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

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.ancient DNA | human evolution | nuclear capture strategy | paleogenetics

Tracing the origin of our species through palaeogenomics

“…These admixture events would have taken place between 80,000 and 50,000 years [36,37]. The separation between Europeans and East Asians would have taken place before the extinction of the Neanderthals, i.e., 30,000 years ago, which is in agreement with the discovery in the cave of Tianyuan in China of a modern human fossil of 40,000 [38]. Different fractions of the Neanderthal genome would have been dispersed in the individuals of European or Asian origin and up to 20% of the Neanderthal genome would still be present collectively in the genomes of modern humans [35].…”

“…In contrast, the genetic contribution of the Denisovans to the present-day northern Asians as well as to the autochthonous Amerindian populations is about 0.2%, and thus about 25 times smaller than that to the Melanesian populations. The same seems to be true for the ancient populations of Northern Asia as deduced from the analysis of the mitochondrial genome and portions of the nuclear genome of the Tianyuan individual from the region of Beijing that was dated to 40,000 years [38]. The distribution in Asia of the populations that carry a portion of the Denisovan genome suggests that the admixture event took place in Southeast Asia and thus that the geographical region inhabited by Denisovans was much larger than the small area where their only remains have been found [40].…”

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

“…Hybridization enrichment was performed as described elsewhere [19] with baits targeting the human mitochondrial genome (3 bp tiling based on NC_001807 as in [17]) using a semiautomated protocol in a 96-well plate set-up on an Evolution P3 (Perkin Elmer, Waltham, MA) for two consecutive rounds. This liquid handler has a 96-well tip head and is therefore suited for steps involving magnetic beads (i.e.…”

“…The oligonucleotide blockers used for each of the respective adapter lengths are specified in the electronic supplementary material, table S1. All other parameters of the hybridization, capture and washing steps and amplifications can be found in the original paper [19]. Each sample was subsequently indexed prior to sequencing with a unique index (pair), using 7-mer index sequences as in Meyer & Kircher [29].…”

“…mtDNA or a set of single nucleotide polymorphisms). To increase the fraction of sequenced molecules that align to subsets of the genome of interest, a standard tool in ancient DNA analysis has become target enrichment via hybridization capture [6,7,[18][19][20][21][22], which in its in-solution form is amenable to being carried out on 96-well plates and processed robotically [23,24]. Parallel handling of many samples, however, increases the opportunity for cross-contamination owing to spillover of liquid from neighbouring wells.…”