Genetic introgression of invasive Pangasius hypophthalmus on native Nigerian fish species

Genetic introgression of invasive <i>Pangasius hypophthalmus </i>on native Nigerian fish species

Abstract

The rapid expansion of aquaculture in Nigeria, particularly farming of the non-indigenous Pangasius hypophthalmus, poses significant genetic risks to native freshwater fish through escapee-mediated hybridization and introgression. This study investigated the genetic impact of escaped P. hypophthalmus on Clarias gariepinus, Oreochromis niloticus, and Heterotis niloticus across 12 stratified sites in the Niger Delta, Benue River, and Kainji Lake. A total of 1,248 fish specimens were genotyped using restriction site-associated DNA sequencing (RAD-seq) on an Illumina NovaSeq 6000 platform, yielding 32,784 high-quality SNPs after filtering in Stacks v2.65. Genetic diversity, population structure, and gene flow were assessed using ARLEQUIN, ADMIXTURE, EIGENSOFT, TreeMix, and IMa3, while hybrid classes were identified with NewHybrids and HyDe. Environmental drivers of admixture were modeled by multiple linear regression, and future diversity trajectories projected using CDPOP simulations over 20 generations. Farm-adjacent native populations showed approximately 30% reduction in heterozygosity, nucleotide diversity, and effective population size relative to controls (ANOVA, p < 0.001). ADMIXTURE detected P. hypophthalmus ancestry in 8–18.4% of farm-adjacent native individuals, absent entirely from control sites. Gene flow was strongly asymmetric, directed from P. hypophthalmus into native species (m = 0.012–0.028). Sixty-two hybrids spanning F1, F2, and backcross generations were identified, with the highest hybridization rate in the Niger Delta (6.25%). Low dissolved oxygen and flood frequency were key admixture predictors (R² = 0.62). Simulations projected a 15–25% genetic diversity loss over 20 generations at current escape rates, reducible by half at 2% escape rates. These findings underscore the urgent need for enhanced containment, genetic monitoring, and adaptive farm management to safeguard Nigeria’s native fish biodiversity.

Ann. Bangladesh Agric. 30(1): 19-32