Biology subjects

Alfaro, R.

Publications and source records attributed to Alfaro, R..

6 recordsLinked to original sources

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↗

bioRxiv2025

Tracing the illicit Peruvian delicacy: proof-of-concept multiplex-PCR for the simultaneous detection of seven commercial Macrobrachium prawn species

The genus Macrobrachium (Decapoda, Palaemonidae) comprises nearly 300 prawn species distributed worldwide. At least nine of these species naturally inhabit the Pacific slope river systems of Peru, where most sustain significant artisanal fisheries and are highly prized as a luxury delicacy in the nations traditional cuisine. Here, we developed and validated a multiplex PCR assay with species-specific primers to identify seven Macrobrachium species of economic importance to Peru. Through robust validation, our assays achieved high specificity and efficiency, enabling fast and simultaneous identification of the seven target species. The utility of our novel multiplex PCR assay was evaluated as a proof-of-concept tool for conducting the first molecular monitoring of species diversity and illegal trade in Peruvian prawns across different commercial sectors. Among the 51 analyzed commercial prawn samples, a total of four species were detected, including M. caementarius (82.4%), M. rosenbergii (11.8%), M. americanum (3.9%), and M. gallus (1.9%). Notably, our molecular monitoring in restaurants revealed the first evidence of illegal trade in native wild-caught prawns in La Libertad region occurring during the reproductive closed season, when only the market of the exotic farmed prawn M. rosenbergii is permitted. These findings underscore the urgent need for enhanced monitoring programs in prawn fisheries in northern Peru, as current efforts are mainly focused on more productive central and southern regions. Our multiplex PCR assay provides a robust and efficient tool that can assist authorities and researchers in monitoring efforts, combating illegal trade, conducting diversity research, and supporting conservation.

genetics↗

bioRxiv2025

A complete mitochondrial genome-based phylogeny of gooseneck barnacles confirms the sister group relationship between the eastern Pacific Pollicipes elegans and the eastern Atlantic P. pollicipes

BackgroundGooseneck barnacles are a fascinating invertebrate group and their taxonomic classification has attracted the attention of several specialists, including Charles Darwin, who was the first to note the close relationship between two species of gooseneck barnacles found on the eastern coasts of the Pacific, Pollicipes elegans, and the Atlantic, P. pollicipes. Additionally, a third species from the eastern Pacific, P. polymerus, was believed to have diverged earlier from the group. Methods and resultsHere, we used genomic short-read sequences publicly available in GenBank to assemble the first complete mitochondrial genome of P. elegans. We conducted a phylogenetic analysis to assess the relationships among its related species and other cirripede species from the superorder Thoracicalcarea. Our phylogenetic findings based on complete mitogenomes reinforce the close relationship between P. elegans and P. pollicipes, with P. polymerus emerging as a basal branch, indicating an earlier divergence from the group. ConclusionsOur analysis provided the first robust phylogenetic assessment of P. elegans, strongly supporting its close relationship with P. pollicipes. Further efforts should aim to sequence the complete mitogenomes of other species within the order Pollicipedomorpha. This endeavor will enable a more comprehensive phylogenetic analysis of this group, whose classification remains a subject of debate.

genomics↗

bioRxiv2025

Complete mitochondrial genome assembly of two searobin species (genus Prionotus) and their phylogenetic relationships (Triglidae: Prionotinae)

Species from the genera Bellator and Prionotus, commonly known as searobins, are marine ray-finned fish that belong to the subfamily Prionotinae. These fish have evolved distinctive morphological features and specialized behaviors that enable them to walk along the seafloor while detecting buried prey. This unique adaptation makes them ideal candidates for studies in evolutionary genetics. However, their phylogenetic relationships remain poorly understood. In this study, we utilized publicly available genomic reads from the GenBank database to assemble the first complete mitochondrial genomes of three searobin species: Bellator militaris, Prionotus alatus, and P. stephanophrys. We conducted a comparative analysis of these mitochondrial genomes, including the first phylogenetic analysis of the Prionotinae based on complete mitogenomic data. The resulting circular contigs measured 16,765 base pairs for B. militaris, 16,602 base pairs for P. alatus, and 16,896 base pairs for P. stephanophrys. The three mitogenomes exhibited a typical vertebrate organization, which includes 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a putative control region. Notably, P. stephanophrys contained an additional tRNA-Leu and an extra non-coding region. A Bayesian phylogenetic analysis grouped all Bellator species into a monophyletic clade within Prionotinae, while the sister taxon Prionotus formed a separate monophyletic subclade. The findings of this research provide valuable insights into the phylogenetic relationships and evolutionary history of the genera Bellator and Prionotus. Clarifying the taxonomy of these species may also support future management and conservation efforts for these economically valuable species.

genomics↗

bioRxiv2024

Development and validation of versatile species-specific primer assays for eDNA monitoring and authentication of 10 commercially important Peruvian marine species

Molecular identification assays provide crucial support in the research and regulation of aquatic resources. Among them, species-specific primers provide strong discriminatory power for fast and simultaneous differentiation between closely related species. In this study, we used interspecific variations detected in two mitochondrial genes to develop species-specific primers for eDNA monitoring and identifying 10 fish and shellfish species commercially available within the Peruvian seafood sector. To ensure versatility and high specificity, our primers were subjected to PCR, qPCR, and sequencing methods, coupled with robust validation assays that included a) an in-silico stage using self-generated and public DNA sequences, b) an in-vitro stage using target species belonging to vouchered specimens, fresh and cooked commercial samples, early life stages, and broad taxa of non-target species, and c) an in-situ stage using eDNA samples from different Peruvian marine ecosystems. Our novel species-specific primers successfully passed the validation process with high efficiency and specificity in unequivocally identifying all target species with 100% accuracy and without cross-species amplifications, thereby making them valuable tools for eDNA monitoring, seafood authentication, and to identify and combat illegal, unreported and unregulated fishing. The identification assays presented herein can be used to support effective fishery management and conservation efforts not only in the Peruvian fishery sector but also in other countries where our target species also occur or are available as imported commodities.

genetics↗

bioRxiv2021

Single-cell immune profiling reveals the impact of antiretroviral therapy on HIV-1-induced immune dysfunction, T cell clonal expansion, and HIV-1 persistence in vivo

Despite antiretroviral therapy (ART), HIV-1 persists in proliferating T cell clones that increase over time. To understand whether early ART affects HIV-1 persistence in vivo, we performed single-cell ECCITE-seq and profiled 89,279 CD4+ T cells in paired samples during viremia and after immediate versus delayed ART in six people in the randomized interventional Sabes study. We found that immediate ART partially reverted TNF responses while delayed ART did not. Antigen and TNF responses persisted despite immediate ART and shaped the transcriptional landscape of CD4+ T cells, HIV-1 RNA+ cells, and T cell clones harboring them (cloneHIV-1). Some HIV-1 RNA+ cells reside in the most clonally expanded cytotoxic T cell populations (GZMB and GZMK Th1 cells). CloneHIV-1+ were larger in clone size, persisted despite ART, and exhibited transcriptional signatures of antigen, cytotoxic effector, and cytokine responses. Using machine-learning algorithms, we identified markers for HIV-1 RNA+ cells and cloneHIV-1+ as potential therapeutic targets. Overall, by combining single-cell immune profiling and T cell expansion dynamics tracking, we identified drivers of HIV-1 persistence in vivo.

immunology↗