Mitochondrial DNA tree calibrated with ancient DNA

Clocking the Human Exodus Out of Africa

The team analyzed 10 well-dated fossils, including a medieval man who lived in France 700 years ago; the 4550-year-old Iceman; two 14,000-year-old skeletons from the tombs of Oberkassel in Germany; three related, modern humans from 31,000 years ago in Dolni Vestonice in the Czech Republic; and an early modern human from 40,000 years ago in Tianyuan, China. [. . .]

The team's method for checking the mutation rate is clever, says geneticist Aylwyn Scally of the Wellcome Trust Sanger Institute in Hinxton, U.K., co-author of one of the studies that calculated the slower mutation rate in living humans. "It's excellent that they have been able to get a better baseline for calibrating the mtDNA mutation rate by looking at ancient DNA."

However, Scally notes, mtDNA is a single genetic lineage, which is not typical of the genome, partly because the mutation rate of mtDNA could be higher because it has a higher proportion of genes under selection than the entire nuclear genome. Krause and one of his collaborators, paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, agree that future work will be needed to resolve the differences in mutation rates in the mtDNA and nuclear genomes. "It is possible that there are things we do not understand about mitochondrial inheritance and mutation patterns," Pääbo says. [. . .]

And that matters, Krause says, because a sense of timing is critical in human evolution. Knowing when modern humans spread out of Africa and into Europe and Asia, for example, allowed Krause and his collaborators to show that the same modern humans were in Europe before and after the glaciers covered that continent—and had the ability to adapt to changing climates. They found that modern humans before and after the last major ice age in Europe share the same mtDNA lineage, making them direct descendants of the same linage. "Out of Africa is one of the major events within human evolution," Krause says. "We need to know when it happened."

The paper:

A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes

Qiaomei Fu, Alissa Mittnik, Philip L.F. Johnson, Kirsten Bos, Martina Lari, Ruth Bollongino, Chengkai Sun, Liane Giemsch, Ralf Schmitz, Joachim Burger, Anna Maria Ronchitelli, Fabio Martini, Renata G. Cremonesi, Jir(í Svoboda, Peter Bauer, David Caramelli, Sergi Castellano, David Reich, Svante Pääbo, Johannes Krause

Background

Recent analyses of de novo DNA mutations in modern humans have suggested a nuclear substitution rate that is approximately half that of previous estimates based on fossil calibration. This result has led to suggestions that major events in human evolution occurred far earlier than previously thought. Results

Here, we use mitochondrial genome sequences from ten securely dated ancient modern humans spanning 40,000 years as calibration points for the mitochondrial clock, thus yielding a direct estimate of the mitochondrial substitution rate. Our clock yields mitochondrial divergence times that are in agreement with earlier estimates based on calibration points derived from either fossils or archaeological material. In particular, our results imply a separation of non-Africans from the most closely related sub-Saharan African mitochondrial DNAs (haplogroup L3) that occurred less than 62–95 kya.

Conclusions

Though single loci like mitochondrial DNA (mtDNA) can only provide biased estimates of population divergence times, they can provide valid upper bounds. Our results exclude most of the older dates for African and non-African population divergences recently suggested by de novo mutation rate estimates in the nuclear genome. [. . .]

We were able to reconstruct three complete and six nearly complete mitochondrial genomes from ancient human remains that were found in Europe and Eastern Asia and span 40,000 years of human history. All Paleolithic and Mesolithic European samples belong to mtDNA hg U, as was previously suggested for pre-Neolithic Europeans [15]. Two of the three individuals from the Dolni Vestonice triple burial associated with the pre-ice age Gravettian culture, namely, 14 and 15, show identical mtDNAs, suggesting a maternal relationship. Furthermore, both individuals display a mitochondrial sequence that falls basal in a phylogenetic tree compared to the post-ice age hunter-gatherer samples from Italy and central Europe, as well as the contemporary mtDNA hg U5 (Figure 1). It has been argued that hg U5 is the most ancient subhaplogroup of the U lineage, originating among the first early modern humans in Europe [18]. Our results support this hypothesis because we find that the two Dolni Vestonice individuals radiocarbon dated to 31.5 kya carry a type of mtDNA that is as yet uncharacterized, sits close to the root of hg U, and carries two mutations that are specific to hg U5. With our recalibrated molecular clock, we date the age of the U5 branch to approximately 30 kya, thus predating the LGM. Because the majority of late Paleolithic and Mesolithic mtDNAs analyzed to date fall on one of the branches of U5 (see also [15]), our data provide some support for maternal genetic continuity between the pre- and post-ice age European hunter-gatherers from the time of first settlement to the onset of the Neolithic. U4, another hg commonly found in Mesolithic hunter-gatherers [15], has so far not been sequenced in a Paleolithic individual, and we find hgs U8 and U2 in pre-LGM individuals but not in later hunter-gatherers. At present, the genetic data on Upper Paleolithic, and especially pre-ice age, populations are too sparse to comment on whether or not this is representative of a change in the genetic structure of the population, perhaps caused by a bottleneck during the LGM and a subsequent repopulation from glacial refugia.