Biology subjects

Santos-Rojas, L. E.

Publications and source records attributed to Santos-Rojas, L. E..

3 recordsLinked to original sources

bioRxiv2026

BATOseq-PE: A public batoid DNA library with the first molecular insights into the cryptic diversity, genetic health, and management of Peruvian marine rays

Batoids (rays, skates, and relatives) are among the most threatened cartilaginous fishes globally, yet the molecular diversity of Peruvian taxa remains poorly evaluated. Furthermore, regional barcode sequences for high-conservation-priority taxa, such as sawfish, manta, and devil rays, are often restricted to private records, hindering essential phylogeographic and population structure assessments. To bridge this gap, we developed BATOseq-PE, the first public genetic reference library for Peruvian marine batoids, covering 14 species sequenced in vitro from local specimens, complemented by a novel in silico assembled mitogenome for Notoraja martinezi. This open-access repository contributes 73 novel COI barcodes, providing robust taxonomic resolution across 15 molecular operational taxonomic units (MOTUs) and Barcode Index Numbers (BINs). Notably, we provide the first Peruvian public records for high-priority species such as Mobula munkiana, Mobula thurstoni, Myliobatis peruviana, Rostroraja velezi, and the first global public barcodes for N. martinezi and Zapteryx xyster. By coupling BATOseq-PE with global datasets, we conducted the first multi-taxa screening for delimitation and phylogeographic assessments on Peruvian batoids, revealing a cryptic lineage within R. velezi and genetic connectivity patterns suggesting female philopatry in Mobula mobular. Finally, by integrating nucleotide diversity into a Genetic Diversity Risk Indicator (GDRI) alongside ecological and fishery data, we identified an alarming trend where heavy fishing pressure overlaps with extinction risk and depleted genetic diversity, allowing us to suggest data-driven, tailored management strategies. BATOseq-PE represents a valuable resource to accelerate taxonomic and population assessments, ultimately fostering ray conservation through the integration of genetic frameworks into fishery management.

genetics↗

bioRxiv2026

Hypanus brevis: a newly resurrected Eastern South Pacific stingray lineage revealed by integrative taxonomy

Hypanus brevis (Garman, 1880) and Hypanus dipterurus (Jordan & Gilbert, 1880) are currently considered as a conspecific lineage of the Eastern Pacific "diamond stingray". This group has been the subject of nomenclatural disputes for about 145 years, with H. brevis accepted as the junior synonym. To clarify the historical confusion surrounding this lineage, we employed an integrative taxonomic approach using specimens from the Eastern North and Eastern South Pacific (ENP and ESP). Both single (COI) and multilocus (COI - 16S rRNA) genetic analyses revealed a distinct evolutionary unit in the ESP. While morphological analyses detected subtle differences between ENP and ESP specimens (e.g., disc length and internostril width), most characters exhibited significant overlap, suggesting low evolutionary divergence. A Bayesian molecular clock analysis estimated this divergence at approximately 5.6 Ma. In accordance with Garmans (1880) original description based on specimens from Paita (northern Peru), we formally resurrect H. brevis from synonymy with H. dipterurus. Our findings suggest an anti-tropical speciation pathway, with core populations of H. brevis and H. dipterurus restricted to the temperate waters of the ESP and ENP, respectively. Notably, a single, fixed COI haplotype was detected in all H. brevis specimens from the north-central Peruvian coast. This result may indicate a severe bottleneck event, raising concerns about the genetic health and long-term viability of this vulnerable species. Finally, we analyzed historical fishery data of H. brevis to infer its current population status, suggesting targeted conservation measures and precautionary management to prevent further loss of genetic diversity.

genetics↗

bioRxiv2021

Non-invasive sex genotyping of paiche Arapaima gigas by qPCR: An applied bioinformatic approach to identify sex differences

Arapaima gigas, one of the largest freshwater fish in the world, is suffering from high fishing pressure and habitat loss, which threaten the conservation status of its natural populations. Of great cultural importance to Amazonian people, the paiche or pirarucu A. gigas is in high demand for its meat, ornamental uses and other byproducts such as scales. Aquaculture is a feasible solution to this dilemma. However, the fact that A. gigas presents no sexual dimorphism until it is 5 years old and its long period to sexual maturity are major obstacles for brood-stock management and fingerling production. Thus, the aim of this study was to develop a molecular tool for non-invasive genotypic sexing of paiche throughout its life cycle. We collected samples from gonads, fins and gill mucus of juvenile specimens from local facilities for histological and molecular analysis. Based on the recently available genome sequence of the paiche and making use of current NGS method, we implemented a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers. We found a Male-Specific Region (MSR), identified as MSR_3728, to be present only in males. Next, we designed two specific sets of primers on this region to identify genotypic sex by qPCR assays. Both primer sets, MSR_107 and MSR_129, detected males with 100% accuracy. Then we developed a duplex qPCR reaction for each primer set along a reference gene, analyzed the melting curves and detected males by observing two distinct peaks, one for MSR_107 or MSR_129 and one for the reference, while females only presented the reference peak. The same results were obtained for gonads, fins and interestingly, a non-invasive source from gill mucus samples. Finally, the gonads were evaluated histologically in a double-blind test, showing 100% accuracy with qPCR assay for identifying males and females. Data clearly demonstrated a novel pipeline approach for identifying DNA sex markers, followed by a quick, non-invasive, cost-effective duplex qPCR method for sexing A. gigas. These results may be valuable to efficient paiche aquaculture and conservation studies, helping to reduce the fishing pressure on its natural populations. Highlights of the manuscript- Implementation of a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers. - Finding of a Male-Specific Region (MSR), present only in males. - Development of a duplex qPCR to identify genotypic sex through non-invasive sampling.

genomics↗