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.

Fig. 1.

Tree of the Tianyuan and 36 present-day mtDNAs belonging to haplogroup B. The bar represents 0.3 substitutions per nucleotide site. Numbers indicate individuals in the tree and the map.

Fig. 2.

Maximum-likelihood tree relating the chromosome 21 sequences of the Tianyuan individual, 11 present-day humans, and the Denisovan genome. The most strongly supported gene-flow event is shown in yellow. Bootstrap support for all internal edges is 100% except for the edge putting Tianyuan outside the four Asians, which is 31%. The scale bar shows 10 times the average standard error of the entries in the covariance matrix.

Fig. 3.

Proportion of alleles shared with the Neandertal and Denisovan genomes for the Tianyuan and present-day individuals. The x axis shows the percent of alleles that match the Neandertal and Denisovan genomes at sites where both of these differ from seven Africans, and the y axis indicates the percent of alleles that match the Denisovan genome where this differs from the Neandertal as well as from the seven Africans.