Analyses of virus migration markers, Denisovan and Neanderthal genes in modern Asians suggest more complex migration routes than southern (coastal) dispersal route to Oceania model

A number of research papers in recent years have been proposing that the finding of variations of Altai Denisovan, Neanderthal genetic introgressions into Asian genes show a migration scenario that does not corroborate the Southern dispersal route hypothesis. Incidentally, these new scenarios are closer to the findings and proposed migration model of virus markers — compare the map immediately below…

Two migration path or pincer models suggested by virus markers by virus

…with the 2012 Alvie’s et al., model below:

Alves I, Šrámková Hanulová A, Foll M, Excoffier L (2012) Genomic Data Reveal a Complex Making of Humans. PLoS Genet 8(7): e1002837.

See excerpts from the abstract and relevant portions of the paper below

We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

Interbreeding between Modern and Archaic Humans

In line with previous studies [10][12]which suggested that some aspects of human genomic diversity were incompatible with a complete replacement of archaic hominins, evidence for admixture between humans and Neanderthals emerged from the first analysis of a complete Neanderthal genome [13]. Indeed, the presence of a significant excess of Neanderthal-derived alleles in Eurasian populations as compared to Africans has been interpreted as resulting from an admixture episode between the ancestors of Eurasians and Neanderthals somewhere in the Middle East [13](Figure 1A). Even though the existence of a very ancient population subdivision in Africa from which both Neanderthals and Eurasians would have emerged could lead to similar patterns [14], the maintenance of such a subdivision over tens of thousands of generations seems unlikely. The sequencing of another archaic hominin from the Denisova cave in the Altaï mountains in Siberia has further revealed that Papua New Guineans showed signs of introgression from this archaic human [15]. Further studies of 33 populations from Southeast Asia and Oceania [16]showed that Denisovan admixture was actually present in other Oceanians, Melanesians, Polynesians, and east Indonesians but was virtually absent in mainland east Asians (but see [17]for evidence of possible Denisovan introgression on the Asian continent). Overall, these genomic analyses of admixture suggest that 1%–3% of the genome of all Eurasians and native Amerindians is of Neanderthal origin [15], and that Papua New Guineans and Australians have another 3.5% of their genome of Denisovan origin [16]. The out-of-Africa model of human evolution, which posited a complete replacement of archaic by modern humans in Eurasia, thus needs to be modified to include a limited assimilation of archaic genes, but the fact that most of the genetic variation observed in extant non-African populations comes from Africa remains true.

…The fact that Denisovan admixture had been first evidenced in Papua New Guineans suggested that admixture had occurred as a single pulse in Southeast Asia, after the separation of the ancestors of Oceanians and other Asians [15], [16](Figure 1A). The analysis of an Australian genome has confirmed the presence of Denisovan admixture in Australians [24]and suggested that admixture occurred during a first early wave of colonization towards Oceania, either in Southeast Asia or earlier in Eurasia (Figure 1B). A reanalysis of a large human SNP database and its comparison with Denisovan-derived alleles has suggested the presence of Denisovan admixture in East Asians, albeit at lower levels than in Oceanians [17], which could have occurred at a different place than for Oceanians, somewhere in East Asia (Figure 1C). Contrastingly, Currat and Excoffier [25]introduced a spatially explicit model of interbreeding between Neanderthals and Eurasians that could occur over the whole Neanderthal range (Figure 1D). They obtained similarly low levels (1%–3%) of Neanderthal introgression in both Europe and China if interspecific exchanges were locally extremely limited (only 200–400 interbreeding events over the >6,000 years of co-existence between the two species). An extension of this scenario to Denisovan admixture would imply that modern humans could have hybridized along all migration routes overlapping with the range(s) of archaic humans (Figure 1D). The fact that the largest levels of Denisovan introgression are found in Oceanians raises the question of a potential discontinuity in the Denisovan range (Figure 1A, 1B) or of a genetic differentiation of archaic hominins living in different ecosystems (Figure 1D). Alternatively, modern humans could have admixed with other hominins [26], and/or inferred hominin introgression could result from the sharing of some derived sites between Neanderthals, Denisovans, and unidentified archaic hominins. A scenario involving an unsampled Eurasian archaic hominin has received support from a recent study [27]showing the presence of a highly divergent (>3 Mya) haplotype of the innate immune gene OAS1. This deep lineage is found at high frequencies in Oceania (and at lower frequencies up to Pakistan). This DNA segment is more closely related (0.6 Mya divergence) to the Denisova sequence than to the Neanderthal sequence, which is itself closer to the human reference sequence. It has been speculated [27]that this fragment had introgressed from a more archaic hominin than Denisovans, who could have been themselves introgressed earlier….

Our understanding of the exact sequence and location of admixture events would highly benefit from a more precise knowledge of the nature and the distribution of Neanderthal segments in our genome. Unfortunately, current estimations of introgression levels are based on a statistic measuring a genome-wide difference in the proportion of archaic-derived alleles between two human populations [13], [14], so that the genomic distribution of introgressed segments is still unknown. However, in addition to the OAS1segment mentioned above [27], several authors have recently argued they had identified candidate regions harboring archaic haplotypes [13], [28], [29]. These regions usually show highly divergent haplotypes with very little evidence for recombination [30]. A dozen genomic regions where Eurasians have haplotypes much more divergent than Africans and a high proportion of derived Neanderthal alleles have been proposed as candidates for Neanderthal introgression [13]. More recently, an X-linked haplotype (B006) in an intron of the dystrophin (dys44) gene, almost absent from Africa but with 9% average frequency outside Africa, has been proposed to be of Neanderthal origin [29]. It is close to the ancestral X haplotype, shares 2/3 of derived alleles with Neanderthals, and has little associated diversity, suggesting a recent origin in humans. Another study has also suggested that several immune-related HLA class I alleles in humans could be of Denisovan origin and that they helped Eurasian populations build their immunity [28]. Whereas the hypothesis of an adaptive introgression is highly seductive, its support is relatively thin. “Denisovan” HLA class I alleles are currently not confined to Oceania but are found widespread in Asia. Moreover, the strongest argued case of Denisovan allelic ancestry (HLA-B*73) is actually not found at all in the Denisovan genome and is presently distributed in western Asia, well in the former Neanderthal range. One should therefore be extremely cautious not to assume that each very divergent haplotype found in humans is necessarily of archaic origin, as cases of incomplete lineage sorting are not rare between higher primates [31], especially in the HLA system where trans-specific polymorphism is facilitated by balancing selection [32]. However, if some introgressed genes were really advantageous, they should have spread and fixed in the human population, but as discussed below there is no widespread signature of strong selective sweeps in Eurasia.

…it is likely that differential admixture should affect population genetic affinities under more complex models of population differentiation. The proper interpretation of human genetic affinities should thus probably be re-evaluated in the light of these results. In particular, the divergence between Africans and Oceanians (showing up to 5% archaic admixture [16]) could be more recent than previously reported (62–75 Kya [24]). It remains unclear whether the method used by Rasmussen et al. [24]to date this divergence is also sensitive to differential introgression, but, if that was the case, the colonization wave to Oceania thought to well predate that towards East Asia [24]could have occurred at roughly the same time once differential admixture had been taken into account.

The paper’s author Clarkson suggests that those early dates of a Middle-Stone-Age-like people are consonant with the previous hypotheses of an early Eurasian split with Papuans (i.e. Abor. Australians’ ancestor) as well as of the incorporation of Neanderthal genes into their lineages. See Chris Clarkson, Richard G. Roberts, Zenobia Jacobs, Ben Manwick, Richard Fullagar, Lee J. Arnold & Qian Hua(2018): Reply to Clarkson et al., (2017), ‘Human occupation of Northern Australia by 65,000 years ago’, Australian Archaeology, DOI:10.1080/03122417.2018.1402884


Many voices and new models disproving the Southern dispersal route model (following the coast of India) have been steadily coming onstream for a while, but it has been difficult to dislodge the consensus model for many decades ever since the latter emerged, and the mountain of media and literature that followed the original model.

Below are some of the literature representing the dissonance with the Southern dispersal hypothesis, the most recent of which being:

Nicolas Zwyns Et al., The Northern Route for Human dispersal in Central and Northeast Asia: New evidence from the site of Tolbor-16, Mongolia
Scientific Reportsvolume 9, Article number: 11759 (2019)


The fossil record suggests that at least two major human dispersals occurred across the Eurasian steppe during the Late Pleistocene. Neanderthals and Modern Humans moved eastward into Central Asia, a region intermittently occupied by the enigmatic Denisovans. Genetic data indicates that the Denisovans interbred with Neanderthals near the Altai Mountains (South Siberia) but where and when they met H. sapiens is yet to be determined. Here we present archaeological evidence that document the timing and environmental context of a third long-distance population movement in Central Asia, during a temperate climatic event around 45,000 years ago. The early occurrence of the Initial Upper Palaeolithic, a techno-complex whose sudden appearance coincides with the first occurrence of H. sapiens in the Eurasian steppes, establishes an essential archaeological link between the Siberian Altai and Northwestern China. Such connection between regions provides empirical ground to discuss contacts between local and exogenous populations in Central and Northeast Asia during the Late Pleistocene.


Although models for H. sapiens’ early dispersals out of Africa emphasize a southern route to Asia1,2,3,4,5, Neanderthal and Modern Human (MH) fossils in Siberia6,7,8,9 suggest that at least two other dispersals took place across the Eurasian steppe north of the Asian high mountains. Given the size of the area considered, human fossils are few but recent studies have suggested that a major change in the regional archaeological record could be indicative of a large-scale human dispersal event. Known as the Initial Upper Palaeolithic (IUP), it refers to the sudden appearance in contiguous regions of a specific blade technology sometimes associated with bone tools and ornaments10,11,12,13,14,15,16,17. How old these assemblages are, and how long the phenomenon lasts are still controversial questions, and little is known about the timing and environmental context of these population movements. Here we present new data following excavations of an archaeological site located in a low altitude pass, the Ikh-Tolborin-Gol, which connects Siberia with northern Mongolia. Our results document the early occurrence of the Upper Paleolithic in Mongolia and provide a chronological reference for population movement across Northeast Asia during the Late Pleistocene.

Excerpts from the Abstract and body of the paper by Sheila Misora et al., Continuity of the microblade technology in the Indian Subcontinent since 45ka: Implications for the dispersal of modern humans

… We extend the continuity of microblade technology in the Indian Subcontinent to 45 ka, on the basis of optical dating of microblade assemblages from the site of Mehtakheri, (22° 13′ 44″ N Lat 76° 01′ 36″ E Long) in Madhya Pradesh, India. Microblade technology in the Indian Subcontinent is continuously present from its first appearance until the Iron Age (~3 ka), making its association with modern humans undisputed. It has been suggested that microblade technology in the Indian Subcontinent was developed locally by modern humans after 35 ka. The dates reported here from Mehtakheri show this inference to be untenable and suggest alternatively that this technology arrived in the Indian Subcontinent with the earliest modern humans. It also shows that modern humans in Indian Subcontinent and SE Asia were associated with differing technologies and this calls into question the “southern dispersal” route of modern humans from Africa through India to SE Asia and then to Australia. ….

The association of microblade technology with modern humans in the Indian Subcontinent is undisputed due to its continuity up to around 3 ka. …Blade technology which has a sporadic but early appearance in the Middle East and Africa [9,10,11,12] is absent from the Indian Acheulian and Middle Palaeolithic. Projectile technology which was an important development in Africa and Europe [13,14] during the post Acheulian period is also virtually absent from the Indian Middle Palaeolithic [15,16]. This suggests that microblade technology is not indigenous to the Indian Subcontinent. Mehtakheri is currently the oldest dated microblade site in the Indian Subcontinent and extends the origin of this technology in the Indian Subcontinent to 44 ± 2 ka based on the weighted average of four dates and ~ 48 ka if the oldest of the dates is accepted as the most accurate as argued below. While microblade technology is associated with modern humans in the Indian Subcontinent, this is not so elsewhere, at least until a much later time period. Modern humans in the Middle East are associated with Middle Palaeolithic technology [17], in Sub-Saharan Africa with the Middle Stone Age [18] and in Southeast Asia [19] and Southern China with core and flake industries [20]. Each of these categories themselves encompasses significant variation. …

Based on our older ages for microblade technology in the Indian Subcontinent, and the arguments presented above, we present the following model for modern human dispersal (as illustrated in Figure 2):

  • 1. During MIS 6 widely dispersed hominin populations with a common ancestor in Homoerectus had differentiated into distinct populations with modern humans and possibly other archaics in Africa, Neanderthals in Europe, Denisovans in temperate Eastern Eurasia and archaic Indians in the Indian Subcontinent and Sundaland (Figure 2.1).

  • 2. During the Interglacial climate of MIS 5, modern humans expanded into Eurasia at the expense of both Neanderthals and Denisovans and reached SE Asia. Due to competition with Indian archaics, modern humans were unable to disperse into the Indian Subcontinent and modern humans reached SE Asia at this time via a northerly route through the Middle East, Central and Eastern Eurasia and Southern China. During this time admixture with both Neanderthals and Denisovans is likely to have occurred in the modern humans reaching SE Asia (Figure 2.2) … Sharp cultural boundaries between the Indian Subcontinent and adjacent areas are not in conformity with a rapid dispersal through India to SE Asia from Africa. Archaeological sites in Arabia and Africa dating to MIS 5 show some distinctive technological features, such as Nubian cores and bifacial projectiles which are absent from any assemblage in the Indian Subcontinent, making it unlikely that modern humans dispersed into the Indian Subcontinent at this time. On the other hand microblade technology or blade technology is attested to at archaeological sites dating to around 60 ka in Africa which have a closer resemblance to the Indian microblade technology. Core and flake assemblages are associated with modern humans in SE Asia and may date back to MIS 5 times. We suggest that the later entry of modern humans into the Indian Subcontinent compared to adjacent regions is because Indian Archaics could easily compete with modern humans during climate conditions favorable to both. …

Finally, if you take into account all of the above recent literature, the above dispersal scenarios are easier to reconcile with recent admixture models and analyses of genetic affinities between both ancient DNA and MtDNA of modern Asians…

… see the analyses of both McColl et al.’s 2018 Ancient genomics reveals four prehistoric migration waves into Southeast Asia as well as Kanzawa-Kiriyama’s 2019 paper, Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan