The evolutionary history and the phylogenetic relationships of many marine species show intricate patterns that challenge traditional views based on isolation by distance. Nonetheless, several groups remain poorly studied, like Bothus (flounders), a widespread and morphologically peculiar genus of Pleuronectiformes. The overlapped traits and the lack of uniformity in the literature hinder the detailed systematics and evolutionary inferences of Bothus species. Here, we combined mitochondrial markers (Cytochrome C Oxidase Subunit I and 16S rRNA genes) and chromosomal data of two species of Bothus from the Southwestern Atlantic to address phylogenetic and biogeographic aspects that might have influenced their diversification when compared to other congeners. All data showed that most samples belonged to Bothus ocellatus, while some specimens, herein regarded as Bothus cf. maculiferus according to their morphology, were similar to the Indo-Pacific species Bothus pantherinus, particularly based on molecular data. Even though the cytogenetic patterns of B. ocellatus were similar to previous reports (2n = 32), the molecular analyses revealed a high haplotype diversity in this taxon, with sympatric lineages within the Caribbean and an allopatric group along the Brazilian coast, consistent with the biodiversity feedback speciation model. On the other hand, Bothus cf. maculiferus presented a distinctive karyotype (2n = 44) that significantly expands the diploid range for this genus. Additionally, the close morphological and genetic relationships between B. cf. maculiferus and B. pantherinus along with divergence time and other bodies of evidence suggest a recent speciation after the invasion of a common ancestor into Atlantic from Southern Africa during the Pleistocene.
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