Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara

Abstract

Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.

Figure 1

The ~7000-year-old individuals from Takarkori Rockshelter in their context. (a) Map of Africa with location of the site (white dot); (b) depositional relations of TK RS H1 and H9 (drawn by F. Del Fattore); details of skull (c) and hands (d) of TK RS H1.

Figure 2

Median Joining Network representing phylogenetic relationships between the Takarkori samples TK RS H1 and TK RS H9 (in red), 8 ancient sequences (names are indicated at the nodes) and 538 modern sequences representing the major mitochondrial lineages and sub-lineages for N macro-haplogroup, indicated in different colours. The reference sequences rCRS and RSRS are represented with black nodes.

Figure 3

Phylogenetic tree constructed for the Takarkori sample TK RS H1 and 209 published complete genomes of ancient and modern samples. The major mitochondrial lineages and sub-lineages for N macro-haplogroup are indicated in different colours as in Fig. 2.

Figure 4

Map of Africa with the alternative models discussed. Haplogroups are indicated in black circles in their probable area of origin. Continuous arrows indicate spread by migration, while dashed arrows indicate molecular differentiation from one haplogroup to another. Dates of origin of haplogroups are indicated in squares. Dates along arrows indicate possible migration time. (a) Haplogroup N differentiates from L3 in the African continent, with a subsequent spread out of Africa. (b) Haplogroups M and N diverged from L3 outside Africa or during the expansion of AMH out of the continent; later migrations during Early Upper Paleolithic and the Neolithic diffusion led some lineages back to North Africa.