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The haplogroups hidden behind other haplogroups
I recently posted about the infertility problems linked to some Y-chromosome haplogroups. In Europe, haplogroups I2b as well as Italian subclades of E1b1b were found to have lower sperm count of motility than other haplogroups. This confirms what I had predicted about some haplogroups' predisposition to conceive more boys (because higher sperm count will result in higher chances of producing a boy than a girl), notably for R1a and R1b.
Ancient Y-DNA from Bronze-age Germany (1000 BCE) showed that I2b was then the dominant Y-haplogroup at the time. I2b is now a minor haplogroup. R1a and R1b have become the two main European haplogroups.
If the reason is that I2b men had less children or just less boys, then R1a and R1b have somehow absorbed the ancient gene pool of I2b by marrying women of I2b lineages. This is how phenotypical traits (from autosomal DNA) managed to get passed from the original Paleolithic I2 population to the new R1a and R1b lineages in western and central Europe. In extreme cases it is completely conceivable that R1b replaced the quasi totality of I2b lineages over the last 3000 or 4000 years.
The Atlantic fringe of Europe, from the British Isles to Iberia, could once have been a predominantly I2 region. I2 men could either have been slaughtered in battle, prevented from reproducing by having their women taken by the new invaders, or simply not able to compete in term of boys fathered. Whatever the relative importance of each factor, it is likely that R1b took wives in the indigenous I2 population. This would explain the continuity in skeletal phenotypes between Paleolithic and modern western Europeans (e.g. elongated skulls).
One could say that the I2 population was genetically absorbed by the new R1b lineages, so that modern R1b Y-chromosome carriers actually have as much or more autosomal DNA from the original I2 people. This could be called "genetic hitch-hiking".
The same process probably happened whenever a new group of invaders arrived with a combination or superior technology and better adapted Y-DNA with a bias towards more males. The original East Asian populations belonged to Y-haplogroups C and D, but were replaced by O lineages, except in remote or isolated regions like the Himalaya, Siberia, Japan and some Austronesian islands. It has been confirmed that haplogroup D carriers suffer from lower sperm count.
O and R people stem from a relatively recent (35,000 years) ancestor in Central Asia. The best explanation for the rift between Caucasian and Mongoloid population around central Asia is that the original O and R people mixed with older populations that already had clearly distinct Caucasian and Mongoloid traits. It is certain from archaeological evidence that the first East Asian Homo Sapiens 60,000 years ago already had Mongoloid traits, and the first Europeans (Cro-Magnons, 45,000 years ago) had Caucasians traits. O and R may represent some 70 to 90% of the lineages today, but their autosomal impact was much less, because their genes were diluted by those of indigenous women.
In Siberia, N and Q might very well have replaced older C lineages, which would explain why N and Q people have Mongoloid traits, like O people, but unlike R people. Haplogroups N, O, P, Q and R all originated from a common ancestor. N, O, P and Q are almost always found side by side to a minority of C and D lineages. R is usually found among E, F, G, H, I and J populations. N, O, P and Q almost always have Mongoloid mtDNA (A, B, C, D, F, G, M7, M8, N9, Y, Z), except in/around Finland, while R1 men typically have Caucasian mtDNA (H, I, J, K, T, U, V, W, X).
The difficulty is to determine whether the original NOPQR population was a unique racial group different from the Mongoloids and Caucasians, and whether they carried unique mtDNA lineages too. I wouldn't be surprised if mtDNA X had a connection with the original NOPQR people, as it is found in all Eurasia, indistinctively among Caucasians and Mongoloids. It is also found among Native North Americans (Y-DNA Q). Its age (30-35,000 years) corresponds to the timeframe of the split between NOP, Q and R.
In Africa, haplogroup E1b1 has replaced most of the older lineages, except in secluded or inhospitable environments (Congolese jungle, desert of Namibia, some valleys of Ethiopia...) where haplogroups A and B survived in greater number. But E1b1 had incorporated part of the gene pool of these A and B populations and is constantly found alongside a minority of A and B men.