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

Abstract

Anatomically modern humans (AMHs) left Africa ~60,000 years ago, marking the first of multiple dispersal events by AMH between Africa and the Arabian Peninsula. The southern dispersal route (SDR) out of Africa (OOA) posits that early AMHs crossed the Bab el-Mandeb strait from the Horn of Africa into what is now Yemen and followed the coast of the Indian Ocean into eastern Eurasia. If AMHs followed the SDR and left modern descendants in situ, Yemeni populations should retain old autochthonous mitogenome lineages. Alternatively, if AMHs did not follow the SDR or did not leave modern descendants in the region, only young autochthonous lineages will remain as evidence of more recent dispersals. We sequenced 113 whole mitogenomes from multiple Yemeni regions with a focus on haplogroups M, N, and L3(xM,N) as they are considered markers of the initial OOA migrations. We performed Bayesian evolutionary analyses to generate time-measured phylogenies calibrated by Neanderthal and Denisovan mitogenome sequences in order to determine the age of Yemeni-specific clades in our dataset. Our results indicate that the M1, N1, and L3(xM,N) sequences in Yemen are the product of recent migration from Africa and western Eurasia. Although these data suggest that modern Yemeni mitogenomes are not markers of the original OOA migrants, we hypothesize that recent population dynamics may obscure any genetic signature of an ancient SDR migration.

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history

“…Consistent with previous findings, our results also indicate that significant gene flow must have occurred between the Levantine and southern Arabian populations (Al‐Abri et al, ; Fernandes et al, ; Fernandes et al, ; Vyas et al, ; Vyas et al, ). This conclusion is supported by Vyas et al () based on ADMIXTURE analyses in which they found that two IACs made up most of the ancestry in these Levantine and southern Arabian populations.…”

Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history

“…Consistent with previous findings, our results also indicate that significant gene flow must have occurred between the Levantine and southern Arabian populations (Al-Abri et al, 2012; Fernandes et al, 2012; Fernandes et al, 2015; Vyas et al, 2017a; Vyas et al, 2016). Regardless of the origin of introgression in the Levant and southern Arabia or the relatedness of the populations in this regions, it would not be expected that selectively-neutral SNPs would maintain such similar frequencies in both regions (Tables S8, S10).…”

Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago

“…Concerning the less frequent L4, L5, and L6 clades, our L4b1a (Iv136) sequence from the Ivory Coast shares tip mutations 789, 7166 and 14935 with geographically close sequences (JQ044848, JQ045081) from Burkina Faso [72]. Likewise, the Arab L4a2 (AR1116) sequence is closely related to other African L4a2 sequences (EU092799, EU092800), and the L4b2a1 (AR197) isolate resulted identical to a sequence (KM986608) from Yemen [73]. From the analysis of partial sequences [53, 74], we can assure representatives of branches L4a1, L4a2 and L4b2 exist in Saudi Arabia.…”