Uedson Pereira Jacobina

Chromosome Mapping of Repetitive Sequences in Rachycentron canadum (Perciformes: Rachycentridae): Implications for Karyotypic Evolution and Perspectives for Biotechnological Uses

The cobia, Rachycentron canadum, a species of marine fish, has been increasingly used in aquaculture worldwide. It is the only member of the family Rachycentridae (Perciformes) showing wide geographic distribution and phylogenetic patterns still not fully understood. In this study, the species was cytogenetically analyzed by different methodologies, including Ag-NOR and chromomycin A3 (CMA3)/DAPI staining, C-banding, early replication banding (RGB), and in situ fluorescent hybridization with probes for 18S and 5S ribosomal genes and for telomeric sequences (TTAGGG)n. The results obtained allow a detailed chromosomal characterization of the Atlantic population. The chromosome diversification found in the karyotype of the cobia is apparently related to pericentric inversions, the main mechanism associated to the karyotypic evolution of Perciformes. The differential heterochromatin replication patterns found were in part associated to functional genes. Despite maintaining conservative chromosomal characteristics in relation to the basal pattern established for Perciformes, some chromosome pairs in the analyzed population exhibit markers that may be important for cytotaxonomic, population, and biodiversity studies as well as for monitoring the species in question.

Chromosomal diversity in tropical reef fishes is related to body size and depth range.

Tropical reef fishes show contrasting patterns of karyotypic diversity. Some families have a high chromosomal conservatism while others show wide variation in karyotypic macrostructure. However, the influence of life-history traits on karyotypic diversity is largely unknown. Using phylogenetic comparative methods, we assessed the effects of larval and adult species traits on chromosomal diversity rates of 280 reef species in 24 families. We employed a novel approach to account for trait variation within families as well as phylogenetic uncertainties. We found a strong negative relationship between karyotypic diversity rates and body size and depth range. These results suggest that lineages with higher dispersal potential and gene flow possess lower karyotypic diversity. Taken together, these results provide evidence that biological traits might modulate the rate of karyotypic diversity in tropical reef fishes.

Morphological and karyotypic differentiation in Caranx lugubris (Perciformes: Carangidae) in the St. Peter and St. Paul Archipelago, mid-Atlantic Ridge

Isolated oceanic islands constitute interesting model systems for the study of colonization processes, as several climatic and oceanographic phenomena have played an important role in the history of the marine ichthyofauna. The present study describes the presence of two morphotypes of Caranx lugubris, in the St. Peter and St. Paul Archipelago located in the mid-Atlantic. Morphotypes were compared in regard to their morphological and cytogenetic patterns, using C-banding, Ag-NORs, staining with CMA3/DAPI fluorochromes and chromosome mapping by dual-color FISH analysis with 5S rDNA and 18S rDNA probes. We found differences in chromosome patterns and marked divergence in body patterns which suggest that different populations of the Atlantic or other provinces can be found in the Archipelago of St. Peter and St. Paul.

Inferring Diversity and Evolution in Fish by Means of Integrative Molecular Cytogenetics

Fish constitute a paraphyletic and profusely diversified group that has historically puzzled ichthyologists. Hard efforts are necessary to better understand this group, due to its extensive diversity. New species are often identified and it leads to questions about their phylogenetic aspects. Cytogenetics is becoming an important biodiversity-detection tool also used to measure biodiversity evolutionary aspects. Molecular cytogenetics by fluorescence in situ hybridization (FISH) allowed integrating quantitative and qualitative data from DNA sequences and their physical location in chromosomes and genomes. Although there is no intention on presenting a broader review, the current study presents some evidences on the need of integrating molecular cytogenetic data to other evolutionary biology tools to more precisely infer cryptic species detection, population structuring in marine environments, intra- and interspecific karyoevolutionary aspects of freshwater groups, evolutionary dynamics of marine fish chromosomes, and the origin and differentiation of sexual and B chromosomes. The new cytogenetic field, called cytogenomics, is spreading due to its capacity to give resolute answers to countless questions that cannot be answered by traditional methodologies. Indeed, the association between chromosomal markers and DNA sequencing as well as between biological diversity analysis methodologies and phylogenetics triggers the will to search for answers about fish evolutionary, taxonomic, and structural features.

Comparative cytogenetics and heterochromatic patterns in two species of the genus Acanthostracion (Ostraciidae: Tetraodontiformes)

Some groups of fish, such as those belonging to the Order Tetraodontiformes, may differ significantly in the amount and location of heterochromatin in the chromosomes. There is a marked variation in DNA content of more than seven-fold among the families of this Order. However, the karyoevolutionary mechanisms responsible for this variation are essentially unknown. The largest genomic contents are present in species of the family Ostraciidae (2.20-2.60pg). The present study cytogenetically characterized two species of the family Ostraciidae, Acanthostracion polygonius and A. quadricornis, using conventional staining, C-bandings, Ag-NOR, CMA(3)/DAPI, AluI, PstI, EcoRI, TaqI and HinfI restriction enzymes (REs) and double FISH with 18S and 5S rDNA probes. The karyotypes of both species showed 2n=52 acrocentric chromosomes (FN=52; chromosome arms) and pronounced conserved structural characteristics. A significant heterochromatic content was observed equilocally distributed in pericentromeric position in all the chromosome pairs. This condition is unusual in relation to the karyotypes of other families of Tetraodontiformes and probability is the cause of the higher DNA content in Ostraciidae. Given the role played by repetitive sequences in the genomic reorganization of this Order, it is suggested that the conspicuous heterochromatic blocks, present in the same chromosomal position and with apparently similar composition, may have arisen or undergo evolutionary changes in concert providing clues about the chromosomal mechanisms which led to extensive variation in genomic content of different Tetraodontiformes families.

A comparative study on karyotypic diversification rate in mammals

Chromosomal rearrangements have a relevant role in organismic evolution. However, little is known about the mechanisms that lead different phylogenetic clades to have different chromosomal rearrangement rates. Here, we investigate the causes behind the wide karyotypic diversity exhibited by mammals. In particular, we analyzed the role of metabolic, reproductive, biogeographic and genomic characteristics on the rates of macro- and microstructural karyotypic diversification (rKD) using comparative phylogenetic methods. We found evidence that reproductive characteristics such as larger litter size per year and longevity, by allowing a higher number of meioses in absolute time, favor a higher probability of chromosomal change. Furthermore, families with large geographic distributions but containing species with restricted geographic ranges showed a greater probability of fixation of macrostructural chromosomal changes in different geographic areas. Finally, rKD does not evolve by Brownian motion because the mutation rate depends on the concerted evolution of repetitive sequences. The decisive factors of rKD evolution will be natural selection, genetic drift and meiotic drive that will eventually allow or not the fixation of the rearrangements. Our results indicate that mammalian karyotypic diversity is influenced by historical and adaptive mechanisms where reproductive and genomic factors modulate the rate of chromosomal change.

Trends on the Karyotype Acrocentrization Within Carangidae (Perciformes): A New Phylogenetic Evidence About a Traditional Marine Paradigm

Carangidae is a morphologically diverse family of marine fish, characterized by stable karyotypes, predominantly with 2n = 48, composed of acrocentric chromosomes (A). This stability is shared with other families of the order Perciformes, which resulted in the hypothesis that 48A is a plesiomorphic karyotype of the group. We tested this hypothesis in the Carangidae family using comparative phylogenetic methods, investigating the evolution of karyotype characters (including chromosome number, morphology, and number of chromosome arms per karyotype [fundamental number, FN]). Our analyses revealed that 2n = 48 is most likely the ancestral chromosome number for the family. However, an extremely variable number of FNs, always above 48, was observed in basal clades within the family and sister groups. On the other hand, the reduced FN = 48 was consistently observed only in the most derived clades, indicating a tendency for acrocentrization. The number of acrocentric chromosomes apparently was accompanied by a trend of reduction in the genome size (1C-value), suggesting that these changes might be correlated. Our data contradict the marine fish hypothesis that the 2n = 48 acrocentric karyotype is plesiomorphic, at least for Carangidae, and reveal the importance for the correct interpretation of karyotype in a temporal and phylogenetic context.

Updated checklist and DNA barcode-based species delimitations reveal taxonomic uncertainties among freshwater fishes from the mid-north-eastern Caatinga ecoregion, north-eastern Brazil

The mid-north-eastern Caatinga is a semiarid freshwater ecoregion in North-eastern Brazil that is dominated by temporary rivers and is currently classified as one of the least ichthyologically-known ecoregions in the world. The present study aimed to provide an updated checklist of mid-north-eastern Caatinga ecoregion (MNCE) freshwater fish species and evaluate their taxonomic identity using morphology, DNA barcoding and multiple species delimitation approaches. After reviewing published studies and ichthyological collections, 119 species were identified. Among these were 94 putatively valid native and 14 non-native species, five undescribed native species, four new records for the MNCE, 11 potential cases of misidentification and 14 species listed as inquirenda. Additionally, 252 individuals from 49 species were barcoded, revealing three potential taxonomic synonyms. The combined molecular approaches estimated a total of 91 native species, although a finalized species list for the MNCE awaits additional taxonomic revisions and field surveys. This study provides the most up-to-date species checklist for the MNCE and a molecular reference database for identifying MNCE fishes with DNA barcodes. Results highlight the need to integrate traditional taxonomy with molecular approaches to correctly identify species, especially in taxonomically problematic ecoregions such as the MNCE.

DNA barcode sheds light on systematics and evolution of neotropical freshwater trahiras

We assessed the presence of independent evolving lineages of the trahira, Hoplias malabaricus, one of the few freshwater fish species having wide distribution in the Neotropics which is the region with the highest global diversity of freshwater fish. To achieve that goal, 58 mitochondrial sequences of cytochrome c oxidase subunit I (COI; DNA barcoding) were generated from collected samples and 85 obtained from public databases, which were analyzed in comparison to chromosomal and geological data. The magnitude of genetic diversity found among different sampling sites was greater than 2%. Molecular species delimitation methods indicated the existence of a least four distinct lineages. The recognised cytotypes did not form monophyletic groups, suggesting that the karyotypic macrostructure could be a homoplastic character. The haplotype relationships suggested secondary contacts between the ecoregions of Northern and Northeastern Brazil that were shaped by coastal routes between adjacent watersheds during the Pleistocene epoch and probable exchanges of their ichthyofaunas. Our results indicated that multiple factors have driven the diversification of H. malabaricus, from ancient geological events linked to the reactivation of tectonic faults to more recent occurrences related to eustatic changes in ocean levels. Ultimately, the magnitude of its genetic diversity suggests the necessity of revising its taxonomic status.