Population history of the Red Sea—genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup

Abstract

Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.

Genetic Stratigraphy of Key Demographic Events in Arabia

“…This was confirmed with whole-mtDNA sequencing of the Eurasian macrohaplogroup N (including its branches X, I, W, N1a, N1b and some R lineages), which is dominant in Arabia, attaining a frequency of 66%–83% [24,32,47,48]. The obvious missing element in those studies was the whole-mtDNA sequencing of Arabian JT lineages, which we have performed here, providing a detailed phylogeographic analysis in Supplemental Material (outline topology in S1 and S2 Figs.…”

“…We performed mtDNA founder analysis for Arabia and neighbouring regions, aiming to ascertain and date the main dispersal episodes. The founder analysis was applied to the unbiased HVS-I database available for the region, and interpreted in the light of the more precise dating information gathered from whole-mtDNA sequences of informative haplogroups [24,32,47,48]. We also updated the phylogenetic trees of haplogroups J, T, L4 and L6, by performing 83 new whole-mtDNA sequences.…”

Early Back-to-Africa Migration into the Horn of Africa

“…Third, in the Eurasian mitochondrial HV1 and R0a lineages there are several sub-haplogroups (HV1a3, HV1b1, R0a2b, R0a2g) that are found in both the HOA and the Arabian Peninsula. Within these shared sub-haplogroup lineages, the HOA and Arabian haplotypes are distinct, suggesting that the migration that brought these lineages into the HOA happened soon after the sub-haplogroups began to diversify at 6–10 ka [38], [39].…”

Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia

“…Additional, previously published Yemeni mitogenomes from the collection of C.J.M. were included as well: 9 were included in all analyses, and another 12 were included in the analyses with additional non-M1/N1 samples (further described below) Musilov a et al, 2011;Al-Abri et al, 2012) (see Supporting Information Table S1 for all Yemeni samples). A set of 310 previously published, comparative modern human mitogenomes from around the world (which are nearly all non-Yemeni), as well as seven Neanderthal and Denisovan mitogenomes, were included in the Bayesian analyses (see Supporting Information Table S2 for all modern comparative samples).…”

“…Specifically, analyses of mitochondrial hypervariable region (HVR) sequences suggest there has been ongoing migration between Yemen and the Horn-of-Africa over the last 3,000-4,000 years as well as broader migration into Yemen from sub-Saharan Africa, South Asia, and western Eurasia Cern y et al, 2008). Furthermore, analyses using whole mitogenome sequences from haplogroups frequently found in Yemen (e.g., HV1, R0a, and R2) indicate Yemeni mitogenome variation may be the product of multiple population expansions within the last 10-15 kya Musilov a et al, 2011;Al-Abri et al, 2012). Additionally, Fernandes et al (2015) argue based on founder analyses that Arabia mitogenomic diversity was influenced by multiple stages of migrations from the Levant, subSaharan Africa, and South Asia over the last 16 kya.…”