Ancestral mitochondrial N lineage from the Neolithic \u2018green\u2019 Sahara

Stefania Vai,Alexander Hübner,Elena Pilli,Martina Lari,Alessandra Modi,Stefania Sarno,Mary Anne Tafuri,Marina Gallinaro,Safaa Mataich,David Caramelli,Donata Luiselli,Giorgio Manzi,Savino Di Lernia

doi:10.1038/s41598-019-39802-1

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.

Highlights

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
The origin of African haplogroup L3, from which N originated, has been dated around 60–70 ka and its expansion in Eastern Africa linked with the exit of Anatomically Modern Humans (AMH) from the continent
The M and N haplogroups, which lie at the base of Eurasian mtDNA diversity, are today globally distributed outside Africa and are dated to around 50–65 ka, very close to the ancestral L3 clade

Summary

Introduction

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. We present newly obtained mitochondrial genomes from two ~7000-yearold individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. African genetic variability is well known only for current times, but local population genetics dynamics and back-migrations from Eurasia could have modified haplotype frequencies, thereby masking ancient genetic scenarios[4,5,6,7] Several variables, such as temperature, pH and salinity, influence molecular degradation[8,9] and environmental conditions in hot and arid regions of Africa do not favour DNA preservation. We extracted DNA from several bone and skin samples (Table S2) and performed a capture enrichment for the mitochondrial genome (mtDNA)

Methods

Results

Conclusion