The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa

Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.
The American Journal of Human Genetics (Impact Factor: 10.93). 02/2012; 90(2):347-55. DOI: 10.1016/j.ajhg.2011.12.010
Source: PubMed


A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The "southern coastal route" model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ∼60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55-24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.

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    • "Fernandes et al. (2012) note that basal lineages of macrohaplogroup N (e.g., N1, N2, and X) are present throughout the Near East and neighboring portions of Africa but appear concentrated specifically within Arabia. These lineages have been dated to around 60 kya, and it has been suggested that they are related to the OOA migration; however, these clades are spread over much of the Near East and are not specific to Yemen or the Horn of Africa/ southern Arabia region (Fernandes et al., 2012). Also, an analysis of nuclear SNP data suggested there were older migrations back into the Horn of Africa that date to at least 23 kya; however, these migrations could not be dated due to the limitations of nuclear data (Hodgson et al., 2014). "
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    ABSTRACT: Objectives: Anatomically, modern humans are thought to have migrated out of Africa ∼60,000 years ago in the first successful global dispersal. This initial migration may have passed through Yemen, a region that has experienced multiple migrations events with Africa and Eurasia throughout human history. We use Bayesian phylogenetics to determine how ancient and recent migrations have shaped Yemeni mitogenomic variation. Materials and methods: We sequenced 113 mitogenomes from multiple Yemeni regions with a focus on haplogroups M, N, and L3(xM,N) as these groups have the oldest evolutionary history outside of Africa. We performed Bayesian evolutionary analyses to generate time-measured phylogenies calibrated by Neanderthal and Denisovan mitogenomes in order to determine the age of Yemeni-specific clades. Results: As defined by Yemeni monophyly, Yemeni in situ evolution is limited to the Holocene or latest Pleistocene (ages of clades in subhaplogroups L3b1a1a, L3h2, L3x1, M1a1f, M1a5, N1a1a3, and N1a3 range from 2 to 14 kya) and is often situated within broader Horn of Africa/southern Arabia in situ evolution (L3h2, L3x1, M1a1f, M1a5, and N1a1a3 ages range from 7 to 29 kya). Five subhaplogroups show no monophyly and are candidates for Holocene migration into Yemen (L0a2a2a, L3d1a1a, L3i2, M1a1b, and N1b1a). Discussion: Yemeni mitogenomes are largely the product of Holocene migration, and subsequent in situ evolution, from Africa and western Eurasia. However, we hypothesize that recent population movements may obscure the genetic signature of more ancient migrations. Additional research, e.g., analyses of Yemeni nuclear genetic data, is needed to better reconstruct the complex population and migration histories associated with Out of Africa. Am J Phys Anthropol, 2015. © 2015 Wiley Periodicals, Inc.
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    • "Fig . 1 ; supplemental Table S1 ) . This is reflected in a sub - stantial Eurasian autosomal component in Eastern Africa , which is also evident to some extent in Kenya ( Pagani et al . 2012 ) . Due to deep ancestry and the distribution of these lineages ( Abu - Amero et al . 2008 ; Brakez et al . 2001 ; Černý et al . 2008 ; Coudray et al . 2009 ; Fernandes et al . 2012 ; Kivisild et al . 2004 ; Olivieri et al . 2006 ; Rhouda et al . 2009 ; Richards et al . 2000 , 2003 ) , none of the West Eurasian mtDNAs found in Uganda has a likely European source , for example , resulting from the heavy European colonial involvement since the 1870s ( Maxon 2009 ) . One possibility is a Bronze - Age dispersal from th"
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    Human Genetics 07/2015; 134(9). DOI:10.1007/s00439-015-1583-0 · 4.82 Impact Factor
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    • "Slow mutation rates yield older dates of divergence and fast mutation rates yield younger dates. For example, estimates from modern human genetic data have ranged between ~84 and 44 ka from mtDNA data (Macaulay et al., 2005; Endicott and Ho, 2008; Endicott et al., 2009; Fernandes et al., 2012; Lippold et al., 2014); ~120 and 60 ka from Y-chromosome data (Lippold et al., 2014; Scozzari et al., 2014), and ~140 and 65 ka from nuclear data (Gutenkunst et al., 2009; Xing et al., 2010; Eriksson et al., 2012; Scally and Durbin, 2012; Reyes-Centeno et al., 2014). Calibration with fossil genomes has now served to constrain these rates for the recent human lineage (Fu et al., 2013b, 2014; Rieux et al., 2014). "
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    ABSTRACT: The modern human expansion process out of Africa has important implications for understanding the genetic and phenotypic structure of extant populations. While intensely debated, the primary hypotheses focus on either a single dispersal or multiple dispersals out of the continent. Here, we use the human fossil record from Africa and the Levant, as well as an exceptionally large dataset of Holocene human crania sampled from Asia, to model ancestor-descendant relationships along hypothetical dispersal routes. We test the spatial and temporal predictions of competing out-of-Africa models by assessing the correlation of geographical distances between populations and measures of population differentiation derived from quantitative cranial phenotype data. Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.
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