Chapter 21 - Nuclear DNA

    In this chapter, we look at what nuclear DNA has to tell us about human origins. Humans have about 25,000 genes, each with an average of 14 alleles, so that makes about 350,000 different nuclear DNA alleles. Most alleles occur in more than one population, but the percentage of individuals in those populations who have them differs. But some alleles are found only in Europeans, others only in Africans and still others only in Asians. It is highly unlikely that alleles that are today found only in Europeans, or only in Asians, arose in Africans. 1 For an allele to have arisen in Africans, be carried by Africans into Europe or Asia, then die out back in Africa would mean that the allele was initially beneficial in Africa, then became harmful (or at least neutral) in Africa while still being beneficial in Eurasia, despite Africa providing a more stable environment.
    If a person has a “population-specific” allele, he most likely acquired it from someone in that population, either because he is a member of that population or because one of his ancestors was (Chapter 4, Rule 11). There can be entire groups of alleles, some from the same gene, and others from different genes, that are population-specific. 2
    Harding (2000) and others studied the MC1R gene, which influences the pigmentation of skin and hair, and therefore its color. The allele for red hair and the allele for blond hair are both found only in Europeans, and Europeans have more alleles for the MC1R gene than do Africans. Africans have only synonymous alleles 3 of MC1R that all code for eumelanin, a pigment that produces dark skin and hair. Although Eurasians also have alleles that code for eumelanin, they don’t have the same alleles for it that the Africans do, plus they also have many alleles for phenomelanin, a red-gold pigment that produces light skin and hair colors. Africans lack alleles for phenomelanin because light skin and hair are disadvantageous in Africa and an African who may have acquired them would have been less likely to survive and leave progeny.
    Thus, the alleles for light skin and hair could not have gotten a foothold in Africa, but only in a population that had lived in Eurasia, and that had lived there long enough for all the various alleles that code for light skin and hair to arise. Since the Eurasian alleles were not strongly positively selected, 4 once those mutations occurred in Eurasia, an additional long time would have been required for the alleles to spread throughout the population to their present high frequency. 5 The 65,000 yrs allowed by OoA for these mutations and their spread to occur is not nearly long enough and afrocentrists exclude the possibility that those mutations were acquired by interbreeding with indigenous Eurasians who already had them. The number of different alleles (“polymorphisms”) in the nuclear DNA of present day non-African populations shows “great time depths,” i.e., they are too many to have resulted from mutations over a period of only 65,000 yrs. (Eswaran, 2005).
    The LCA of Africans and non-Africans for the MC1R gene is about 1 mya, 6 which means that Africans and non-Africans split into two separate populations at least that long ago, not 65,000 ya, as held by OoA. Several Eurasian MC1R alleles are 250,000 to 100,000 yrs old, and the allele for red hair is about 80,000 yrs old, 7 so a Eurasian population must have existed that had those alleles that long ago. Harding (2000) concludes that, “…an incompatibility arises between estimated ages in the range of 250,000 – 100,000 years, for non-African MC1R allelic variation, and ages, from fossil evidence, of ≤100,000 years for the dispersal of modern humans outside Africa and the Middle East.”
    For OoA to be correct, not only must all of the African-specific alleles disappear from all the Eurasian populations in 65,000 yrs, but a whole new collection of Eurasian-specific alleles must arise within that time. Although some individual European-specific and Asian-specific alleles might appear in the huge numbers of people who have those alleles today in less than 65,000 yrs, that is not possible for the entire collection of European and Asian specific alleles. Thus, either some of those alleles evolved in another species of Homo, such as the Neanderthals, then entered the Hss lineage by interbreeding less than 65,000 ya or there was no replacement of Eurasians by Africans and OoA is wrong. There is no evidence that some of the traits coded for by those alleles were even useful in Eurasians, so there would not have been strong selection for them 8 and, without strong selection, much more time would have been required for them to spread throughout the Eurasian population. 9
    In fact, there is no plausible model for the conversion of African nuclear DNA into European and Asian nuclear DNA, and there is no evidence that there ever were Eurasians who had any African-specific alleles. For example, European and Asian skulls do not show traits that are unique to African skulls, 10 and traces of African-specific alleles, such as wooly hair, are not found in modern Eurasians whose ancestors have not interbred with Africans.
    Many, even most, of the nuclear alleles that have been globally surveyed arose prior to even 200,000 ya, before Hs allegedly even arose in Africa. 11 This strongly suggests either that Eurasians got those alleles by interbreeding with archaic humans or, more likely, that Hss did not arise in Africa, but in Eurasia.

    Not only are there mtDNA haplotypes, there are also nuclear DNA haplotypes. During the formation of the egg and sperm, chromosome pairs (one from the father and one from the mother) are broken up into small pieces, some of the pieces from each parent are interchanged, then the pieces are recombined to re-form the chromosomes, a process called “crossover” (p. 26). Small chunks of this nuclear DNA, however, are not broken up into pieces, but are inherited as chunks, called “haplotypes”; a group of these haplotypes is called a “haplogroup.” Thus, in this way haplotypes and haplogroups maintain their integrity from generation to generation the same way that mtDNA from the mother and the Y-chromosome from the father do, though they all gradually accumulate mutations. There are about 100,000 haplogroups in each individual’s genome and, since haplogroups of different populations accumulate different mutations, an individual’s race can be determined by checking only the locations on the DNA where these mutations have occurred.
    By comparing similarities and differences in the haplogroups of different populations it is possible to determine which haplotype is the oldest and estimate how old it is. For example, there were several versions of a haplotype within the gene PDHA1. The different versions fell into a tree that branched 1.8 mya, one branch of which branched again 200,000 ya. (Harris, E.E., 1999; Harding, 1999). But if all humans were a single group in Africa 65,000 ya, as OoA holds, it would not be possible for there to be humans alive today who have versions of a haplotype that branched twice before that date, but there are. And this haplotype is only one of many that contradict OoA. The only way to explain these haplotypes and still retain the basis of OoA, that man originated in Africa, is to say that the ancient variations were picked up by interbreeding with other, older species of man, such as Neanderthals in Europe and erectus in East Asia. However, any significant interbreeding with other species of man would invalidate an exclusively African origin for modern man.

                            Haplogroup D
    Nuclear haplogroup D is another haplogroup that is a problem for OoA. Haplogroup D, one of the haplogroups in nuclear macrohaplogroup M, is found in Caucasians and Asians, but is rare or absent in Africans. The gene microcephalin (MCPH1) on Chromosome 8, which regulates brain size during development, is one of the genes within this haplogroup. Haplogroup D is believed to have arisen about 1.1 mya, possibly in the ancestors of Neanderthals, who may have mated with Hss about 37,000 ya. (Evans, 2006). It is so advantageous that about 70% of the Eurasians living today have it. 12

                         Y Chromosome Haplogroups
    Before we leave nuclear DNA, let’s look at the nuclear DNA on the Y chromosome. Since mtDNA is transmitted through the female line, mapping the variations in it in people across the globe tells us the geographical journeys of women. Similarly, Y chromosome DNA is transmitted through the male line and tells us where men went. It does not tell the same story that mtDNA tells because men did much more exploring than women. Men frequently went to new lands without their women, then mated with native women, so that their descendants had native mtDNA and the explorers’ Y chromosome DNA. Figure 21-1 (Underhill, 2001) shows the world-wide distribution of different variations of the Y chromosome.

Figure 21-1

    The amount of each color in the circles is proportional to the number of men in that location who had the variation indicated by that color. Note that olive, the major color in Africa, appears outside of Africa only around the Mediterranean, suggesting that Africans did not migrate out of Africa, except as slaves taken to those areas. 13 Bright red and dark blue are unique to Africa, which also suggests that there were no migrations out of Africa; those variations may have been brought in to Africa by primitive hominoids (Section IV) who died out elsewhere but whose Y-DNA still continues in Africa.
    The orange and yellow European colors indicates that European men lived in the Middle East, North Africa, Georgia of the former U.S.S.R., 14 India, southeast Asia, Australia, and North America; where they originated will be discussed in Chapter 24. (The orange and yellow men may have been members of a single population.) Green is the dominant color in the Americas, and the small amounts of green in the Old World suggest its origins in Western Asia, then migrating into northern India and southern Siberia, and possibly the Ainu in Japan. From the large amounts of pink in eastern Asia one might expect substantial amounts of pink in the Americas, but it is not there; this suggests that the pink Asians were not inclined to explore much and that less evolution occurred in the pink Asians than in the orange and yellow Europeans.

Chapter 22

Table of Contents


1. “Subsequent data from the nuclear genome not only fail to support this model [Out-of-Africa], they do not support any simple model of human demographic history.” (Eswaran, 2005). Back

2.  A few examples: The Duffy antigen Fy (a-b-) is very rare among whites, but is found in nearly all Africans; an allele, 35delG, of the gene GJB2, occurs only in Europeans and Jews; alleles of genes that provide lactose tolerance and HIV resistance are rare outside Europe (Libert, 1998); certain alleles that cause a number of diseases are found almost exclusively among Ashkenazi Jews. Also see (Hinds, 2006). Back

3. I.e., the alleles have different A-C-G-T sequences, but code for the same polypeptide. See Appendix. Back

4. The afrocentrists argue that the Eurasian alleles spread quickly throughout the Eurasian population because they were strongly selected, but no evidence for strong selection was found. “For many European and Asian individuals, variant MC1R alleles contribute to both lighter skin color and sun sensitivity. However, we found no statistical evidence that MC1R diversity [i.e., the large number of alleles in Eurasians] has been enhanced by selection, either in its apparently high levels or in its haplotype frequency distribution patterns.” That is, there was no evidence that having those alleles was advantageous. Back

5. Harding (2000) calculates that it took at least a hundred thousand years, and possibly more than twice that long, for just one of these alleles to reach its current frequency. Back

6.  “Both African and non-African data suggest that the time to the most recent common ancestor is ~1 million years …” (Harding, 2000). Back

7. “These estimates suggest that the MC1R variants Val60Leu, Val92Met, and Arg163Gln may trace back to ancestors in Eurasian populations existing 250,000 - 100,000 years ago. … For the European red hair-associated Arg151cys and Arg160Trp variants, we estimate an age of ~80,000 years;” (Harding, 2000). Back

8. The traditional test for selection (Tajima’s D statistics; Tajima, 1989) does not show strong selection. (Harding, 2000). Other tests for selection have not been useful as they show too many other alleles being strongly selected. Back

9.  The 7R allele of the CG4 gene is a good example. It appeared in the Hss lineage perhaps only 50,000 ya, but it would have taken many times as long for its ancestral allele to evolve, step by step, through all of its several intermediate forms and become the 7R form. Back

10. Except the Grimaldi skeletons, discussed in Chapter 26. Back

11. E.g., b-globin, MC1R, PDHA1, Dys44, Y-chromosome haplotypes, etc. Back

12. Percentages are likely higher in Europe and north Asia and lower in southern Asia. Back

13.  A small number of Africans were even brought into India as slaves; they were later freed and are now called “Sidis.” Back

14. Note the great diversity of Y-DNA in Georgia, which suggests considerable evolution took place there, which will be discussed in Chapter 24. Back