Tilapia species play a pivotal role in the development of aquaculture in Tanzania. However, knowledge of their genetic diversity and population structure remains limited. In addition, unregulated movement of fingerlings and broodstock between farms, as well as introductions from hatcheries into natural water bodies, has led to species mixing and unintentional hybridization events. Therefore, assessing population structure and genetic diversity is essential, thereby supporting both conservation and aquaculture management. In this study, we analyzed double-digest Restriction-site Associated DNA sequencing (ddRAD-seq) data compiled from previously published studies to distinguish between two tilapia species: Nile tilapia ( Oreochromis niloticus ) and Rufiji tilapia ( Oreochromis urolepis urolepis ), and to investigate their genetic diversity and population structure across Tanzania. A total of 550 fish samples from 27 sites were included in the study. Genetic diversity indices revealed that Rufiji tilapia populations exhibited a broader range and overall higher genetic diversity (He = 0.078–0.326; Ho = 0.075–0.228) compared to Nile tilapia populations. Introduced Nile tilapia populations showed lower diversity (He = 0.068–0.149; Ho = 0.073–0.140), while native Nile tilapia populations displayed moderate levels (He = 0.067–0.218; Ho = 0.067–0.190). Population structure and genetic differentiation analyses using PCA, F ST , and STRUCTURE provided evidence of admixture between native Nile tilapia and Rufiji tilapia populations. High F ST values were observed between Rufiji and Nile tilapia populations, except for two Rufiji populations (Mindu and Wami), which showed signs of ongoing gene flow between the two species. Ancestry-informative markers (AIMs) further supported the occurrence of hybridization between Rufiji and Nile tilapia species. The detected AIM revealed F1 hybrids in the Mindu population, with hybrid index (HI) values ranging from 0.40 to 0.47 and interclass heterozygosity (Hc) between 0.70 and 0.78. Overall, hybridization was widespread, with F1 hybrids and potentially multiple generations of backcrosses toward the parental populations P1 (Victoria) and P2 (Nyamisati). Overall, our results provide a solid foundation for the development of a tilapia breeding program and the conservation of wild genetic resources in Tanzania.
Kajungiro et al. (Fri,) studied this question.