Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes

International audienceThe evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes covering the three domains of life makes it possible to contrast these predictions with empirical data. We performed a systematic analysis of the phylogenetic relationships of ancestral eukaryotic genes with archaeal and bacterial genes. In contrast with previous studies, we emphasize the critical importance of methods accounting for statistical support, horizontal gene transfer, and gene loss, and we disentangle the processes underlying the phylogenomic pattern we observe. We first recover a clear signal indicating that a fraction of the bacteria-like eukaryotic genes are of alphaproteobacterial origin. Then, we show that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group. We also provide evidence that eukaryotes branch close to the last archaeal common ancestor. Our results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria. Overall, they leave only two possible interpretations, respectively, based on the early-mitochondria hypotheses, which suppose an early endosymbiosis of an alphaproteobacterium in an archaeal host and on the slow-drip autogenous hypothesis, in which early eukaryotic ancestors were particularly prone to horizontal gene transfers

Magnetic nanoparticles as efficient bulk pinning centers in type-II superconductors

Enhancement of flux pinning by magnetic nanoparticles embedded into the bulk of type-2 superconductor is studied both theoretically and experimentally. Magnetic part of the pinning force associated with the interaction between a spherical magnetic inclusion and an Abrikosov vortex was calculated in the London approximation. Calculations are supported by the experimental results obtained on sonochemically modified MgB2 superconductor with embedded magnetic Fe2O3 nanoparticles and compared to MgB2 with nonmagnetic Mo2O5 pinning centers of similar concentration and particle size distribution. It is shown that ferromagnetic nanoparticles result in a considerable enhancement of vortex pinning in large-kappa type-2 superconductors.Comment: PDF, 14 page

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

Homologous genes originate from a common ancestor through vertical inheritance, duplication, or horizontal gene transfer. Entire homolog families spawned by a single ancestral gene can be identified across multiple genomes based on protein sequence similarity. The sequences, however, do not always reveal conclusively the history of large families. To study the evolution of complete gene repertoires, we propose here a mathematical framework that does not rely on resolved gene family histories. We show that so-called phylogenetic profiles, formed by family sizes across multiple genomes, are sufficient to infer principal evolutionary trends. The main novelty in our approach is an efficient algorithm to compute the likelihood of a phylogenetic profile in a model of birth-and-death processes acting on a phylogeny

Interpreting the Effect of Stimulus Parameters on the Electrically Evoked Compound Action Potential and on Neural Health Estimates

Abstract: Variations in the condition of the neural population along the length of the cochlea can degrade the spectral and temporal representation of sounds conveyed by CIs, thereby limiting speech perception. One measurement that has been proposed as an estimate of neural survival (the number of remaining functional neurons) or neural health (the health of those remaining neurons) is the effect of stimulation parameters, such as the interphase gap (IPG), on the amplitude growth function (AGF) of the electrically evoked compound action potential (ECAP). The extent to which such measures reflect neural factors, rather than non-neural factors (e.g. electrode orientation, electrode-modiolus distance, and impedance), depends crucially upon how the AGF data are analysed. However, there is currently no consensus in the literature for the correct method to interpret changes in the ECAP AGF due to changes in stimulation parameters. We present a simple theoretical model for the effect of IPG on ECAP AGFs, along with a re-analysis of both animal and human data that measured the IPG effect. Both the theoretical model and the re-analysis of the animal data suggest that the IPG effect on ECAP AGF slope (IPG slope effect), measured using either a linear or logarithmic input-output scale, does not successfully control for the effects of non-neural factors. Both the model and the data suggest that the appropriate method to estimate neural health is by measuring the IPG offset effect, defined as the dB offset between the linear portions of ECAP AGFs for two stimuli differing only in IPG

Economic evaluation of three systems of alimentation used in finishing lambs

Eighteen castrated male lambs of the Texel breed were randomly diestribut3ed among the following treatments: T1 = confinement; T2 = pasture with supplementation; T3 = pasture without supplementation. At 144 days of age the lambs were slaughtered after a 12hr fast. Live weight at slaughter and warm carcass weight were lower (P≤0.05) for T3 lambs compared with those confined or supplemented at pasture, which resulted in lower gross income. Profitability in relation to liveweight was higher (P≤0.05) for the lambs on pasture without supplementation relative to T1, whereas the profitability in relation to carcass weight numerically was higher for both T1 and T2 than for T3. The availability of herbage dry matter at the end of the experiment was 326% higher for the supplementation treatment than without supplementation (T2 vs. T3). (Portuguese

Interpreting the Effect of Stimulus Parameters on the Electrically Evoked Compound Action Potential and on Neural Health Estimates

Abstract: Variations in the condition of the neural population along the length of the cochlea can degrade the spectral and temporal representation of sounds conveyed by CIs, thereby limiting speech perception. One measurement that has been proposed as an estimate of neural survival (the number of remaining functional neurons) or neural health (the health of those remaining neurons) is the effect of stimulation parameters, such as the interphase gap (IPG), on the amplitude growth function (AGF) of the electrically evoked compound action potential (ECAP). The extent to which such measures reflect neural factors, rather than non-neural factors (e.g. electrode orientation, electrode-modiolus distance, and impedance), depends crucially upon how the AGF data are analysed. However, there is currently no consensus in the literature for the correct method to interpret changes in the ECAP AGF due to changes in stimulation parameters. We present a simple theoretical model for the effect of IPG on ECAP AGFs, along with a re-analysis of both animal and human data that measured the IPG effect. Both the theoretical model and the re-analysis of the animal data suggest that the IPG effect on ECAP AGF slope (IPG slope effect), measured using either a linear or logarithmic input-output scale, does not successfully control for the effects of non-neural factors. Both the model and the data suggest that the appropriate method to estimate neural health is by measuring the IPG offset effect, defined as the dB offset between the linear portions of ECAP AGFs for two stimuli differing only in IPG

Superfluid fraction in an interacting spatially modulated Bose-Einstein condensate

At zero temperature, a Galilean-invariant Bose fluid is expected to be fully superfluid. Here we investigate theoretically and experimentally the quenching of the superfluid density of a dilute Bose-Einstein condensate due to the breaking of translational (and thus Galilean) invariance by an external 1D periodic potential. Both Leggett's bound fixed by the knowledge of the total density and the anisotropy of the sound velocity provide a consistent determination of the superfluid fraction. The use of a large-period lattice emphasizes the important role of two-body interactions on superfluidity

An ethnoarchaeological study of livestock dung fuels from cooking installations in northern Tunisia

Livestock dung is a valuable material in many rural communities worldwide. In our research area, the site of Althiburos and its surroundings, now el Médéïna, in northwestern Tunisia, dung is the main source of fuel for domestic purposes, primarily the processing and cooking of foods. Ovicaprine dung is daily used in traditional mud tannur type ovens, namely tabouna. The archaeological record shows that mud constructed cooking installations were common during the first millennium BC. Previous studies of phytoliths and dung spherulites at Numidian Althiburos suggested the use of vegetal and fecal matter for fuel purposes. We present here the results of the continuation study based on the comparison between archaeological results (a selection of cooking installations, six hearths and two mud ovens) and those obtained from the ethnographic study of dung fuel materials from the site area. The present study builds up on ethnographic observations and informal interviews (dung collection, management, storage, waste disposal and cooking and baking activities), temperature measurements within the burning fuel, as well as modern material sampling (fresh dung, burned pellets, dung ashes and fuel trash paths) which was followed by integrated studies of phytoliths and calcitic microfossil analyses (dung spherulites and wood ash pseudomorphs) for comparative purposes. The results obtained provided direct evidence regarding the type of fuel sources: dung, wood and a mixing of dung and vegetal matter (wood and agricultural by-products). Dung was used as source of fuel material across time (from the Early Numidian occupation phase, 10th–9th century BC, to the last centuries BC) and space (in different excavation areas and type of installations). Such integrated studies demonstrate the value of combining different microarchaeological techniques and the use of ethnoarchaeological material from site areas

ENSO impact on northwest African upwelling

One of the most robust ENSO teleconnections is that linking SST anomalies in the equatorial Pacific and Tropical North Atlantic (TNA) in boreal spring. While the role played by the wind-evaporation-SST (WES) feedback in maintaining the ENSO-related SST anomalies over the TNA is well understood, many questions remain open about the signature of this ENSO teleconnection on the northwest African upwelling system and its role for the further response during the spring season along the whole TNA. This issue is analyzed here in both observations and CGCM models with different nominal resolution (CMIP6 HighResMIP simulations). In particular, the relevance of the mean state variability in the tropical Atlantic for modulating the northwest African upwelling response to ENSO has been assessed in depth. Furthermore, and considering the exceptional ecological importance of this upwelling area, the ENSO-related influence on the spatio-temporal variability of round sardinella (the dominant fish species in terms of abundance) has been also analyzed. To this aim, an end-to-end strategy which combines models of physics (hydrodynamic), lower trophic levels (nutrient-plankton) and upper trophic levels (sardinella), is used. All these analyses highlight from both climate and ecological perspectives, the relevance of better understanding the ENSO-northwest African upwelling teleconnection.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech