Using hominin introgression to trace modern human dispersals

Abstract

The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace's Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.

Keywords: anthropology; archaic introgression; genetics; human evolution.

Fig. 1.

Proposed route of AMH movement out of Africa, around 60 to 50 ka (1, 4), following areas of savannah-like habitat reconstructed from BIOME4 CO₂ climate models (https://www.paleo.bristol.ac.uk/ummodel/data/bbc_all_triff_rev_dyn/standard_new_plots/bbc_all_triff_rev_dyn_biome4_co2_ann_msy_jav.html). Around 55 to 50 ka, a small founding AMH population met and interbred with Neandertals somewhere in western Eurasia (blue circled N), resulting in a Neandertal genomic signal of around 2% that was subsequently distributed globally outside of Africa (1, 2, 4). Sometime after the first event, the AMH population split, with one of the branches leading to the ancestors of Europeans and the other to the common ancestor of South and East Asians, Australo-Papuans, and related populations. Genetic data (33) suggest that as the latter moved across South Asia, it experienced an initial introgression event (purple circled 1) with an unknown hominin (EH1) that was genetically roughly equidistant to Denisovans and Neandertals. The resulting genomic signal (estimated to have originally been 2.6 to 3.4%) is detected in groups as geographically distant as South Asians, Andaman Islanders, and Aboriginal Australians (33), so we have tentatively positioned the event in northern India. In East Asia, a subsequent introgression with a Denisovan group closely related to the Altai specimen also appears to have taken place (red circled 3).

Fig. 2.

Yellow and red arrows indicate the inferred route of AMH movement through ISEA around 50 ka (44) (shown with lowered sea levels), following reconstructed areas of savannah-like habitat as above. Modern-day hunter-gatherer populations with genetic data are shown in red, and farming populations are shown in black. The estimated genomic content of EH1 (purple), Denisovan (red), EH2 (brown), and nonarchaic (gray) in modern-day populations (28, 33, 40, 42) is shown in pie charts, as a relative proportion to that seen in Australo-Papuans (full circles). Gray All populations containing large amounts of Denisovan genomic content are found east of Wallace’s Line. Independent introgression events with Denisovan groups are inferred for both the common ancestor of Australo-Papuan, Philippines, and ISEA populations (red circled 2) and, separately, for the Philippines (red circled 4). The signal for a separate introgression with an unknown hominin on Flores, recorded in genomic data from modern-day populations, remains less secure (brown-circled 5). The precise location of introgression events 2, 4, and 5 currently remains unknown. Pie charts with black borders have estimated hominin proportions.

Fig. 3.

Recent hominin introgression events in SEA. The phylogenetic tree shows approximate relationships and date estimates for the various events with extinct hominins and modern-day AMH populations. Five inferred hominin introgression events are shown, starting with the Neandertal around 55 to 50 ka (blue-circled N), followed by EH1 (purple-circled 1). The ancestor of Australo-Papuans, Philippines, and other ISEA groups is then inferred to have experienced admixture with Denisovans (red-circled 2), followed by a subsequent event (red-circled 4) detected just in Philippines hunter-gatherer populations. A separate Denisovan introgression is also detected in East Asian populations (red-circled 3). A further contribution from an unknown hominin (EH2) may be recorded in the genomes of modern-day short-statured populations on Flores but remains unclear (brown-circled 5) (42). The phylogenetic relationships among the extinct hominins remains uncertain, but appear to be of roughly similar genetic divergence, occurring around 400 ka (11). We suggest the timing of the above events is constrained between the initial Neandertal introgression at 55 to 50 ka and the colonization of Australia at 50 ka (1, 4).