Phylogeny of Denisovans, Neanderthals, and Modern Humans: An Alternative Hypothesis Based on the Uniparental Genetic Topology

The genome-based tree topology of the modern human–Neanderthal–Denisovan triad places Neanderthals and Denisovans as sister clades and modern humans as the outgroup. In contrast, the mtDNA and NRY phylogenies support modern humans and Neanderthals as the closest groups; for resolving this discrepancy in favor of the genomic phylogeny, different introgression phenomena have been proposed. One is admixture between a very divergent archaic population and the Denisovans, resulting in complete substitution of Denisovan uniparental markers by archaic ones without affecting the Denisovan nuclear genetic background. A second proposes admixture between Neanderthals after their separation from Denisovans and early modern humans, resulting in a population that retained the uniparental markers of early modern humans but incorporated the nuclear genome of early Neanderthals. However, when strong sex bias is invoked to substitute one of the uniparental markers, the fixation of the other sex marker is concomitantly impeded. Furthermore, the massive introduction of the nuclear genome of one group into other group cannot occur without the simultaneous massive introduction of at least one of its uniparental markers. Here, we demonstrate that all these difficulties disappear if we accept that the phylogeny deduced from the mtDNA and NRY lineages is a possible alternative and attribute the nuclear topology to population structure, incomplete lineage sorting, and secondary introgression affecting each group differently. The genetic affinities recently found between derived Erectus populations and Denisovans in eastern Asia territories that, at that time, were not occupied by Neanderthals or early modern humans and the growing possibility that modern humans and Neanderthals shared a common ancestor in northern Africa, an area without any clue of Denisovan presence, also support the genetic tree topology deduced from uniparental markers.