Home > DNA, Paleoanthropology > Y-DNA: How valid is the evidence for recent Out of Africa replacements?

Y-DNA: How valid is the evidence for recent Out of Africa replacements?

December 6, 2009

At first sight, the global distribution of Y-DNA haplogroups fairly well corresponds to an Out of Africa scenario of Human evolution. Older haplogroups, baptized  A and B, are virtually limited to Africa and apart from a deficiency or absence of African DE forms in comparison to Eurasia, there is a reasonable match with the pretty extreme Recent Out of Africa scenario that asserts modern man originated in Africa quite recently, driving all other contemporary human species into extinction.

A closer look at the distribution of Y-DNA haplogroups downstream F and even all of E in comparison to DE would suggest massive back migrations to Africa early in human prehistory. At least this would still leave haplogroups A and B as unequivocally African. Especially B is associated to primitive African tribes, while only minor amounts of A1 have been found outside Africa, so far only sporadically in NW Europe.

Microcephalin-1 distribution

The distribution of autosomal microcephalin-1, also referred to as Haplogroup D (not to be confused with Y-DNA haplogroup D), seems to support the concept of moderate backmigrations rather than an exclusive African development, accounting for all derived modern human genetic variation. Microcephalin-1 may have arrived as an archaic introgression into the Homo Sapiens genepool, having a possible genetic distance to non-microcephalin-1 haplotypes of 1.7 million years ago (Evans 2006). The evolutionary advantages above other types are disputed and probably non-existent, what would define the gene essentially as a neutral marker. According to autosomal calculations, the gene originated more or less contemporaneous to a time calculated when the most prolific Y-DNA haplogroups already branched off (37.000 years ago). The moderate microcephalin-1 values in Africa (~30%) could only be reconciled with Hg E backmigrations if by then microcephalin-1 was still absent in the  genepool of Hg E populations. This is plausible since according to Karafet Haplogroup E already branched off from DE at about 52,500 years ago.

Considering the character of microcephalin-1 as a fairly neutral autosomal marker, the introgression should have happened in a time of expansion and accelerated gene flow, thus in a direction generally outward with regard to Africa. However, the reconstructed succession of events would rather put the gravity of the modern human origin and expansion in Asia, well after the impetus of African expansion. A tendency of lower microcephalin-1 values in some SE Asiatic areas, that encompass tribal communities presenting reminiscent Hg D, would in the Recent Single Origin view attest the residue of the earliest African immigrants that expanded before microcephalin-1 was incorporated in their ancestral group. The hypothesized introgression thus seems to have happened elsewhere and much after these first expansions, most probably among Y-DNA CF groups. These in turn must have branched off from a common stock as DE as early as 65,000 years ago, about 30,000 years before the introgression. However, this would turn the premises of the Recent Single Origin hypothesis upside down since this would imply that African backmigrations already started before European Neanderthal was driven to extinction by modern human immigrants. The arrival of new groups west of the Iron Gates of the Donau is not confirmed to have happened before 32,000 years ago.

These dates and the wide range of CF haplogroups that attest a maximum association to microcephalin-1 would be contradictory to the neutrality of this gene. The ancestral group where introgression took place can hardly be reduced to a bottlenecked population where microcephalin-1 gained prevalence, unless this population already comprised a wide range of CF haplogroups on the eve of their expansion.  The neutrality of microcephalin-1 implies a migrational expansion and even in Africa we can’t find so much sub-saharan Y-DNA that derives from CF (C is virtually absent) as to propose a tight link to F-related backmigrations. Something appears to be wrong.

Part of the anthropological and autosomal genetic data seem to favour multiregionalist scenarios, though Y-DNA is often cited as the decisive counterargument. It has been tried to find old Hg A and Hg B (Y-DNA) elsewhere in the world to indicate the continuity with early humans. Still the occurrences found are virtually restricted to Africa. A complicated model of Y-DNA related geneflow could be devised to account for the current Y-DNA haplogroup distribution, though even a pretty strong CF related association to microcephalin-1 as an autosomal markers fails to support the hypothesis CF already branched off in Africa. Like DE, CF didn’t leave unequivocal traces behind in Africa and their common ancestor could have left Africa a long time before in the main Out of Africa event linked to modern humans in the Recent Single Origin hypothesis, that thus should be dated conform Karafet et al. at about 70 kya. The above implies that the expansion of modern humans out of Africa at most could have been a one wave event.

Assuming a correlation of microcephalin-1 to the distribution of modern Y-DNA, I am inclined to pinpoint the introgression geographically in the neighbourhood of East Turkestan. Neutrality should imply a pocket of related CF Y-DNA groups that passed through a bottleneck. I gather that an association between Australian C4-populations and microcephalin-1 still awaits verification. Otherwise, a non-neutral behavior of microcephalin-1 should be assumed, affecting the distribution of Y-DNA haplogroups D, C, E and F in different ways.

In a non-neutral scenario of the dispersion of microcephalin-1, the main agent to the expansion might have been still undifferentiated Hg F. Probably Hg C is slightly too old to have been much more than one of the intermediaries in the spreading event, Hg C3 being the most successful agent among the Hg C-subclades. The main agents, however, remain the Hg F subclade family. Unless Hg F derives from a parent Hg CF that is especially close to Hg C3, the picture that evolves in this hypothesis is of a tiny region probably in the neighbourhood of Turkestan where Hg C and Hg F can be inferred to have occurred all close together and well outside the range of Hg D and “maybe” Hg DE. An important expansion by geneflow of Y-DNA from this confined region could at least explain why most current Y-DNA groups are young and genetically related. However, it is still difficult to link a late CF expansion everywhere and to the same degree to the swamping of pre-CF groups other than DE or D. CF expansion thus appears congruent to more recent events that seem to be related to the habitation of new geographical niches by people that carried microcephalin-1, initially with their gravity in cold, northern climates.

Any close tie between microcephalin-1 and contemporary Y-DNA haplogroups should have dragged Hg F+ to the west (including ancestral Hg K2) and Hg C3 to the north, by migration or geneflow. To Hg D, the closeness to the center might have safeguarded its survival for being well behind the full impact of the wave of advance that – according to Fisher(1937) – follow a strict mathematical pattern of outward increasing frequencies, leaving only the center virtually unaltered. Lower microcephalin-1 frequencies in most of the regions where Y-DNA Hg D has a patchy distribution suggests that there is no evidence of Y-DNA Hg D having actively participated in spreading the microcephalin-1 gene, or to have spread by any “recent” geneflow whatsoever. In contrast, the patchy distribution of Y-DNA K2-M70 in Africa “may be a remnant of a more widespread occupation. Subsequent demic events introducing chromosomes carrying the E3b-M35, E3a-M2, GM201, and J-12f2 haplogroups may have overwhelmed the K2-M70 representatives in some areas.” – J. R. Luis et al.,2004: thus potentially accounting for microcephalin-1 in Africa due to K2 backmigrations.

The picture that emerges of is not fully consistent with the assumptions of the Recent Out of Africa model. The implied dominant position of African populations didn’t last long and was soon superseded by backmigrations that even brought exogenetic DNA from Asia. Moreover, the dating results for Y-DNA can’t be synchronized easily with autosomal DNA and only very globally with the dating results of mtDNA.

Y-DNA evidence against multiregionalism departs from the accepted age of the non-recombining Y-DNA mutations involved, and subsequently tries to verify the results of other disciplines, in this case paleoanthropology. Nobody ever bothered to reverse the verification. We could as well depart from paleoanthropology and verify our current level of understanding of the human genome.

So far, dating was globally based on three assumptions:

– Y-DNA is susceptible to random change since it virtually consists of 100% junk
– Mutation rates can be derived from the number of substitutions found between a chimpanzee sequence and a human sequence
– The Out of Africa scenario can be used as a circular argument to calibrate the age.

Later I will go into deeper detail to indicate the folly of each of these assumptions. The first efforts to come to a verification of mutation rates were indeed designed to indicate that the mutation rate should apply as an average to the whole Y-DNA (Xue et al., 2009). Unfortunately no full genome verification has been applied yet, in the latter study only 30% Y-DNA (~10MB) was tested. Lower rates up to factor 3 are still possible, though this will be hardly enough for Y-DNA mutation rates to be fully consistent to alternative evolutionary scenarios like the Early Out of Africa or Back and Forth theories, that depart from a common ancestor at about 2.7 million years ago, in  Africa. Multiregional populations that were not fully replaced much later by African arrivals of modern humans would possibly attest similar mutation counts at a maximum of 3% junk Y-DNA that can mutate freely against 97% “evolutionary” Y-DNA that remains fixed by selective forces. Could our ignorance of Y-DNA approximate 97%, or does our failure to produce credible Y-DNA dates that approximate tangible Out of Africa results have to do with our ignorance of how Y-DNA evolved?

Just imagine that Y-DNA Hg A and Hg B was already present in Africa, while Homo Erectus developed in Asia and returned in Africa about 1.8 million years ago to meet and breed there with older Human lineages. This would correspond to a scenario where DE and CF developed from M168 emigrants that already coexisted with A and B populations in Africa. Since M168 was indeed attested in Africa, in this scenario the main backmigration thus would have been contemporaneous to Homo Erectus/Ergaster and Y-DNA Hg E. In Africa they would have mixed with Homo Habilis, while the returning Homo Erectus only represented a subset of the Eurasian Homo Erectus: Hg D and Hg CF already branched off when they returned.

Unfortunately the Recent Single Origin scenario doesn’t give such a perfect fit to the genetic record. The flip-side of the apparent match between the current Y-DNA distribution and the paleo-anthropological evidence, however, is the recent dating of the genetic record.


  • Patrick D. Evans et al. – Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans, 2005, link
  • Patrick D. Evans et al. – Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage, 2006, link
  • Tatiana M. Karafet et al. – New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree, 2008, link
  • J. R. Luis et al. – The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors of Human Migrations, 2004, link
  • Y-Chromosome Phylogenetic Tree (FamilyTreeDNA), 2008, link
  • Yali Xue et al. – Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree, 2009, link
Categories: DNA, Paleoanthropology