45,000-Year-Old Modern Human Genome from Western Siberia is the Earliest Yet

Svante Pääbo's team has produced the earliest Homo sapiens genome so far, extracted from a directly radiocarbon-dated femur found in western Siberia. Two AMS dates on the collagen combined to produce a calibrated date of 46,880-43,210 cal BP. Stable C and N isotope analyses indicate a diet based on C3 plants and animals that ate them. The bone is from a male whose mtDNA falls near the root of the R haplogroup, which is widespread in modern Europe and Asia. The Y chromosome is similarly ancestral a widespread Eurasian haplogroup. They called the specimen  "Ust'-Ishim" after the location in which it was recovered.

The authors find that the individual was probably related to or derived from an early population involved in the dispersal of modern humans out of Africa. Principal components analyses (PCAs) of the autosomal DNA suggest this guy was more closely related to non-Africans than Africans. In fact, when comparing the autosomal DNA only to modern non-Africans the authors observe that the specimen falls near the origin of the graph (of the first two components) and interpret that to indicate that he was equally-closely related to all modern non-Africans.

There may, however, be a better interpretation. In both PCA plots the Ust'-Ishim genome fell closest to modern Central and South Asians, which would make sense too, given the location of the find. I haven't read the Supplementary materials yet (they're 115 pages long), but I did review Section 10, which addresses this issue. To my mind, the results of the admixture analysis shown in Supplementary Figure S10.3 do indeed suggest that the Ust'-Ishim genome is closest to Central Asians, such as the Pathan, Sindhi, Burusho, Hazara, and Uygur. (The ethnic labels come from the article.) These are all central Asian peoples from Pakistan, Afghanistan, and western China. The match between the bars representing those peoples and the Ust'-Ishim genome is not perfect (the former are missing a purple patch and a bit of dark blue that appear in the ancient genome), but to me that match it does seem markedly more similar than the others. Unfortunately, the subsequent phylogenetic analyses do not address this question as they do not include central Asian genomes. So, I'm not sure I agree with the authors' interpretation that this new specimen is equally related to all Eurasians. If the Ust'-Ishim individual is more closely related to central Asians than to others, it implies a remarkable degree of geographic stability. This is an obvious hypothesis that probably should have been addressed. I hope it is investigated in the future.

They also found a 2.3 +/- 0.3% Neanderthal admixture, showing that their inter-species cuddling had already taken place by 45,000 BP. Curiously, given the date and location, there was no Denisovan admixture. The percentage of Neanderthal admixture is a bit higher than in modern humans, but not by much. As one would expect, the characteristic length of the Neanderthal DNA segments is substantially greater (~1.8-4.2 x) in the Ust'-Ishim genome than in modern ones, because the fragments were subsequently broken up further by recombination. Actually, this fragmentation process can provide an estimate of the length of time since the admixture took place, which the authors estimate as 232-430 generations earlier, or 50,000-60,000 BP, using a 29-year generation length. This corresponds approximately to some estimates of the time of expansion of modern humans out of Africa, but post-dates the putatively early modern humans from Skhul and Qafzeh. Some longer Neanderthal segments in the Ust'-Ishim genome imply that later admixture events also occurred. Interestingly, Figure 5 in the article illustrates homozygous versus heterozygous Neanderthal-derived alleles in the Ust'-Ishim genome compared to several modern ones. The Neanderthal alleles in the ancient genome are all heterozygous whereas some of the modern ones are homozygous. This makes sense, as one would expect by chance alone (panmixia) that heterozygous derived alleles would be more common earlier in the gene flow process. Probabilistically, it would take time for homozygosity to develop. Figure 5 only shows Chromosome 12, but it is suggestive.

Because the specimen is directly dated, it could be used (along with other specimens) to help calibrate the "genetic clock" that calculates age of genetic divergence from mutation rates, and the authors did so. The new estimates of mutation rates in autosomal DNA from this study are lower (slower) than some, possibly implying a longer time interval since the split from archaic human relatives.They also provided new Y Chromosome and mtDNA mutation rate estimates.

Finally, it is noteworthy that the authors find that the Ust'Ishim individual was not more closely related to the Andaman Islanders than he was to modern East Asians or Native Americans. I say this is noteworthy because some documentaries have made, in my opinion, far too much of the Andaman Islanders' genes as evidence for a coastal, southern migration route for early modern humans.

Quite the interesting article. Here's the reference:

Fu, Qiaomei, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L. F. Johnson, Ayinuer Aximu-Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-García, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F. G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola & Svante Pääbo (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514: 445-450. doi:10.1038/nature13810.

Denisovan DNA East of Wallace's Line

As naturally and inevitably as gators eat the dogs of careless owners in Florida, the one time I carelessly leave town for personal reasons--to attend the wedding of Honduran friends in Louisiana--Science ejaculates a gob of interesting articles. There are too many of them to review in one post, so I will tackle them one at a time and hope to finish one day.

First up is this discussion in the "Perspectives" section:

Cooper, A. and C. B. Stringer (2013). Did the Denisovans Cross Wallace's Line? Science 342: 321-323.

Wallace's Line is the imaginary boundary that winds north to south through the islands of modern Indonesia marking the frontier between the mainland Asian fauna to the west and the Austronesian ecosystems to the east. Cooper and Stringer attempt to explain why small "remnant" Denisovan DNA is only found in modern human populations east of the Wallace line when the only known Denisovan lived far away in southwest Siberia. The characteristics of the Denisovan DNA sequence imply a large and diverse population in Asia. The authors, however, reject the obvious idea that most east and southeast Asian peoples once had Denisovan DNA that was later "overwritten" by subsequent gene flows. Their evidence for rejecting this interpretation is pretty strong: the DNA of isolated, remote, and evidently "indigenous" Asian populations thought to predate later migrations, such as that of the Andaman Islanders, lacks Denisovan DNA, precisely where one might most confidently expect it to be found. Moreover, recent analysis of the ancient DNA from a Chinese specimen dating from ca. 40,000 ya shows no trace of Denisovan introgression. They therefore suggest that the Denisovans who crossed the Wallace Line encountered the ancestors of Homo floresiensis, the hobbits, who were there at least 800,000 ya if not 1 mya. Perhaps, they conjecture, the Denisovan DNA signal was better preserved east of the Wallace Line because of the small size of the populations involved, which might have encouraged interbreeding, or because of selective advantages conferred by some of the genes upon rapidly advancing human populations. I didn't find their final answer to be very satisfying, but their control of the data was impressive and their discussion thought-provoking.