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Category Archives: Denisova

Neanderthals, Denisovans and everything else

A recent analysis of the nuclear DNA of a Neanderthal toe from Altai has caused widespread interest.
Kay Prüffer et al., The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013. Pay per viewLINK [doi:10.1038/nature12886]
The story of a finger and a toe
Both the Denisovan and Neanderthal DNA sequences discussed in this paper come from small bones found at the same location: Denisova cave, Altai Republic. The Denisovan sequence that revolutionized human paleogenetics a few years ago corresponds to a finger phalanx bone of some 50,000 years ago. The less notorious Neanderthal sequence discussed in this study corresponds to a toe imal phalanx, which was found in a lower layer in the same gallery of the same cave, and hence should be older.
This is very interesting to underscore because it seems to imply that Neanderthals were in Altai and specifically in Denisova cave very early, at dates similar to those we find in West Asia (Tabun excepted) and they may even be older than Denisovans in the very cave that gave them their name.
The toe sequence was found in a previous study to have Neanderthal mtDNA, closely related to the lineages of European Neanderthals of various dates and sites. Instead the finger mtDNA (Denisovan) was derived from a more ancient branch of humankind than the very point of split between Neanderthals and modern humans (H. sapiens) and has been recently shown to be related to European H. heidelbergensis from Atapuerca
Notes in red are mine.
This study focuses on the autosomal DNA of both Neanderthals and Denisovans. Unlike mtDNA, whose phylogenetic position is simple and quite straightforward, autosomal or nuclear DNA (nDNA) is extremely much more complex to understand because of its recombining nature, requiring of statistical approaches, which may get extremely complex and potentially subject to premise biases. When comparing two individuals this gets largely simplified but it is a lot more complex when doing the same with larger samples.
And that is precisely what this study does: comparing one Denisovan, several Neanderthals and also several modern humans. Therefore it is a very complex paper and the authors necessarily assume some evaluation risks, which nevertheless are discussed in depth in the supplemental material, a methodology of the Pääbo team that we can’t but greatly appreciate.
Age estimates
The study makes two age estimates, one based on a very conservative and truly unbelievable Pan-Homo split date of 6.5 Ma BP and the other based on observed per generation mutation rates, which happens to be perfectly coincident with a Pan-Homo split of 13 Ma BP, the oldest extreme of Langergraber’s estimate. This coincidence alone is of enough relevance for all molecular clock approaches, because it effectively demands the doubling of all age estimates based on the ridiculously short 6.5 Ma Pan-Homo split supposition. 
Red outlines are mine. Click to enlarge.
It also produces a semi-reasonable San-West African age estimate of c. 86-130 Ka, although I would think it a bit older in fact or at the very least at the top end. This highlights the severe difficulties of such molecular clock estimates, because a 4 Ma divergence between the alleged introgressing mystery archaic in the Denisovan genome, seems out of the question according on the archaeological and paleontological record, which only documents Homo species since c. 2 Ma ago, half that time (within the estimate but clearly very far from the top end).
Altai Neanderthal inbreeding
An important finding of this study is that the studied individual was extremely inbred, with parents in effective relationship comparable to that of grandparent and grandchild or half siblings. This inbreeding tendency, even if extreme, is not so strange in populations that have experienced founder effect bottlenecks and small population sizes. The Denisovan and the modern human Karitiana people are not so extreme but range in the lower end of double first cousins level of genetic relationship between the parents. Other Native Americans like the Mixe are close to that range, while the other compared populations, Papuans and Sardinians, show much lower levels of inbreeding.
Whatever we may think of Altai Neanderthal inbreeding, their drift parameter is still very low when compared with European Neanderthals. This is not discussed in the paper but such extreme drift also seems to imply extreme inbreeding issues in European Neanderthals, even if these may have other causes such as an extremely strong founder effect or whatever.
Bonobo-specific segments were removed, so the bonobo position is not realistic.
Inferred population history
Both populations leading to the Altai Neanderthal and Denisovans, but not modern humans, appear to have gone through a strong decline in population size since hundreds of millennia ago. The Denisovan decline seems to begin c. 800 Ka ago while the Neanderthal one may have begun c. 500 Ka ago. While this is coincident with a general expansion of the H. sapiens branch (still undifferentiated in Africa), peaking around c. 250 Ka ago before differentiation and relative decline. In their words:

All genomes analysed show evidence of a reduction in population size that occurred sometime before 1.0 million years ago. Subsequently, the population ancestral to present-day humans increased in size,whereas the Altai and Denisovan ancestral populations decreased further in size. It is thus clear that the demographic histories of both archaic populations differ substantially from that of present-day humans.

Neanderthal and Denisovan admixture in modern humans

The new tests confirm in essence the previous findings: there is significant Neanderthal introgression in modern humans descending from the migrants out of Africa and there is also significant Denisovan one among Australasian populations.

Additionally and with some caution, the authors think that much lesser Denisovan introgression (of around 0.2%) is found among East Asians and that these, as well as Native Americans, show slightly more Neanderthal admixture than West Eurasians. In my understanding this may be caused by minor African flow to West Eurasia after the admixture event (and/or residual “First Arabian” persistence) and I would think that measuring South Asians would help to clarify this issue (because African admixture is negligible in the subcontinent but they are also distinct from East Asians).

These measurements are so weak that the authors agree to all kind of cautions about them in any case.

In addition to all this, the supplemental material (section 13) also detects tiny, almost homeopathic, amounts of Neanderthal gene flow to Yorubas (~0.02%), obviously mediated by H. sapiens backflow from Asia and Europe into parts of Africa, which eventually influenced other African populations. An even more diluted amount may also be present among the Mbuti Pygmies.

Altai Neanderthal admixture in Denisovans

This issue is not really explained in the paper as such, and we have to reach out to the Supplemental Information chapter 15 in order to grasp it.

It is clear that the Altai Neanderthals are closer to Denisovans than other Neanderthals are by approx. the following fractions (directly deduced from the raw affinities listed in fig. S6a.2):

  • 2% more than Mezhmaiskaya
  • 7% more than Vindija (avg.)
  • 9% more than El Sidrón
Feldhofer appears closer instead but this sequence was not used by the authors in most tests because it has too dubious quality.

In section 15 of the supplementary material, using complex methodology and lamenting the lack of a second Denisovan sample which would be most useful, they estimate a minimal 0.5% (Altai) Neanderthal introgression in Denisovans, with strong warnings that this could well be quite higher. I don’t know why they are not even considering a more direct approach, but I would dare to guesstimate the introgression to be close to 8% from the above raw data, assuming that there are no further complexities at play, such as other Heidelbergensis introgression in European Neanderthals, etc. The drift parameter (see above) does not seem to be one such complexity because Mezhmaiskaya is almost as drifted as Vindija yet it is consistently much closer, as it seems to correspond to its specific relatedness to Altai Neanderthals in mtDNA (and possibly also in nDNA if it is admixture what causes their pseudo-tree positioning closer to the root, what would be typical).

Note in blue is mine.

Mystery archaic genetic flow into Denisovans

The authors find that some 0.5-8% of the Denisovan genome appears to come from another hominin, which split from the human trunk even earlier.

We caution that these analyses make several simplifying assumptions. Despite these limitations, we show that the Denisova genome harbors a component that derives from a population that lived before the separation of Neanderthals, Denisovans and modern humans. This component may be present due to gene flow, or to a more complex population history such as ancient population structure maintaining a larger proportion of ancestral alleles in the ancestors of Denisovans over hundreds of thousands of years.


Later in the discussion section they ponder further the implications of this finding:

The evidence suggestive of gene flow into Denisovans from an unknown hominin is interesting. The estimated age of 0.9 to 4 million years for the population split of this unknown hominin from the modern human lineage is compatible with a model where this unknown hominin contributed its mtDNA to Denisovans since the Denisovan mtDNA diverged from the mtDNA of the other hominins about 0.7–1.3 million years ago41. The estimated population split time is also compatible with the possibility that this unknown hominin was what is known from the fossil record as Homo erectus. This group started to spread out of Africa around 1.8 million years ago42, but Asian and African H. erectus populations may have become finally separated only about one million years ago43. However, further work is necessary to establish if and how this gene flow event occurred.


Going to the detail of the matter (i.e. supplemental material sections 16a and 16b), one of the key details is that present-day Africans share more derived alleles with Neanderthals than with Denisovans. This can only be explained because Denisovans have other archaic ancestry prior to their apparent divergence from Neanderthals or (what is about the same) because Denisovans diverged themselves prior to the Neanderthal-Sapiens split, what is what the mtDNA (unlike the nDNA) suggests. However the difference, even if consistent across comparisons, is too small (a few percentage points) to be attributed to the later scenario.

This means that Denisovans appear to be at nDNA level some sort of an independent branch of proto-Neanderthals with some other but minor archaic admixture. Instead at mtDNA level they appear to be unrelated to Neanderthals and related instead to H. heidelbergensis (a detail not discussed in this paper because it is a too recent independent discovery).

There are still many details to explore but, in principle, it would seem that the Denisovan branch appears to be a divergent proto-Neanderthal one (maybe related to the Hathnora hominin, which looks very much Neanderthal) with lesser other archaic (H. heidelbergensis?) admixture, which nevertheless remained prominent in their mtDNA for whatever accidental reason.

Whether the H. heidelbergensis population of Atapuerca responds to this same profile (i.e. they were Denisovans too) or belongs instead to the “other archaic” population which introgressed in the Denisovan genome remains to be solved. So far we only know the mitochondrial lineage and this one may be misleading, as seems to be the case with the Denisova hominin.

Note in red is mine

Modern human genetic evolution

Benefiting from the high quality of the archaic genomes of Altai, the authors cataloged a long list of simple mutations exclusive to our species: 31,389 single nucleotide substitutions and 4,113 short insertions and deletions (indels). Additionally they found other 105,757 substitutions and 3,900 indels shared by 90% of their modern human sample of 1094 individuals.

They suggest some lines for future research in this regard, maybe focusing on genes known to influence brain development or regions that could show signs of positive selection. These preliminary lines of research are explored in SI-20, noticing potential selection in genes that affect the ventricular zone of the brain and cell proliferation in fetal brain development.

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The Denisovans were not alone

H. heidelbergensis from Atapuerca
Cranium 5 “Miguelón”
(CC by José Manuel Benito)
About half an hour ago, somewhat cryptic comments in this blog and my email woke me up, more abruptly than I would have desired maybe, to a new game-breaking finding: researchers have sequenced the mtDNA of a 400,000 years old Homo heidelbergensis from Atapuerca (Iberian Peninsula, Europe) and it was not at all like most would have expected.
Mathhias Mayer et al., A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 2013. Pay per viewLINK [doi:10.1038/nature12788]

Abstract

Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils2, 3, consisting of at least 28 individuals4 dated to over 300,000 years ago5. The skeletal remains share a number of morphological features with fossils classified as Homo heidelbergensis and also display distinct Neanderthal-derived traits6, 7, 8. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans9, 10, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.

The key figure is this one, which phylogenetically relates the newly sequenced mtDNA with the known Homo ones:

Figure 4: Bayesian phylogenetic tree of hominin mitochondrial relationships based on the Sima de los Huesos mtDNA sequence determined using the inclusive filtering criteria.
All nodes connecting the denoted hominin groups are supported with posterior probability of 1. The tree was rooted using chimpanzee and bonobo mtDNA genomes. The scale bar denotes substitutions per site.

It has been argued by all sides (myself included) that the H. heidelbergensis of Atapuerca and other European locations are ancestral to Neanderthals. Some say that also to H. sapiens, while others argue that ours is a wholly distinct line, derived from H. rhodesiensis, and yet others claim that H. rhodesiensis is not different from H. heidelbergensis in spite of being older and rooted, it seems, in South Africa.
The clear evidence for migrations out of Africa, before our species, is limited to two periods: (1) the c. 1.8 Ma old migration of H. erectus/georgicus with Olduwayan technology (mode 1, “choppers”), and (2) the c. 1 Ma old migration of H. ergaster/antecessor (sometimes also confusingly called H. erectus) with Acheulean technology (mode 2, typically “hand axes”). Archaeological evidence for later migrations does not exist.
See: Late human evolution maps at Leherensuge.
So we could well ask, if H. heidelbergensis is not ancestral to Neanderthals, then where do Neanderthals come from?
It must be answered that we do not know yet if H. heidelbergensis is or not ancestral to Neanderthals or in what degree it is. The mitochodrial (maternal) lineage may well be misleading in this sense. Denisovans themselves were much more related to Neanderthals via autosomal (nuclear) DNA than the mtDNA, so it may also be the case with European Heidelbergensis.
In fact it is still possible that these individuals represent some sort of admixture between older and newer layers of human expansion. But there is no clear answer yet. What is clear is that no Neanderthals have these mitochondrial sequences but others closer to those of H. sapiens – and this is the most puzzling part in fact. 
But one thing is clear: the World is much bigger than just Europe, and that was also the case back in Paleolithic times. Our answer may well lay under the sands of some tropical desert, the waters of the sea or whatever other place in Asia or Africa.
Even if we’d find the “missing link”, so to say, we might not be able to discern it as such without genetic sequencing and that is often not even possible at all. However this pioneer research, as well as its precursors on a bear also from Atapuerca and a 700,000 years old horse (the true record of ancient DNA recovery), give us some hope of getting an improved, even if sometimes perplexing, understanding of the complexity of the human adventure.
 

Nearly complete sequence of a Neanderthal from Altai

A 99.9% complete Neanderthal genome from a toe bone found at Denisova Cave (Altai, Southern Siberia).

A high-quality Neandertal genome sequence


The genome sequence was generated from a toe bone discovered in Denisova Cave in southern Siberia in 2010. The bone is described in Mednikova (Ethnology & Anthropology of Eurasia 2011. 39: 129-138).


DNA sequences were generated on the Illumina HiSeq platform and constitute an average 50-fold coverage of the genome. 99.9% of the 1.7GB of uniquely mappable DNA sequences in the human genome are covered at least ten times.
Contamination with modern human DNA, estimated from mitochondrial and nuclear DNA sequences, is around 1%.


The figure shows a tree relating this genome to the genomes of Neandertals from Croatia, from Germany and from the Caucasus as well as the Denisovan genome recovered from a finger bone excavated at Deniosva Cave. It shows that this individual is closely related to these other Neandertals. Thus, both Neandertals and Denisovans have inhabited this cave in southern Siberia, presumably at different times. 

One may wonder: how can they know it is a Neanderthal and not a “Denisovan”? Because of the close genetic affinity with other Neanderthals from Europe:

It is still possible, considering its position in the tree that the Altai Neanderthal had minor “Denisovan” admixture. But it would be very minor in any case. 

 
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Posted by on March 25, 2013 in aDNA, Altai, Denisova, Neanderthal

 

More Neanderthal admixture details

The main conclusion of this new study seems to be that East Asians have normally more Neanderthal admixture than South or West Eurasians. Also the Maasai from East Africa have been shown to have minor Neanderthal admixture, consistent with the also minor Eurasian genetic component they have.
Jeffrey D. Wall et al., Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans. Genetics 2013. Freely accessible at the time of writing thisLINK [doi: 10.1534/genetics.112.148213]

Abstract

Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

There is a sentence in page 8 in which the authors claim that:

By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.

However I fail to see it in the D-statistic graphs, which show less than 15% more Neanderthal admixture in Eastern Asians than in Europeans (on average and discounting error margins, which strongly overlap). It may be therefore another case of hair-splitting.
Instead the evidence of weak Neanderthal admixture (via minor Eurasian  genetic influence) in the Maasai of East Africa seems more solid: while error margins of Maasai and Luhya do overlap, the main blocs do not.

Figure 3. Summary of significance tests for average values of D. Positive values indicate that the second sequence is more similar to the Neanderthal genome than the first sequence. In all parts, the box plots indicate the range of D values obtained for pairs of individuals from the populations indicated. Parts A and B are box plots of individual D statistics computed for each individual from the specified population compared with each Yoruban. The p values are from the randomization test, Test 1, of significant differences in the average D values for different pairs of populations. Parts C and D show box plots of individual D statistics computed for every pair of individuals in the specified populations. The p values are from the randomization test, Test 2, of significant differences of the average D from 0. See also Table 2.

It is surely convenient to look carefully at all the data, including the supplementary materials, before jumping to any strong conclusions. Among them I found more interesting fig. S1:

Figure S1: Box plot of the D-statistics for Analyses A and B for the set (Afr, X), where X was any of the non-African populations,
CEU or TSI (Europeans, green), CHB or JPT (East Asians, blue), or GIH (South Asian, pink) (PDF, 222 KB).

As we can see here, the error margins continue overlapping very strongly, but, assuming that we can jump to conclusions based on the norm (thick black line), which is assuming some risks indeed but also the only way to (tentatively) agree with the authors’ conclusion of greater Neanderthal admixture among East Asians, then the causes should be:
  1. Founder effect among East Asians, known to have less overall genetic diversity and suspected to have undergone some extra (mild?) bottleneck at their ancient origins.
  2. Low-level African (and surely also early OoA residuals from West Asia) admixture among West Eurasians, notably Tuscans (TSI) in these samples but also to some extent all Europeans (incl. CEU). This has the effect of increasing genetic diversity but also of slightly diluting Neanderthal admixture. The control here are Indians (GIH), which show slightly more Neanderthal admixture than Europeans (but are still closer to these than to East Asians also in this aspect).
Indians (who don’t seem to have any post-OoA African admixture, unlike Europeans and West Asians, who have it at variable low levels) suggest that factor #2 (dilution) weights only somewhat and therefore that factor #1 (East Asian founder effect) must be considered the main one instead. 
But, unless someone can point me where I am wrong, I fail to see neither the alleged 40% excess Neanderthal admixture in Orientals nor why would these results question the single admixture episode (or period) at the origins of migration out of Africa (OoA).

To finish this entry, it must be mentioned that the authors could only detect at most the tiniest fraction of Denisovan admixture among the sampled populations (i.e. nothing relevant and with no regional differences). However they did not research, admittedly, the South China populations suggested to have slight more Denisovan input by  Skoglund and Jakobsson 2011.
See also:

 

Tianyuan, mtDNA B and the formation of Far Eastern peoples

The genetic study of the ancient man of Tianyuan is already online, as I commented yesterday in a quick update.
Qiaomei Fu et al., DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 2013. Open accessLINK [doi: 10.1073/pnas.1221359110]

Abstract

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Mitochondrial DNA

Part of fig. 1
And the old guy (or is it a woman?) happened to carry the matrilineage (mtDNA) B, more specifically B4’5, defined by a relatively long deleted block at positions 8281-8289 (this excludes B6 now linked with R11 and also the other relative of all them R24, see PhyloTree for details). However within B4’5 the lineage could not further be resolved within the modern haplogroups, so it is neither B4 nor B5 but a third branch of the same haplogroup. 
The authors actually talk of “haplogroup B” but they explicitly mention a deletion of a 9-bp motif (5′-CCCCCTCTA-3′, revised Cambridge reference sequence positions 8,281–8,289) as well as a substitution at position 16,189, what makes it unmistakable B4’5 per the current PhyloTree build.
The tree to the right illustrates this fact, placing Tianyuan man’s lineage hanging directly from the root of this haplogroup that, beyond reasonable doubt, coalesced somewhere in East Asia (probably SE Asia, with Laos and Hainan being good references judging on diversity) some time before this person lived and died near what today is Beijing. 
What does it tell us? Really nothing new, at least within the parameters I have been managing: it confirms that the expansion of mtDNA B4’5 was already happening back in that time and that it had reached more or less its current area of expansion in East Asia (American and Oceanian B variants expanded later, of course). It also implies that its ancestors R and N, which experienced important successive expansions in the course of the colonization of Eurasia by our species had expanded  at an even earlier date (again nothing new to me but a nice confirmation anyhow).
On the other hand, this person’s particular matrilineage went eventually extinct later on. This again does not tell us too much because it is something to expect with the course of time, especially at low population densities, as was the case in the Paleolithic. He can still be ancestral to modern peoples in the area and elsewhere but not by a purely mother-to-daughter line – at least not that we know. 

Chromosome 21 autosomal DNA
Because of the poor state of the DNA, the researchers had a difficult time sequencing it (technical details in the paper), however they managed to reconstruct a good deal of chromosome 21, which they used to compare with modern humans and also with Neanderthals and the so-called Denisovans
The result places Tianyuan closer to modern Far Eastern populations than to the rest of modern humans. This clearly indicates that the process of division in various more or less homogeneous subcontinental-sized populations was already somewhat advanced. 

Fig. 2. Maximum-likelihood tree relating the chromosome 21 sequences of the Tianyuan individual, 11 present-day humans, and the Denisovan genome. The most strongly supported gene-flow event is shown in yellow. Bootstrap support for all internal edges is 100% except for the edge putting Tianyuan outside the four Asians, which is 31%. The scale bar shows 10 times the average standard error of the entries in the covariance matrix.
While it is generally acknowledged that Papuans cluster at very deep level with East Asians, the authors are not fully persuaded of the exactitude of this tree, particularly in this aspect. They declare:


We note, however, that the relationship of the Tianyuan and Papuan individuals is not resolved (bootstrap support 31%). Further work is necessary to clarify whether this reflects the age of the Tianyuan individual relative to the divergence between modern human populations.

The caveat is particularly relevant because the colonization of New Guinea is at least as old as 49,000 years ago, some ten millennia before Tianyuan, what does not fit too well with the tree at that level of detail, assuming (as I do) that modern Papuans are direct unmixed descendants of those early settlers. Papuans do carry at high frequencies a related matrilineage (P also basal descendant from R) but that is also true of modern Europeans and they appear more distant in the tree above.
A good contrast to understand better the difficulties in getting a good picture from autosomal DNA, especially one so old, is table 1:

Here we can appreciate the differences and proximities by another measure. The closest compared modern person to Tianyuan man is a Karitiana, followed closely by the Han and, surprisingly, by the Sardinian and the French, and only then the Dai and Papuan. 
The distance of the Karitiana to Tianyuan man is still greater than that with not just the Han or the Dai but also the Europeans. However this can be argued to be because Native Americans must have a deep dual East Asian and West Eurasian origin, the latter via Altai (Y-DNA Q, mtDNA X2).
Let’s check the Han then, who are not believed to have any meaningful West Eurasian admixture. Curiously the paradox happens again: the Han is somewhat closer to Europeans by this measure than to Tianyuan, and even their comparison with the Papuan shows up slightly less differentiated. 
This is admittedly harder to explain but we can conclude that either (a) this method can only grasp affinity/divergence to some degree or (b) that the Tianyuan partial genome indicates a very preliminary level of continental differentiation. Or (c) both. Of course time is the main cause of genetic differentiation and by no means we can imagine that such an ancient individual would be too similar to his modern plausible descendants but, on the other hand, all (including Tianyuan mtDNA) indicates that the process of continental differentiation was already well developed 40,000 years ago (most European ancestry must come from people living in Europe or West Asia back then) so we can either blame subtle flows like Siberian migrations that have kept both genetic pools somewhat closer than in pure isolation or we must assume that the measure is not too exact.
Admixture with other human species
The paper also deals with Denisovan and Neanderthal admixture, finding that Tianyuan man was within the modern range for both parameters in East Asia. 
This is very important because it ratifies the mainstream model of two minor admixture episodes: (1) with Neanderthals at the exit from Africa and prior to the Great Eurasian Expansion (so all non-Africans, including Tianyuan man, have very similar levels of Neanderthal admixture today) and (2) with a relative of Denisovans (Homo erectus?) maybe in Indonesia affecting only (or almost only) the aboriginal peoples of Oceania (and Filipino Negritos but not the other so-called Negritos from Malaysia or the Andaman, who are not particularly related anyhow).
(As a side note notice that the Denisovan-like gene flow into Papuans in fig. 2 appears to hang not from the end of the branch but from a very high position, suggesting it was a relative and not the known Denisovans of Altai themselves who became admixed into Papuans and other Oceanian populations, probably a relative living in the route to Australasia).

Update: Marnie just published a mention of a previous work on Tianyuan 1, which focuses on the isotopic evidence for a fish-based diet. 

 

Ancient North Chinese from 40,000 years ago closely related to modern locals

Tianyuan Cave (source)
The information is sketchy as of now but the news in the press indicate that an Homo sapiens from Tianyuan Cave, near Beijing, whose fragmented remains were discovered in 2003, was closely related to modern East Asians and Native Americans. 
The paper is not yet online but the information released to the media strongly suggests that East Asians were already distinct from other populations some 40,000 years ago. This would seem to be based on the sequencing of the mitochondrial DNA and the explicit mention of Native Americans indicates that the lineage must be A, B, C or D (X, the fifth and less common matrilineage of Native Americans, is not found in East Asians, with some exceptions from Siberia, so we can exclude it safely). 

Ancient DNA from cell nuclei and maternally inherited mitochondria
indicates that this individual belonged to a population that eventually
gave rise to many present-day Asians and Native Americans, says a team
led by Qiaomei Fu and Svante Pääbo, evolutionary geneticists at the Max
Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

This would seem to discard some adventurous hypothesis floating around about tremendous demographic changes in the Paleolithic and afterwards, at least for this region. Probably not even when “mode 4” technology arrived to the region (from Altai) c. 30,000 years ago. 
In other words: the seeds of modern populations were already there c. 40,000 years ago in East Asia (and surely also in most other regions) and, even if they may have changed somewhat, they have remained the same at least to some notable degree.
Furthermore, the autosomal DNA also seems to have been sequenced to at least some degree because the researchers state that Denisovan and Neanderthal genetic inputs are at the same levels as modern North Chinese (i.e. some 0% and 2.5% respectively):

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003,
carries roughly the same small proportions of Neandertal and Denisovan
genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

Or in the words of the Max Plank Institute:

The genetic profile reveals that this early modern human was related to
the ancestors of many present-day Asians and Native Americans but had
already diverged genetically from the ancestors of present-day
Europeans. In addition, the Tianyuan individual did not carry a larger
proportion of Neanderthal or Denisovan DNA than present-day people in
the region.

This also seems to discard models implying Denisovan admixture happening in Siberia or NE Asia and would indirectly support my own hypothesis of admixture with Homo erectus (for which Denisovans, plausibly an Erectus-Neanderthal hybrid, would be just a proxy) in or near Indonesia.
Sources: Science News, Max Plank Institute.

Update (Jan 22): the paper is already online and is open access (cool!)  I don’t think I have time to discuss it today but will do tomorrow without doubt (other than the sky falls on my head, you know).

 

Variation in human (modern and archaic) and chimpanzee lipoprotein APOE

This new study has some interest in understanding some details, of metabolic relevance, of the genetics of humans and our closest relatives:
Annick McIntosh et al., The Apolipoprotein E (APOE) Gene Appears Functionally Monomorphic in Chimpanzees (Pan troglodytes). PLoS ONE 2012. Open access ··> LINK [doi:10.1371/journal.pone.0047760]

Abstract

Background

The human apolipoprotein E (APOE) gene is polymorphic, with three primary alleles (E2, E3, E4) that differ at two key non-synonymous sites. These alleles are functionally different in how they bind to lipoproteins, and this genetic variation is associated with phenotypic variation for several medical traits, including cholesterol levels, cardiovascular health, Alzheimer’s disease risk, and longevity. The relative frequencies of these alleles vary across human populations, and the evolution and maintenance of this diversity is much debated. Previous studies comparing human and chimpanzee APOE sequences found that the chimpanzee sequence is most similar to the human E4 allele, although the resulting chimpanzee protein might function like the protein coded for by the human E3 allele. However, these studies have used sequence data from a single chimpanzee and do not consider whether chimpanzees, like humans, show intra-specific and subspecific variation at this locus.

Methodology and Principal Findings

To examine potential intraspecific variation, we sequenced the APOE gene of 32 chimpanzees. This sample included 20 captive individuals representing the western subspecies (P. troglodytes verus) and 12 wild individuals representing the eastern subspecies (P. t. schweinfurthii). Variation in our resulting sequences was limited to one non-coding, intronic SNP, which showed fixed differences between the two subspecies. We also compared APOE sequences for all available ape genera and fossil hominins. The bonobo APOE protein is identical to that of the chimpanzee, and the Denisovan APOE exhibits all four human-specific, non-synonymous changes and appears functionally similar to the human E4 allele.

Conclusions

We found no coding variation within and between chimpanzee populations, suggesting that the maintenance of functionally diverse APOE polymorphisms is a unique feature of human evolution.

The relevant details are all in table 1:

Table 1. Variation at key APOE functional sites in Homo and Pan.
There is uncertainty about the correctness of the only known Neanderthal triplet.
Even if E4 seems to be the ancestral type, E3 is the most common allele in our species, ranging from 50% in most populations to as much as 90% among some tribes.