SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses.

BACKGROUND: The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. RESULTS: To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. CONCLUSIONS: The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature.

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range.

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still-neglected taxonomic condition for this lineage/species.

Characterization of a new cytotype and ocurrence of a B microchromosome in two spot astyanax, Astyanax bimaculatus Linnaeus, 1758 (Characiformes: Characidae).

Although Astyanax bimaculatus is the most representative species of the genus in the Amazon region, there are no cytogenetic studies of A. bimaculatus species in Amazon region. Thus, we aimed to analyse the chromosome complements of specimens from this area using classic and molecular cytogenetic approaches. The results revealed the existence of a distinct cytotype and this is the first report of the occurrence of a B microchromosome in the species. Overall, these data indicate that the karyotypic evolution of this species is complex, involving the occurrence of chromosomal rearrangements.

Revisiting the phylogeny of the genus Lolliguncula Steenstrup 1881 improves understanding of their biogeography and proves the validity of Lolliguncula argus Brakoniecki & Roper, 1985.

The biogeography of American loliginid squids has been improved in recent years, but certain key taxa have been missing. Given that the most accurate phylogenies and estimates of divergence times of common ancestors depend heavily on good taxonomic coverage we have reanalyzed the genus Lolliguncula in light of new samples that increase the geographic and taxonomic coverage. New sequences were produced using standard methods to update an existing dataset for COI, 16S and Rhodopsin markers. Data was analyzed using various species delimitation methods, rigorous phylogenetic analyses and estimates of divergence times between clades. Within Lolliguncula we recover five monophyletic lineages that relate to the known species L. argus, L. diomedeae, L. panamensis, L. brevis North Atlantic and L. brevis South Atlantic. Except when using low divergence thresholds in ABGD, species delimitation methods only identify four of these lineages as distinct species, grouping L. argus and L. diomedeae as a single species. However, considering the reciprocal monophyly, recent divergence time estimate and morphological diagnoses we refrain from synonymizing L. argus within L. diomedeae, considering them very recently diverged species. The biogeography of the American loliginids is discussed, wherein basal cladogenesis in both Lolliguncula and Doryteuthis occur between the Atlantic and Pacific about 45 mya, with subsequent speciation around 20 mya associated with seafloor changes during the formation of the Caribbean. The recent speciation between L. argus and L. diomedeae is associated to oceanic environmental changes associated with glaciation, deep sea cooling and tropical upwelling.

The roles of vicariance and dispersal in the differentiation of two species of the Rhinella marina species complex.

The high levels of Neotropical biodiversity are commonly associated with the intense Neogene-Quaternary geological events and climate dynamics. Here, we investigate the evolutionary history of two species of Neotropical closely related amphibians (R. horribilis and R. marina). We combine published data with new mitochondrial DNA sequences and multiple nuclear markers, including 12 microsatellites. The phylogenetic analyses showed support for grouping the samples in two main clades; R. horribilis (Central America and Mexico) and R. marina (South America east of the Andes). However, the phylogenetic inferences also show an evident mito-nuclear discordance. We use Approximate Bayesian Computation (ABC) to test the role of different events in the diversification between the two groups recovered. We found that both species were affected primarily by a recent Pleistocene divergence, which was similar to the divergence estimate revealed by the Isolation-with-Migration model, under persistent bidirectional gene flow through time. We provide the first evidence that R. horribilis is differentiated from the South American R. marina at the nuclear level supporting the taxonomic status of R. horribilis, which has been controversial for more than a century.

Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt.

The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.

Range distribution and contributions to taxonomy of Elops smithi (ELOPIFORMES: ELOPIDAE).

This study presents the first record of Elops smithi for northern Brazil. The evidence suggests this species is being misidentified incorrectly as Elops saurus in estuaries of the Western Atlantic Ocean. Here, morphological, molecular, and cytogenetic evidence identified all ladyfish specimens from one estuary in the region as E. smithi. Thus, at least Elops smithi occurs in the northern coast of Brazil and it is recommended that specimens from this region identified as E. saurus be further investigated with genetic and cytogenetic tools in order to assure a correct species identification.

Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae).

Lepidothrix is the most diverse genus of the family Pipridae, with eight recognized species. Although the genus' monophyly has been supported by both molecular and morphological characters, phylogenetic relationships and species limits within Lepidothrix remain uncertain. In the present study, we combined molecular sequences of mitochondrial (ND2 and COI) and nuclear (MYO, G3PDh and I5BF) markers in a multilocus analysis, to evaluate relationships and inter-specific limits among L. iris, L. nattereri, and L. vilasboasi, which are known to hybridize in eastern Amazonia. The results revealed a complex pattern, whereby events of secondary contact and gene flow after isolation and genetic and phenotypic differentiation prevented the recuperation of reciprocal monophyly among the studied taxa. The mitochondrial data indicate that L. nattereri is divided into two non-sister groups, one monophyletic, and the other, paraphyletic, with L. iris iris being more closely related to one of the two L. nattereri groups, while L. iris eucephala forms an undifferentiated clade with L. vilasboasi, probably resulting from an extensive process of mitochondrial introgression. In agreement with a previous study based on Single Nucleotide Polymorphism (SNP) data, mitochondrial haplotype networks also support that L. vilasboasi does not represent a recent "hybrid swarm" between L. iris and L. nattereri, but instead a genetically divergent lineage with a separate species status. Finally, the sister relationship recovered herein between L. iris iris and some western populations of L. nattereri currently in allopatry is also apparently explained by mitochondrial introgression, as also supported for nuclear genes by SNP data, indicating a complex scenario of past contact and gene flow between currently geographically distant Lepidothrix lineages.

Realized niche shift during a global biological invasion.

Accurate forecasts of biological invasions are crucial for managing invasion risk but are hampered by niche shifts resulting from evolved environmental tolerances (fundamental niche shifts) or the presence of novel biotic and abiotic conditions in the invaded range (realized niche shifts). Distinguishing between these kinds of niche shifts is impossible with traditional, correlative approaches to invasion forecasts, which exclusively consider the realized niche. Here we overcome this challenge by combining a physiologically mechanistic model of the fundamental niche with correlative models based on the realized niche to study the global invasion of the cane toad Rhinella marina. We find strong evidence that the success of R. marina in Australia reflects a shift in the species' realized niche, as opposed to evolutionary shifts in range-limiting traits. Our results demonstrate that R. marina does not fill its fundamental niche in its native South American range and that areas of niche unfilling coincide with the presence of a closely related species with which R. marina hybridizes. Conversely, in Australia, where coevolved taxa are absent, R. marina largely fills its fundamental niche in areas behind the invasion front. The general approach taken here of contrasting fundamental and realized niche models provides key insights into the role of biotic interactions in shaping range limits and can inform effective management strategies not only for invasive species but also for assisted colonization under climate change.

Molecular evidence of two new species of Eleotris (Gobiiformes: Eleotridae) in the western Atlantic.

Fishes of the genus Eleotris present highly conserved morphology, which may make their recognition difficult. Here, two cryptic Eleotris lineages from five locations along the coast of Brazil were identified using the COI gene and two nuclear fragments. High bootstrap and posteriori values supported those lineages, and the genetic distance of COI varied from 6% between the two lineages to 14.1% from other western Atlantic Eleotris species, such as E. pisonis, E. amblyopsis and E. perniger. The reciprocal monophyly for both types of markers, the divergences between those lineages and the other Eleotris species from the Brazilian coast may, in fact, represent two new cryptic species. The cryptic lineages and currently recognized species were collected in distinct environments, reinforcing the need for further sampling to understand the real distribution of each taxon.

Molecular phylogeny and diversification of a widespread Neotropical rainforest bird group: The Buff-throated Woodcreeper complex, Xiphorhynchus guttatus/susurrans (Aves: Dendrocolaptidae).

The genus Xiphorhynchus is a species rich avian group widely distributed in Neotropical forests of Central and South America. Although recent molecular studies have improved our understanding of the spatial patterns of genetic diversity in some species of this genus, most are still poorly known, including their taxonomy. Here, we address the historical diversification and phylogenetic relationships of the X. guttatus/susurrans complex, using data from two mitochondrial (cyt b and ND2) and one nuclear (ß-fibint7) genes. Phylogenetic relationships were inferred with both gene trees and a Bayesian-based species tree under a coalescent framework (∗BEAST). With exception of the nuclear ß-fibint7 gene that produced an unresolved tree, both mtDNA and the species tree showed a similar topology and were congruent in recovering five main clades with high statistical support. These clades, however, are not fully concordant with traditional delimitation of some X. guttatus subspecies, since X. g. polystictus, X. g. guttatus, and X. g. connectens are not supported as distinct clades. Interestingly, these three taxa are more closely related to the mostly trans-Andean X. susurrans than the other southern and western Amazonian subspecies of X. guttatus, which constitutes a paraphyletic species. Timing estimates based on the species tree indicated that diversification in X. guttatus occurred between the end of the Pliocene and early Pleistocene, likely associated with the formation of the modern Amazon River and its main southern tributaries (Xingu, Tocantins, and Madeira), in addition to climate-induced changes in the distribution of rainforest biomes. Our study supports with an enlarged dataset a previous proposal for recognizing at least three species level taxa in the X. guttatus/susurrans complex: X. susurrans, X. guttatus, and X. guttatoides.

Comparative cytogenetics of microsatellite distribution in two tetra fishes Astyanax bimaculatus (Linnaeus, 1758) and Psalidodon scabripinnis (Jenyns, 1842).

Background: The main cytogenetic studies of the Characidae family comprise the genera Astyanax and Psalidodon involving the use of repetitive DNA probes. However, for the microsatellite classes, studies are still scarce and the function of these sequences in the genome of these individuals is still not understood. Thus, we aimed to analyze and compare the distribution of microsatellite sequences in the species Astyanax bimaculatus and Psalidodon scabripinnis. Methods: We collected biopsies from the fins of A. bimaculatus and P. scabripinnis to perform cell culture, followed by chromosome extraction, and mapped the distribution of 14 microsatellites by FISH in both species. Results and Discussion: The diploid number observed for both species was 2n = 50, with an acrocentric B microchromosome in A. bimaculatus and a metacentric B chromosome in P. scabripinnis. Regarding FISH, 11 probes hybridized in the karyotype of A. bimaculatus mainly in centromeric regions, and 13 probes hybridized in P. scabripinnis, mainly in telomeric regions, in addition to a large accumulation of microsatellite hybridization on its B chromosome. Conclusion: Comparative FISH mapping of 14 microsatellite motifs revealed different patterns of distribution both in autosomes and supernumerary chromosomes of A. bimaculatus and P. scabripinnis, suggesting independent evolutionary processes in each of these species, representing excellent data on chromosome rearrangements and cytotaxonomy.

DNA barcoding for the assessment of marine and coastal fish diversity from the Coast of Mozambique.

The ichthyological provinces of Mozambique are understudied hotspots of global fish diversity. In this study, we applied DNA barcoding to identify the composition of the fish fauna from the coast of Mozambique. A total of 143 species belonging to 104 genera, 59 families, and 30 orders were identified. The overall K2P distance of the COI sequences within species ranged from 0.00% to 1.51%, while interspecific distances ranged from 3.64% to 24.49%. Moreover, the study revealed 15 threatened species according to the IUCN Red List of Threatened Species, with elasmobranchs being the most represented group. Additionally, the study also uncovered four new species that were not previously recorded in this geographic area, including Boleophthalmus dussumieri, Maculabatis gerrardi, Hippocampus kelloggi, and Lethrinus miniatus. This study represents the first instance of utilizing molecular references to explore the fish fauna along the Mozambican coast. Our results indicate that DNA barcoding is a dependable technique for the identification and delineation of fish species in the waters of Mozambique. The DNA barcoding library established in this research will be an invaluable asset for advancing the understanding of fish diversity and guiding future conservation initiatives.

First neurotranscriptome of adults Tambaquis (Colossoma macropomum) with characterization and differential expression between males and females.

The Tambaqui is one of the most representative Amazon fish species, being highly exploited in fisheries, aquaculture and as a research model. Nonetheless, data about functional genome are still required to evaluate reproductive and nutrition parameters as well as resistance to pathogens. The of next-generation sequencing has allows assessing the transcriptional processes in non-model species by providing comprehensive gene collections to be used as a database in further genomic applications and increased performance of captive populations. In this study, we relied on RNAseq approach to generate the first transcriptome of the telencephalon from adult males and females of Colossoma macropomum, resulting in a reference dataset for future functional studies. We retrieved 896,238 transcripts, including the identification of 267,785 contigs and 203,790 genes. From this total, 91 transcripts were differentially expressed, being 63 and 28 of them positively regulated for females and males, respectively. The functional annotation resulted in a library of 40 candidate genes for females and 20 for males. The functional enrichment classes comprised reproductive processes (GO:0,048,609; GO:0,003,006; GO:0,044,703; GO:0,032,504; GO:0,019,953) being related to sex differentiation (e.g., SAFB) and immune response (e.g., SLC2A6, AHNAK, NLRC3, NLRP3 and IgC MHC I alpha3), thus indicating that the genes in the neurotranscriptome of Tambaqui participate in sex differentiation and homeostasis of captive specimens. These data are useful to design the selection of genes related to sex determination and animal welfare in raising systems of Tambaqui.

Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species.

Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.

New molecular evidence supports the species status of Kaempfer's Woodpecker (Aves, Picidae).

Kaempfer's Woodpecker (Celeus obrieni) is the only species of the genus Celeus endemic to Brazil. The description of this taxon as a subspecies of the Rufous-headed Woodpecker (Celeus spectabilis) was based on a single specimen. While C. obrieni and C. spectabilis are now considered separate species based on morphological and limited molecular evidence, no study has critically tested the reciprocal monophyly and degree of evolutionary independence between these taxa with several specimens. Herein, fragments of the mitochondrial and nuclear DNA of three recently-collected specimens of C. obrieni were analyzed to evaluate the degree of evolutionary differentiation of this taxon with respect to C. spectabilis. The results confirm the reciprocal monophyly between the specimens of C. obrieni and C. spectabilis. The genetic divergence values for the two taxa also support their classification as independent species, given that they are greater than the values recorded among other closely-related but separate species of the same genus. Estimates of the divergence time between C. obrieni and C. spectabilis indicate that cladogenesis occurred in the mid-Pleistocene, during a period of major climatic fluctuations and landscape change, consistent with the hypothesis of a corridor of open bamboo dominated forests and woodland stretching.

Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction.

Molecular genetic techniques are an effective monitoring tool, but high-quality DNA samples are usually required. In this study, we compared three different protocols of DNA extraction: NaCl (saline); phenol-chloroform and commercial kit (Promega)-from three biological tissues of five individuals of Lutjanus purpureus under two methods of storage. The evaluated items included DNA concentration and purity, processing time and cost, as well as the obtaining of functional sequences. The highest average values of DNA concentration were obtained using the saline procedure and the commercial kit. Pure DNA was only obtained using the saline protocol, evaluated by the ratio of 260/280. The saline and phenol-chloroform protocols were the least expensive methods. The commercial kit costs are counterbalanced by the short time required. The procedure based on phenol-chloroform presented the worst results regarding DNA yield and the time required to perform all steps. The saline and commercial kit protocols showed similar results concerning the amount and quality of extracted DNA. Therefore, the final choice should be based on the available financial resources and the available time for carrying out each procedure of DNA extraction.

DNA barcode reveals occurrence of threatened species and hidden diversity on Teleost fish trade in the Coastal Amazon.

This study aimed to identify the teleost fish species sold in Bragança, a major fishing hub on the north coast of Brazil. The COI gene analysis was performed for the identification of fish species. The local market uses common names that are not accurate and do not reflect the diversity of the species. 204 sequences were obtained, with 119 haplotypes. 83 species were identified by comparing with public databases and constructing phylogenetic trees, with Carangidae being the most prevalent family. The study also found Haemulon atlanticus, Menticirrhus cuiaranensis and Hoplias misioneira, a newly described species from the Amazon basin, among the samples. Additionally, 73 commercial names were recorded, including 10 categories, and the illegal trade of Epinephelus itajara was detected. The DNA Barcode method proved to be effective for discriminating the species. The study highlights that common and commercial names are vague and underestimate the fish diversity, and that Brazil needs to revise its regulations for commercial and scientific names.

Molecular characterization of juvenile fish from the Amazon estuary using DNA barcoding approach.

The efficiency of the DNA barcoding relies on sequencing fragment of the Cytochrome C Subunit I (COI) gene, which has been claimed as a tool to biodiversity identification from distinct groups. Accordingly, the goal of this study was to identify juvenile fish species along an estuary of Caeté River in the Brazilian Blue Amazon based on. For this purpose, we applied the DNA barcoding and discuss this approach as a tool for discrimination of species in early ontogenetic stages. A 500-bp fragment was obtained from 74 individuals, belonging to 23 species, 20 genera, 13 families and seven orders. About 70% of the 46 haplotypes revealed congruence between morphological and molecular species identification, while 8% of them failed in identification of taxa and 22% demonstrated morphological misidentification. These results proved that COI fragments were effective to diagnose fish species at early life stages, allowing identifying all samples to a species-specific status, except for some taxa whose COI sequences remain unavailable in public databases. Therefore, we recommend the incorporation of DNA barcoding to provide additional support to traditional identification, especially in morphologically controversial groups. In addition, periodic updates and comparative analyses in public COI datasets are encouraged.

Molecular characterisation of dengue virus type 1 reveals lineage replacement during circulation in Brazilian territory.

Dengue fever is the most important arbovirus infection found in tropical regions around the world. Dispersal of the vector and an increase in migratory flow between countries have led to large epidemics and severe clinical outcomes, such as dengue haemorrhagic fever and dengue shock syndrome. This study analysed the genetic variability of the dengue virus serotype 1 (DENV-1) in Brazil with regard to the full-length structural genes C/prM/M/E among 34 strains isolated during epidemics that occurred in the country between 1994-2011. Virus phylogeny and time of divergence were also evaluated with only the E gene of the strains isolated from 1994-2008. An analysis of amino acid differences between these strains and the French Guiana strain (FGA/89) revealed the presence of important nonsynonymous substitutions in the amino acid sequences, including residues E297 (Met→Thr) and E338 (Ser→Leu). A phylogenetic analysis of E proteins comparing the studied isolates and other strains selected from the GenBank database showed that the Brazilian DENV-1 strains since 1982 belonged to genotype V. This analysis also showed that different introductions of strains from the 1990s represented lineage replacement, with the identification of three lineages that cluster all isolates from the Americas. An analysis of the divergence time of DENV-1 indicated that the lineage circulating in Brazil emerged from an ancestral lineage that originated approximately 44.35 years ago.