Ancient human genome sequence of an extinct Palaeo-Eskimo

Abstract

We report here the genome sequence of an ancient human. Obtained from approximately 4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20x, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.

Figure 1. Sample details

a, Location of the Saqqaq Culture site Qeqertasussuk, north-western Greenland (after ref. 15). b, Saqqaq hair sample. c, Saqqaq and modern hair shafts on a comparison microscope. d, Comparative cross-sections of modern Caucasian and Saqqaq hairs. e, Carbon and nitrogen isotope measurements on the Saqqaq hair (brown square, Qt 86 profile C 85/261:12 Oxford; pink triangle, Qt 86 profile C 85/261:12 Bradford), another Saqqaq hair sample from a similar context (green diamond, Qt 87 FB 20/20), six ancient Thule (Inuit) samples (purple circle), published data on modern Uummannaq (Greenland) omnivores (orange diamond), and modern Danish omnivores (blue square) and vegans (orange circle). Saqqaq and Thule are shown as averages of 2–3 replicates (Supplementary Information). Error bars, s.d. f, Calibrated ages (before present) on the Saqqaq hair and associated reindeer (Rangifer tarandus) bones, plotted using the INTCAL04 calibration curve, are shown. The human hair dates are calibrated twice, one using a correction for the marine reservoir effect (Supplementary information).

Figure 2. Data summary

a, Flow diagram summarizing our data pipeline. b, Distribution of all reads among the major taxonomic groups. c, Cumulative distribution of reads across the genome, for all positions (black), only repeat regions (blue) or exclusive repeat regions (green). d, The read depth (green) varies along the chromosomes. e, Much of this variation can be attributed to the repetitive structure of the genome and is especially pronounced in highly repetitive regions, for example, flanking the centromere, but is also observed in regions with genes (shades of blue). f, Simple repeats, here (CAGC)_n (grey), are common in assembly gaps and therefore cause alleviated read depths. In contrast, a recent segmental duplication (black, with differences in red) will prevent reads from mapping uniquely and lower the read depth.

Figure 3. Population genetics and phylogenetics

a, Locations of the studied populations are shown with the most relevant populations indicated by name (numbers in circles correspond to the nr column in Supplementary Table 12). b, PCA plot (PC1 versus PC2) of the studied populations and the Saqqaq genome. c, Ancestry proportions of the studied 492 individuals from 35 extant American and Eurasian populations and the Saqqaq individual as revealed by the ADMIXTURE program with K = 5. Each individual is represented by a stacked column of the five proportions, with fractions indicated on the y axis. The analysis assumes no grouping information. The samples are sorted by region/population only after the analysis. For better readability the Saqqaq individual is shown in three columns. Populations added to the published collection are shown in bold. Red dots in the expanded plot indicate four individuals whose ancestry proportion pattern showed the highest correlation (Kendall τ >0.95; P <0.05) with that of the Saqqaq individual. d, The phylogenetic tree of Y chromosome haplogroup Q. The position of the Saqqaq individual is ascertained by markers shown on the tree. Information for markers shown in parentheses is missing and their status is therefore inferred. Haplogroup names are according to ref. 38; hash symbol indicates error in reference (Supplementary information).