BioDeepTime : a database of biodiversity time series for modern and fossil assemblages

We thank the Paleosynthesis Project and the Volkswagen Stiftung for funding that supported this project (Az 96 796). M.C.R. acknowledges the German Research Foundation (DFG) for funding through the Cluster of Excellence ‘The Ocean Floor – Earth's Uncharted Interface’ (EXC 2077, grant no. 390741603). E.E.S. acknowledges funding from Leverhulme Trust grant RPG-201170, the Leverhulme Prize and the National Science Research Council grant NE/V011405/1. Q.J.L. and L.N. acknowledge support from the Youth Innovation Promotion Association (2019310) and the Chinese Academy of Sciences (CAS-WX2021SF-0205). A.M.P. acknowledges funding from the Leverhulme Trust through research grant RPG-2019-402. M.D. acknowledges funding from Leverhulme Trust through the Leverhulme Centre for Anthropocene Biodiversity (RC-2018-021) and a research grant (RPG-2019-402), and the European Union (ERC coralINT, 101044975). L. H. L. acknowledges funding from the European Research Council (macroevolution.abc ERC grant no. 724324). K.H.P acknowledges funding from the National Science Foundation Graduate Research Fellowship Program (DGE-2139841). H.H.M.H. acknowledges support from Peter Buck Postdoc Fellowship, Smithsonian Institution. A.T. acknowledges funding from the Slovak Research and Development Agency (APVV 22-0523) and the Slovak Scientific Grant Agency (VEGA 02/0106/23).Motivation We have little understanding of how communities respond to varying magnitudes and rates of environmental perturbations across temporal scales. BioDeepTime harmonizes assemblage time series of presence and abundance data to help facilitate investigations of community dynamics across timescales and the response of communities to natural and anthropogenic stressors. BioDeepTime includes time series of terrestrial and aquatic assemblages of varying spatial and temporal grain and extent from the present-day to millions of years ago. Main Types of Variables Included BioDeepTime currently contains 7,437,847 taxon records from 10,062 assemblage time series, each with a minimum of 10 time steps. Age constraints, sampling method, environment and taxonomic scope are provided for each time series. Spatial Location and Grain The database includes 8752 unique sampling locations from freshwater, marine and terrestrial ecosystems. Spatial grain represented by individual samples varies from quadrats on the order of several cm2 to grid cells of ~100 km2. Time Period and Grain BioDeepTime in aggregate currently spans the last 451?million years, with the 10,062 modern and fossil assemblage time series ranging in extent from years to millions of years. The median extent of modern time series is 18.7?years and for fossil series is 54,872?years. Temporal grain, the time encompassed by individual samples, ranges from days to tens of thousands of years. Major Taxa and Level of Measurement The database contains information on 28,777 unique taxa with 4,769,789 records at the species level and another 271,218 records known to the genus level, including time series of benthic and planktonic foraminifera, coccolithophores, diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates. There are to date 7012 modern and 3050 fossil time series in BioDeepTime. Software Format SQLite, Comma-separated values.Publisher PDFPeer reviewe

Hepatitis C-associated B-cell non-Hodgkin lymphomas. Epidemiology, molecular signature and clinical management

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Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Multi-messenger Observations of a Binary Neutron Star Merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ∼ 1.7 {{s}} with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of {40}-8+8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 {M}ȯ . An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ∼ 40 {{Mpc}}) less than 11 hours after the merger by the One-Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ∼10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ∼ 9 and ∼ 16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC 4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta.</p

Dinâmica de diversificação de Placentalia (Mammalia): integrando o registro fóssil com filogenias moleculares

The effects of intrinsic traits on the diversification dynamics have been extensively investigated, with several traits being associated with increase in diversification. On the other hand, the possible negative effects of traits on the diversification of a lineage have been for the most part overlooked. Here we used both the fossil record and molecular data to study the diversification dynamics of Placentalia, focusing on the orders in decline of diversity, and investigated different mechanisms that might control the evolutionary success of the 21 placental orders. More specifically we: 1- determined which of the 21 orders of Placentalia are in decline of diversity (i.e., Decline model); 2- investigated whether the Decline model has a phylogenetic signal; 3- tested the hypothesis that the differences in body size are related to the Decline model; 4- tested the hypothesis that the orders in Decline have lower morphological disparity; 5- investigated whether the orders in decline of diversity, inferred from the fossil record, are the ones with higher extinction risk nowadays. Our analysis indicate that the majority of the orders of placental mammals have a pattern consistent with the Decline model and, although the Decline model is not equally distributed among the placental superorders, there was no significant phylogenetic signal for the orders in diversity decline. We found a positive correlation between the Decline model and the average body size which is in line with previous studies on body size evolution. We argue that such results suggest a complex evolutionary dynamics: larger body size appears to be an evolutionary attractor with lineages showing a tendency to increase in size, however, the increase in body size would be counterbalanced by a higher propensity to Decline. Moreover, we found a the negative correlation between the Decline model and morphological variation. We suggest that such results could indicate two possible scenario: (i) the low morphological variation would cause lineages to loose diversity; (ii) the low morphological variation would be the product of decrease in diversity through extinction selectivity. Finally, we found no correlation between the extinction risk of extant species and the deep time diversity decline, which suggests that the drivers of the current and the past Decline are not the sameO efeito de caracteres intrínsecos na dinâmica de diversificação foram extensamente investigados e diversos caracteres foram associados com aumentos na diversificação. Contudo, os possíveis efeitos negativos de um caractere sobre a diversificação de uma linhagem foram em grande parte ignorados. No presente trabalho integramos o registro fóssil com dados moleculares para estudar a dinâmica de diversificação de Placentalia, focando nas ordens em declínio de diversidade, e investigamos possíveis mecanismos responsáveis por gerar os padrões de diversificação encontrados. Mais especificamente nós: 1- determinamos quais das 21 ordens de Placentalia estão em declínio de diversidade (i.e., Declínio); 2- investigamos se o Declínio apresenta um sinal filogenético; 3- testamos a hipótese de que o tamanho do corpo está relacionado com o Declínio; 4- testamos a hipótese de que as ordens em Declínio possum menor disparidade morfológica; 5- investigamos se as ordens em Declínio, inferido a partir do registro fóssil, são as mesas com maior risco de extinção na atualidade. Nossas análises indicam que a maioria das ordens de mamíferos placentários apresentam um signal consistente com o Declínio e, embora o Declínio não esteja igualmente distribuído entre as superorderns de Placentalia, não há um signal filogenético significativo para as ordens em Declínio. Nossos resultados indicam uma correlação positiva entre o Declínio e o tamanho corporal médio de cada ordem que está de acordo com estudos prévios sobre evolução do tamanho do corpo. Argumentamos que estes resultados sugerem uma dinâmica de evolução complexa: tamanho corpóreo grande seria um atrator evolutivo que gera a tendência das linhagens aumentarem de tamanho, todavia, o aumento do tamanho do corpo seria contrabalançado pela maior susceptibilidade ao Declínio. Outrossim, encontramos uma correlação negativa entre o Declínio e a variação morfológica. Argumentamos que essa correlação poderia indicar dois possíveis cenários: (i) a baixa variação morfológica seria responsável pela redução no número de linhagens e tornaria as ordens mais susceptíveis ao declínio de diversidade; (ii) a baixa variação morfológica teria sido gerada pela diminuição da diversidade. Por último, o risco de extinção das espécies atuais não está correlacionado com o Declínio, o que sugere que os mecanismos responsáveis pelo Declínio no passado e no presente não são os mesmos

Subspecies richness and diversity gradients: A case study with birds

Implementation of a Bayesian version of the protracted birth-death diversification model and the latitudinal diversity gradient in birds

Summer workshop 1: Reproducible research through Open Science

This hosts materials associated with an online webinar introducing the core concepts of Open Science and Reproducibility, and providing an introduction to the OSF online collaboration platfor

On the mismatch in the strength of competition among fossil and modern species of planktonic Foraminifera

AimMany clades display the macroevolutionary pattern of a negative relationship between standing diversity and diversification rates. Competition among species has been proposed as the main mechanism that explains this pattern. However, we currently lack empirical insight into how the effects of individual‐level ecological interactions scale up to affect species diversification. Here, we investigate a clade that shows evidence for negative diversity‐dependent diversification in the fossil record and test whether the clade's modern communities show a corresponding signal of interspecific competition.LocationWorld's oceans.Time periodHolocene.Major taxa studiedPlanktonic Foraminifera (Rhizaria).MethodsWe explore spatial and temporal ecological patterns expected under interspecific competition. Firstly, we use a community phylogenetics approach to test for signs of local competitive exclusion among ecologically similar species (defined as closely related or of similar shell sizes) by combining species relative abundances in seafloor sediments. Secondly, we analyse whether population abundances of co‐occurring species covary negatively through time using sediment trap time‐series spanning 1–12 years.ResultsThe great majority of the assemblages are indistinguishable from randomly assembled communities, showing no significant spatial co‐occurrence patterns regarding phylogeny or size similarity. Through time, most species pairs correlated positively, indicating synchronous rather than compensatory population dynamics.Main conclusionsWe found no detectable evidence for interspecific competition structuring extant planktonic Foraminifera communities. Species co‐occurrences and population dynamics are likely regulated by the abiotic environment and/or distantly related species, rather than intra‐clade density‐dependent processes. This interpretation contradicts the idea that competition drives the clade's macroevolutionary dynamics. One way to better integrate community ecology and macroevolution is to consider that diversification dynamics are influenced by groups that interact ecologically even when distantly related

Homologous versus heterologous interactions in the bicomponent staphylococcal γ-haemolysin pore(1)

Staphylococcal γ-haemolysin HlgA–HlgB forms a β-barrel transmembrane pore in cells and in model membranes. The pore is formed by the oligomerization of two different proteins and a still debated number of monomers. To clarify the topology of the pore, we have mutated single residues – placed near the right and left interfaces of each monomer into cysteine. The mutants were labelled with fluorescent probes, forming a donor–acceptor pair for FRET (fluorescence resonance energy transfer). Heterologous couples (labelled on complementary left and right interfaces) displayed a marked FRET, suggesting extensive HlgA–HlgB or HlgB–HlgA contacts. Heterologous control couples (with both components labelled on the same side) showed absent or low FRET. We found the same result for the homologous couple formed by HlgA [i.e. HlgA–HlgA in the presence of wt (wild-type) HlgB]. The homologous HlgB couple (HlgB–HlgB labelled on left and right interfaces and in the presence of wt HlgA) displayed a transient, declining FRET, which may indicate fast formation of an intermediate that is consumed during pore formation. We conclude that bicomponent pores are assembled by alternating heterologous monomers