Biology subjects

Silva, F. E.

Publications and source records attributed to Silva, F. E..

7 recordsLinked to original sources

bioRxiv2025

Refining Feulgen: low-cost and accurate genome size measurements for everyone

Feulgen image analysis densitometry (FIAD) has been extensively used for decades to measure genome sizes, but is usually considered less precise and less reproducible compared to other methods such as flow cytometry (FCM). However, FCM requires fresh tissue samples, which is a major impediment to using it on specimens collected in the field far from the lab. By contrast, FIAD works on ethanol-preserved samples kept at room temperature, which is a huge advantage for biodiversity genomics. In this study, we present refinements on the Feulgen protocol and downstream analyses that produce measurements at least as reliable and precise as those obtained using whole-genome sequencing. We illustrate it by measuring for the first time the genome size of the red bald uakari monkey Cacajao rubicundus using the American cockroach Periplaneta americana and the black garden ant Lasius niger as standards.

genomics↗

bioRxiv2025

First Comprehensive Examination of the Molecular Phylogenetics of Saki Monkeys, Genus Pithecia Desmarest, 1804, Reveals an Unexpectedly Low Taxonomic Diversity

Saki monkeys (Pithecia) are found exclusively in the Amazon, ranging from the Guiana Shield in the east to the Andean foothills in the west. The taxonomy of this genus is complex due to indeterminate type localities, numerous synonyms, sexual dichromatism and considerable geographical diversity in coat colour patterns. Previous assessments have indicated two to four species and a variable few subspecies based on morphological analyses of museum specimens. Just two species have been consistently recognised--Pithecia pithecia and Pithecia monachus. This study presents the first comprehensive molecular phylogeny of the genus, using mitochondrial cytochrome b sequences from 137 individuals across their range and a ddRADseq genomic analysis on 34 individuals. The phylogenetic results revealed three main clades: (1) Guiana Shield sakis, (2) Sedimentary Basin and Brazilian Shield sakis, and (3) a basal P. albicans south of the Rio Solimoes. The ddRADseq data further clarified species boundaries and relationships, identifying six distinct species: P. chrysocephala and P. pithecia sensu Hershkovitz (1987) on the Guiana Shield; P. albicans in central Amazonia south of the Rio Solimoes; P. monachus in western Amazonia; P. irrorata between the rios Purus, Tapajos, and Juruena; and P. vanzolinii in a limited area east of the Rio Jurua.

zoology↗

bioRxiv2025

The Sleep-Mood Connection: Temperament Modulates Neuroinflammation, Clock Genes, and Dopaminergic Receptors Expression in Rats

Temperament may influence mood disorder risk under sleep disturbances. Using high- and low-exploratory rats as a temperament model, we examined the effects of paradoxical sleep deprivation (PSD) on mood behaviors, neuroinflammation, oxidative stress, clock genes, and dopamine receptor expression. Eighty male Wistar rats were screened for exploratory activity, while 20 were classified as high (HE) and 21 as low (LE) exploratory based on open-field performance. HE and LE rats were subjected to PSD or remained undisturbed (controls). Behavioral assessments included impulsivity, risk-taking, anhedonia, and forced swim test (FST) performance. Neurobiological analyses measured hippocampal lipid peroxidation, pro-inflammatory markers (IL-6, TLR4), gene expression of Clock, Tph2, Tdo2, and protein expression of D1, and D2, which regulate, respectively, circadian rhythms, serotonin synthesis, tryptophan metabolism, and dopaminergic signaling--key pathways implicated in mood disorders. HE rats showed increased impulsivity, risk-taking, and exploratory behaviors, resembling mania, while LE rats exhibited avoidance. PSD intensified these traits, heightening risk-taking in HE rats and inducing depressive-like behaviors in LE rats, including anhedonia and FST immobility linked to reduced Tph2 expression. Both groups had post-PSD working memory deficits. Neurobiologically, HE+PSD rats showed increased lipid peroxidation, neuroinflammation (IL-6, TLR4), and upregulation of Clock and DRD1 genes, while LE+PSD rats had elevated hippocampal Tdo2 expression. Temperament shapes PSD-induced behavioral and neurobiological effects. HE rats showed mania-like traits, while LE rats exhibited depressive behaviors. PSD impaired working memory in both. Oxidative stress, inflammation, and gene expression changes highlight distinct vulnerabilities and potential therapeutic targets for mood disorders.

animal behavior and cognition↗

bioRxiv2025

The genomic landscape of spider monkeys and northern muriquis from a conservation perspective

BackgroundMost populations of spider monkeys (Ateles) and muriquis (Brachyteles), two Neotropical primate genera, are under severe anthropogenic threats. Yet, taxon-wide population-level studies leveraging their degree of endangerment linked to their genetic diversity patterns and demographic history are lacking. To properly address this, there is a need to expand from morphological and genetic marker-based studies. ResultsWe generated high-coverage genome sequencing for 58 individuals sampled across 8 Atelidae species, in the first population-wide study of all extant spider monkey species, in the wild and captivity, alongside northern muriquis (Brachyteles hypoxanthus). Additionally, we present a high-contiguity reference genome for Ateles hybridus. Here, we observe the overall levels of genetic diversity and genetic load of the analyzed populations do not align to their IUCN endangerment category. Moreover, we show that in the wild, genetic load is overall higher compared to the captive populations analyzed. Then, we depict two main trans and cis-Andean sister clades in Ateles, and further structure and dynamics outlined by the Madeira River in the latter clade. Lastly, we find that genes in highly divergent regions between Ateles and B. hypoxanthus are involved in central nervous system development and photorreception. ConclusionsOur study shows i) the lack of concordance between the genetic diversity levels and extinction risk of these populations, suggestive of recent and strong external drivers; ii) increased genetic load in the wild in contrast to effective captive management, indicating mostly past demographic events; iii) structure and dynamics in spider monkeys that agrees with common biogeographical patterns and iv) genetic divergence between Ateles and Brachyteles potentially linked to distinct environmental light levels.

genomics↗

bioRxiv2023

Whole genome approach to the structure and dynamics of Cacajao wild populations

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into bald and black uakaris, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of uakari populations. Beyond increasing their representation, with this work we explored the effects of the Amazon rainforests dynamism on platyrrhine species.

evolutionary biology↗

bioRxiv2023

The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genus Cacajao)

AimWestern Amazonia is a region that underwent several landscape changes during the Quaternary. While Riverine Barrier Hypothesis is traditionally used to explain the influence of rivers on speciation, processes such as river rearrangements have been overlooked to explain the geographic distribution and evolutionary history of the Amazonia biota. Here we test how river rearrangements in western Amazonia influenced the evolutionary history of uakari monkeys, a primate group most associated with seasonally flooded forests in western Amazonia. LocationWestern Amazonia TaxonThe uakari monkey (genus Cacajao) MethodsWe performed a continuous phylogeographic analysis using 77 cytochrome b sequences and used digital elevation models to identify the role of landscape and riverscape characteristics in the geographic distribution of Cacajao. Finally, we used genome-wide SNPs variation (ddRADseq) to investigate population structure, gene flow and demographic history in three Cacajao species that were impacted by river rearrangements. ResultsOur continuous phylogeographical reconstruction points that the ancestral Cacajao lineage occupied the flooded forests of the Solimoes River at [~]1.7 Mya, and descendant lineages dispersed throughout western Amazonia more recently. We identified gene flow among both black and bald-headed uakari populations, even across rivers considered barriers (e.g., the Negro River). Landscape analysis showed that river rearrangements influenced the geographic distribution and population structure in Cacajao. The demographic analysis indicates that C. calvus, C. amuna, and C. rubicundus went through a population decline in the last 70 Kya and have a low effective population size. Main conclusionOur results support that the river rearrangements have shaped the geographic distribution and divergence of recently diverged Cacajao lineages. Landscape and riverscape changes, along with retractions of the flooded forests, isolated some Cacajao populations in floodplain areas. Our study also suggests that these events led to the recent population decline in species with a restricted geographic distribution.

evolutionary biology↗

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↗