Current genetic evidence suggests that when AMHs first moved through the area, they interbred with EH1 in South Asia, Denisovans in ISEA and the Philippines, and potentially with EH2 on Flores. Strikingly, of these hominid groups, only the Denisovans are currently known, and even here the evidence comes only from genomics. The region was clearly inhabited by several hominid groups that likely lived in relative isolation from each other for hundreds of thousands of years and apparently brought unique patterns of ancestry to the current populations. Teixeira and Cooper's (2019) study examines the use of genetic signals from the introgression of archaic hominins (including Neanderthals and Denisovans) as a tool to reconstruct the migration of anatomically modern humans (AMH) from Africa. The ancestral AMH of all Asian and Australo-Pacific populations interbred with EH1, resulting in a shared genomic signal of 2.6-3.4% of the ancestral EH1 (purple in Fig. 1). This signal, although diluted, can still be detected in modern Indian, Andaman and East Asian populations (33). This initial event appears to have been followed by a second phase of intermixing between the ancestral Australo-Papuans (after separation from other Asian populations) and a group of Denisovans more closely related to the sequenced Altaic individual, generating an additional genomic contribution of ~1.6% (33) (highlighted in red by number 2 in Fig. 2). Previous studies have shown that modern ISEA populations have genomic content of Denisovans roughly proportional to their Australo-Papuan ancestors (28), suggesting that they originated from the same secondary. Major findings: Neanderthal introgression (55-50 thousand years ago): AMH's first contact with Neanderthals occurred in western Eurasia. All modern humans outside Africa have ~2% Neanderthal DNA, indicating that introgression occurred in a small, original founding population. Complicated Denisovan heritage: the highest levels of their DNA (~3-6%) were found in Australian Aborigines and Papuans. Denisovans, although known mainly from the Denisov cave in Siberia, probably inhabited much of eastern Asia. They are not found in Europe. At least two waves of Denisovan introgression:One involves the common ancestor of the South Asian and Oceania populations, originating from a "distant" Denisovan source. The second wave (Altaic) occurred later in the ancestors of the Australopapulcans. New unknown hominin (EH1): Research suggests the existence of a third archaic hominin, genetically equally distant from Neanderthals and Denisovans, with whom AMH probably crossed in northern India. Its genetic signals have been detected in populations of India, the Andaman Islands and East Asia. Independent introgression in the Philippines: Hunter-gatherers from the Philippines show distinct traces of Denisovan DNA, suggesting a third independent wave of introgression. Potential introgression from another hominin (EH2) on Flores: Local population shows unique genetic components that may be from an unknown, highly divergent archaic hominin. No evidence of archaic hominins in Sahulu (Australia and New Guinea): Despite the high level of archaic DNA in the current population, there is no archaeological evidence of archaic hominins on the continent - indicating earlier introgression before the arrival of AMH. Summary: The genomes of modern humans contain traces of multiple and geographically diverse interbreeding with archaic hominins. Analysis of these signals makes it possible to reconstruct the routes and timing of AMH migrations, particularly in Asia and Oceania, revealing the presence of at least two unknown hominin groups (EH1 and EH2), neither of which has yet been identified in the fossil record.
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