Always on the lookout for genetic markers that contradict the mainstream assumption that America was populated by some very small bands of migrants that had remained in splendid isolation in Beringia for several millennia until the end of the last Ice Age, I came across a paper (Pereira, dos Santos and Junho Pena, 2006)  which looks into the human X chromosome (interesting because all of us carry at least one copy - women carry two). The global pattern of a marker they identified is quite odd; please read on below:
A new marker DXS225
The paper describes how the authors found a region with a low recombination rate and within that region they identified a novel polymorphic Alu insertion which was later named DXS225.
The insertion allele is the mutation, and the archaic ancestral form, found in our distant chimpanzee relatives is the "pre-insertion allele".
Interestignly, there are some specifc groups that lack the modern mutation, (well, modern is not the best word for it, because it appeared 100 kya) shown in the table below :
DXS225 has two allelic states, one is the "archaic pre-insertion (marked as 0 or -) and the other is the "mutated or modern" Alu insertion allele (marked as 1 or +). 
Table showing only those populations in each region that only carry the archaic pre-insertion allele and not the "modern" insertion.
It is interesting because the "ancient" African groups San, Bantu and Yoruba don't carry the modern mutation, but it is also found among the Dai in Yunnan, China, the Northern Italians, the Papuans and four out of five Amerindian groups! The other African, European, Middle Eastern, Central Asian and East Asian as well as Oceanian populations carried both alleles at different ratios.
What is necessary is to explain why the "ancient" Africans, Dai, Papuans, Northern Italians and Amerindians do not carry the modern allele.
The map below shows the global distribution, the populations lacking the modern allele are marked: 
The polymorphic nature of DXS225 (poly: many, morph: kinds; there are two variants of it: with and without insertion) and its absence in chimps, is taken by the authors as having taken place after our split from the other non-hominids; since it is "found in polymorphic frequencies all over the world..."  they conclude that it took place among modern humans some time before the Out of Africa (OoA) event some 100 kya.
The same team wrote a second paper on this allele (2007)  where they estimate the time of the most recent common ancestor as 182 ky (56.7 to 479 ky)* and the date that the DSX225 mutation took place: 94,4 ky (24,3 to 310 ky)*.  Which the authors find "compatible" with the OoA dates*.
* Comment. Just look at the error bars on this calculation! it spans from a putative OoA date to the split with Neanderthals! The mutation date also ranges from the time the world was fully peopled to a date 300 kya which possibly predates modern humans. This goes to show all the uncertainties that exist in the models used -see my post criticising models.
2. Amerindian singularity
Regarding its pan-global distribution there is a glaring exception: Native Americans: "among the five Amerindian populations [...] only the Karitiana showed presence of the Alu insertion".  So the "modern" allele is found all over the world but is absent in America except for only one group, the Karitiana... why?
The authors explains this singularity as follows:
- Karitiana are not pure Amerindians, they admixed with Europeans and Africans (former slaves) in the early 1900s and these introduced the Alu insertion into their genome, add to this that it is a small inbred tribe. 
- All other Native Americans lost the inseriton in a pre-hispanic founder effect. So the people who entered America did not carry this allele.
They then eliminated the Karitiana from further analysis in their study!
But what about the Papuans, Dai, Northern Italians and the African groups. Nothing is said about them, no explanations are offered, but I would expect them.
Maybe the Karitiana are an admixture of extra-American genes, but the "founder effect" should be justified. As we will see below, statistically a 25% of a given population carry the mutated allele. Are we to expect that these people died out while migrating into America, (not only that, the founder effect spans Y chromosome hgs., mtDNA hgs, etc. it is indeed a fantastic excuse to explain away what is unexplainable!).
Diversity. DXS225 has a "low level of genetic structure"  suggesting that it is neutral to natural selection and that "the variations in insertion allele frequencies among populations result from genetic drift" , which is true if you look at the data for all groups except the Native Americans and Papuans, because these other groups have a very small degree of variability.
But when you look at Papuans and Native Americans, the situation is different. The authors' second paper delved in this matter when they combined DXS225 with other markers and defined several haplotypes which were analyzed using AMOVA, and, again found two regional exceptions to the general lack of genetic variation: Oceania and America (sans the Karitiana of course).
A strange finding because the variation is very large: Oceania had a 14.95% and the American Natives a 15.29% of "among-populations within-regions variation"; as a reference, the values were -0,59 in East Asia 1,06 for Eurasia and 1.99 Africa. That is almost a difference of an order of magnitude (tenfold).
This is exactly the opposite you'd expect in the American population which orthodoxy (and the paper  itself) have defined as subjected to "a significant bottleneck that led to a large reduction of haplotypic diversity" , it is a situation which does perplex the authors:
They find it "difficult to ascertain the meaning of this relatively elevated component" in Oceania because only two populations were studied. Well, why didn't they add more populations to the study to elucidate the matter?
Of course, American diversity is easily explained with the usual excuse: the"high levels of genetic drift"  that characterize its populations. They are excused from having to justify anything.
I believe however that the high diversity (note that these haplogroups they defined combines several markers and not only DXS225) is due to admixture with archaic hominins which carry long evolved mutations which have had plenty of time to evolve: both in Oceania (New Guinea) and the Americas... I am thinking Homo erectus here.
The facts of these two papers are that there is a mutation (DXS225) in modern humans' X chromosomes, that ~25% carry and the other roughly 75% do not carry. Averages that make sense:
The following image shows how a man develops a chance mutation in his X chromosome and after 2 generations it appears in 4 of his 16 grandchildren: 4⁄16 = 25% carrying the mutation.
Statistically a 75% of the people would not carry the mutation and 25% would. But (see the table further up), the numbers show a different panorama:
- 75.0% Theoretical average statistical value
- 74.4% Africa
- 74.3% East Asia
- 81.0% Oceania
- 64.0% Europe
- 90.7% America
- 59.3% Middle East
- 65.3% Central Asia
- 70.6% Global Average
Further down we look into the transmission of the allele: it is matrilineal, those with more daughters will transmit more of the allele to future generations. But is this the cause for Europeans, Central Asians and Middle Eastern populations in having a much lower "archaic allele" value? (i.e. they had more daughters?) while Amerindians and Oceanians have a higher ratio of the archaic allele because they had more sons?.
Maybe the differences are due to admixture with archaic populations that did not have the modern mutation: Amerindians and Oceanians admixed with, say, H. erectus in their respective territories and took up their X chromosomes with the archaich pre-insertion variant, diluting the modern allele that they carried with them...
Getting back to DXS225, the archaic form is the lack of this insertion: chimpanzees do not carry it.
Neither do several populations within Africa, 100% of their members do not have the mutation. Since genetic diversity is highest accepted as being highest in Africa , this should not surprise us. An archaic form could be conserved in some groups which do not carry the "modern" mutation that appeared almost 100 kya, maybe it appeared in others that migrated out of Africa and many that stayed behind lacked the mutation or even admixed with archaic African populations (Mendez et al., 2013 ) and therefore had a higher influx of the archaic pre-insert variant.
It is not found among the Papuans either. These people (see my most recent post on haplogroup C, C2 haplotype) reached their territory in New Guinea very soon after leaving Africa their Y chromosome haplogroup C2 is unique to them and very old. They could have retained the non-mutated allele too.
The Dai in South China, Thailand and Myanmar are intriguing. These people are either indigenous to their territory or originated in South China and moved there . This region is probably the homeland of the C* Y chromosome paragroup, the point it split into its haplotypes (C1 to C5), including the C2 found among Papuans and the C3 found in America.
What role do the Northern Italians from Bergamo have in this plot? I am at a loss. Maybe these people have C6 (the European branch of hg. C)?
Amerindians have haplotype C3 (North America) at very low frequencies and C3* in Soth America. And all have DXS225.
I mention the C hg. because in my previous post I conjectured a link between haplogroup C and Homo erectus. As we see the allele also follows the pattern of hg. C, but not because of the haplogroup itself -see below- but because it is the rang e once occupied by Homo erectus
No link between DXS225 and Y chromosome haplogroups
Unfortunately I can not make a link between a mutation in the X chromosome and Y chromosome haplogroups. The explanation is below:
The image further up shows us that the men (Man 1) carrying the X mutation (green X chromosome) do not pass it on to their sons (male descent) or his grandchildren born from those sons, so there is no link between Y chromosome haplotype of men carrying the mutated allele and the allele. The boys born from Man 1 do not carry the Allele. This is interesting, it is transmitted via women: Man 1's daughters.
His daughters will receive the mutation (green colored X), and they will of course carry the same haplogroup as their mother, Woman 1, (pink squares). Their children if boys, will have the Y chromosome haplogroup of their fathers (which may or may not be the same as that of their grandfather). So this shows there is no link between Y chromosome hgs. and the allele.
Regarding the descent via Man 1's daughters: Half of the granddaughters born from his daughters will carry the mutation and so will half of his daughters' sons; all of them will carry the mtDNA of their mother, Woman 1.
The most interesting scenario is the one that suggests that a non-human archaic homin left Africa long before this allele evolved (I am thinking H. erectus). They took the coastal route to New Guinea, South East Asia and onwards into America. Y chromosome haplogroup C marks their course (yes, some spread into Europe, where some Northern Italians still carry it).
It remained back in Africa too among H. erectus or related groups. Later with the evolution of modern Humans, the mutation appeared and spread globally, overlaying the C hg archaic allele carriers with other more recent haplogroups and modern populations carrying the allele at a 25% ratio. It did not erase the archaicn pre-insertion mutation however: three out of every four modern humans carry the archaic type. Some groups remained isolated from the mutation and suffered no admixture. Maybe it is not neutral (we have seen that it is found at very high frequencies in N. Guinea and America) and is subject to natural selection and this contributes to its survival despite the presence of the mutation.
America peopled by H. erectus received waves of H. sapiens with this insertion mutation, but the archaic form prevailed. Were the erectus better adapted to the New World conditions?
 Rinaldo Wellerson Pereira, Simone Silva dos Santos Lopes and Sérgio Danilo Junho Pena, (2006). A novel polymorphic Alu insertion embedded in a LINE 1 retrotransposon in the human X chromosome (DXS225): identification and worldwide population study.
Genet. Mol. Res. 5 (1): 63-71
 Ibid. (2007) A Worldwide Phylogeography for the Human X Chromosome. PLoS ONE 2(6): e557. doi:10.1371/journal.pone.0000557
Brenna M. Henn, (2011). Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. vol. 108 no. 13 5154–5162, doi: 10.1073/pnas.1017511108
 Sun H, Zhou C, Huang X, Lin K, Shi L, et al. (2013). Autosomal STRs Provide Genetic Evidence for the Hypothesis That Tai People Originate from Southern China. PLoS ONE 8(4): e60822. doi:10.1371/journal.pone.0060822
 Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
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