DNA barcoding reveals taxonomic uncertainties and cryptic lineages of fish from the Mearim River basin, Maranhão, Brazil

Abstract The Mearim River, located in the Northeast region of Brazil, constitutes a hydrographic basin of considerable socioeconomic and ecological importance and is characterized by a high diversity of fish species, including several endemics. However, most studies conducted in this basin have focused predominantly on taxonomic surveys and species inventories. Consequently, knowledge regarding the genetic characterization of the species that compose its ichthyofauna remains limited. To address this gap, the present study employed DNA barcoding to identify and characterize the ichthyofaunal diversity of the Mearim River basin and its tributaries. An average of 20 campaigns trips were conducted between 2014 and 2020, resulting in the capture of 2,412 individuals. A total of 914 sequences were obtained for a 640 bp (bp) fragment of the mitochondrial COI gene, corresponding to 74 species, 67 genera, 33 families, and 10 orders. Molecular species delimitation analyses recovered between 74 and 77 operational taxonomic units (OTUs). According to the ASAP, bPTP, and GMYC models, there was an increase in molecular entities compared to the number of species identified using morphological criteria, indicating the presence of hidden diversity and potential misidentifications. In contrast, the ABGD method recovered a number of molecular entities equivalent to the total number of species delimited based on morphological criteria. The results obtained in this study contribute significantly to reducing knowledge gaps regarding the genetic diversity of species for which no information was previously available in this basin, providing support for the development of management and conservation strategies for regional fisheries resources.