Short IBD segments shared between Humans, Neanderthals and Denisovans in Africa and Eurasia

[Argang]

To test for an enrichment of Denisova, Neanderthal or Archaic matching segments they used Fisher’s exact test for count data. The "Admixed Americans" they refer to are various South American nationals. For other populations it seems that Denisovan and Neanderthal segments grow in number with distance to Africa (Africans-> Europeans -> East Asians).

Denisovans: Amerindians seem to have more than Europeans which would explain the result for "Admixed Americans". Denisovan segments peak in South Chinese among the tested populations, which makes sense since they are closest to Papuans who have highest Denisovan levels in the planet. Africans have the least Denisovan. No visible geographical clines in Europe.
http://s27.postimg.org/3ocnh524y/deni.jpg

Neanderthals: Besides the main cline of Africans to non-Africans, there's a secondary cline with increasing amount of Neanderthal IBD towards north. Africans have the least segments, and "Admixed Americans" have less than Europeans.
http://s16.postimg.org/rkozcb4pg/nean.jpg

We analyze the sharing of very short identity by descent (IBD) segments between humans,
Neandertals, and Denisovans to gain new insights into their demographic history. Short IBD
segments convey information about events far back in time because the shorter IBD segments are,
the older they are assumed to be.

A DNA segment is identical by state (IBS) in two or more individuals if they all have identical nucleotide sequences in this segment. An IBS segment is
identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor, that is, the segment has the same ancestral origin in these individuals.



http://biorxiv.org/content/biorxiv/early/2014/04/07/003988.full.pdf

[Longbowman]

Yes, the Mongoloids are the most non-Sapiens of the three primary races. Interesting.

[Argang]

Yes, the Mongoloids are the most non-Sapiens of the three primary races. Interesting.

I think Mbuti pygmies are the top contender for purest Homo Sapiens on the planet now that there's evidence of West Eurasian in the Khoisan.

[Longbowman]

I think Mbuti pygmies are the top contender for purest Homo Sapiens on the planet now that there's evidence of West Eurasian in the Khoisan.

Southeast Asians are the least sapiens.

[Kale]

I thought pygmies inherited a couple percent from some unknown species?

[Argang]

I thought pygmies inherited a couple percent from some unknown species?

I think the idea was that most SSA groups did. It's not really researched yet, since no one has found remains of such a hominid.

[Kale]

Rhodesia?

[Longbowman]

Rhodesia?

Old name for Zimbabwe.

[Kale]

Old name for Zimbabwe.

Old name for buttcheeks.

[Longbowman]

Old name for buttcheeks.

What

[Kale]

What
http://xenohistorian.faithweb.com/genesis/rhodesianman.jpg

[Longbowman]

http://xenohistorian.faithweb.com/genesis/rhodesianman.jpg

where do buttcheeks come into it?

[Kale]

where do buttcheeks come into it?

You got it all backwards.

[Argang]

A new study proposes that Neanderthals were much less heterozygous and had a smaller gene pool than modern humans.

http://s4.postimg.org/zad3qdhi5/heteroz.jpg

They also did a PCA comparing Neanderthals and Denisovan to modern humans from Europe, Africa and Asia.

Principal components 1 and 2 contain 38.04% and 14.65% of the total variation respectively and seem to mark species differences, Sapiens populations cluster together, Neanderthals cluster together and Denisovan is on its own.

PC3 and PC4 represent 8.96% and 6.06% of the variation and there we start seeing significant differences between modern humans. Neanderthals and Denisovan still are separate from modern humans but much closer to Europeans and Asians than to Africans.
Assuming the supplementary information uses the same three populations for PCA's and homozygosity tests, it seems that the reference individuals for Africa are Mandenka, Dinka and Yoruba, for Europe they're French, Sardinian and Italian-American, and for Asia Han, Dai and Papuan. It would have been nice to have North European, South Asian and Amerindian references but w/e
http://s22.postimg.org/r4690s529/pca.png
source:
http://www.pnas.org/content/suppl/2014/04/17/1405138111.DCSupplemental/pnas.1405138111.sapp.pdf

[Argang]

This study suggests Eurasians have also admixture from pre-Neanderthal archaic hominins.

http://arxiv.org/abs/1404.7766



Introgressions from Neanderthals and Denisovans were detected in modern humans. Introgressions from other archaic hominins were also implicated, however, identification of which poses a great technical challenge. Here, we introduced an approach in identifying introgressions from all possible archaic hominins in Eurasian genomes, without referring to archaic hominin sequences. We focused on mutations emerged in archaic hominins after their divergence from modern humans (denoted as archaic-specific mutations), and identified introgressive segments which showed significant enrichment of archaic-specific mutations over the rest of the genome. Furthermore, boundaries of introgressions were identified using a dynamic programming approach to partition whole genome into segments which contained different levels of archaic-specific mutations. We found that detected introgressions shared more archaic-specific mutations with Altai Neanderthal than they shared with Denisovan, and 60.3% of archaic hominin introgressions were from Neanderthals. Furthermore, we detected more introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes. Above results suggested a complex admixture history among hominins. The proposed approach could also facilitate admixture research across species.

If that's right, Mbuti and Yoruba reinforce their status as purest Homo Sapiens I quess.