Biology subjects

Santos, F. R.

Publications and source records attributed to Santos, F. R..

5 recordsLinked to original sources

bioRxiv2025

Chromosome-level genome assembly of the Brazilian merganser (Mergus octosetaceus), a rare and elusive waterfowl species

BackgroundThe Brazilian merganser (Mergus octosetaceus) is a critically endangered bird, with fewer than 250 mature individuals remaining in fragmented populations of the Cerrado biome in Brazil. It is an ecologically demanding species that requires clear water of fast-flowing rivers for diving and foraging, and riverside cavities for nesting. Technical and logistical challenges have restricted sampling and research to few genetic studies so far. The genetic results consistently revealed a low genetic diversity and high inbreeding in the species. Besides, the lack of a reference genome has precluded deeper evolutionary and conservation genetic analyses for the species. ResultsWe generated the first high-quality, chromosome-level genome assembly for Mergus octosetaceus using PacBio HiFi long reads and Arima Hi-C data from a female specimen. The assembly is 1.25 Gb in length, is highly complete, scoring 98.9% of BUSCO completeness, and includes both sex chromosomes (Z and W). Annotated repetitive elements comprise 18.94% of the genome, with evidence of recent activity, particularly among LINEs and LTRs retrotransposons. We also produced and annotated the complete mitochondrial genome, identifying 37 genes and the control region. Comparative synteny analysis with other Anatidae species revealed strong chromosomal conservation, with several inversion events in macrochromosomes. Demographic history reconstruction indicated fluctuations in effective population size, with significant reductions overlapped by major temperature changes, highlighting potential climate sensitivity of this lineage. ConclusionThis reference genome provides a fundamental resource for M. octosetaceus, enabling insights into genome evolution, chromosomal dynamics within Anatidae, and past population history. It is a remarkable foundation for future research and conservation strategies for managing and restoring this critically endangered species.

evolutionary biology↗

bioRxiv2023

Complete phylogeny of Micrathena spiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation

The Neotropical region is the most diverse on the planet, largely due to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to play a role in generating this diversity; these include Andean orogeny, closure of the Panama Isthmus, the hypothesized GAARlandia land bridge, and putative historical connections among currently isolated forests. Micrathena spiny spiders (Araneidae) include [~]120 species distributed mostly in forests from Mexico to Argentina, including the Antilles. Here, we use it as a model to study the biogeographic history of Neotropical rainforests by estimating a complete, dated phylogeny using morphological data for all species and molecular data for a subsample of 79 species. This resulted in a phylogeny that is mostly robust and supports most of the previously recognized species groups, although with uncertainty in the phylogenetic position of some species, especially those lacking sequences. The genus began diversifying about 25 million years ago. We use an event-based approach and biogeographic stochastic mapping to estimate ancestral distributions and the timing and direction of dispersal events, and to identify areas where diversity was generated, while accounting for phylogenetic uncertainty. Andean cloud forests generated the majority of species through in-situ speciation, but the Amazon was the major source of species for adjacent areas through dispersal; on the other extreme, the Dry Diagonal received species from other areas but generated very little diversity. Species exchange between Central and South America was intense, with [~]23 dispersal events beginning at least 20 million years ago, indicating that Micrathena dispersed between these continents before closure of the Isthmus of Panama. We also inferred [~]4 over-water dispersal events from Central and North America to the Antilles, which happened in the last 20 million years, and thus much after the proposed age of the GAARlandia land bridge. We identified an important species exchange route between the Amazon and the Atlantic forests. Sampling all species of the genus was fundamental to some of the conclusions above, especially in identifying the Andes as the area that generated the majority of species. This study highlights the importance of a solid and complete taxonomic sampling in biogeographic studies.

evolutionary biology↗

bioRxiv2020

New genetic insights about hybridization and population structure of hawksbill and loggerhead turtles from Brazil

An extremely high incidence of hybridization among sea turtles is found along the Brazilian coast. To understand this atypical phenomenon and its impact on sea turtle conservation, research focused in the evolutionary history of sea turtles is fundamental. We assessed high quality multilocus haplotypes of 143 samples of the five species of sea turtles that occur along the Brazilian coast to investigate the hybridization process and the population structure of hawksbill (Eretmochelys imbricata) and loggerhead turtles (Caretta caretta). The multilocus data were initially used to characterize interspecific hybrids. Introgression (F2 hybrids) was only confirmed in hatchlings of F1 hybrid females (hawksbill x loggerhead), indicating that introgression was either previously overestimated and F2 hybrids may not survive to adulthood, or the first-generation hybrid females nesting in Brazil were born as recent as few decades ago. Phylogenetic analyses using nuclear markers recovered the mtDNA-based Indo-Pacific and Atlantic lineages for hawksbill turtles, demonstrating a deep genetic divergence dating from the early Pliocene. In addition, loggerhead turtles that share a common feeding area and belong to distinct Indo-Pacific and Atlantic mtDNA clades present no clear genetic differentiation at the nuclear level. Finally, our results indicate that hawksbill and loggerhead rookeries along the Brazilian coast are likely connected by male-mediated gene flow.

genetics↗

bioRxiv2019

Manatee genomics supports a special conservation area in the Guianas coastline under the influence of the Amazon River plume

The West Indian manatee (Trichechus manatus) occurs along the Atlantic coastline and adjacent freshwater systems of South, Central and North America, from Alagoas (Brazil) to Florida (USA) and Greater Antilles. The Amazonian manatee (Trichechus inunguis) is the only Sirenian adapted exclusively to freshwater and endemic to the Amazon River basin. Previous studies have reported hybrids between T. inunguis and T. manatus close to the mouth of the Amazon River, composing a likely extensive hybrid zone along the Guianas coast of South America under the influence of the Amazon River plume. We have used ddRAD SNP data, and sequences of nuclear and mtDNA loci to characterize the genomic composition of manatees along the French Guiana coastline. We found this population to be formed by introgressed or later generation interspecific hybrids, and also describe the first T. inunguis found outside the Amazon River basin. Our results indicate that T. inunguis can survive in the Amazon River plume and have colonized independent water streams of the Guianas coastline where they likely hybridize with T. manatus. This hypothesis offers a plausible explanation for the known extension of the hybrid zone between the two species along the Guianas coastline. It also reinforces the importance of the Amazon plume, which flows westwards to the Guianas coastline and favors the dispersion of the freshwater species. This habitat functions as a large estuary-like system that provides an ecological continuum from Amazon River mouth to the disconnected waterflows of the Guianas, which deserves a status of special conservation area.

genomics↗

bioRxiv2017

Rapid antidepressant effects of the psychedelic ayahuasca in treatment-resistant depression: a randomised placebo-controlled trial

Major Depressive Disorder affects about 350 million people worldwide, and about one-third of the patients are considered treatment-resistant. Furthermore, available antidepressants take usually two weeks for the onset of their antidepressant effect. Recent open label trials show that psychedelics, such as ayahuasca and psilocybin, hold promise as fast-onset antidepressants. Although promising, these studies were not controlled for the placebo effect. To address this issue, and to further test the antidepressant effects of ayahuasca, we conducted a parallel arm, double-blind randomised placebo-controlled trial, in patients with treatment-resistant major depression. Thirty-five patients with treatment-resistant major depression received a single dose of ayahuasca or placebo. We measured as primary outcome the change in the Hamilton Depression Rating scale (HAM-D) seven days after the dosing session, and as secondary outcomes the changes in Montgomery-[A]sberg Depression Rating Scale (MADRS), and response rates at one day (D1), two days (D2) and seven days (D7) after dosing, and remission rates at D7. This study is registered with http://clinicaltrials.gov (NCT02914769). We observed robust evidence of rapid antidepressant effects of a single dosing session with ayahuasca when compared to placebo. HAM-D scores at D7 were significantly lower in patients treated with ayahuasca than in those treated with placebo (p=0{middle dot}019; Cohens d=0{middle dot}98). MADRS scores were significantly reduced in the ayahuasca group compared to the placebo group at all endpoints (at D1 and D2, p=0{middle dot}04; at D7, p<0{middle dot}0001). Between-group effect sizes increased from D1 to D7 (D1: Cohens d=0{middle dot}84; D2: Cohens d=0{middle dot}84; D7: Cohens d=1{middle dot}49). Response rates were high for both groups at D1 and D2, and were significantly higher in the ayahuasca group only at D7 (64% vs. 27%; OR = 4{middle dot}95; p = 0{middle dot}04; NNT = 2{middle dot}66). Remission rate was not significantly different between groups. Our study provides new evidence of rapid antidepressant effects of ayahuasca for treatment-resistant major depression.

clinical trials↗