The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence ( 2%), pointing to at least 23 strong candidates for new species. Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.

/pdf/can-dna-barcoding-accurately-discriminate-megadiverse-1zv7n7ka79.pdf

Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna

Polyploidy, the multiplication of entire setsof chromosomes beyond the normal set of two,has occurred extensively, independently, and isoften repeated in many groups of fish, from thesharks to the higher teleosts. While there areseveral ways that a polyploid fish can develop,environmental change and hybrid stabilizationmay play a large role in the initiation of anew polyploid species. Despite its prevalence,the importance of polyploidy in the evolutionof the fishes is unclear. Polyploidy is morecommon in the lower teleosts than the higherteleosts, possibly due to an advantage gainedthrough decreased specialization in the lowerteleosts, a decreased viability of polyploidyin the higher fish, or both. Polyploid fishcould gain an advantage over diploid fishthrough increased heterozygosity, divergence ofduplicate genes, and/or increased expression ofkey physiological proteins. While polyploidfish do not differ considerably from diploidsphenotypically, they may be at a disadvantage,or certain advantages may be lessened due to anoverall decrease in cell number. This papersummarizes all polyploid species of fish knownto-date, and discusses the possible roles andpathways for establishment of polyploidy in theevolution of the fishes.

Occurrence of polyploidy in the fishes

This paper is aimed at underlining the limited knowledge available about the physiology of triploid fishes compared with diploids. Whereas many aspects (induction, detection, growth, resistance to diseases, etc.) in the production and rearing of triploid fishes have widely been developed and described in the literature, other numerous questions of ecophysiology remain in abeyance, and the study of triploid cells physiology is still in its infancy. Triploid fishes can be considered as models worthwhile for physiological investigations not only for the economical stake in relation to the development of triploid fishes rearing, but also for the cytological and molecular features of their tissues and organs. The functional implications of these features have been poorly studied although they are potential areas of applied and/or fundamental studies.

The physiology of triploid fish: current knowledge and comparisons with diploid fish

Fluorescence in situhybridisation (FISH) and double FISH experiments were carried out to ascertain the chromosomal distribution pattern of the 45S and 5S ribosomal (r) DNAs in four populations of the characid fish Astyanax scabripinnis – a group considered to be a species complex for its wide karyotypical and morphological diversity. The results regarding the 45S rDNA agreed with this hypothesis, since these sites showed intra- and inter-populational, numerical and positional variations. However, the data obtained with the 5S rDNA probe revealed a highly conserved chromosomal distribution pattern of these sequences among individuals of each population, as well as among the populations analysed. We consider this contrasting situation as a functional divergence between 45S and 5S ribosomal DNAs, which may reflect the localisation of these sequences in distinct nuclear compartments, leading them to undergo differentiated evolutionary processes.

Conserved 5S and variable 45S rDNA chromosomal localisation revealed by FISH in Astyanax scabripinnis (Pisces, Characidae).

Fish exhibit the greatest diversity of all vertebrates, making this group extremely attractive for the study of a number of evolutionary questions. Fish genomes have intrinsic characteristics that may be responsible for the amazing diversity of fish species observed, but little is known about their structure and organization. A large amount of data from mapping of repetitive DNA sequences of several species has been generated, providing an important source of information for better understanding the involvement of repetitive DNA sequences in chromosomal organization. Almost all classes of repeated DNAs have been mapped in fishes, and all fish genomes analyzed contain at least one, mostly all types of repetitive DNAs. DNA sequence data combined with the chromosomal mapping of these repeated elements by means of cytogenetic techniques can provide a clearer picture of the genome, which is not yet clearly defined, even if already sequenced. In this chapter, we do not aim to analyze all available data on the chromosomal distribution of repetitive DNAs in fish species, but instead wish to draw attention to the impact of repetitive DNA sequences on fish karyotyping and genome evolution, with a particular focus on B chromosome origin and maintenance and on the differentiation of sex chromosomes. We also discuss the integration of chromosome analysis and genomic data, which represents a promising tool for fish cytogenomics.

Chromosomal Distribution and Evolution of Repetitive DNAs in Fish

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.2004.01832.x

Cytogenetic studies in two populations of Astyanax altiparanae (Pisces, Characiformes).

A cytogenetic and morphometric study of four populations of characid fish assigned to the "complex" of Astyanax scabripinnis originating from three riverine basins, namely Ivai (populations A and B), Paranapanema (C) and Parana (D), was carried out. Karyological analysis showed the diploid chromosome number 2n = 48 for population B and 2n = 50 for the remaining populations. All populations under study differed in the composition of karyotypes and C-banding patterns. Canonical variable analysis used to assess the morphometric data revealed that 1) the four populations under study were entirely discriminated from each other and 2) the coefficients that most contributed to this pattern were standard length, rostrodorsal distance, eye diameter and snout length. The results indicate that the differences in karyotypes were paralleled by the morphological differentiation of the populations under study and contributed to the problem of systematics of A. scabripinnis "complex".

Cytogenetic and morphometric differences in populations of Astyanax "scabripinnis" (Pisces, Characidae) from Maringá region, PR, Brazil

Chromosomes of Astyanax scabripinnis from the Tatupeba stream, Ivai basin (state of Parana, Brazil), were analyzed. Astyanax scabripinnis population presents 3 different diploid numbers (2n = 46, 48 and 50) and B chromosomes in each cytotype. Eighty per cent of the females among individuals of cytotype I (2n = 50) has a metacentric B macrochromosome, whereas three different types of B chromosomes were identified in individuals of cytotype II (2n = 48). Cytotype III (2n = 46) showed two B chromosomes of different morphologic types (metacentric macrochromosomes and acrocentric) in all specimens and cells analyzed. Constitutive heterochromatin pattern for the three cytotypes showed weak markings in centromeric regions and conspicuous blocks in the telomere regions of ST and A chromosomes. Whereas C-banding showed that B chromosomes were totally or partially heterochromatic, a discussion on their behavior and origin was also undertaken.

Sympatric occurrence of three cytotypes and four morphological types of B chromosomes of Astyanax scabripinnis (Pisces, Characiformes) in the River Ivaí Basin, state of Paraná, Brazil.

https://www.jstage.jst.go.jp/article/cytologia1929/66/3/66_3_299/_pdf

Karyotype and B Chromosome of Rhamdia Species (Pisces, Pimelodidae) Endemic in the River Iguacu Basin.

Cytogenetic studies of three species of the Pimelodidae family were carried out. The results showed a diploid chromosome number of 2n = 46 for Pimelodellu spl, 2n = 52 for Pimelodellu sp2 and 2n = 50 for Pinirampus pirinumpu. Chromosome polymorphism was detected by of G-banding analysis in Pimeladella spl and by C-banding in P. pirinampu. In Pimelodellu spl the 12th chromosome pair presented three G-bands on the long arm while its homologous showed only two G-bands. The 21st chromosome pair of P. pirinampu showed centromeric and interstitial heterocromatin block on one of the homologues and absence of an interstitial on other. However, the latter presented a telomeric band. In both cases the polymorphism was detected in all specimens analyzed. A deletion and an inversion rearrangement are suggested, respectively. A single NOR system was observed for three species. Considerations about the karyotype variability and evolution of the Pimelodidae family are presented.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.2000.00103.x

Isabel Cristina Martins-Santos

Papers

Cytogenetic studies in two populations of Astyanax altiparanae (Pisces, Characiformes).

Cytogenetic and morphometric differences in populations of Astyanax "scabripinnis" (Pisces, Characidae) from Maringá region, PR, Brazil

Sympatric occurrence of three cytotypes and four morphological types of B chromosomes of Astyanax scabripinnis (Pisces, Characiformes) in the River Ivaí Basin, state of Paraná, Brazil.

Karyotype and B Chromosome of Rhamdia Species (Pisces, Pimelodidae) Endemic in the River Iguacu Basin.

Chromosome polymorphism in species of the Pimelodidae family (Pisces, Siluriformes)