Biology subjects

Rodrigues, A. E. S.

Publications and source records attributed to Rodrigues, A. E. S..

3 recordsLinked to original sources

bioRxiv2025

Geographical variation in mitogenomes of the largetooth sawfish Pristis pristis: challenges and perspectives for conservation efforts

Sawfishes (Pristidae) have been severely impacted by coastal development and unregulated fisheries and are considered Critically Endangered by the IUCN Red List. Environmental DNA (eDNA) analyses have shown potential for monitoring elasmobranch species, with various studies focusing on using species-specific approaches to detect Pristis species. However positive detection using existing probes has not been confirmed in some geographic regions where they would be expected. Here, we aimed to test whether mutations at key sites have been detrimental to species-specific detection of P. pristis (Linnaeus, 1758) using the existing probe set. To test this hypothesis mitogenomes were assembled that were found to follow the typical pattern of vertebrate mitogenomic organization. Phylogenetic trees showed similar topologies and confirmed geographic mitochondrial variation in P. pristis. Mismatches for the published 12S species-specific probe set for P. pristis were identified that prevent amplification of positive control samples from Brazil. However, ddPCR detection of the positive control was possible using a newly designed species-specific probe set. This study highlights how geographical variation can severely impact the success of generally applying species-specific detection systems developed based on data from only one geographical region. The new mitogenomes and species-specific probe set developed here may also contribute to improving the potential to map and monitor these Critically Endangered species across the globe. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/639618v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1fb30fborg.highwire.dtl.DTLVardef@4cd3a8org.highwire.dtl.DTLVardef@1dbd985org.highwire.dtl.DTLVardef@a5d7d3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

ecology↗

bioRxiv2024

Molecular identification of whole squids and calamari at fairs and markets in regions of Latin America

In recent decades, the commercial importance of cephalopods has increased considerably, being an important fishing resource around the world. However, during the preparation for commercialization of those species, especially those sold in markets, they suffer the process known as "calamari" which includes removing and separating the head, arm, skin or even having the body structure cut into rings, which ends up making it difficult or often prevents the identification of the species, which can lead to replacements. In this sense, the present study aimed to use the large ribosomal region, rrnL (also known as 16S rDNA) to genetically identify cephalopod species sold in markets and fairs in Latin America. Whole and processed samples were collected from supermarkets and directly from local fishers the approximate collection location. Each generated sequence was submitted to the website Genbank for molecular comparison and included in the database for subsequent genetic identification. Comparison of sequences using the Blastn revealed the presence of eight species that are widely traded in the Latin American region. Our results indicate labeling errors in samples from the State of Para that contained the species Dosidicus gigas (d Orbigny, 1823) found only in the Pacific Ocean and were generically labeled as "National Lula". No type of substitution was found among the samples that were being sold at fairs and markets, only labeling errors. Thus, our results demonstrate the effectiveness of the rrnL for identifying species and evaluating labeling errors.

genetics↗

bioRxiv2023

The role of Miocene-Pleistocene environmental change in diversification of the genus Hypoclinemus Chabanaud, 1928.

The Neotropical region stands out as one of the most taxonomically diverse areas on the planet, garnering significant attention in the context of marine incursions and their role in shaping this diversity. Among marine-derived taxa, pleuronectiform fishes exhibit distinctive morphological characteristics that have attracted significant scientific interest. However, the biogeography of Hypoclinemus mentalis, initially described as Solea mentalis and subsequently assigned to the genus Achirus, was eventually reclassified into its current monotypic genus due to its limited distribution in freshwater environments, in contrast to the species of Achirus. The broad distribution of a single species across multiple South American river basins positions H. mentalis as an ideal candidate for biogeographic studies within South America, with an emphasis on the detection of cryptic lineages associated with major drainage basins. In our study, we employed mitochondrial and nuclear markers to investigate the potential existence of such lineages within the broader context of a molecular phylogeny that encompasses all valid genera in the flatfish family Achiridae. Our findings reveal that Hypoclinemus comprises seven operational taxonomic units (OTUs), as deduced from specimens collected across the majority of its documented range. Furthermore, our phylogeographic analyses support the hypothesis that colonization of freshwater habitats occurred through connections between the Caribbean Sea and Lake Pebas approximately 21.28 million years ago. Moreover, we observed that differentiation of lineages within the Hypoclinemus genus was significantly influenced by pronounced sea level fluctuations during the Plio-Pleistocene epoch, underscoring the impact of glaciations and interglacial periods on the biogeographic patterns.

evolutionary biology↗