Mutation rate of the nuclear genome is getting a fossil calibration

The SMBE 2014 conference is showcasing a presentation where a 45,000 year old genome is being fully sequenced by Fu et al. and where the sequence will be used to calibrate, to my knowledge for the first time, the mutation rate of the nuclear genome.

Previously, Fu et al. (2013) had calibrated the Mitochondrial genome's mutation rate by using some 10 non-African fossils as a reference, with results by and large in compliance with previously established mutation rate estimates.

The rate of accumulation of SNPs on the YDNA, will thus be the last remaining thing to get a fossil calibration. Once we get that, temporal based analysis using these calibrated mutation rates should gain a much more solid basis.

O-15

The complete genome sequence of a 45,000-year-oldmodern human from Eurasia

Qiaomei Fu ^{1 ,2}, Bence Viola^{1 ,3}, Heng Li^{5 ,6}, Priya Moorjani⁶, Flora Jay⁴, Aximu Ayinuer-Petri¹, Susan Keates⁸, Yaroslav V. Kuzmin⁷, Montgomery Slatkin⁴, David Reich^{5 ,6}, Janet Kelso¹, Svante Pääbo¹  

¹Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, ²Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Beijing, China, ³Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, ⁴Department of Integrative Biology, University of California, Berkeley, USA, ⁵Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA, ⁶Department of Genetics,Harvard Medical School, Boston, USA, ⁷Institute of Geology & Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, ⁸University Village, Columbia, USA

We have sequenced to high coverage the genome of a femur recently discovered near Ust-Ishim in Siberia. The bone was directly carbon-dated to 45,000 years before present. Analyses of the relationship of the Ust-Ishim individual to present-day humans show that he is closely related to the ancestral population shared between present-day Europeans and present-day Asians. The over-all amount of genomic admixture from Neandertals is similar to that in present-day non-Africans and there is no evidence for admixture from Denisovans. However, the size of the genomic segments of Neandertal ancestry in the Ust-Ishim individual is substantially larger than in present-day individuals. From the size distribution of these segments we estimated that this individual lived about 200-400 generations after the admixture with Neandertals occurred. The age of this genome allows us to directly assess the mutation rate in the different compartments of the human genome. These results will be presented and discussed.

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