Biology subjects

Sampaio, I.

Publications and source records attributed to Sampaio, I..

4 recordsLinked to original sources

bioRxiv2024

Phylogeography of the electric rays of the family Narcinidae (Gill, 1862): systematic review and evidence of the dispersal routes to America.

The electric rays belonging family Narcinidae are a cosmopolitan group, which has come under increasing scrutiny in relation to the taxonomic composition of the family and its phylogenetic position within the order Torpediniformes. Phylogeographic inferences can provide important insights into the present-day distribution of the narcinid species, as well as the systematics of the group. In this context, the present study evaluates the evolutionary and biogeographic history of the family Narcinidae, inferring distribution patterns and the molecular systematics of these organisms based on the DNA barcode. The results of the analysis indicate that the electric rays originated in the Central Indo-Pacific realm, with all other dispersal events beginning from this region. Two different dispersal routes were observed for the American narcinids. The first route was from the Central Indo-Pacific realm to the Pacific Ocean and then the Caribbean Sea, prior to the closure of the Isthmus of Panama. The second route start on Central Indo-Pacific realm passed South Africa continent before crossing the Atlantic. The principal torpediniform lineages diversified between the end of the Cretaceous and the early Paleocene, with the present-day narcinid taxa arising and diversifying between 25 and 20 Mya. The present study confirms the lack of monophyly in the Narcinidae, validates the genus Narcinops, and restricts the occurrence of the genus Narcine to the coastal environments of the Americas, which emphasizes the need for the review and revalidation of the synonym Syrraxis for the narcinids of the Central/Western Indo-Pacific realm. This study also describes additional lineages for Narcine entemedor and Narcine maculata and validates the occurrence of three species (Narcinesp., Narcine brasiliensis, and Narcine bancroftii) in the Atlantic Ocean, based on the published data, and emphasizes the need for a definitive description of Narcine sp.

evolutionary biology↗

bioRxiv2023

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases. One Sentence SummaryDeep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

genomics↗

bioRxiv2023

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human-specific. This study will open a wide range of research avenues for future primate genomic research. One-Sentence SummaryThe whole genome sequences of 233 primate species provide insight into the determinants of genetic diversity, phylogenomics, and human uniqueness.

genomics↗

bioRxiv2020

Volatiles defenses of Amazon Azteca ants (repellent ants)

Azteca ants are widely distributed in the neotropics and have been utilized as natural insect repellent for centuries. Azteca oils provide natural defense against herbivores in mutualistic interactions between ants and their host trees. While chemical characterization of oil secretions revealed a composition dominated by iridoids and ketones, the volatile emissions from Azteca ants, and therefore the active gas-phase semiochemicals, remain uncharacterized. In this study, we determined the composition of volatile emissions from a sample of an Azteca ant nest near the Rio Negro in the central Amazon. We found Azteca emissions were composed of a blend of methyl cyclopentyl and methyl cyclopentenyl based volatiles previously identified in Azteca oil extracts as potent alarm pheromones. The ketone 6-methyl-5-hepten-2-one, which also waspreviously identified as a major component of the Azteca oil, was found to be the dominant volatile emitted. For the first time, we report emissions of the highly volatile ketones 2,3-butadione and acetoin from the Azteca nest. Our study has important implications for the better understanding of the ecology and defense strategies of Azteca ants in herbivore defense and provides a base for future commercial applications involving Azteca ant essential oils as natural insect repellents.

plant biology↗