|Fig. 1 – click to expand|
Category Archives: Eurasia
AbstractSignals of archaic admixture have been identified through comparisons of the draft Neanderthal and Denisova genomes with those of living humans. Studies of individual loci contributing to these genome-wide average signals are required for characterization of the introgression process and investigation of whether archaic variants conferred an adaptive advantage to the ancestors of contemporary human populations. However, no definitive case of adaptive introgression has yet been described. Here we provide a DNA sequence analysis of the innate immune gene STAT2 and show that a haplotype carried by many Eurasians (but not sub-Saharan Africans) has a sequence that closely matches that of the Neanderthal STAT2. This haplotype, referred to as N, was discovered through a resequencing survey of the entire coding region of STAT2 in a global sample of 90 individuals. Analyses of publicly available complete genome sequence data show that haplotype N shares a recent common ancestor with the Neanderthal sequence (∼80 thousand years ago) and is found throughout Eurasia at an average frequency of ∼5%. Interestingly, N is found in Melanesian populations at ∼10-fold higher frequency (∼54%) than in Eurasian populations. A neutrality test that controls for demography rejects the hypothesis that a variant of N rose to high frequency in Melanesia by genetic drift alone. Although we are not able to pinpoint the precise target of positive selection, we identify nonsynonymous mutations in ERBB3, ESYT1, and STAT2—all of which are part of the same 250 kb introgressive haplotype—as good candidates.
(Slashed out text is edited: wrong notions)
Rs1883832 – whose T variant is almost exclusively non-African Rs4810485 – whose T variant is also almost exclusively non-African Rs2066808 – whose T variant is dominant outside Africa but also somewhat common in Africa Rs1927914 – whose T variant is dominant outside Africa but also somewhat common in Africa Rs10983755 – whose A variant is almost exclusive of East Asians
Update: I just got a copy of the paper, so I share these key figures:
We can see in them that the genomic positions at 55,030,689, 55,030,712 and 55,036,471 do not seem to correspond with the SNPs listed in SNPedia (so my previous inference was wrong, it seems).
We can also see in the map how the haplotype N is distributed in what would seem to be random founder effects.
There is a chance that the Denisova variant (haplotype D) is found in some Papuans but being described by just a single transition this is not certain.
As you know I dislike molecular-clock-o-logy, which I consider close to pseudoscience but considering that there has been some paper recently claiming (as they usually do: as if it was rocket science instead of a mere educated guess) low divergence ages for Neanderthals and H. sapiens, I feel almost obliged to mention that this paper estimates the haplotype divergence at some 500-731 Ka., what, after correcting for the usual under-estimate of the Pan-Homo divergence, can be consistent with the classical archaeological understanding of the Neanderthal-Sapiens divergence before a million years ago, with the spread of Acheulean and H. heidelbergensis.
- Elder daughters: one coding region mutation downstream of N: N1’5, N9, N11, S and R. Notice that among these R holds a special place, not for any phylogenetic reason but because it has a scatter as wide as that of her mother N, suggestive of a very early coalescence and some sort of association between both expansions.
- Two mutations downstream of N: N10 and O.
- Four mutations downstream of N: N2 (incl. W), A and X.
- Extremely long stems, rare clades without any known node under N: N8, N13, N14, N21, N22.
|1.- Estimated coalescence of basal subhaplogroups of N|
|2.- Possible origins of mtDNA N (blue flowers): A – ‘raw’ geometric centroid, B – corrected against directionality.|
|3.- Scatter of N (deep blue) and R (cyan) subhaplogroups. The flower indicates the possible common origin.|
Lots of cobbles have been found in a gully near Dmanisi, Georgia, the oldest known site of Homo erectus (or habilis or georgicus) in Eurasia. The cobbles could not have arrived there naturally and are not found in other areas of the site (Olduwayan style tools have been found instead).
- Cambodian 4.4%
- Mongolian 4%
- Han Chinese 3.2%
- French and Sardinians 2.6%
- Melanesians 2.5%
- Karitianas 0.9%
Update (Dec 25): it may well be only 4.8% of total archaic admixture if Denisovans were hybrids of Neanderthals and H. erectus (see here – scroll to near bottom).
… we propose the following scenario: a first hominin occupation of the cave more than 50,000 radiocarbon years ago by the Denisova hominins, and a second occupation during the Upper Palaeolithic, at 30,000 years BP or later, probably by modern humans.
Update (Dec 23): Denisova mtDNA “modern”?
Dienekes mentions today that Niccolo Caldararo has published an article at Nature (freely available as PDF) suggesting that the Denisova mtDNA sequence may be corrupt. If this would be true, then the sequence would be that of a H. sapiens.
This could explain some of the anomalies in the autosomal NJ tree and related age estimates, that would make Chinese and French (for instance) diverging by more than 500,000 years, what is totally absurd.
However, considering that a very similar sequence was successfully sequenced also for the tooth, this claim seems less likely.
Still many questions remain open because there are issues such as the divergence estimates for various H. sapiens, specially Eurasian H. sapiens, that just do not make any sense at all. So I’d say it’s best to lay back a bit and wait patiently for more brilliant insights, which will no doubt come.
Update (Dec 25): see this new review for a more elaborate review of mine on this matter, including some intriguing hypothesis I am launching, partly on feedback provided by commenters.
AbstractDomestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.
|Fig. 2 – Ancient horse mtDNA haplotypes with timeline and region|
Update (Apr 6 2011): see also to this more recent post: Horse’s double origins, on new research supporting by means of autosomal DNA diversity the double origin in the steppes and SW Europe of modern horses.