Phylogenetic Relationships, Genetic Diversity, and Neutrality Tests of Nigerian Cattle Populations in Taraba State

The research investigated the genetic diversity and genetic neutrality of cattle populations in Taraba State, Nigeria. The study analyzed 100 reference populations, and 28 blood samples were used for mitochondrial DNA sequencing using Flinders Technology Associates (FTA) paper, which covered five locations (Iware, Wukari, Donga, Gembu, and Jalingo) and five breeds (Bokoloji, Muturu, Red Bororo, White Fulani, Adamawa Gudali). The research utilized Tajima's Neutrality Test, Tajima's Relative Rate Clock Test, and phylogenetic analysis to determine patterns of molecular evolution and population structure. The analysis of location-based neutrality showed that all populations tested positive for Tajima's D, with Iware recording 2.73 D value, Wukari showing 3.33 D value, Donga presenting 1.99 D value, and Gembu achieving 4.04 D value. The nucleotide diversity (π) measured between 0.5759 in Donga and 0.6781 in Gembu, indicating moderate to high genetic variability, whereas Wukari and Gembu displayed the most segregating sites with S = 778 and 779. The findings demonstrate evolution that deviates from neutral patterns due to three factors: balancing selection, population subdivision, and historical demographic patterns. The breed-based analysis produced positive Tajima's D results, reaching peak values in White Fulani (D = 4.49) and Red Bororo (D = 4.05), with both breeds showing high nucleotide diversity (π = 0.6535 and 0.6989, respectively). The Bokoloji (D = 1.25) and Muturu (D = 1.00) results showed reduced polymorphism levels, with S = 562 and 512. The Tajima's Clock Test results showed that evolutionary rates differed significantly between study locations. Iware showed the highest number of identical sites (202) and very few divergent sites (6), but a pronounced imbalance in unique substitutions, specially in sequence A (536). Wukari, Donga, and Gembu showed more divergent sites, with their total counts reaching 244, 229, and 193 respectively, while their unique differences among sequences appeared to be distributed more evenly, which proved the molecular clock predictions to be less accurate. The analysis of phylogenetic relationships demonstrated that different breeds of cattle from different regions showed shared ancestry together with genetic mixing from different populations. The research results demonstrate that Taraba State cattle populations possess high genetic diversity together with non-neutral evolutionary patterns and different rates of evolutionary change, which affect both conservation efforts and breeding programmes.