Maternal Genetic Diversity and Population Structure of Four Jordanian Subpopulations Revealed by Mitochondrial DNA Variation

Background/Objectives: Jordan’s geographical position at the crossroads of the Southern Levant, Arabian Peninsula, and Africa has contributed to its complex demographic and population interactions and genetic admixture. This study aimed to investigate the maternal genetic structure among four Jordanian subpopulations: Fellahin (Farmers), Bedouins (Nomads), Alnawar (Banu Murra), and Beer Al-Saba Bedouins. Methods: A total of 192 unrelated participants, 48 from each subpopulation, were analyzed after required ethical approvals. Three mitochondrial DNA regions (the D-loop, cytochrome b, and cytochrome c oxidase subunit 1) were amplified and sequenced. The predicted maternal haplogroups were assigned using the online HaploGrep 3 tool. Further genetic structure and diversity analyses were assessed through Multidimensional Scaling (MDS) analysis based on the FST distance matrix, along with a Principal Coordinate Analysis (PCoA). The studied subpopulations were also compared with other populations from the Levant, the Arabian Peninsula, North Africa, East and West Africa, and Europe. Results: The most frequent predicted haplogroup was U in Fellahin (18.75%) and Bedouins (22.92%), H in Alnawar (Banu Murra) (18.75%), and U in Beer Al-Saba Bedouins (20.83%). Maternal genetic diversity was high among the four studied subpopulations, with an average value of 0.9. MDS analysis placed the Jordanian subpopulations within the broader maternal genetic landscape of the Levant and Arabian Peninsula, while also revealing population-specific differentiation, particularly among the Bedouins of Beer Al-Saba. PCoA further showed substantial overlap among Fellahin and Bedouins, partial differentiation of Beer Al-Saba Bedouins, and broader dispersion among Alnawar (Banu Murra) individuals. Interestingly, in comparison with selected Roma subgroups, Alnawar (Banu Murra) showed greater similarity in the predicted mitochondrial haplogroup composition with other Jordanian groups than most of the selected Roma reference populations. Conclusions: The obtained results showed substantial maternal genetic diversity within the studied Jordanian subgroups and highlight the influence of distinct demographic histories on the mitochondrial variation. The study also provides additional mtDNA data that may support future development of population-specific mitochondrial reference datasets for forensic applications in Jordan.