Untangling the Tangled Bank: A Novel Method for Partitioning the Effects of Phylogenies and Traits on Ecological Networks

Understanding how evolutionary and ecological processes shape species interaction networks remains as one of the main challenges in eco-evolutionary studies. Here, we present an integrative analytical framework to partition the effects of phylogenies and functional traits on the structure of ecological networks. The method combines fuzzy set theory and matrix correlation, implemented under a Monte Carlo framework. We designed a simulation study in order to estimate the accuracy of the methods proposed here, measuring Type I Error rates. The simulation study shows that the method is accurate, i.e., incorrectly rejecting a true null hypothesis in ~5% of the cases and falling within the confidence interval. We illustrate our framework using data from a seed dispersal network from southern Brazil. Our analyses suggest that birds must have specific traits in order to consume their plant resources, and that phylogenetic resemblance has no explanatory power for species traits and species interactions in this seed-dispersal network.     

Testing an Ethnobiological Evolutionary Hypothesis on Plant-Based Remedies to Treat Malaria in Africa

The malaria hypothesis, which addresses a strong selective pressure on human genes resulting from a chain of processes that originated with the practice of agriculture, is an example of an evolutionary consequence of niche construction. This scenario has led us to formulate the following questions: Are the genetic adaptations of populations with a history of contact with malaria reflected in the local medical systems? Likewise, could environmental changes (deforestation) and the incidence of malaria result in an adaptive response in these local health care systems? We collected secondary data for the entire African continent from different databases and secondary sources and measured the response of health care systems as the variation in the richness of antimalarial medicinal plants. Our results did not indicate a cause-and-effect relationship between the tested variables and the medical systems, but a subsequent analysis of variance showed an increase in the mean of medicinal plants in regions with a higher incidence of malaria prior to disease control measures. We suggest that this response had a greater impact on local medical knowledge than other variables, such as genetic frequency and deforestation.     

Chronic Stress Causes Sex-Specific and Structure-Specific Alterations in Mitochondrial Respiratory Chain Activity in Rat Brain

Chronic restraint stress (CRS) induces a variety of changes in brain function, some of which are mediated by glucocorticoids. The response to stress occurs in a sex-specific way, and may include mitochondrial and synaptic alterations. The synapse is highly dependent on mitochondrial energy supply, and when mitochondria become dysfunctional, they orchestrate cell death. This study aimed to investigate the CRS effects on mitochondrial respiratory chain activity, as well as mitochondrial potential and mass in cell body and synapses using hippocampus, cortex and striatum of male and female rats. Rats were divided into non-stressed (control) and stressed group (CRS during 40 days). Results showed that CRS increased complex I–III activity in hippocampus. We also observed an interaction between CRS and sex in the striatal complex II activity, since CRS induced a reduction in complex II activity in males, while in females this activity was increased. Also an interaction was observed between stress and sex in cortical complex IV activity, since CRS induced increased activity in females, while it was reduced in males. Glucocorticoid receptor (GR) content in cortex and hippocampus was sexually dimorphic, with female rats presenting higher levels compared to males. No changes were observed in GR content, mitochondrial potential or mass of animals submitted to CRS. It was concluded that CRS induced changes in respiratory chain complex activities, and some of these changes are sex-dependent: these activities are increased in the striatal mitochondria by CRS protocol mainly in females, while in males it is decreased.

     

Host bromeliads and their associated frog species: Further considerations on the importance of species interactions for conservation

Bromeliads constitute a good example of symbiosis with organisms that spend their entire life cycle inside the plants, and often depend on them to breed. The bromeliads benefit from this interaction by increasing their nutrients intake. Conservation efforts tend to focus on a single endangered species, but in symbiotic associations, the viability of one species depends on that of the other. Based on IUCN criteria, any species that depends on another to complete its life cycle should be assigned a conservation status equivalent to that of the host taxon, where appropriate. We gathered published plus fieldwork data on the frog-bromeliad mutualism and compiled a checklist of 99 bromeligenous frogs species associated to 69 bromeliad hosts, and found threatened bromeliads hosting non-threatened frogs. We found that 62% bromeligenous frogs inhabit unspecified bromeliads. Finally, we propose strategies for improving understanding and conservation of the frog-bromeliad mutualism.     

Neoleucinodes elegantalis (Lepidoptera: Crambidae): an organism invisible to the defences of tomato fruits

Insect–plant interactions involving species of the genus Solanum have been intensively studied, resulting in several articles on insect–plant interactions. However, the interactions between herbivores and the fruits of Solanum lycopersicum (tomato) are not well known. Neoleucinodes elegantalis is a borer that causes great yield losses in S. lycopersicum crops because of the direct damage that it causes to the fruits and the difficulty of controlling it. In the field, the outside of a tomato fruit infested with the larvae of N. elegantalis is visually similar to uninfested fruits. Even a minor injury by herbivores can elicit a defensive response. Due to the lack of studies on interactions between fruit borers and S. lycopersicum, our aim in this study was to determine the locations of S. lycopersicum fruit in which the N. elegantalis larvae prefer to feed. An evaluation of nutritional sources was done through histochemical and biochemical tests and the defensive response of the S. lycopersicum fruit to attack by N. elegantalis larvae was evaluated through the detection of protease inhibitors (PIs) and lipoxygenase (LOX) activity. Our results show that the columella region is preferred by the N. elegantalis larvae and that this region has a nutritional source. Furthermore, attack by N. elegantalis larvae in the columella does not induce a significant increase in lipoxygenase activity and PIs. Thus, our results provide a better understanding of the interaction between the larvae of N. elegantalis and S. lycopersicum fruits and a better understanding of the evolution of plant–herbivore interactions, with an emphasis on the choice of feeding location as a strategy to avoid plant defences.     

Bat species diversity and distribution in a disturbed regime at the Lake Bogoria National Reserve,Kenya

Human population growth drives intrusion and progressive conversion of natural habitats for agriculture. We evaluated human impacts on bat species diversity and distribution among four vegetation types in and around Lake Bogoria National Reserve between November 2012 and July 2013. Plants were surveyed using the Braun–Blanquet cover/abundance method, whereas bats were sampled using standard mist nets erected on poles at ground level. Floristic similarity analysis revealed three broad vegetation assemblages, namely riverine vegetation, farmland and Acacia woodland/Acacia–Commiphora woodland. Two hundred and 33 bats representing eleven species in eleven genera and seven families were recorded. These were Epomophorus minimus, Rhinolophus landeri, Hipposideros caffer, Cardioderma cor, Lavia frons, Nycteris hispida, Chaerephon pumilus, Mops condylurus, Neoromicia capensis, Scotoecus hirundo and Scotophilus dinganii. Species richness estimators indicated that sampling for bats at ground level was exhaustive. Bat species richness and diversity were highest in the more structurally complex Acacia woodland compared to more homogenous farmlands where we recorded only common and generalist species that often occur in open habitats. The higher bat species richness and diversity in the Acacia woodland as compared to farmland underscore the importance of remnant natural savannah woodlands in the conservation of bats and other elements of biodiversity .     

Complexity and algorithms for copy-number evolution problems

Background

Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome’s copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis.

Results

We model the evolution of a tumor by segmental deletions and amplifications, and gauge distance from profile \(\mathbf {a}\) to \(\mathbf {b}\) by the minimum number of events needed to transform \(\mathbf {a}\) into \(\mathbf {b}\). Given two profiles, our first problem aims to find a parental profile that minimizes the sum of distances to its children. Given k profiles, the second, more general problem, seeks a phylogenetic tree, whose k leaves are labeled by the k given profiles and whose internal vertices are labeled by ancestral profiles such that the sum of edge distances is minimum.

Conclusions

For the former problem we give a pseudo-polynomial dynamic programming algorithm that is linear in the profile length, and an integer linear program formulation. For the latter problem we show it is NP-hard and give an integer linear program formulation that scales to practical problem instance sizes. We assess the efficiency and quality of our algorithms on simulated instances.

Availability

https://github.com/raphael-group/CNT-ILP

     

Bond length pattern associated with charge carriers in armchair graphene nanoribbons

The geometry configuration of charged armchair graphene nanoribbons (AGNRs) is theoretically investigated in the framework of a two-dimensional tight-binding model that includes lattice relaxation. Our findings show that the charge distribution and, consequently, the bond length pattern is dependent on the parity of the nanoribbon width. In this sense, the lattice distortions decrease smoothly for increasingly wider GNRs. As should be expected, AGNRs belonging to a particular family present similar patterns for the bond lengths. The interplay between the electron-phonon coupling and band gap is also investigated. The results show that the electron-phonon coupling strength is fundamental to promote the transition from metallic towards semiconducting-like behavior for the band gap. Most important, such strength is crucial on defining the degree of lattice distortions in AGNRs.     

Hox2 Genes Are Required for Tonotopic Map Precision and Sound Discrimination in the Mouse Auditory Brainstem

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