Characterization and phylogenetic analysis of the mitochondrial 12S rRNA gene sequences of Aphaniops dispar

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The Arabian killifish ( Aphaniops dispar ) is a resilient freshwater species capable of surviving extreme environments, making it a valuable model for studying evolutionary adaptation in challenging environments. This study provides baseline genetic information of A. dispar populations from Saudi Arabian Wadis (Saul and Zaban) based on mitochondrial 12S rRNA gene sequencing. Our analyses of the 542 bp fragment revealed 58 polymorphic sites. Pairwise genetic distances (Kimura 2-parameter) indicated moderate divergence (0.00–0.12), with the highest differentiation observed between wadi saul populations. Analysis of molecular variance (AMOVA) showed significant genetic structuring, with 67.3% of variation attributed to regional differences. ABBA-BABA tests on genome-wide single nucleotide polymorphism (SNP) data revealed historical hybridization with Aphaniops fasciatus (D = 0.32, p < 0.001). While the 12S rRNA marker confirms broad phylogeographic patterns, these findings highlight the value of multi-faceted genomic approaches for understanding the evolution of A. dispar . To our knowledge, this is the first report of A. dispar on genetic diversity in the Asir region of Saudi Arabia.