Scale dependence of temporal biodiversity change in modern and fossil marine plankton

Aim Biodiversity dynamics comprise evolutionary and ecological changes on multiple temporal scales from millions of years to decades, but they are often interpreted within a single time frame. Planktonic foraminifera communities offer a unique opportunity for analysing the dynamics of marine biodiversity over different temporal scales. Our study aims to provide a baseline for assessments of biodiversity patterns over multiple time-scales, which is urgently needed to interpret biodiversity responses to increasing anthropogenic pressure. Location Global (26 sites). Time period Five time-scales: multi-million-year (0-7 Myr), million-year (0-0.5 Myr), multi-millennial (0-15 thousand years), millennial (0-1,100 years) and decadal (0-32 years). Major taxa studied Planktonic foraminifera. Methods We analysed community composition of planktonic foraminifera at five time-scales, combining measures of standing diversity (richness and effective number of species, ENS) with measures of temporal community turnover (presence-absence-based, dominance-based). Observed biodiversity patterns were compared with the outcome of a neutral model to separate the effects of sampling resolution (the highest in the shortest time series) from biological responses. Results Richness and ENS decreased from multi-million-year to millennial time-scales, but higher standing diversity was observed on the decadal scale. As predicted by the neutral model, turnover in species identity and dominance was strongest at the multi-million-year time-scale and decreased towards the millennial scale. However, contrary to the model predictions, modern time series show rapid decadal variation in the dominance structure of foraminifera communities, which is of comparable magnitude as over much longer time periods. Community turnover was significantly correlated with global temperature change, but not on the shortest time-scale. Main conclusions Biodiversity patterns can be to some degree predicted from the scaling effects related to different durations of time series, but changes in the dominance structure observed over the last few decades reach higher magnitude, probably forced by anthropogenic effects, than those observed over much longer durations

Chamber formation leads to Mg/Ca banding in the planktonic foraminifer <i>Neogloboquadrina pachyderma</i>

Many species of planktonic foraminifera show distinct banding in the intratest distribution of Mg/Ca. This heterogeneity appears biologically controlled and thus poses a challenge to Mg/Ca paleothermometry. The cause of this banding and its relation with chamber formation are poorly constrained and most of what we know about intratest Mg/Ca variability stems from culture studies of tropical, symbiont-bearing foraminifera. Here we present data on the non-spinose, symbiont-barren Neogloboquadrina pachyderma from the subpolar North Atlantic where wintertime mixing removes vertical gradients in temperature and salinity. This allows investigation of biologically controlled Mg/Ca intratest variability under natural conditions. We find that intratest Mg/Ca varies between <0.1 and 7 mmol/mol, even in winter specimens. High Mg/Ca bands occur at the outer edge of the laminae, indicating reduced Mg removal at the end of chamber formation. Our data thus provide new constraints on the timing of the formation of such bands and indicate that their presence is intrinsic to the chamber formation process. Additionally, all specimens are covered with an outer crust consisting of large euhedral crystals. The composition of the crust is similar to the low Mg/Ca bands in the laminar calcite in winter and summer specimens, indicating a tight biological control on crust formation and composition. Nevertheless, despite high intratest variability, the median Mg/Ca of summertime tests is higher than that of wintertime tests. This provides support for Mg/Ca paleothermometry, but to improve the accuracy of paleotemperature estimates biological effects on Mg incorporation need to be better accounted fo

Constructing bi-plots for random forest:Tutorial

Current technological developments have allowed for a significant increase and availability of data. Consequently, this has opened enormous opportunities for the machine learning and data science field, translating into the development of new algorithms in a wide range of applications in medical, biomedical, daily-life, and national security areas. Ensemble techniques are among the pillars of the machine learning field, and they can be defined as approaches in which multiple, complex, independent/uncorrelated, predictive models are subsequently combined by either averaging or voting to yield a higher model performance. Random forest (RF), a popular ensemble method, has been successfully applied in various domains due to its ability to build predictive models with high certainty and little necessity of model optimization. RF provides both a predictive model and an estimation of the variable importance. However, the estimation of the variable importance is based on thousands of trees, and therefore, it does not specify which variable is important for which sample group.The present study demonstrates an approach based on the pseudo-sample principle that allows for construction of bi-plots (i.e. spin plots) associated with RF models. The pseudo-sample principle for RF. is explained and demonstrated by using two simulated datasets, and three different types of real data, which include political sciences, food chemistry and the human microbiome data. The pseudo-sample bi plots, associated with RF and its unsupervised version, allow for a versatile visualization of multivariate models, and the variable importance and the relation among them. (c) 2020 Elsevier B.V. All rights reserved.</p

High‐resolution Mg/Ca and δ 18 O patterns in modern Neogloboquadrina pachyderma from the Fram Strait and Irminger Sea

Neogloboquadrina pachyderma is the dominant species of planktonic foraminifera found in polar waters and is therefore invaluable for paleoceanographic studies of the high latitudes. However, the geochemistry of this species is complicated due to the development of a thick calcite crust in its final growth stage and at greater depths within the water column. We analyzed the in situ Mg/Ca and δ18O in discrete calcite zones using LA‐ICP‐MS, EPMA and SIMS within modern N. pachyderma shells from the highly dynamic Fram Strait and the seasonally isothermal/isohaline Irminger Sea. Here we compare shell geochemistry to the measured temperature, salinity and δ18Osw in which the shells calcified to better understand the controls on N. pachyderma geochemical heterogeneity. We present a relationship between Mg/Ca and temperature in N. pachyderma lamellar calcite that is significantly different than published equations for shells that contained both crust and lamellar calcite. We also document highly variable SIMS δ18O results (up to a 3.3‰ range in single shells) on plankton tow samples which we hypothesize is due to the granular texture of shell walls. Finally, we document that the δ18O of the crust and lamellar calcite of N. pachyderma from an isothermal/isohaline environment are indistinguishable from each other, indicating that shifts in N. pachyderma δ18O are primarily controlled by changes in environmental temperature and/or salinity rather than differences in the sensitivities of the two calcite types to environmental conditions

Effects of Ethanol and Acetaldehyde on Tight Junction Integrity: In Vitro Study in a Three Dimensional Intestinal Epithelial Cell Culture Model

Background: Intestinal barrier dysfunction and translocation of endotoxins are involved in the pathogenesis of alcoholic liver disease. Exposure to ethanol and its metabolite, acetaldehyde at relatively high concentrations have been shown to disrupt intestinal epithelial tight junctions in the conventional two dimensional cell culture models. The present study investigated quantitatively and qualitatively the effects of ethanol at concentrations detected in the blood after moderate ethanol consumption, of its metabolite acetaldehyde and of the combination of both compounds on intestinal barrier function in a three-dimensional cell culture model. Methods and Findings: Caco-2 cells were grown in a basement membrane matrix (Matrigel (TM)) to induce spheroid formation and were then exposed to the compounds at the basolateral side. Morphological differentiation of the spheroids was assessed by immunocytochemistry and transmission electron microscopy. The barrier function was assessed by the flux of FITC-labeled dextran from the basal side into the spheroids' luminal compartment using confocal microscopy. Caco-2 cells grown on Matrigel assembled into fully differentiated and polarized spheroids with a central lumen, closely resembling enterocytes in vivo and provide an excellent model to study epithelial barrier functionality. Exposure to ethanol (10-40 mM) or acetaldehyde (25-200 mu M) for 3 h, dose-dependently and additively increased the paracellular permeability and induced redistribution of ZO-1 and occludin without affecting cell viability or tight junction-encoding gene expression. Furthermore, ethanol and acetaldehyde induced lysine residue and microtubules hyperacetylation. Conclusions: These results indicate that ethanol at concentrations found in the blood after moderate drinking and acetaldehyde, alone and in combination, can increase the intestinal epithelial permeability. The data also point to the involvement of protein hyperacetylation in ethanol- and acetaldehyde-induced loss of tight junctions integrity

Thermalisation of a two-dimensional photonic gas in a 'white-wall' photon box

Bose-Einstein condensation, the macroscopic accumulation of bosonic particles in the energetic ground state below a critical temperature, has been demonstrated in several physical systems. The perhaps best known example of a bosonic gas, blackbody radiation, however exhibits no Bose-Einstein condensation at low temperatures. Instead of collectively occupying the lowest energy mode, the photons disappear in the cavity walls when the temperature is lowered - corresponding to a vanishing chemical potential. Here we report on evidence for a thermalised two-dimensional photon gas with freely adjustable chemical potential. Our experiment is based on a dye filled optical microresonator, acting as a 'white-wall' box for photons. Thermalisation is achieved in a photon number-conserving way by photon scattering off the dye-molecules, and the cavity mirrors both provide an effective photon mass and a confining potential - key prerequisites for the Bose-Einstein condensation of photons. As a striking example for the unusual system properties, we demonstrate a yet unobserved light concentration effect into the centre of the confining potential, an effect with prospects for increasing the efficiency of diffuse solar light collection.Comment: 15 pages, 3 figure

Bose-Einstein condensation of photons in an optical microcavity

Bose-Einstein condensation, the macroscopic ground state accumulation of particles with integer spin (bosons) at low temperature and high density, has been observed in several physical systems, including cold atomic gases and solid state physics quasiparticles. However, the most omnipresent Bose gas, blackbody radiation (radiation in thermal equilibrium with the cavity walls) does not show this phase transition, because the chemical potential of photons vanishes and, when the temperature is reduced, photons disappear in the cavity walls. Theoretical works have considered photon number conserving thermalization processes, a prerequisite for Bose-Einstein condensation, using Compton scattering with a gas of thermal electrons, or using photon-photon scattering in a nonlinear resonator configuration. In a recent experiment, we have observed number conserving thermalization of a two-dimensional photon gas in a dye-filled optical microcavity, acting as a 'white-wall' box for photons. Here we report on the observation of a Bose-Einstein condensation of photons in a dye-filled optical microcavity. The cavity mirrors provide both a confining potential and a non-vanishing effective photon mass, making the system formally equivalent to a two-dimensional gas of trapped, massive bosons. By multiple scattering off the dye molecules, the photons thermalize to the temperature of the dye solution (room temperature). Upon increasing the photon density we observe the following signatures for a BEC of photons: Bose-Einstein distributed photon energies with a massively populated ground state mode on top of a broad thermal wing, the phase transition occurring both at the expected value and exhibiting the predicted cavity geometry dependence, and the ground state mode emerging even for a spatially displaced pump spot