Abstract
The control region of the mitochondrial DNA haplotype frequencies were significantly different among the two separate lagoon populations of Oreochromis alcalicus grahami in Lake Magadi and of O. a. alcalicus from lake Natron, and DNA fingerprint similarity indices were significantly higher for intra-population comparisons of the two Magadi lagoon populations and the Lake Natron population than the inter-population similarity indices among these populations. A modified Fst measure indicated population sub-division and the phylogeographic partitioning of the VNTR fragments observed were unique to specific populations further indicating substantial genetic differentiation. The lagoon populations within Lake Magadi demonstrated the same degree of genetic differentiation as either of these populations did to the outgroup (the Lake Natron population). There appears to be limited gene flow between Lake Magadi tilapia populations and this population structure has important implications for protecting locally adapted populations within this unique ecosystem.
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