Mito‐Nuclear Discordance and Species Boundaries in the Freshwater Fish Genus <i>Cyprinion</i> Revealed by Genome‐Wide <scp>SNPs</scp>

ABSTRACT The cyprinid genus Cyprinion , comprising nine species distributed from the Indus drainage across the Iranian Plateau to Mesopotamia and the Arabian Peninsula, exhibits contentious species boundaries due to extensive morphological overlap and limited molecular data. In this study, we integrated mitochondrial DNA ( COI ) sequences and genome‐wide single nucleotide polymorphism (SNP) data to investigate the phylogenetic relationships, taxonomy, and biogeography of six species: C. acinaces , C. kais , C. macrostomum , C. microphthalmum , C. mhalense , and C. muscatense . Mitochondrial analyses revealed extremely shallow divergence among C. macrostomum , C. kais , C. acinaces , and C. tenuiradius , sharing identical or closely related haplotypes. In contrast, genome‐wide SNP analyses resolved most taxa as distinct genomic clusters. Clustering and gene‐flow analyses identified five major genetic groups and revealed patterns consistent with historical introgression, particularly between C. macrostomum and C. acinaces . Despite shallow mitochondrial divergence, genome‐wide SNP analyses revealed differentiation among several taxa, providing preliminary support for lineage divergence. However, these interpretations remain constrained by limited genomic sampling, and alternative explanations including incomplete lineage sorting cannot be excluded. Our results further refine biogeographic hypotheses for Cyprinion species, suggesting that recent dispersal and historical connectivity among Mesopotamian, Iranian, and Arabian drainages may have been facilitated by palaeodrainage systems active during the Late Pleistocene. In addition, analysis of unpublished GenBank COI sequences suggests that C. tenuiradius , previously considered restricted to northern Persian Gulf drainages, may also occur on the Arabian Peninsula. This study provides the first genomic framework for understanding the taxonomy and biogeography of Cyprinion in western Asia.