Claudio Oliveira

Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna

BackgroundThe 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.ResultsOf 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%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.ConclusionsOur 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.

Identification of a new repetitive element in the sex chromosomes of Leporinus elongatus (Teleostei: Characiformes: Anostomidae): new insights into the sex chromosomes of Leporinus

Leporinuselongatus represents an interesting model for studies on chromosome evolution since it possesses a conspicuous ZZ/ZW sex chromosome system that has been characterized mainly by basic cytogenetic techniques. In the present study we describe a dispersed repetitive element (named LeSpeI) related to the sex chromosomes of L.elongatus. Females revealed clusters of LeSpeI on the long arm of the W chromosome and in the acrocentric NOR-bearing chromosome pair. In males, the signal was restricted to the pericentromeric region of the NOR-bearing chromosomes. Considering the results obtained in the present study using FISH, NOR and C-banding, together with findings from previous studies, it can be inferred that the sex chromosome system of L. elongatus is still undergoing an evolutionary process. The data suggest novelties in relation to the sex chromosomes of the genus Leporinus with the description of a multiple sex chromosome system involving the NOR-bearing chromosomes. Therefore, it is hypothesized that the simple ZW chromosome system previously described for L. elongatus rather is a multiple Z1Z1Z2Z2/Z1W1Z2W2 system.

Supernumerary Chromosomes, Robertsonian Rearrangement and Multiple NORs in Corydoras Aeneus (Pisces, Siluriformes, Callichthyidae)

SUMMARYCytogenetic studies in four samples of Corydoras aetteus from tributaries of the Tiete River in the upper Parana System, Brazil (rivers Araqua, Corumbatai, Capivara and Alambari) evidenced a diploid number of 2n = 60 and 2n = 61 plus a variable number of 0 to 3 small supernumeraries or B chromosomes. The variability in the A complement was due to the occurrence of a Robertsonian rearrangement. The supernumerary chromosomes were almost totally C-band positive. The analysis of male meiotic cells showed the occurrence of 29 bivalents and one trivalent in the individuals heterozygous for the Robertsonian rearrangement and of univalents in the individuals with supernumerary chromosomes. Four chromosome pairs are involved in nucleolar organization. All the 4 samples presented supernumerary chromosomes, but the Robertsonian rearrangement was restricted to the rivers Araqua and Corumbatai.

Comparative Chromosome Mapping of U2 snRNA and 5S rRNA Genes in Gymnotus Species (Gymnotiformes, Gymnotidae): Evolutionary Dynamics and Sex Chromosome Linkage in G. pantanal

A comparative mapping of U2 small nuclear RNA (snRNA) and 5S ribosomal RNA (rRNA) genes was performed in 6 Gymnotus species. All species analyzed presented the U2 snDNA organized in conspicuous blocks and not co-located with rRNA genes. In addition, 5 species showed the U2 snDNA located in a single pair of chromosomes, which seems to be a conserved trait in this genus. Conversely, G. pantanal was the only species displaying several terminal signals in different chromosome pairs, including the X1 sex chromosome but not the Y chromosome. This is the first report of U2 snRNA genes in sex chromosomes of fishes. The absence of sites in the Y chromosome of G. pantanal indicates a possible loss of terminal segments of the chromosomes involved in the Y formation.

Nuclear DNA content of thirty species of Neotropical fishes

The present paper reports nuclear DNA content in 30 Neotropical freshwater fish species and summarizes the data on other Neotropical species presented in the literature. Among Neotropical fishes, the nuclear DNA content ranges from 1.04 ± 0.09 pg/nucleus in Corydoras cf. simulatus (2n = 62) to 248.0 pg/nucleus in Lepidosiren paradoxa (2n = 38). A general analysis of the data obtained in the present study for each species showed that DNA measurements were practically constant at the individual level, while significant differences were observed among individuals of the same population. This observation was valid for all species analyzed and was more evident in those species that presented other karyotypic particularities such as sex chromosomes or supernumerary chromosomes. The importance of changes in nuclear DNA content in the evolutionary process of Neotropical fishes is discussed.

Evolution of the commutation concept associated with the development of flow analysis

Abstract Evolution of the commutation concept has lead to the proposal and development of different generations of flow analyzers. Since the inception of the air-segmented flow systems till the availability of modern flow injection, sequential-injection and other flow-based analytical systems, a noteworthy improvement of the commutating devices has been noted. Multi-functional manifold is described as a polyvalent approach for methodology implementation in a flow analyzer. It permits the investigation of mixing conditions under different flow patterns (unsegmented, segmented, monosegmented) with optional exploitation of the stopped-flow approach. For this purpose, spectrophotometric or turbidimetric measurements eventually affected by Schlieren noise were considered. Potentialities and limitations of the manifold are discussed in relation with methods based on relatively fast or slow chemical reactions. As applications, phosphate and chloride determinations in plant digests and natural waters were selected. The manifold is characterized by high versatility and may work in connection with different flow configurations. Development will certainly lead to simple, versatile and miniaturized analyzers, able to run samples in a personalized fashion. In addition, random reagent selection, full automation, expansion of the analytical application range and increasing potentialities of the already existing methodologies are devised.

Multicommutation in flow analysis. Part 4. Computer-assisted splitting for spectrophotometric determination of copper and zinc in plants

Abstract An improved splitting process in flow analysis accomplished by means of a computer controlled three-way solenoid valve is proposed. This valve is located at the splitting site, and defines the flow pattern and the portions of the processed sample delivered to each emergent stream. As an application, the simultaneous spectrophotometric determination of copper and zinc in plant digests was selected. The method is based on metal complexation with cyanide, differential kinetics of decomplexation, and reaction with Zincon. The proposed system is very stable and handles 45 samples per hour which corresponds to 0.27 mg Zincon per determination. Precise measurements (r.s.d. = 0.7% and 1.7% for first and second peaks) are obtained within 0.00–1.00 mg 1 −1 Cu and 0.00–2.00 mg 1 −1 Zn. Detection limits are 0.05 and 0.04 mg l −1 for Cu and Zn. Results are in agreement with standard reference materials.

Karyotypic diversity in four species of the genus Gymnotus Linnaeus, 1758 (Teleostei, Gymnotiformes, Gymnotidae): physical mapping of ribosomal genes and telomeric sequences

Abstract Conventional (Giemsa, C-Banding, Ag-NORs, CMA3) and molecular (5S rDNA, 18S rDNA, telomeric sequences) cytogenetic studies were carried out in specimens of ten distinct fish populations of the genus Gymnotus (Gymnotus sylvius Albert and Fernandes-Matioli, 1999, Gymnotus inaequilabiatus Valenciennes, 1839, Gymnotus pantherinus Steindachner, 1908, and G. cf. carapo Linnaeus, 1758) from different Brazilian hydrographic basins. Gymnotus sylvius presented a diploid number of 40 chromosomes (22m+12sm+6st), Gymnotus pantherinus presented 52 chromosomes (32m+18sm+2st), while Gymnotus inaequilabiatus (42m+10sm+2a)and Gymnotus cf. carapo (38m+12sm+4st) presented 54 chromosomes. The C-banding technique revealed centromeric marks in all chromosomes of all species. Besides that, conspicuous blocks of heterochromatin were found interstitially on the chromosomes of Gymnotus inaequilabiatus, Gymnotus cf. carapo,and Gymnotus pantherinus. All four species showed single nucleolus organizing regions confirmed by results obtained through Ag-NORs and FISH experiments using 18S rDNA probes, which showed the NORs localized on the first chromosome pair in Gymnotus inaequilabiatus, Gymnotus cf. carapo,and Gymnotus pantherinus, and on pair 2 in Gymnotus sylvius. CMA3 staining revealed additional unrelated NORs marks in Gymnotus sylvius and Gymnotus pantherinus. The 5S rDNA probes revealed signals on one pair in Gymnotus sylvius and two pairs in Gymnotus pantherinus; Gymnotus inaequilabiatus had about seventeen pairs marked, and Gymnotus cf. carapo had about fifteen pairs marked. It is considered that the high amount of heterochromatin identified in the chromosomes of Gymnotus inaequilabiatus and Gymnotus cf. carapo could have facilitated the dispersion of 5S rDNA in these species. Interstitial signals were detected on the first metacentric pair of Gymnotus sylvius by telomeric probes (TTAGGG)n indicating the possible occurrence of chromosomal fusions in this species. The present study reveals valuable cytotaxonomic markers for this group and allows a more precise evaluation of the processes involved in the karyotype differentiation and the interrelationships among different species of the genus Gymnotus.

Chromosomal mapping of repetitive DNA and cytochrome C oxidase I sequence analysis reveal differentiation among sympatric samples of Astyanax fasciatus (Characiformes, Characidae).

The genus Astyanax is a specious Neotropical fish group, occurring from the south area of the United States to Argentina. During the past few years, intensive studies on representatives of this group have been performed, broadening the genetic, taxonomic and biogeographical knowledge considerably. However, phylogenetic relationships among many species remain uncertain. Significant karyotypic variations occur in A. bimaculatus, A. scabripinnis and A. fasciatus, suggesting the existence of species complexes. Samples with different diploid numbers may be found in A. fasciatus and, in some cases, morphological differentiation among them is not easily verified due to the absence of clear diagnostic characteristics. In the present study, the organization of the A. fasciatus genome from the Tietê River, Mogi das Cruzes, SP, Brazil, was analyzed, describing the karyotype structure and the chromosomal mapping of 18S and 5S ribosomal DNA (rDNA), H1 and H3 histones genes, telomeric DNA, and Rex3 transposable element. Sequencing of the cytochrome c oxidase I (COI) gene was also performed. Chromosomal analyses highlighted the occurrence of 2 distinct karyomorphs in the referred population, one with 2n = 46 and the other with 2n = 48 chromosomes. Furthermore, physical mapping of the repetitive sequences and nucleotide analysis of the COI gene reinforce the genomic differentiation between those karyomorphs and corroborate the existence of 2 different lineages morphologically similar to A. fasciatus living in sympatry.

Flow analysis with accuracy assessment

Abstract The concept of accuracy assessment is exploited in flow analysis. The resulting system is based on multi-commutation because multiple sample processing is involved. The manifold includes different quasi -independent methods and permits recovery tests to be performed on every sample. Results are then intrinsically more accurate and additional information on the sample matrix is provided. The feasibility of the approach is demonstrated in the large scale determination of chloride in river water samples presenting high variability in matrix composition and/or in acidity. The spectrophotometric mercury thiocyanate-Fe(III) method and the turbidimetric method based on the precipitation with silver ions are implemented in a single manifold and a 40.00 mg l −1 Cl − intermittent stream is added in-line to each sample for producing recovery data. Analysis of the four recorded analytical signals permits evaluation and eventual compensation of matrix effects. The final result is calculated after considering the results obtained by two different methods, and the eventual correction of matrix effects. The proposed system is very robust, handles 25 samples per hour and yields precise results between 0.50 and 10.0 mg l −1 Cl − . Potentialities and limitations of the approach are discussed.