Tianyuan autosomal data

I had checked a few times after the Tianyuan paper came out, and it seems that the data from it is now publicly available. The data appears to be in SRA format; see instructions on how to convert to SAM format in the link.

Ancient DNA from Tianyuan Cave

Another new PNAS paper that hasn't yet appeared in the journal website. Still, from this description at ScienceNews this appears to be Very Important, as it pertains to a 40,000-year-old modern human, which, if I'm not mistaken is the oldest modern human tested so far:

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 Paabo, evolutionary geneticists at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

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.

The Max Planck press release adds some information:

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.

This is an important finding because some published demographic models had Europeans and East Eurasians diverging as recently as ~20 thousand years ago. It now appears that they did so already at around the time of the Upper Paleolithic revolution, when unambiguous evidence of modern humans across Eurasia exists.

UPDATE I: While we wait for this paper to appear on the PNAS website, it might be useful to wonder whether the Tianyuan sample might fall on the East Asian/Amerindian group or the more general "Ancestral South Indian" (ASI)/East Eurasian group.

According to current dating, haplogroup M itself is ~50 thousand years old, and most of the subclades therein coalesce to younger than 40ky times. It's possible that the Tianyuan sample dates from a period where ASI/East Asian differentiation had only just begun or was just about to begin.

The press release makes clear that Tianyuan was already "Asian" rather than generalized Eurasian, proving that East/West Eurasian differentiation had begun by ~40kya. It will be interesting to see whether it can be placed on a more specific "East Eurasian" group rather than a generalized "Asian" one.

UPDATE II: The paper is now online.

UPDATE III: From the paper:

Thus, it is related to the mtDNA that was ancestral to present-day haplogroup B (Fig. 1), which has been estimated to be around 50,000 y old (18) (50. 7 ka BP; 95% CI: 38.1–68.3 ka BP). We note that the age of the Tianyuan individual is compatible with this date.

So, it appears to be within macro-haplogroup N, with haplogroup B being, I think, a fairly unambiguously East Asian/Native American clade of the phylogeny. It will certainly be interesting to see how the much more successful -and younger- M subclades ended up dominating East Eurasia.

UPDATE IV: The TreeMix analysis clearly places Tianyuan within the Asian group, but does not resolve whether Papuans are an outgroup to East Asians/Tianyuan:

I guess that is expected (see my UPDATE I), since Tianyuan dates from a period where within-Asia differentiation had only just begun or was about to begin.

UPDATE V: With respect to sharing of alleles with archaic Eurasian hominins, the Tianyuan sample is within the modern range of variation.

PNAS doi: 10.1073/pnas.1221359110

DNA analysis of an early modern human from Tianyuan Cave, China

Qiaomei Fu et al.

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.

Link

Earliest human footwear (Tianyuan and Sunghir)

Journal of Archaeological Science (Article in Press)
doi:10.1016/j.jas.2007.12.002

See also Earliest shoe wearers and 40,000 year old human from China.

Anatomical evidence for the antiquity of human footwear: Tianyuan and Sunghir

Erik Trinkaus and Hong Shang

Trinkaus [Trinkaus, E., 2005. Anatomical evidence for the antiquity of human footwear use. J. Archaeol. Sci. 32, 1515–1526] provided a comparative biomechanical analysis of the proximal pedal phalanges of western Eurasian Middle Paleolithic and Middle Upper Paleolithic humans, in the context of those of variably shod recent humans. The anatomical evidence indicated that supportive footwear was rare in the Middle Paleolithic but became frequent by the Middle Upper Paleolithic. Based on that analysis, additional data are provided for the Middle Upper Paleolithic (not, vert, similar27,500 cal BP) Sunghir 1 and the earlier (not, vert, similar40,000 cal BP) Tianyuan 1 modern humans. Both specimens exhibit relatively gracile middle proximal phalanges in the context of otherwise robust lower limbs. The former specimen reinforces the association of footwear with pedal phalangeal gracility in the Middle Upper Paleolithic. Tianyuan 1 indicates a greater antiquity for the habitual use of footwear than previously inferred, predating the emergence of the Middle Upper Paleolithic.

Link

40,000 year old human from China

From EurekAlert:

Researchers at Washington University in St. Louis and the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing have been studying a 40,000-year-old early modern human skeleton found in China and have determined that the "out of Africa" dispersal of modern humans may not have been as simple as once thought.

The research result will be published in the Proceedings of the U.S. National Academy of Sciences on April 3.

Erik Trinkaus, Professor of Anthropology at Washington University in St. Louis, his colleague Hong Shang, and others at the IVPP examined the skeleton, recovered in 2003 from the Tianyuan Cave, Zhoukoudian, near Beijing City.

The skeleton dates to 42,000 to 38,500 years ago, making it the oldest securely dated modern human skeleton in China and one of the oldest modern human fossils in eastern Eurasia.

The specimen is basically a modern human, but it does have a few archaic characteristics, particularly in the teeth and hand bone. This morphological pattern implies that a simple spread of modern humans from Africa is unlikely, especially since younger specimens have been found in Eastern Eurasia with similar feature patterns.

According to Trinkaus and Shang, "the discovery promises to provide relevant paleontological data for our understanding of the emergence of modern humans in eastern Asia."