The genus Hypostomus has a broad geographic distribution in Brazilian rivers and comprises armored catfishes with a very complicated taxonomy due to the absence of morphological autapomorphies. The existence of nearly 10 allopatric populations with different karyotypes suggests that Hypostomusancistroides represents a species complex in the Upper Paraná River basin. In this paper, an unusual karyotype of an isolated H. aff. ancistroides population was investigated. All specimens of this sample have 2n = 66 chromosomes except for 1 male with 2n = 67, most likely due to a supernumerary chromosome. In this population, the sexes are dimorphic, the males are heterogametic, and an XX/XY sex chromosome system is present. Phylogenetic analysis using mitochondrial and nuclear DNAs indicated that this population forms a monophyletic group separate from the other populations of H.ancistroides and may represent an incipient species.

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Several cytogenetic markers show chromosomal diversity in the fish such as “armoured catfish”. Although studies have characterized many species in the major genera representing these Siluridae, particularly in the genus Hypostomus Lacépède, 1803, trends in chromosome evolution of this group remain unclear. The Paraíba do Sul river basin contains the armoured catfish Hypostomus affinis Steindachner, 1877, which is unique because of its distribution of repetitive DNAs, the 5S and 18S rDNA. Identified samples and registered collections in Brazilian museums were identified as the same typological species, while we observed wide variations in the physical location of this gene in the karyotype based on fluorescent in situ hybridization results. In this study, we propose that these species can represent evolutionarily independent units, as these fish frequently undergo processes such as dispersion and vicariance and that the rDNA is associated with DNA that spreads in the genome, such as transposons. Additionally, the absence of gene flow due to the distance of the sample location could intensify evolutionary processes. The phenotypes found for the 18S rDNA showed minor changes in relation to the number of sites between the lower and upper drainage regions of Paraíba do Sul. The large difference in the number of sites found for the 5S rDNA entered the same region (upper drainage of the basin) and the literature data could represent a population dynamics where an expansion of the 5S rDNA sites provides an extinct or non-sampled cytotype in this work.

The Hypostomini tribe comprises a single genus, Hypostomus, which possibly contains several monophyletic groups because of significant morphological variation and a variety of diploid numbers and karyotype formulas. The objective of this study was to infer evolutionary relationships among some species of Hypostomus found in the Paraná River basin and subsequently to identify chromosomal synapomorphies in the groupings formed. Two nuclear genes, rag1 and rag2, and two mitochondrial genes, mt-co1 and mt-cyb, were used to establish evolutionary relationships. Phylogenetic trees were inferred using the maximum likelihood (ML) method for mt-co1 and Bayesian analysis (BA) for all genes concatenated. Both phylogenetic trees showed two large monophyletic clades within Hypostomus. These clades are based on chromosome number, where haplogroup I contains individuals with 66–68 chromosomes, and haplogroup II contains species with 72–80 chromosomes. A third monophyletic haplogroup was also observed using ML, formed by H. faveolus and H. cochliodon, which present 2n = 64, reinforcing the separation of groups in Hypostomus by diploid number. Robertsonian rearrangements were responsible for forming the different diploid numbers and for the diversity of karyotype formulas. The groups based on traditional morphological taxonomy are considered artificial in this study; the staining pattern, which separates the two large groups morphologically and is supported by little chromosomal evidence, was instead determined to show homoplasy. Ag-NORs are predominantly multiple and located on st/a chromosomes, along with 18S rDNA sites; 5S rDNA sites are often seen in an interstitial position, following the trend already described for vertebrates.