Reconsideration of the “Out of Africa” Concept as Not Having Enough Proof

Anatole A. Klyosov

The Academy of DNA Genealogy, Newton, USA.

DOI: 10.4236/aa.2014.41004                

Abstract

This is an overview of the “Out of Africa” (OOA) concept and the concept is based upon experimental data. The article shows that said concept is based on data which are—as a rule—interpreted by the OOA proponents in a one-sided manner, that is to “prove” the OOA concept. The Y-chromosomal haplogroup tree in its most ancient part includes a number of nodes-haplogroups, which in the current classification are named A0-T, A1, and A1b. Bearers of those haplogroups are not identified in Africa or elsewhere. However, those three haplogroups are assigned by the proponents of the OOA “by default” to be the “African” haplogroups, which “automatically” makes all non-Africans “African descendants”. In fact, each of the three haplogroups represents a split into African and non-African haplogroups. As a result, the evolution (Y-chromosomal) tree produced at least five waves of migrants to Africa (haplogroups A00, A0, A1a, A1b1, and B), while the rest of the tree consists of four non-African (by origin) haplogroups, that is A0-T, A1, A1b, and BT, along with the downstream subclades of the latter. The tree is confirmed by the analysis employing STR (Short Tandem Repeat) and SNP (Single Nucleotide Polymorphism) mutations of the Y-chromosome. Indeed, according to many data, the tree shows a deep split between African and non-African (by origin) lineages. The last split, from haplogroup A1b (into African A1b1 and non-African—by origin—B) occurred 160,000 ± 12,000 years before present. Haplogroup B is by origin a non-African haplogroup, which is very distant—time-wise—from haplogroups A, by at least 250 - 300 thousand years, and could not possibly have descended from haplogroups A1a or A1b1, or their subclades. A similar pattern is observed with the mtDNA haplogroup tree, which shows a deep split between African L0 and non-African (by origin) haplogroups L1-L6. The article shows how recent OOA studies (as well as earlier ones) employ biased interpretations to artificially “prove” the OOA concept. The article shows that the same data can be—and more justifiably—interpreted as incompatible with the OOA concept, and giving support for a “into Africa” concept. It seems that from times of Neanderthals (seemingly having pale skin and fair hair, based on the identified Neanderthal MCR1 melanocortin receptor), our ancestors, of both Africans and non-Africans current populations, lived outside of Africa, apparently in Eurasia or maybe in Europe.

Keywords

Y-Chromosome; mtDNA; Mutations; Haplotypes; Haplogroups; STR; SNP; Out-of-Africa; Into-Africa; SHV-1 (Simplex Herpes Virus)

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Arredi, B., Poloni, E. S., Paracchini, S., Zerjal, T., Fathallah, D. M., Makrelouf, M., Pascali, V. L., Novelletto, A., & Tyler-Smith, C. (2004). A predominantly neolithic origin for Y-chromosomal DNA variation in North Africa. American Journal of Human Genetics, 75, 338-345. http://dx.doi.org/10.1086/423147
[2]	Atkinson, Q. D. (2011). Phonemic diversity supports a serial founder effect model of language expansion from Africa. Science, 332, 346-349. http://dx.doi.org/10.1126/science.1199295
[3]	Behar, D. M., van Oven, M., Rosset, S., Metspalu, M., Loogvali, E. L., Silva, N. M., Kivisild, T., Torroni, A., & Villems, R. (2012). A “copernican” reassessment of the human mitochondrial DNA tree from its root. American Journal of Human Genetics, 90, 675-684. http://dx.doi.org/10.1016/j.ajhg.2012.03.002
[4]	Behar, D. M., Villems, R., Soodyall, H., Blue-Smith, J., Pereira, L., Metspalu, E., Scozzari, R. et al. (2008). The dawn of human matrilineal diversity. American Journal of Human Genetics, 82, 1130-1140. http://dx.doi.org/10.1016/j.ajhg.2008.04.002
[5]	Benazzi, S., Douka, K., Fornai, C., Bauer, C. C., Kullmer, O., Svoboda, J. et al. (2011). Early dispersal of modern humans in Europe and implications for Neanderthal behaviour. Nature, 479, 525-528. http://dx.doi.org/10.1038/nature10617
[6]	Campbell, M. C., & Tishkoff, S. A. (2010). The evolution of human genetic and phenotypic variation in Africa. Current Biology, 20, R166-R173. http://dx.doi.org/10.1016/j.cub.2009.11.050
[7]	Cann, R. (2013). Y weigh in again on moden humans. Science, 341, 465-467. http://dx.doi.org/10.1126/science.1242899
[8]	Cann, R. L., Stoneking, M., & Wilson, A. C. (1987). Mitochondrial DNA and human evolution. Nature, 325, 31-36. http://dx.doi.org/10.1038/325031a0
[9]	Carrigan, D., & Hammer, M. F. (2006). Reconstructing human origins in the genomic era. Nature Reviews Genetics, 7, 669-680. http://dx.doi.org/10.1038/nrg1941
[10]	Chiaroni, J., Underhill, P. A., & Cavalli-Sforza, L. L. (2009). Y-chromosome diversity, human expansion, drift, and cultural evolution. Proceedings of the National Academy of Sciences of the United States of America, 106, 20174-20179. http://dx.doi.org/10.1073/pnas.0910803106
[11]	Cruciani, F., Trombetta, B., Massaia, A., Destro-Bisol, G., Sellitto, D., & Scozzari, R. (2011). A revised root for the human Y chromosomal phylogenetic tree: The orogin of patrilineal diversity in Africa. American Journal of Human Genetics, 88, 814-818. http://dx.doi.org/10.1016/j.ajhg.2011.05.002
[12]	Cruciani, F., Trombetta, B., Sellitto, D., Massaia, A., Destro-Bisol, G., Watson, E., Colomb, E. B., Dugoujon, J. M., Moral, P., & Scozzari, R. (2010). Human Y chromosome haplogroup R-V88: A paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages. European Journal of Human Genetics, 18, 800-807. http://dx.doi.org/10.1038/ejhg.2009.231
[13]	Curnoe, D., Xueping, J., Herries, A. I. R., Kanning, B., Tacon, P. S. C., Zhende, B., Fink, D. et al. (2012). Human remains from the Pleistocene-holocene transition of Southwest China suggest a complex evolutionary history for East Asians. PLOS ONE, 7, Article ID: e31918. http://dx.doi.org/10.1371/journal.pone.0031918
[14]	Edmonds, C. A., Lillie, A. S., & Cavalli-Sforza, L. L. (2004). Mutations arising in the wave front of an expanding population. Proceedings of the National Academy of Sciences of the United States of America, 101, 975-979. http://dx.doi.org/10.1073/pnas.0308064100
[15]	Fernandes, V., Alshamali, F., Alves, M., Costa, M. D., Pereira, J. B., Silva, N. M., Cherni, L., Harich, N., Cerny, V., Soares, P., Richards, M. B., & Pereira, L. (2012). The Arabian cradle: Mitochondrial relicts of the first steps along the Southern route out of Africa. American Journal of Human Genetics, 90, 347-355. http://dx.doi.org/10.1016/j.ajhg.2011.12.010
[16]	Forster, P. (2004). Ice Ages and the mitochondrial DNA chronology of human dispersals: A review. Philosophical Transactions of Royal Society B, 359, 255-264. http://dx.doi.org/10.1098/rstb.2003.1394
[17]	Forster, P., Torroni, A., Renfrew, C., & Rohl, A. (2001). Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Molecular Biology and Evolution, 18, 1864-1881. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003728
[18]	Francalacci, P., Morelli, L., Angius, A., Berutti, R., Reinier, F., Atzeni, R., Pilu, R. et al. (2013). Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science, 341, 565-569. http://dx.doi.org/10.1126/science.1237947
[19]	Grine, F. E., Bailey, R. M., Harvati, K., Nathan, R. P., Morris, A. G., Henderson, G. M., Ribot, I., & Pike, A. W. G. (2007). Late Pleistocene human skull from Hofmeyr, South Africa, and modern human origins. Science, 315, 226-229. http://dx.doi.org/10.1126/science.1136294
[20]	Grine, F. E., Gunz, P., Betti-Nash, L., Neubauer, S., & Morris, A. G. (2010). Reconstruction of the late Pleistocene human skull from Hofmeyr, South Africa. Journal of Human Evolution, 59, 1-15. http://dx.doi.org/10.1016/j.jhevol.2010.02.007
[21]	Hammer, M. (2013). Human hybrids. Scientific American, 308, 66-71. http://dx.doi.org/10.1038/scientificamerican0513-66
[22]	Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C., & Wall, J. D. (2011). Genetic evidence for archaic admixture in Africa. Proceedings of the National Academy of Sciences of the United States of America, 108, 15123-15128. http://dx.doi.org/10.1073/pnas.1109300108
[23]	Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C., & Wall, J. D. (2011). Genetic evidence for archaic admixture in Africa. Proceedings of the National Academy of Sciences of the United States of America.
[24]	Hayden, E. C. (2013). African genes tracked back. Nature, 500, 514. http://dx.doi.org/10.1038/500514a
[25]	Hellenthal, G., Auton, A., & Falush, D. (2008). Inferring human colonization history using a copying model. PLOS Genetics, 4, Article ID: e1000078. http://dx.doi.org/10.1371/journal.pgen.1000078
[26]	Henn, B. M., Gignoux, C. R., Jobin, M., Granka, J. M., Macpherson, J. M., Kidd, J. M., Rodríguez-Botigué, L., Ramachandran, S., Hon, L., Brisbin, A., Lin, A. A., Underhill, P. A., Comas, D., Kidd, K. K., Norman, P. J., Parham, P., Bustamante, C. D., Mountain, J. L., & Feldman, M. W. (2011). Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proceedings of the National Academy of Sciences of the United States of America, 108, 5154-5162. http://dx.doi.org/10.1073/pnas.1017511108
[27]	Higham, T., Compton, T., Stringer, C., Jacobi, R., Shapiro, B., Trinkaus, E., Chandler, B., Groning, F., Collins, C., Hillson, S., O’Higgins, P., FitzGerald, C., & Fagan, M. (2011). The earliest evidence for anatomically modern humans in North-Western Europe. Nature, 479, 521-524. http://dx.doi.org/10.1038/nature10484
[28]	Hublin, J. J. (2011). African origin. Nature, 476, 395. http://dx.doi.org/10.1038/476395a
[29]	Hudjashov, G., Kivisild, T., Underhill, P. A., Endicott, P., Sanchez, J. J., Lin, A. A., Shen, P., Oefner, P., Renfrew, C., Villems, R., & Forster, P. (2007). Revealing the prehistoric settlement of Australia by Y-chromosome and mtDNA analysis. Proceedings of the National Academy of Sciences of the United States of America, 104, 8726-8730. http://dx.doi.org/10.1073/pnas.0702928104
[30]	Jobling, M. A., & Tyler-Smith, C. (2003). The human Y-hromosome: An evolutionary marker comes of age. Nature Reviews Genetics, 4, 598-612. http://dx.doi.org/10.1038/nrg1124
[31]	Ke, Y., Su, B., Song, X., Lu, D., Chen, L., Li, H., Qi, C. et al. (2001). African origin of modern humans in East Asia: A tale of 12,000 Y chromosomes. Science, 292, 1151-1153. http://dx.doi.org/10.1126/science.1060011
[32]	King, T. E., Parkin, E. J., Swinfield, G., Cruciani, F., Scozzari, R., Rosa, A., Lim, S. K., Xue, Y. L., Tyler-Smith, C., & Jobling, M. A. (2007). Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy. European Journal of Human Genetics, 15, 288-293. http://dx.doi.org/10.1038/sj.ejhg.5201771
[33]	Klyosov, A. A. (2009). DNA genealogy, mutation rates, and some historical evidences written in Y-chromosome: I. Basic principles and the method. Journal of Genetic Genealogy, 5, 186-216.
[34]	Klyosov, A. A. (2011). The slowest 22 marker haplotype panel (out of the 67 marker panel) and their mutation rate constants employed for calculations timespans to the most ancient common ancestors. Proceedings of the Russian Academy of DNA Genealogy, 4, 1240-1257.
[35]	Klyosov, A. A. (2012). Ancient history of the Arbins, bearers of haplogroup R1b, from Central Asia to Europe, 16,000 to 1500 years before present. Advances in Anthropology, 2, 87-105. http://dx.doi.org/10.4236/aa.2012.22010
[36]	Klyosov, A. A., & Rozhanskii, I. L. (2012a). Re-examining the “Out of Africa” theory and the origin of Europeoids (Caucasoids) in light of DNA genealogy. Advances in Anthropology, 2, 80-86. http://dx.doi.org/10.4236/aa.2012.22009
[37]	Klyosov, A. A., & Rozhanskii, I. L. (2012b). Haplogroup R1a as the Proto Indo-Europeans and the legendary Aryans as witnessed by the DNA of their current descendants. Advances in Anthropology, 2, 1-13. http://dx.doi.org/10.4236/aa.2012.21001
[38]	Kolb, A. W., Ane, C., & Brandt, C. R. (2013). Using HSV-1 genome phylogenetics to track past human migrations. PLoS ONE, 8, Article ID: e76267. http://dx.doi.org/10.1371/journal.pone.0076267
[39]	Lachance, J., Vernot, B., Elbers, C. E., Ferwerda, B., Froment, A., Bodo, J. M., Lema, G., Fu, W.Q., Nyambo, T. B., Rebbeck, T. R., Zhang, K., Akey, J. M., & Tishkoff, S. A. (2012). Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell, 150, 457-469. http://dx.doi.org/10.1016/j.cell.2012.07.009
[40]	Lalueza-Fox, C., Rompler, H., Caramelli, D., Staubert, C., Catalano, G., Hughes, D., Rohland, N., Pilli, E., Longo, L., Condemi, S., de la Rasilla, M., Fortea, J., Rosas, A., Stoneking, M., Schoneberg, T., Bertranpetit, J., & Hofreiter, M. (2007). A Melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science, 318, 1453-1455. http://dx.doi.org/10.1126/science.1147417
[41]	Li, H., & Durbin, R. (2011). Inference of human population history from individual whole genome sequences. Nature, 475, 493-496. http://dx.doi.org/10.1038/nature10231
[42]	Majumder, P. P. (2010). The human genetic history of South Asia. Current Biology, 20, R184-R187. http://dx.doi.org/10.1016/j.cub.2009.11.053
[43]	Mellars, P. (2011). The earliest modern humans in Europe. Nature, 479, 483-485. http://dx.doi.org/10.1038/479483a
[44]	Mendez, F. L., Krahn, T., Schrack, B., Krahn, A. M., Veeramah, K. R., Woerner, A. E., Fomine, F. L. M., Bradman, N., Thomas, M. G., Karafet, T. M., & Hammer, M. F. (2013). An African American paternal lineage adds an extremely ancient root to the human y chromosome phylogenetic tree. American Journal of Human Genetics, 92, 454-459. http://dx.doi.org/10.1016/j.ajhg.2013.02.002
[45]	Moorjani, P., Patterson, N., Hirschhorn, J. N., Keinan, A., Hao, L., Atzmon, G., Burns, E., Ostrer, H., Price, A. L., & Reich, D. (2011). The history of African gene flow into Southern Europeans, Levantines, and Jews. PLOS Genetics, 7, Article ID: e1001373. http://dx.doi.org/10.1371/journal.pgen.1001373
[46]	Ottoni, C., Primativo, G., Kashani, B. H., Achilli, A., Martinez-Labarga, C., Biondi, G., Torroni, A., & Rickards, O. (2010). Mitochondrial haplogroup H1 in North Africa: An early holocene arrival from Iberia. Plos ONE, 5, Article ID: e13378. http://dx.doi.org/10.1371/journal.pone.0013378
[47]	Patin, E., Laval, G., Barreiro, L. B., Salas, A., Semino, O., Santachiara-Benerecetti, S., Kidd, K. K. et al. (2009). Inferring the demographic history of African farmers and Pygmy hunter-gatherers using a multilocus recequencing data set. PLOS Genetics, 5, 1-13. http://dx.doi.org/10.1371/journal.pgen.1000448
[48]	Poznik, G. D., Henn, B. M., Yee, M. C., Sliwerska, E., Euskirchen, G. M., Lin, A. A., Snyder, M., Quintana-Murci, L., Kidd, J. M., Underhill, P. A., & Bustamante, C. D. (2013). Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science, 341, 562-565. http://dx.doi.org/10.1126/science.1237619
[49]	Ramachandran, S., Deshpande, O., Roseman, C. C., Rosenberg, N. A., Feldman, M. W., & Cavalli-Sforza, L. L. (2005). Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proceedings of the National Academy of Sciences of the United States of America, 102, 15942-15947. http://dx.doi.org/10.1073/pnas.0507611102
[50]	Rightmire, G. P. (2009). Middle and later Pleistocene hominins in Africa and Southwest Asia. Proceedings of the National Academy of Sciences of the United States of America, 106, 16046-16050. http://dx.doi.org/10.1073/pnas.0903930106
[51]	Rito, T., Richards, M. B., Fernandes, V., Alshamali, F., Cerny, V., Pereira, L., & Soares, P. (2013). The first modern human dispersals across Africa. PLoS ONE, 8, Article ID: e80031.
[52]	Sahoo, S., Singh, A., Himabindu, G., Banerjee, J., Sitalaximi, T., Gaikwad, S., Trivedi, R., Endicott, P., Kivisild, T., Metspalu, M., Villems, R., & Kashyap, V. K. (2006). A prehistory of Indian Y-chromosomes: Evaluating demic diffusion scenarios. Proceedings of the National Academy of Sciences of the United States of America, 103, 843-848. http://dx.doi.org/10.1073/pnas.0507714103
[53]	Scozzari, R., Massaia, A., D’Atanasio, E., Myres, N.M., Perego, U.A., Trombetta, B., & Cruciani, F. (2012). Molecular dissection of the basal clades in the human Y chromosome phylogenetic tree. PLoS ONE, 7, Article ID: e49170. http://dx.doi.org/10.1371/journal.pone.0049170
[54]	Shi, W., Ayub, Q., Vermeulen, M., Shao, R. G., Zuniga, S., van der Gaag, K., de Knijff, P., Kayser, M., Xue, Y., & Tyler-Smith, C. (2010). A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations. Molecular Biology and Evolution, 27, 385-393. http://dx.doi.org/10.1093/molbev/msp243
[55]	Skoglund, P. (2013). Reconstructing the human past using ancient and modern genomes. Uppsala Disssertation from the Faculty of Science and Technology, Uppsala Universitet, Acta Universitatis Upsaliensis, Uppsala, 52 p.
[56]	Soares, P., Ermini, L., Thompson, N., Normina, M., Rito, T., Rohl, A., Salas, A., Oppenheimer, S., Macaulay, V., & Richards, M. B. (2009). Correcting for purifying selection: An improved human mitochondrial molecular clock. American Journal of Human Genetics, 84, 740-759.
[57]	Stewart, J. R., & Stringer, C. B. (2012). Human evolution out of Africa: The role of refugia and climate change. Science, 335, 1317-1321. http://dx.doi.org/10.1126/science.1215627
[58]	Stoneking, M., & Delfin, F. (2010). The human genetic history of East Asia: Weaving a complex tapestry. Current Biology, 20, R188-R193. http://dx.doi.org/10.1016/j.cub.2009.11.052
[59]	Tattersall, I. (2009). Human origins: Out of Africa. Proceedings of the National Academy of Sciences of the United States of America, 106, 16018-16021. http://dx.doi.org/10.1073/pnas.0903207106
[60]	Thomson, R., Pritchard, J. K., Shen, P., Oefner, P. J., & Feldman, M. (2000). Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data. Proceedings of the National Academy of Sciences of the United States of America, 97, 7360-7365. http://dx.doi.org/10.1073/pnas.97.13.7360
[61]	Underhill, P. A., Shen, P., Lin, A. A., Jin, L., Passarino, G., Yang, W. H., Kauffman, E. et al. (2000). Y-chromosome sequence variation and the history of human populations. Nature Genetics, 26, 358-361. http://dx.doi.org/10.1038/81685
[62]	Vigilant, L., Stoneking, M., Harpending, H., Hawkes, K., & Wilson, A. C. (1991). African populations and the evolution of human mitochondrial DNA. Science, 253, 1503-1507. http://dx.doi.org/10.1126/science.1840702
[63]	Wei, W., Ayub, Q., Xue, Y., & Tyler-Smith, C. (2013). A comparison of Y-chromosomal lineage dating using either resequencing or Y-SNP plus Y-STR genotyping. Forensic Science International: Genetics, 7, 568-572. http://dx.doi.org/10.1016/j.fsigen.2013.03.014
[64]	Xue, Y., Zerjal, T., Bao, W., Zhu, S., Lim, S. K., Shu, Q., Xu, J. J., Du, R. F., Fu, S. B., Li, P., Yang, H. M., & Tyler-Smith, C. (2005). Recent spread of a Y-chromosomal lineage in Northern China and Mongolia. American Journal of Human Genetics, 77, 1112-1116. http://dx.doi.org/10.1086/498583
[65]	Yotova, V., Lefebvre, J. F., Moreau, C., Gbeha, E., Hovhannesyan, K., Bourgeois, S., Bedarida, S. et al. (2011). An X-linked haplotype of Neandertal origin is present among all non-African populations. Molecular Biology and Evolution, 28, 1957-1962. http://dx.doi.org/10.1093/molbev/msr024