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Mitochondrial DNA Structure in the Arabian Peninsula

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Mitochondrial DNA Structure in the Arabian Peninsula

Khaled K Abu-Amero et al. BMC Evol Biol.

Abstract

Background: Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3.

Results: To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source.

Conclusion: Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.

Figures

Figure 1
Figure 1
Map of the Arabian Peninsula showing the Saudi regions and Arabian countries studied.
Figure 2
Figure 2
Phylogenetic tree based on complete M1 sequences. Numbers along links refer to nucleotide positions. A, C, G indicate transversions; "d" deletions and "i" insertions. Recurrent mutations are underlined. Regions not analyzed are in parenthesis. Star differs from rCRS [62, 63] at positions: 73, 263, 303i, 311i, 489, 750, 1438, 2706, 4769, 7028, 8701, 8860, 9540, 10398, 10873, 10400, 11719, 12705, 14766, 14783, 15043, 15301, 15326, 16223 and 16519. GenBank accession numbers of the subjects retrieved from the literature are: 43 Oli (EF060354), 30 Oli (EF060341) and 40 Oli (EF060351) from Olivieri et al. [37]; 626 God (EF184626), 635 God EF184635 and 637 God (EF184637) from Gonder et al. [39]; and 957 Goz (DQ779926) from González et al. [38].
Figure 3
Figure 3
Phylogenetic tree based on complete M sequences. Numbers along links refer to nucleotide positions. A, C, T indicate transversions; "d" deletions and "i" insertions. Recurrent mutations are underlined. Regions not analyzed are in parenthesis. Star differs from rCRS [62, 63] at positions: 73, 263, 303i, 311i, 489, 750, 1438, 2706, 4769, 7028, 8701, 8860, 9540, 10398, 10873, 10400, 11719, 12705, 14766, 14783, 15043, 15301, 15326, 16223 and 16519. GenBank accession numbers of the subjects retrieved from the literature are: C182 Sun (AY922276), T135 Sun (AY922287), R58 Sun (AY922299), C56 Sun (AY922274), and C51 Sun (AY922261) from Sun et al. [20]; ON96 Tan (AP008599) from Tanaka et al. [40]; 45 VHP (DQ404445) from van Holst Pellekaan et al. [25]; DQ07 Mer (DQ137407), DQ99 Mer (DQ137399) from Merriwether et al. [24]; AY85 Ing (AY289085) from Ingman and Gyllensten [22]; Au38 Hud (EF495222) from Hudjashov et al. [26]; and 201 Abu (DQ904234) from Abu-Amero et al. [31].
Figure 4
Figure 4
Phylogenetic tree based on complete J1b sequences. Numbers along links refer to nucleotide positions. T indicates transversion and "i" insertions. Recurrent mutations are underlined. Regions not analyzed are in parenthesis. Star differs from rCRS [62, 63] at positions: 73, 263, 295, 311i, 489, 750, 1438, 2706, 4216, 4769, 7028, 8860, 10398, 11251, 11719, 12612, 13708, 14766, 15326, 15452A, 16069 and 16126. GenBank accession numbers of the subjects retrieved from the literature are: R80 Pal (AY714033) and B30 Pal (AY714035) from Palanichamy et al. [18]; 498 Her (EF657673) and 501 Her (EF657678) from Herrnstad et al. [64]; 238 Cob (AY495238), 231 Cob (AY495231), 234 Cob (AY495234), 235 Cob (AY495235), 232 Cob (AY495232), 236 Cob (AY495236), 237 Cob (AY495237) and 233 Cob (AY495233) from Coble et al. [65]; L21 and L170 from Rose et al. [66]; 181 Fin (AY339582) and 180 Fin (AY339581) from Finnilä et al. [50]; 7 Est from Esteitie et al. [67]; 87 MM (AF381987) from Maca-Meyer et al. [6]; 488 (DQ282488), 489 (DQ282489), 490 (DQ282490), 492 (DQ282492) and 491 Jus (DQ282491) from Just et al. [68].
Figure 5
Figure 5
Reduced median network relating J1b HVSI sequences. The central motif (star) differs from rCRS at positions: 16069 16126 16145 16222 16261 for HVI control region. Numbers along links refer to nucleotide positions minus 16000: homoplasic mutations are underlined. The broken lines are less probable links due to mutation recurrence. Size of boxes is proportional to the number of individuals included. Codes are: Am = Armenian, Ar = Saudi Arab, Bd = Bedouin Arab, Eg = Egyptian, Ge = Georgian, In = Iranian, Iq = Iraqi, Jo = Jordanian, Ka = Kazakhs, Ki = Kirghiz, Ku = Kurd, Mo = Moroccan Berber, NC = Caucasian, Om = Omani, Pa = Palestinian, Qa = Qatar, Sy = Syrian, Ta = Tajik, Tm = Turkmen, Tn = Tunisian, Tu = Turk, UA = United Arab Emirates, UZ = Uzbek, Ye = Yemeni.
Figure 6
Figure 6
Graphical relationships among the studied populations. MDS plot based on FST haplogroup distances. Codes are: Ce = Central Saudi Arab, Dz = Druze, Et = Ethiopian, Ke = Kenyan, No = Northern Saudi Arab, Nu = Nubian, SE = Southeastern Saudi Arab, Su = Sudan, We = Western Saudi Arab. Others codes as in Figure 5.

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