdna M, and y-dna D, Loschbur is mtdna U (descended from N) and y-dna I. The only thing earlier than M and N, is various types of L...and y-dna D and I only meet up back at CT*, leaving only A or B as earlier splits.

[Rochefaton]

If I recall correctly, Y-DNA D is found mainly in the Tibetans, Japanese and Andamanese Islanders, and DE* has been found in both Tibetan and African populations. I wouldn't rule out some form of Y-DNA E being related to the elusive group we call the "Basal Eurasians" simply due to Y-DNA D's frequency peaks in modern populations.

[Kale]

Well here's another problem I have with Basal Eurasian and its hypothetical link with haplogroup E... On a global PCA, African Pygmies form one pole, and the rest of Africa is on a long trail towards West Eurasia, more specifically Sardinia.
http://4.bp.blogspot.com/-unaJATtPLV4/T2jLIx5utbI/AAAAAAAAErY/vtoOrMfBmUA/s1600/1_2.png
Africans (excluding North Africans and some Sahelian populations) show no sign of anything relating to West Eurasia at all. The only thing that could possibly be dragging them that way is ancestry related to the bearers of haplogroup E, the supposed Basal people. Now look at the PCA again. Why would Sardinia be the end point of this long trail? They are supposed to be only around 40% basal. Why would Orcadians and Sardinians plot so close to each other with such a huge difference (25% or something) of ancestry fro ma hugely divergent clade?

P.S> Why is this site so god damn slow today?!/

[Hevo]

Wasn't there a recent study that K-M526 and the derived P-M45 most likely originated in South East Asia and then migrated north? It looks like based on these results it's more likely that it's origin lies actually in Siberia although we need more ancient gnomes from South East Asia to be certain i guess.

[Kale]

The recent study suggested K2b originated in Southeast Asia, nothing about K* itself.

[Hevo]

The recent study suggested K2b originated in Southeast Asia, nothing about K* itself.

But isn't K-M526 K2?

[Kale]

O yes I'm sorry. He's 6 unknown mutations up from K2*.