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L3 basic lineages migrated back to Africa, new human origin model, Cabrera 2018
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[QUOTE]Originally posted by the lioness,: [QB] https://www.biorxiv.org/content/biorxiv/early/2017/12/13/233502.full.pdf (pre print) [b]Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago. [/b] 2018 Vicente M Cabrera, View ORCID ProfileJulia Patricia Marrero Rodriguez, View ORCID ProfileKhaled K Abu-Amero, Jose M Larruga doi: https://doi.org/10.1101/233502 Abstract Background: After three decades of mtDNA studies on human evolution the only incontrovertible main result is the African origin of all extant modern humans. In addition, a southern coastal route has been relentlessly imposed to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, that out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion. Consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basic L3 lineages around 70 kya. Results: The coalescence ages of all Eurasian (M,N) and African L3 lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. A Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. It seems better to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions: These results are congruent with a model proposing an out-of-Africa of early anatomically modern humans around 125 kya. A return to Africa of Eurasian fully modern humans around 70 kya, and a second Eurasian global expansion by 60 kya. Climatic conditions and the presence of Neanderthals played key roles in these human movements. Results: The coalescence ages of all Eurasian (M,N) and African 28 L3 lineages, both around 71 kya, are not significantly different. The 29 oldest M and N Eurasian clades are found in southeastern Asia 30 instead near of Africa as expected by the southern route hypothesis. 31 The split of the Y-chromosome composite DE haplogroup is very 32 similar to the age of mtDNA L3. A Eurasian origin and back 33 migration to Africa has been proposed for the African Y- 34 chromosome haplogroup E. Inside Africa, frequency distributions of 35 maternal L3 and paternal E lineages are positively correlated. This 36 correlation is not fully explained by geographic or ethnic affinities. It 37 seems better to be the result of a joint and global replacement of the 38 old autochthonous male and female African lineages by the new 39 Eurasian incomers. [b]A new mtDNA model about the origin and dispersion of Homo 693 sapiens[/b] 694 At mtDNA level, the sampling and data accumulated during the last 695 thirty years, including those contributed by ancient DNA studies, 696 allow us to propose a more detailed model of the origin and 697 worldwide spread of modern humans than the ones proposed three 698 decades ago. There are three fossil series in northwest, northeast, 699 and southern Africa that chronologically and morphologically 700 recapitulated the evolution of Homo sapiens from early archaic 701 around 600 kya to early moderns by 200 kya [123]. The recent 702 dating of Middle Stone Age tools (315 ± 34 kya) and early modern 703 human fossils (286 ± 32 kya) from Jebel Irhoud in Morocco, places 704 the emergence of our species, and of the Middle Stone Age, close in 705 time and long before the age of about 200 kya previously suggested 706 for the common origin of all humans in eastern Africa [124]. These 707 data coincide in time with the existence of an old Y-chromosome 708 lineage (A00) detected in samples of western-central African 709 ascendance and dated 338 kya (95% CI: 237-581 kya), remarkably 710 older than common estimates based on the Y-chromosome and 711 mtDNA TMRCAs [125]. The fact that the following more divergent Y- 712 chromosome A lineages (A0, A1a) also have a western-central bioRxiv preprint first posted online Dec. 13, 2017; doi: http://dx.doi.org/10.1101/233502. 713 African location, strongly supports this region as the origin of an 714 ancestral human population from which the ancestors of early 715 modern humans emerged [90, 103]. The most ancient splits and 716 spreads of the mtDNA lineages also situated the hypothetical origin 717 of all extant maternal lineages around this area. Although the 718 earliest L0 clade diverged around 145 kya (Additional file 1: Table 719 S3) and had its first expansions in southern Africa (L0d, L0k), the 720 subsequent splits gave rise to L1 and L5 around 131 kya and 123 721 kya spreading to western and eastern Africa respectively. These 722 long range African dispersions place its putative origin somewhere 723 in Central Africa (Figure 1a). The same "centre-of-gravity" argument 724 was used by other authors to suggest a Central African origin [126]. 725 It is worth mentioning that while ancestral southern African 726 Khoesan-speaking population still maintain high frequencies of 727 primitive L0d and k lineages [94, 106, 127, 128], and that in the 728 hunter- gatherer populations of central-western Africa the L1c 729 haplogroup is dominant [108, 109], L5 in eastern Africa has today 730 only a marginal presence [114, 129], most probably due to its 731 displacement produced by more recent waves of better adapted 732 incomers. The presence of L5 in southern Africa and eastern Mbuti 733 pygmies [70, 109, 118, 127] is the result of later migrations. Most 734 probably, next split, around 100 kya, also occurred in Central Africa 735 resulting in sister clusters L2 and L3'4'6 that, respectively, produced 736 initial westward and eastward expansions (Figure 1a). Although the 737 oldest L2 lineages have been sampled in western Africa [130], 738 today, as result of successive spreads inside the continent, this 739 clade has a pan-African range [119]. In eastern Africa, the cluster 740 L3'4'6 was the embryo of the full Eurasian maternal diversity. Its first 741 split was haplogroup L6 that nowadays is a rare eastern lineage with bioRxiv preprint first posted online Dec. 13, 2017; doi: http://dx.doi.org/10.1101/233502. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. 742 a deep founder age (about 100 kya) but a rather recent expansion 743 (about 25 kya). It has been found at frequencies below 1% in 744 Egyptians [131], Somalis [132], Kenyan [133], and eastern Nilotes 745 from Uganda [114]. Mean frequency rise in Ethiopia (3.15 ± 1.15 %) 746 with a maximum (15.8%) in Ongota, an extinguishing linguistic 747 isolate of uncertain adscription [129]. Outside Africa L6 has not been 748 detected in the Levant [134]. It is present in the Arabian Peninsula at 749 frequencies below 1% in Saudi samples but raises 12% in some 750 Yemeni samples [135]. Attending to the L6 phylogeny (Additional file 751 2: Figure S1), it seems that not all the Yemeni lineages are a subset 752 of the eastern African lineages as there is at least one for which its 753 common node coincides with the expansion of the whole 754 haplogroup. Based on its peculiar phylogeography, the possibility 755 that L6 could have originated from the same out-of-Africa southern 756 migration that colonized Eurasia was suggested [135]. If this were 757 the case, this early L6 expansion would give genetic support to the 758 reported presence of modern humans in the Arabian Peninsula, 759 around 125 kya, based on archaeological evidence [12–14]. This 760 suggestion also enjoys climatic support as this period coincides with 761 humid environmental conditions in Arabia [136]. However, it seems 762 that this possible human expansion did not extend beyond the 763 Peninsula as L6 derived lineages have not yet been detected across 764 Eurasia. The return to arid conditions, most probably, caused the 765 decline of the populations carrying the L6 lineage that had to retreat 766 to refuge areas as the highlands of Yemen and Ethiopia until more 767 favorable conditions made possible their subsequent recovery in 768 eastern Africa and Yemen. The long mutational stem that precedes 769 the expansion of L6 (Additional file 2: Figure S1), would faithfully 770 represent that strong and long bottleneck. Next phylogenetic bioRxiv preprint first posted online Dec. 13, 2017; doi: http://dx.doi.org/10.1101/233502. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. 771 bifurcation produced the ancestors of L3 and L4 haplogroups 772 (Additional file 2: Figure S1). Nowadays, the highest frequencies 773 and diversities of L4 are found in eastern Africa, but it has spread 774 over the entire continent (Table 3). Besides, it has been detected at 775 frequencies below 1% in the Levant [137], and the Arabian 776 Peninsula [74, 138]. Most probably, as consequence of drift effects, 777 some populations show outstanding frequencies of L4. In western 778 Africa, Samoya (28.6%) and Kassena (21.2%) samples, speakers of 779 the Gur linguistic family, stand out [72]. In Ethiopia, the cases of the 780 Omotic-speaking Hamer (18.2%), the Cushitic-speaking Daasanach 781 (22.2%), and the Nilotic-speaking Gumuz (24.0%) and Nyangatom 782 (21.6%) are also remarkable [129, 139]. However, without any 783 doubt, are the Tanzanian click-speaking Hadza (58%) and Sandawe 784 (43%) whom show the highest values for L4 in Africa [111–113], 785 this, together with the elevated frequencies that Hadza (50%) and 786 Sandawe (15%) present for the Y-chromosome haplogroup B-M112 787 [140], points to human expansions from the North as those that most 788 strongly influenced the gene pool of these groups. Attending to the 789 age of bifurcation from L3 (around 95 kya), it could be thought that 790 these L4 expansions occurred before our proposed return to Africa 791 of L3 basic lineages. However, as the main spreads of its 792 descendant clusters L4a (54.8 kya) and L4b (48.9 kya) [94, 138] had 793 taken place around the same time window that the majority of the L3 794 and L2 branches in Africa, the most probable explanation is that 795 improved climatic conditions after 60 kya motivated a global 796 demographic growth on the African continent. Noticed that the 797 evidence for an L3 first expansion in East Africa [89] is likewise in 798 support of the out-of-Africa scenario than of a Eurasian back-flow as 799 proposed here. We hypothetically situated the L3'4 node in bioRxiv preprint first posted online Dec. 13, 2017; doi: http://dx.doi.org/10.1101/233502. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. 800 northeast Africa or the Near East (Figure 1a) to allow an out-of- 801 Africa of the pre-L3 clade. The Y-chromosome CDEF ancestor had 802 to be its male counterpart. Other female and male lineages could 803 have moved with them but, presumably gone extinct without 804 contributing either to the maternal or paternal gene pools of the 805 living human populations of Eurasia. 806 Under the scenario proposed here, early anatomically modern 807 humans went out of Africa around 125 kya with a simple Middle 808 Stone Age technology that was not superior to that manufactured by 809 the Neanderthals. Favored by mild climatic conditions, these African 810 pioneers progressed through West Asia and reached Central Asia 811 overlapping in its way with the southern geographic range occupied 812 by the Neanderthals. A new vision of the fossil and archaeological 813 records of those regions [88, 141, 142] might uncover the path 814 followed by those early African colonizers. At favorable conditions 815 for both hominin groups, we might predict limited exchange of skills, 816 lithic technology, and sex. However, when after 75 kya glacial 817 environments became dominant, Neanderthals had to retreat 818 southwards pushing out humans in its way. Confronted with the 819 northern foothills of the Himalayas, humans moved in two directions, 820 westwards to return to Africa, and eastwards to reach southeastern 821 Asia across China (Figure 1b). The second part of this model has 822 been already outlined in precedent articles [53–55]. [/QB][/QUOTE]
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