Genetic Diversity and Conservation Genomics of Nile Crocodile Populations in Nigerian River Systems

The Nile crocodile is increasingly rare across Nigerian freshwater ecosystems due to historical overhunting and ongoing habitat loss, yet the genetic diversity and population structure of remaining Nigerian crocodile populations are entirely uncharacterised, limiting both captive breeding and wild population management strategies. This study examines the genetic diversity, population structure, and connectivity of Nile crocodile populations in three Nigerian river systems: the Niger River in Kogi State, the Benue River in Benue State, and the Taraba River in Taraba State. Non-invasive sampling using tissue from skin shed and faecal DNA was supplemented by blood sampling of captive-held individuals at Jos Wildlife Park. Microsatellite genotyping using twelve polymorphic loci was performed for 87 individuals. Bayesian clustering, principal coordinate analysis, and F-statistics were used to characterise population structure and gene flow. Results reveal three genetically distinct population clusters corresponding approximately to the three river systems, with limited contemporary gene flow between the Niger River population and the Benue-Taraba cluster. Genetic diversity levels were moderate overall, lower in the Niger River population, suggesting past bottleneck effects consistent with historical hunting records. The Taraba River population showed the highest allelic richness and heterozygosity, supporting its designation as a priority conservation unit. Assignment tests suggest no recent admixture with West African dwarf crocodile, confirming species identification. The study recommends prioritising the Taraba River population for in situ protection and recommends captive breeding draw from genetically underrepresented populations. Keywords: Nile crocodile, genetic diversity, conservation genomics, population structure, Nigeria