Phylogeography and Population Genetics of the African Manatee in Nigerian Coastal Waters

The African manatee (Trichechus senegalensis) is a critically understudied aquatic mammal whose population structure and genetic diversity in Nigerian coastal waters and freshwater systems remain almost entirely unknown. This knowledge gap constrains the development of effective species management strategies and limits Nigeria's contribution to regional manatee conservation. This study investigates the phylogeography and population genetics of African manatees in the Nigerian coastal zone, spanning the Cross River, Niger Delta, and Lagos Lagoon systems, representing the South South and South West geopolitical zones. Non-invasive genetic samples were collected from manatee excreta, sloughed skin, and biopsy biopsies obtained from individuals identified through underwater observation and community interviews over 18 months. Mitochondrial DNA sequences and microsatellite markers were analyzed to assess genetic diversity, population structure, and connectivity. Bayesian clustering analysis identifies two genetically differentiated manatee populations within Nigerian waters, separated at the Niger Delta corridor. Evidence of restricted gene flow between the Cross River system and the Niger Delta populations is significant, suggesting that historical land use changes and waterway fragmentation have reduced connectivity. Genetic diversity indices indicate that the Cross River population may be experiencing early-stage inbreeding. The study recommends targeted conservation interventions to maintain connectivity between genetic units and prioritizes the Cross River system as a high-priority conservation zone for African manatee protection. Keywords: African manatee, population genetics, phylogeography, Nigeria, aquatic mammal conservation