Characterisation of Mitochondrial DNA and Y-STR Variation in the Libyan Population

Despite the distinct strategic geographical location of Libya linking North Africa with the Middle East and Europe with sub-Saharan Africa and rich human settlement history, the genetic diversity in Libya has not been well studied compared to other North African populations.

To shed light on the genetic composition of the modern populations in Libya and investigate human migration patterns and arrival time of different ethnic and geographic groups, samples were collected and analysed for 3 ethnic groups including Berber, Arab and African groups in Libya. 375 hypervariable sequence mitochondrial DNA (mtDNA) fragments were analysed by Sanger sequencing, 199 samples were selected for whole mitogenome next-generation sequencing and 219 samples had 23 Y chromosomal STR loci variations analysed.

Data analysis showed that both female and male lineages in Libya correlated with their geographical region in North Africa. However, the analysis showed that both lineages experienced a different pattern of gene flow that led to the absence of correlation between their ancestral origin where mitochondrial DNA showed a dominance of Eurasian lineages including N1, R0, HV, V, H, J, T, U, K, and X and moderate influence of sub-Saharan lineages including L0, L1, L2, L3, and L4. The paternal genome-wide diversity was mainly constituted by dual components; indigenous North African lineage haplogroup E-M81 and the Arabic components J (xJ1a,J2)-M304. The analysis also showed that the distributions of some maternal lineages statistically correlated with ethnicity such as haplo group U6 for Libyan Berber, haplogroup L for African Libyans and haplogroups R0a for Arab group. Furthermore, founder analysis of complete mtDNA genome show that all the Berber populations have local roots involved in the first settlement of the current population in Libya during Iberomaurusian period ~22,000 years ago including haplogroups U6 and M1 and have received multiple maternal lineages from West Europe during the last glacial warming, Levant components during the Holocene and in Neolithic associated with the spread of agriculture. Neutrality tests confirmed the evidence of a recent population expansion in Libya that is probably attributed to the major Arab arrival in 7th and 10th centuries. Age estimation and founder analysis of mtDNA also revealed that the majority of current sub-Saharan lineages found in Libya were probably recently introduced associated with the trans-Saharan slave trade that was started in the seventh century. In addition, there were a few lineages that were most likely introduced in Libya with the spread of Iberomaurusian expansion culture from the Levant (haplogroup L2) and during the early Holocene after a humid period (haplogroup L1).

With regards to the analysis of the Libyan Berber populations maternal lineages, the Zuwara population experienced high levels of genetic drift resulting in a small number of haplotypes elevated to high frequencies as demonstrated by haplogroups J1c. In contrast, the Libyan Arabs being relative newcomers to Libya had much higher levels of diversity among them.

Overall, the newly presented data in this study refines the knowledge about Libyan population history and serves as a basis for comparison with other populations and contributes to the establishment of databases suitable for forensic casework where mtDNA and Y-STR information might be helpful.