Transposable elements (TEs) have the potential to produce broad changes in the genomes of their hosts, acting as a type of evolutionary toolbox and generating a collection of new regulatory and coding sequences. Several TE classes have been studied in Neotropical cichlids; however, the information gained from these studies is restricted to the physical chromosome mapping, whereas the genetic diversity of the TEs remains unknown. Therefore, the genomic organization of the non-LTR retrotransposons Rex1, Rex3, and Rex6 in five Amazonian cichlid species was evaluated using physical chromosome mapping and DNA sequencing to provide information about the role of TEs in the evolution of cichlid genomes. Physical mapping revealed abundant TE clusters dispersed throughout the chromosomes. Furthermore, several species showed conspicuous clusters accumulation in the centromeric and terminal portions of the chromosomes. These TE chromosomal sites are associated with both heterochromatic and euchromatic regions. A higher number of Rex1 clusters were observed among the derived species. The Rex1 and Rex3 nucleotide sequences were more conserved in the basal species than in the derived species; however, this pattern was not observed in Rex6. In addition, it was possible to observe conserved blocks corresponding to the reverse transcriptase fragment of the Rex1 and Rex3 clones and to the endonuclease of Rex6. Our data showed no congruence between the Bayesian trees generated for Rex1, Rex3 and Rex6 of cichlid species and phylogenetic hypothesis described for the group. Rex1 and Rex3 nucleotide sequences were more conserved in the basal species whereas Rex6 exhibited high substitution rates in both basal and derived species. The distribution of Rex elements in cichlid genomes suggests that such elements are under the action of evolutionary mechanisms that lead to their accumulation in particular chromosome regions, mostly in heterochromatins.

We present karyotypic characteristics and report on the occurrence of ZZ/ZW sex chromosomes in Ancistrus ranunculus (rio Xingu) and Ancistrus sp. "Piagaçu" (rio Purus), of the Brazilian Amazon. Ancistrus ranunculus has a modal number of 2n=48 chromosomes, a fundamental number (FN) of 82 for both sexes, and the karyotypic formula was 20m+8sm+6st+14a for males and 19m+9sm+6st+14a for females. Ancistrus sp. "Piagaçu" presented 2n=52 chromosomes, FN= 78 for males and FN= 79 for females. The karyotypic formula was 16m+8sm+2st+26a for males and 16m+9sm+2st+25a for females. The high number of acrocentric chromosomes in karyotype of Ancistrus sp. "Piagaçu" differs from the majority of Ancistrini genera studied so far, and may have resulted from pericentric inversions and translocations. The lower number of chromosomes in A. ranunculus indicates that centric fusions also occurred in the evolution of Ancistrus karyotypes. We conclude that karyotypic characteristics and the presence of sex chromosomes can constitute important cytotaxonomic markers to identify cryptic species of Ancistrus. However, sex chromosomes apparently arose independently within the genus and thus do not constitute a reliable character to analyze phylogenetic relations among Ancistrus species. Nós apresentamos características cariotípicas e registramos a ocorrência de cromossomos sexuais ZZ/ZW em Ancistrus ranunculus (rio Xingu) e Ancistrus sp. "Piagaçu" (rio Purus), da Amazônia Brasileira. Ancistrus ranunculus teve um número modal de 2n=48 cromossomos, um número fundamental (NF) de 82 para ambos os sexos, e a fórmula cariotípica 20m+8sm+6st+14a para machos e 19m+9sm+6st+14a para fêmeas. Ancistrus sp. "Piagaçu" apresentou 2n=52 cromossomos, NF=78 para machos e NF= 79 para fêmeas. A fórmula cariotípica foi de 16m+8sm+2st+26a para machos e 16m+9sm+2st+25a para fêmeas. O alto número de cromossomos acrocêntricos no cariótipo de Ancistrus sp. "Piagaçu" difere da maioria dos gêneros de Ancistrini estudada até o momento, e pode ter resultado de inversões pericêntricas e translocações. O número mais baixo de cromossomos em A. ranunculus indica que fusões cêntricas também ocorreram na evolução dos cariótipos de Ancistrus. Nós concluímos que as características cariotípicas e a presença de cromossomos sexuais podem constituir marcadores citotaxonômicos importantes para identificar espécies crípticas de Ancistrus. Entretanto, cromossomos sexuais aparentemente surgiram de forma independente dentro do gênero e, deste modo, não constituem um caráter confiável para ser usado em análises de relações filogenéticas entre espécies de Ancistrus

Cichla monoculus, Cichla temensis (peacock bass or tucunare), and its presumed hybrids, were cytogenetically analyzed. The fish were collected at three distinct sites in the central Amazon basin, namely in the Uatuma (C. monoculus, C. temensis and their natural hybrid), Jau (C. temensis), and Solimoes rivers (C. monoculus). The two species and the natural hybrid showed the same diploid number, 2n=48 acrocentric chromosomes. Single NORs were detected in the distal region of the long arm in all three species. However, in C. monoculus, the NOR was found on the second pair of the complement, in C. temensis, on the third pair and in the hybrid two NOR patterns were found, one on the second pair and the other on the third pair of chromosomes. The two species and the hybrid have their constitutive heterochromatin located in the pericentromeric region of all chromosomes and an interstitial C-band located on the largest chromosome pair. The great similarity in the chromosome number and morphology, chromosome size class differences, the NOR patterns and C-banding suggested chromosomal stasis during speciation and hybridization of Cichla.

Cytogenetic data obtained for Serrasalmus rhombeus revealed two cytotypes (cytotype 1 and cytotype 2) at four sampling sites. Cytotype 1 consists of 2n = 60, 20M + 24SM + 6ST + 10A and was detected in specimens from Negro River (Anavilhanas Islands), Solimões River (Camaleão Lake), confluence of Negro and Solimões Rivers (Catalão Lake), and Uatumã River. Cytotype 2 consists of 2n = 58, 22M + 24SM + 2ST+10A and was detected in specimens from Catalão and Camaleão Lakes. In Cytotype 2, the first chromosome pair was almost twice the size of second pair, and the constitutive heterochromatin pattern of each cytotype is distinct. The two cytotypes occurred sympatrically at Catalão and Camaleão Lakes, and no intermediates between the cytotypes were detected, suggesting each cytotype represents a different fish species.

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA₃/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.