Comparison of simulated and reconstructed variations in East African hydroclimate over the last millennium

The multi-decadal to centennial hydroclimate changes in East Africa over the last millennium are studied by comparing the results of forced transient simulations by six general circulation models (GCMs) with published hydroclimate reconstructions from four lakes: Challa and Naivasha in equatorial East Africa, and Masoko and Malawi in southeastern inter-tropical Africa. All GCMs simulate fairly well the unimodal seasonal cycle of precipitation in the Masoko-Malawi region, while the bimodal seasonal cycle characterizing the Challa-Naivasha region is generally less well captured by most models. Model results and lake-based hydroclimate reconstructions display very different temporal patterns over the last millennium. Additionally, there is no common signal among the model time series, at least until 1850. This suggests that simulated hydroclimate fluctuations are mostly driven by internal variability rather than by common external forcing. After 1850, half of the models simulate a relatively clear response to forcing, but this response is different between the models. Overall, the link between precipitation and tropical sea surface temperatures (SSTs) over the pre-industrial portion of the last millennium is stronger and more robust for the Challa-Naivasha region than for theMasoko-Malawi region. At the inter-annual timescale, last-millennium Challa-Naivasha precipitation is positively (negatively) correlated with western (eastern) Indian Ocean SST, while the influence of the Pacific Ocean appears weak and unclear. Although most often not significant, the same pattern of correlations between East African rainfall and the Indian Ocean SST is still visible when using the last-millennium time series smoothed to highlight centennial variability, but only in fixed-forcing simulations. This means that, at the centennial timescale, the effect of (natural) climate forcing can mask the imprint of internal climate variability in large-scale teleconnections

A method for ensemble expansion and improved definition of forecast distributions from climate simulations

Because of the inherently chaotic nature of the atmosphere, ensemble simulations are required to characterize a model’s response to the prescribed boundary forcing in probabilistic terms, particularly if the focus is on the probabilities of extreme events. At the same time, substantial computer resources are needed to produce routinely ensemble seasonal climate forecasts of sufficient size to make suitably reproducible estimates of such probabilities. We describe a method for artificially expanding the effective number of members in ensemble climate simulations on a seasonal basis, thereby reducing uncertainty in estimated probability distributions. As described here, the method involves calculating seasonal statistics using monthly values from all possible combinations of ensemble members. Under certain assumptions, this method is able to increase the effective ensemble size of an N-member M-month seasonal forecast by a factor of (asymptotically) M. One key assumption in this regard is that, aside from the effects of prescribed boundary conditions, the month-to-month values from a particular ensemble member are linear independent. This paper describes the behaviour of the ensemble expansion technique using both idealized and actual ensemble forecast data under a variety of conditions, drawing comparisons with an alternative parametric approach for ensemble expansion. A method for testing the assumption of linear independence in model simulations is also presented

Conditional probabilities, relative operating characteristics, and relative operating levels

The relative operating characteristic (ROC) curve is a highly flexible method for representing the quality of dichotomous, categorical, continuous, and probabilistic forecasts. The method is based on ratios that measure the proportions of events and nonevents for which warnings were provided. These ratios provide estimates of the probabilities that an event will be forewarned and that an incorrect warning will be provided for a nonevent. Some guidelines for interpreting the ROC curve are provided. While the ROC curve is of direct interest to the user, the warning is provided in advance of the outcome and so there is additional value in knowing the probability of an event occurring contingent upon a warning being provided or not provided. An alternative method to the ROC curve is proposed that represents forecast quality when expressed in terms of probabilities of events occurring contingent upon the warnings provided. The ratios used provide estimates of the probability of an event occurring given the forecast that is issued. Some problems in constructing the curve in a manner that is directly analogous to that for the ROC curve are highlighted, and so an alternative approach is proposed. In the context of probabilistic forecasts, the ROC curve provides a means of identifying the forecast probability at which forecast value is optimized. In the context of continuous variables, the proposed relative operating levels curve indicates the exceedence threshold for defining an event at which forecast skill is optimized, and can enable the forecast user to estimate the probabilities of events other than that defined by the forecaster

Simulation of recent global temperature trends [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Observations show that global average tropospheric temperatures have been rising during the past century, with the most recent portion of record showing a sharp rise since the mid-1970s

Climate-driven coral reorganisation influences aggressive behaviour in juvenile coral-reef fishes

Globally, habitat degradation is altering the abundance and diversity of species in a variety of ecosystems. This study aimed to determine how habitat degradation, in terms of changing coral composition under climate change, affected abundance, species richness and aggressive behaviour of juveniles of three damselfishes (Pomacentrus moluccensis, P. amboinensis and Dischistodus perspicillatus, in order of decreasing reliance on coral). Patch reefs were constructed to simulate two types of reefs: present-day reefs that are vulnerable to climate-induced coral bleaching, and reefs with more bleaching-robust coral taxa, thereby simulating the likely future of coral reefs under a warming climate. Fish communities were allowed to establish naturally on the reefs during the summer recruitment period. Climate-robust reefs had lower total species richness of coral-reef fishes than climate-vulnerable reefs, but total fish abundance was not significantly different between reef types (pooled across all species and life-history stages). The nature of aggressive interactions, measured as the number of aggressive chases, varied according to coral composition; on climate-robust reefs, juveniles used the substratum less often to avoid aggression from competitors, and interspecific aggression became relatively more frequent than intraspecific aggression for juveniles of the coral-obligate P. moluccensis. This study highlights the importance of coral composition as a determinant of behaviour and diversity of coral-reef fishes

A new physical interpretation of optical and infrared variability in quasars

Changing-look quasars are a recently identified class of active galaxies in which the strong UV continuum and/or broad optical hydrogen emission lines associated with unobscured quasars either appear or disappear on timescales of months to years. The physical processes responsible for this behaviour are still debated, but changes in the black hole accretion rate or accretion disk structure appear more likely than changes in obscuration. Here we report on four epochs of spectroscopy of SDSS J110057.70-005304.5, a quasar at a redshift of $z=0.378$ whose UV continuum and broad hydrogen emission lines have faded, and then returned over the past $\approx$20 years. The change in this quasar was initially identified in the infrared, and an archival spectrum from 2010 shows an intermediate phase of the transition during which the flux below rest-frame $\approx$3400\AA\ has decreased by close to an order of magnitude. This combination is unique compared to previously published examples of changing-look quasars, and is best explained by dramatic changes in the innermost regions of the accretion disk. The optical continuum has been rising since mid-2016, leading to a prediction of a rise in hydrogen emission line flux in the next year. Increases in the infrared flux are beginning to follow, delayed by a $\sim$3 year observed timescale. If our model is confirmed, the physics of changing-look quasars are governed by processes at the innermost stable circular orbit (ISCO) around the black hole, and the structure of the innermost disk. The easily identifiable and monitored changing-look quasars would then provide a new probe and laboratory of the nuclear central engine.Comment: 13 pages, 4 figures, 3 tables. Published in MNRAS. All code and data links on GitHub, https://github.com/d80b2t/WISE_L

Accurate design of translational output by a neural network model of ribosome distribution

Synonymous codon choice can have dramatic effects on ribosome speed and protein expression. Ribosome profiling experiments have underscored that ribosomes do not move uniformly along mRNAs. Here, we have modeled this variation in translation elongation by using a feed-forward neural network to predict the ribosome density at each codon as a function of its sequence neighborhood. Our approach revealed sequence features affecting translation elongation and characterized large technical biases in ribosome profiling. We applied our model to design synonymous variants of a fluorescent protein spanning the range of translation speeds predicted with our model. Levels of the fluorescent protein in budding yeast closely tracked the predicted translation speeds across their full range. We therefore demonstrate that our model captures information determining translation dynamics in vivo; that this information can be harnessed to design coding sequences; and that control of translation elongation alone is sufficient to produce large quantitative differences in protein output

Impacts of speciation and extinction measured by an evolutionary decay clock

The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution1,2. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates the simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the ‘big five’ mass extinction events2, seven additional mass extinctions, two combined mass extinction–radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations1,3, we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions4, evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay4 (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life’s decay-clock debt