Biology subjects

Silva, A.

Publications and source records attributed to Silva, A..

6 recordsLinked to original sources

bioRxiv2018

Dioecy in plants: an evolutionary dead end? Insights from a population genomics study in the Silene genus

About 15,000 angiosperm species ([~]6%) have separate sexes, a phenomenon known as dioecy. Early work reported a lower species richness in dioecious compared to non-dioecious sister clades, which was taken to suggest that dioecy might be an evolutionary dead end. More recently, phylogenetic analyses using different methodologies have challenged this conclusion. Here, we used a population genomics approach to look for evidence of evolutionary handicaps of dioecy in the Silene genus at the molecular level. We obtained RNA-seq data of individuals from several populations in 13 closely related species with different breeding systems: seven dioecious, three hermaphroditic and three gynodioecious species. We show that dioecy is associated with increased genetic diversity and a higher selection efficacy both against deleterious and for beneficial mutations while controlling for differences in population size. We conclude that, in the Silene genus, dioecious species bear no sign of mutational burden or upcoming extinction. On the contrary, dioecious species harbor a higher potential for adaptation than their non-dioecious relatives. Our results do not support the evolutionary dead end hypothesis and re-open the question why dioecy is rare in angiosperms.\n\nSignificance statementDioecy (=separate sexes) is much rarer in flowering plants compared to animals and other organisms. The \"dead-end hypothesis\" states that dioecious plant populations might experience evolutionary handicaps such as low seed dispersal (as only 50% of the individuals, the females, contribute), which might cause high genetic drift, low adaptation and ultimately extinction. Here we tested this hypothesis by focusing on the genus Silene and by comparing the population genetics of 13 dioecious and non-dioecious species. We found that dioecious Silene species exhibit lower genetic drift and more adaptation compared to their non-dioecious relatives. Our results thus reject the dead-end hypothesis and re-open the question of why dioecy is rare in flowering plants.

evolutionary biology↗

bioRxiv2018

Effect of cadmium accumulation on the performance of plants and of herbivores that cope differently with organic defences

Some plants can accumulate in their shoots metals that are toxic to most other organisms. This ability may serve as a defence against herbivores. Although both metal accumulation and the production of organic defences may be costly to the plant, the two mechanisms may interact on their effect on herbivores. However, this interplay between metal-based and classical organic defences remains overlooked.\n\nTo fill this gap, we studied the interactions between tomato (Solanum lycopersicum), a plant that accumulates cadmium, and two spider-mites, Tetranychus urticae and T. evansi that respectively induce and suppress organic plant defences, measurable via the activity of trypsin inhibitors. We exposed plants to different concentrations of cadmium and measured their effect on mites and plants. The oviposition of both spider-mite species was higher on plants exposed to low concentrations of Cd than on control plants but decreased at concentrations above 0.5 mM. Therefore, herbivores with contrasting responses to organic defences responded similarly to metal accumulation by the plants. On the plant, despite clear evidence for Cd accumulation, we did not detect any effect of Cd on traits that reflect the general response of the plant, such as biomass, water content and carbon/nitrogen ratio. Still, we found an effect of Cd supply upon the quantity of soluble sugars and leaf reflectance changes that may reflect structural modifications in the cells. In turn, these changes in plant traits interfered with the performance of spider mites feeding on those plants.\n\nAdditionally, we show that the induction and suppression of plant defences by spider mites was not affected by Cd supply to the plants. Furthermore, the effect of metal supply on spider-mite performance was not affected by previous infestation. Together, our results suggest no interaction between metal-based and organic plant defences, on our system. This may be useful for plants living in heterogeneous environments, as they may use one or the other defence mechanism, depending on their relative performance in each environment. This may be relevant to studies on the interactions between herbivores and plants, from physiology to ecology.

ecology↗

bioRxiv2018

Molecular tools for phytoplankton monitoring samples

HABs can have severe impacts in fisheries or human health by the consumption of contaminated bivalves. Monitoring assessment (quantitative and qualitative identification) of these organisms, is routinely accomplished by microscopic identification and counting of these organisms. Nonetheless, molecular biology techniques are gaining relevance, once these approaches can easily identify phytoplankton organisms at species level and even cell number quantifications. This work tests 12 methods/kits for genomic DNA extraction and seven DNA polymerases to determine which is the best method for routinely use in a common molecular laboratory, for phytoplankton monitoring samples analyses. From our work, Direct PCR master mix for tissue samples, proved to be the most adequate by its velocity of processivity, practicability, reproducibility, sensitiveness and robustness. However, brands such as Omega Biotek, GRISP, Qiagen and MP Biomedicals also showed good results for conventional DNA extraction as well as all the Taq brands tested (GRISP, GE Healthcare Life Sciences, ThermoFisher Scientific and Promega). Lugols solution, with our tested kits did not show negative interference in DNA amplification. The same can be said about mechanical digestion, with no significant differences among kits with or without this homogenization step.

molecular biology↗

bioRxiv2018

Stepping into a dangerous quagmire: environmental determinants of human-lancehead pit vipers (Bothrops genus) contact resulting in injuries, Brazilian Amazon

Despite significant and successful efforts in Brazil regarding snakebites in the areas of research, antivenom manufacture and quality control, training of health professionals in the diagnosis and clinical management of bites, little is known about determinants of snakebites incidence in order to further plan interventions to reduce the impact of this medical condition. Understanding the complexity of ecological interactions in a geographical region is important for prediction, prevention and control measures of snakebites. The aim of this investigation is to describe spatial distribution and identify environmental determinants of human- lancehead pit vipers (Bothrops genus) contact resulting in injuries, in the Brazilian Amazon. Aggregated data by municipality was used to analyze the spatial distribution of Bothrops bites cases and its relationship with geographic and environmental factors. Eight geo-environmental factors were included in the analysis as independent variables: (1) tree canopy loss increase; (2) area with vegetation cover; (3) area covered by water bodies; (4) altitude; (5) precipitation; (6) air relative humidity; (7) soil moisture; and (8) air temperature. Human- lancehead pit vipers (Bothrops genus) contact resulting in envenomings in the Amazon region is more incident in lowlands [-0.0006827 (IC95%: -0.0007705; - 0.0005949), p<0.0001], with high preserved original vegetation cover [0.0065439 (IC95%: 0.0070757; 0.0060121), p<0.0001], with heaviest rainfall [0.0000976 (IC95%: 0.0000925; 0.0001026), p<0.0001] and higher air relative humidity [- 0.0081773 (IC95%: -0.0107681; -0.0055865), p<0.0001]. This association is interpreted as the result of the higher forest productivity and abundance of pit vipers in such landscapes.\n\nAuthor summaryDespite successful efforts in Brazil regarding snakebites in the areas of research, antivenom manufacture and quality control and training of health professionals, little is known about determinants of snakebites incidence in order to further plan interventions to reduce the impact of this medical condition. Understanding the complexity of ecological interactions in a geographical region is important for prediction, prevention and control measures of snakebites. The aim of this study is to describe spatial distribution and identify environmental determinants of human- lancehead pit vipers (Bothrops genus) contact resulting in injuries, in the Brazilian Amazon. An increase in the forest productivity with a higher availability of some types of prey, such as frogs and amphibians, anurans and lizards, was suggested as a cause for the higher snake abundance in the rainy season. Probably due to the higher forest productivity and abundance of pit vipers in such landscapes, human-lancehead pit vipers contact resulting in envenomings in the Amazon region is more incident in lowlands, with high preserved original vegetation cover, with heaviest rainfall and higher air relative humidity.

animal behavior and cognition↗

bioRxiv2018

Improving Metagenomic Assemblies Through Data Partitioning: a GC content approach

Assembling metagenomic data sequenced by NGS platforms poses significant computational challenges, especially due to large volumes of data, sequencing errors, and variations in size, complexity, diversity and abundance of organisms present in a given metagenome. To overcome these problems, this work proposes an open-source, bioinfor-matic tool called GCSplit, which partitions metagenomic sequences into subsets using a computationally inexpensive metric: the GC content. Experiments performed on real data show that preprocessing short reads with GCSplit prior to assembly reduces memory consumption and generates higher quality results, such as an increase in the N50 metric and the reduction in both the L50 value and the total number of contigs produced in the assembly. GCSplit is available at https://github.com/mirand863/gcsplit.

bioinformatics↗

bioRxiv2017

A convergent depression vulnerability pathway encoded by emergent spatiotemporal dynamics

Fluctuations in brain local field potential (LFP) oscillations reflect emergent network-level signals that mediate behavior. Cracking the code whereby these LFP oscillations coordinate in time and space (spatiotemporal dynamics) to represent complex behaviors would provide fundamental insights into how the brain signals emotional processes at the network level. Here we use machine learning to integrate LFP activity acquired concurrently from seven cortical and subcortical brain regions into an analytical model that predicts the emergence of depression-related behavioral dysfunction across individual mice subjected to chronic social defeat stress. We uncover a spatiotemporal dynamic network in which activity originates in prefrontal cortex (PFC) and nucleus accumbens (NAc, ventral striatum), relays through amygdala and ventral tegmental area (VTA), and converges in ventral hippocampus (VHip). The activity of this network correlates with acute threat responses and brain-wide cellular firing, and it is enhanced in three independent molecular-, physiological-, and behavioral-based models of depression vulnerability. Finally, we use two antidepressant manipulations to demonstrate that this vulnerability network is biologically distinct from the networks that signal behavioral dysfunction after stress. Thus, corticostriatal to VHip-directed spatiotemporal dynamics organized at the network level are a novel convergent depression vulnerability pathway.

neuroscience↗