East Africa is a key region in human evolutionary history, serving as a major corridor for population movements within and out of the continent and characterised by extensive genetic, ecological, and ethnolinguistic diversity. Kenya represents a complex population interface shaped by successive waves of migration and admixture. Hunter-gatherer (HG) descendant groups, now largely confined to highland forest regions following displacement by Nilotic and Bantu expansions, remain underrepresented in genomic studies and reference databases. Consequently, their population dynamics and maternal connectivity, both locally and across Africa, remain poorly understood. To address this gap, we generate whole mitochondrial genomes from HG descendant communities, specifically the Okiek and Dorobo groups inhabiting the Kenyan highland forests.

We analysed complete mitochondrial genomes from n = 250 individuals from HG descendant (Okiek, Dorobo), Nilotic (Maasai, Kalenjin) and Bantu-speaking (Luhya) populations. These data provide high-resolution mitogenome profiles for inclusion in EMPOP and improve the representation of East African populations in forensic and population genetic reference frameworks.

Population genetic diversity parameters (haplotype diversity (H), number of sequences (K), number of segregating sites (S), nucleotide diversity (π), and associated estimators of female effective population size (θK, θS, θπ)) are estimated using Arlequin v3.5. Haplogroup frequency profiling, haplotype sharing, and comparisons with regional datasets (e.g Ethiopia and Tanzania) were performed. Spatial patterns were modelled using kriging interpolation in R with packages gstat and automap, while population structure was assessed using ΦST, AMOVA, multidimensional scaling (MDS), and correspondence analysis using FactoMineR for an extended regional dataset.

Preliminary results show regional and sub-regional variation among Okiek groups, with Mau Forest populations characterised by higher frequencies of L3-L5  and M1 lineages, and Mt. Elgon Okiek predominated by L0a and L3-L4. In the Mau region, Okiek and Dorobo populations share dominant haplogroups (M1a1f and L4b), while maintaining a heterogeneous haplogroup composition, indicating both signals of shared ancestry and population-specific maternal lineage variation. Bantu-speaking Luhya are dominated by L3 lineages, whereas neighbouring Nilotic groups display a more even distribution, showing elevated frequencies for haplogroups L2a and L4b specifically.

Overall, these preliminary findings indicate evident shared maternal ancestry alongside emerging signals of fine-scale population structure among HG-descendant groups of the Kenyan highlands and neighbouring communities.

Authors

• Mohaimin Kasu (University of the Western Cape, South Africa)
• Toni November (University of the Western Cape, South Africa)
• Denis Misiko Mukhongo (Alupe University, Kenya)
• Maria Eugenia D'Amato (University of the Western Cape, South Africa)