Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture

To isolate regions with Neanderthal ancestry, we considered segments identified in five European populations that have at least 30 putatively introgressed variants that could be compared to the Altai Neanderthal genome and had a match rate of at least 30% to the Altai Neanderthal allele.

“To isolate regions with Neanderthal ancestry, as recommended by Browning et al.36, we (1) considered segments identified in these five populations that have at least 30 putatively introgressed variants that could be compared to the Altai Neanderthal genome and (2) had a match rate of at least 30% to the Altai Neanderthal allele36.”

Denisovan components in Papuans exhibit deep divergence from the reference Altai Denisovan genome, providing evidence for multiple Denisovan introgression events across time and space.

“these components exhibit a deep divergence from the reference Altai Denisovan genome, providing strong evidence for the occurrence of multiple Denisovan introgression events across time and space [6, 7].”

The HAR202 region shows signatures of introgression in populations from East Asia.

“We analyzed chromosome 14 in every population from this database and found that the HAR202 region shows signatures of introgression in populations from East Asian (Fig. 2b; supplementary table S1, Supplementary Material online and supplementary fig. S2, Supplementary Material online).”

In Europeans, archaic ancestry is consistent with contributions by a single population of Neanderthals through one or more pulses.

“In Europeans, archaic ancestry is consistent with contributions by a single population of Neanderthals 3 through one or more pulses [4][5][6][7] .”

Denisovan-like ancestry is the result of multiple introgression events from different source populations.

“We find support for the hypothesis that Denisovan-like ancestry is the result of multiple introgression events from different source populations (9, 10).”

Prior studies have suggested that Denisovan-like haplotype blocks in humans have two or three distinct sources with different levels of divergence to the Denisovan genome, with the best-matching haplotype blocks in East Asia.

“Prior studies have suggested that Denisovan-like haplotype blocks in humans have two or three distinct sources with different levels of divergence to the Denisovan genome, with the best-matching haplotype blocks in East Asia (9, 10).”

Analyses using NIMs identified by a different approach gave concordant results.

“We repeated these analyses using NIMs that had been identified using a different approach (Browning et al., 2018) and obtained concordant results (‘Appendix 5’).”

No hit was found within the most probable candidate genomic regions for Neanderthal introgression.

“No hit was found within the most probable candidate genomic regions for Neanderthal introgression [31–33].”

Using Mbuti as an outgroup, the S prime statistic detected SLC30A9 as a candidate for introgression in both Europeans and East Asian samples from HGDP-CEPH.

“we next computed the S prime statistic [31] in the Europeans and East Asian samples available in the Human Genome Diversity Panel (HGDP-CEPH) [37], using the Mbuti as an outgroup, and detected the SLC30A9 as a candidate for introgression in both groupings”

Most studies of archaic introgression have relied on the GRCh37 human reference genome.

“However, most studies of archaic introgression have relied on the GRCh37 human reference genome [8, 10, 11, 13, 14, 20].”