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Although crocodilians have attracted enormous attention in other research fields, from the cytogenetic point of view, this group remains understudied. Here, we analyzed the karyotypes of eight species formally described from the Alligatoridae family using differential staining, fluorescence in situ hybridization with rDNA and repetitive motifs as a probe, whole chromosome painting (WCP), and comparative genome hybridization. All Caimaninae species have a diploid chromosome number (2n) 42 and karyotypes dominated by acrocentric chromosomes, in contrast to both species of Alligatorinae, which have 2n = 32 and karyotypes that are predominantly metacentric, suggesting fusion/fission rearrangements. Our WCP results supported this scenario by revealing the homeology of the largest metacentric pair present in both Alligator spp. with two smaller pairs of acrocentrics in Caimaninae species. The clusters of 18S rDNA were found on one chromosome pair in all species, except for Paleosuchus spp., which possessed three chromosome pairs bearing these sites. Similarly, comparative genomic hybridization demonstrated an advanced stage of sequence divergence among the caiman genomes, with Paleosuchus standing out as the most divergent. Thus, although Alligatoridae exhibited rather low species diversity and some level of karyotype stasis, their genomic content indicates that they are not as conserved as previously thought. These new data deepen the discussion of cytotaxonomy in this family.

In the fish genus Hoplias, two major general groups can be found, one of which is formed by the “common trahiras” (Hoplias malabaricus group) and the other by the “giant trahiras” (Hoplias lacerdae group, in addition to Hoplias aimara), which usually comprises specimens of larger body size. Previous investigations from the giant trahiras group recovered 2n = 50 meta/submetacentric chromosomes and no sex chromosome differentiation, indicating a probable conservative pattern for their karyotype organization. Here, we conducted comparative cytogenetic studies in six giant trahiras species, two of them for the first time. We employed standard and advanced molecular cytogenetics procedures, including comparative genomic hybridization (CGH), as well as genomic assessments of diversity levels and phylogenetic relationships among them. The results strongly suggest that the giant trahiras have a particular and differentiated evolutionary pathway inside the Hoplias genus. While these species share the same 2n and karyotypes, their congeneric species of the H. malabaricus group show a notable chromosomal diversity in number, morphology, and sex chromosome systems. However, at the same time, significant changes were characterized at their inner chromosomal level, as well as in their genetic diversity, highlighting their current relationships resulting from different evolutionary histories.

Lebiasinidae fishes have been historically neglected by cytogenetical studies. Here we present a genomic comparison in eleven Lebiasinidae species, in addition to a review of the ribosomal DNA sequences distribution in this family. With that, we develop ten sets of experiments in order to hybridize the genomic DNA of representative species from the genus Copeina, Copella, Nannostomus, and Pyrrhulina in metaphase plates of Lebiasina melanoguttata. Two major pathways on the chromosomal evolution of these species can be recognized: (i) conservation of 2n = 36 bi-armed chromosomes in Lebiasininae, as a basal condition, and (ii) high numeric and structural chromosomal rearrangements in Pyrrhulininae, with a notable tendency towards acrocentrization. The ribosomal DNA (rDNA) distribution also revealed a marked differentiation during the chromosomal evolution of Lebiasinidae, since both single and multiple sites, in addition to a wide range of chromosomal locations can be found. With some few exceptions, the terminal position of 18S rDNA appears as a common feature in Lebiasinidae-analyzed species. Altogether with Ctenoluciidae, this pattern can be considered a symplesiomorphism for both families. In addition to the specific repetitive DNA content that characterizes the genome of each particular species, Lebiasina also keeps inter-specific repetitive sequences, thus reinforcing its proposed basal condition in Lebiasinidae.

Although fishes have traditionally been the subject of comparative evolutionary studies, few reports have concentrated on the application of multipronged modern molecular cytogenetic techniques (such as comparative genomic hybridization = CGH and whole chromosome painting = WCP) to analyze deeper the karyotype evolution of specific groups, especially the historically neglected small-sized ones. Representatives of the family Lebiasinidae (Characiformes) are a notable example, where only a few cytogenetic investigations have been conducted thus far. Here, we aim to elucidate the evolutionary processes behind the karyotype differentiation of Pyrrhulina species on a finer-scale cytogenetic level. To achieve this, we applied C-banding, repetitive DNA mapping, CGH and WCP in Pyrrhulina semifasciata and P. brevis. Our results showed 2n = 42 in both sexes of P. brevis, while the difference in 2n between male and female in P. semifasciata (♂41/♀42) stands out due to the presence of a multiple X1X2Y sex chromosome system, until now undetected in this family. As a remarkable common feature, multiple 18S and 5S rDNA sites are present, with an occasional synteny or tandem-repeat amplification. Male-vs.-female CGH experiments in P. semifasciata highlighted the accumulation of male-enriched repetitive sequences in the pericentromeric region of the Y chromosome. Inter-specific CGH experiments evidenced a divergence between both species’ genomes based on the presence of several species-specific signals, highlighting their inner genomic diversity. WCP with the P. semifasciata-derived Y (PSEMI-Y) probe painted not only the entire metacentric Y chromosome in males but also the X1 and X2 chromosomes in both male and female chromosomes of P. semifasciata. In the cross-species experiments, the PSEMI-Y probe painted four acrocentric chromosomes in both males and females of the other tested Pyrrhulina species. In summary, our results show that both intra- and interchromosomal rearrangements together with the dynamics of repetitive DNA significantly contributed to the karyotype divergence among Pyrrhulina species, possibly promoted by specific populational and ecological traits and accompanied in one species by the origin of neo-sex chromosomes. The present results suggest how particular evolutionary scenarios found in fish species can help to clarify several issues related to genome organization and the karyotype evolution of vertebrates in general.

In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages, making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family.

Previous geoetic studies cooducted with migratory fish populatioos from dowostream of the Três Marias dam io the São Fraocisco River Basio (Brazil) have documeoted the occurreoce of populatioo structuriog, as reported for Brycon orthotaenia aod Prochilodus argenteus, two commercially importaot species io this basio. We revisited the geoetic structure of these species usiog microsatellites. B. orthotaenia was sampled duriog the spawoiog seasoo aod was aoalyzed usiog five heterologous microsatellites. P. argenteus was collected io the ooo-reproductive seasoo aod geoetic aoalysis was cooducted usiog teo species-specific microsatellites. For both species, geoetic diversity betweeo collectioo sites was similar. Coosideriog B. orthotaenia, F ST aod R ST estimates aod the Bayesiao aoalysis demoostrated sigoificaot differeoces betweeo sites. Two well-defioed populatioos were ideotified io the study area, iodicatiog populatioo structuriog for this species. No sigoificaot differeoces were fouod for P. argenteus. These data provide ioformatioo for koowledge regardiog geoetic structure of migratory fish species, which may cootribute toward the cooservatioo besides the uoderstaodiog the biology aod ecology of these importaot fishery resources. Estudios geoéticos aoteriores realizados coo poblaciooes de peces migratorios de aguas abajo de la represa de las Tres Marías eo la cueoca del río Sao Fraocisco (Brasil) hao documeotado casos de estructuracióo geoética, como se ha descrito para Brycon orthotaenia y Prochilodus argenteus, dos especies de importaocia comercial. Se revisó la estructura geoética de estas especies utilizaodo microsatélites. Se obtuvieroo muestras de B. orthotaenia duraote la temporada de desove y se aoalizaroo mediaote cioco microsatélites heterólogos. Muestras de P. argenteus fueroo recogidas eo la temporada oo reproductiva y el aoálisis geoético se realizó utilizaodo diez microsatélites específicos para P. argenteus. Para ambas especies, la diversidad geoética eotre los sitios de recoleccióo fue similar. Coosideraodo a B. orthotaenia, las estimaciooes FST y RST y el aoálisis Bayesiaoo demostraroo difereocias sigoificativas eotre los sitios. Se ideotificaroo dos poblaciooes bieo defioidas eo el área de estudio, iodicaodo uoa estructuracióo de la poblacióo de esta especie. No se eocootraroo difereocias sigoificativas para P. argenteus. Estos datos proporciooao ioformacióo para el cooocimieoto sobre la estructura geoética de las especies de peces migratorios, que puede cootribuir a la cooservacióo, además de la compreosióo de la biología y ecología de estos importaotes recursos pesqueros.

Financiadora de Estudos e Projetos A preliminary genetic linkage map was constructed for the species Prochilodus argenteus, an endemic fish from the São Francisco river basin, using 23 microsatellite markers in a progeny with 95 individuals from a single cross by the pseudo-testcross strategy. The male and female parents were collected in different regions, downstream of the dam of the Três Marias (MG). Only 11 (52.4%) markers grouped in some linkage group and the the remaining was unlinked. Twenty-one (91.5%) markers appeared to segregate according to Mendelian inheritance, and only two (8.7%) showed segregation distortion. The map covered 297.58 cM of the genome, according to the Kosambi s function. The number of linkage groups (3) found in this study was much lower than expected for the species (equivalent to the haploid number of chromosomes, n = 27), demonstrating the importance of using a larger number of molecular markers in future studies. The data obtained in this work will be compiled with the marks obtained by AFLP by Rojas (2008) in order to obtain a denser genetic map. Although the number of linkage groups found have been lower than expected for the species, the results can be considered promising for the Brazillian Fish Genetics, since genetic mapping studies are virtually absent in Neotropical fish. Um mapa genético preliminar foi construído para a espécie Prochilodus argenteus, um peixe endêmico da bacia hidrográfica do rio São Francisco, através de 23 marcadores moleculares microssatélites em uma progênie com 95 indivíduos provenientes de um único cruzamento através da estratégia pseudo-testcross . Os genitores masculino e feminino foram coletados em diferentes regiões, à jusante da barragem de Três Marias (MG). Apenas 11 (52.4%) marcadores foram alocados em algum grupo de ligação e os restantes não estavam ligados. Vinte e um (91.5%) marcadores segregaram de acordo com a herança mendeliana e apenas dois (8.7%) apresentaram distorção da segregação. O mapa cobriu 297.58 cM do genoma, de acordo com a função de Kosambi. O número de grupos de ligação (3) encontrado no presente trabalho foi muito inferior ao esperado para a espécie (equivalente ao número de cromossomos haplóides, n = 27), demonstrando a importância da utilização de um número maior de marcadores moleculares em estudos futuros. Os dados obtidos no presente trabalho serão compilados com as marcas AFLP obtidas por Rojas (2008), visando um mapa genético mais denso. Embora o número de grupos de ligação encontrado tenha sido inferior ao esperado para a espécie, os resultados podem ser considerados como promissores na área de Genética de Peixes do Brasil, já que estudos de mapeamento genético são praticamente inexistentes em peixes neotropicais.

Financiadora de Estudos e Projetos Introduction of hatchery fish in river has been the major using strategy for river fishery rehabilitation, working to attenuate river damage in short time. But there are effective risks about their efficiency and results, concerning the pool gene preservation and illness proliferation, beyond others ecologies and economics aspects. At São Francisco river, during two decades it was used this kind of procedure with some species of fish, but there are no quantitative data about their efficiency. Prochilodus argenteus, popular known as Curimatápacu, is pointed as the most important economic specie at São Francisco basin, responsible for 50% of all fishery production. Therefore, this project goals to trace the genetic profile of a Prochilodus argenteus hatchery population, looking for identify stock genetic variability through 13 SSR loci previous described, and to compare theses data with others described in literature from wild stocks. Tests made with Microchecker, Genepop, and Fsat softwares detected low homozygosis; reduced allelic variability when compared with wild population; increase in heterozygosis when compared with expected; and negative inbreed coefficient, these data got a trace for bottleneck phenomena in a cultured population, and Bottleneck software tests confirm this hypothesis. When the same test was ruled with wild population data results very far from those found in hatchery populations, give a high reliability. To conclude, at cultured and/or management programs are necessary the knowledge of genetic profile population (hatchery or wild) to prevent damaging introgression in wild population and consequently extinction. These data can be used to made fishery river rehabilitation program more efficient, and so, adding with information to fish procreation, industrial fishery and biologic fish conservation studies. O repovoamento de rios é uma das estratégias que vem sendo frequentemente usada para a reabilitação pesqueira, atuando como uma medida mitigadora de curto prazo, embora envolva riscos relativos à eficiência do programa quanto aos seus resultados, à preservação do pool genético e à possibilidade de introdução de doenças, além de outros aspectos ecológicos e econômicos. No rio São Francisco, esta prática vem sendo realizada há mais de duas décadas com algumas espécies de peixes. No entanto, não existem relatos quantitativos de sua eficiência. Prochilodus argenteus, conhecido popularmente como curimatã-pacu, constitui uma espécie de relevante valor econômico para a bacia do São Francisco, representando cerca de 50% de toda produção de pescado. O presente trabalho teve como objetivo traçar o perfil genético de uma população de cultivo de Prochilodus argenteus, visando identificar a variabilidade genética deste estoque. Foram utilizados 13 loci de microssatélites previamente descritos na literatura e seus dados foram comparados com os de população selvagem de trabalhos anteriores. Testes feitos com os programas Microchecker, Genepop e Fstat detectaram baixa homozigose, redução da variabilidade alélica quando comparada a estoques naturais, um número aumentado de heterozigotos quando comparado com o esperado e coeficiente de endogamia negativo, tais dados apontam para um possível efeito gargalo (bottleneck) recente na população cultivada. Testes feitos com o programa Bottleneck confirmaram essa hipótese. Resultado de tais teste se tornaram muito expressivos, quando o mesmo teste foi feito com dados de uma população selvagem para parâmetros de comparação. Os dados obtidos no presente trabalho demonstram que programas de manejo e cultivo do Prochilodus argenteus necessitam de um conhecimento do perfil genético da população (de cultivo ou selvagem), para que não haja introgressão deletéria na população selvagem com seu posterior declínio. Discussões sobre recuperação de ambientes aquáticos mostram que ações integradas são necessárias para que de fato se tenha uma efetiva recuperação desses ambientes. Dados genéticos poderão subsidiar e viabilizar programas de peixamentos mais eficientes e, assim, contribuir com estudos relacionados ao manejo de pesca, piscicultura e conservação biológica deste peixe.