A comparison of random draw and locally neutral models for the avifauna of an English woodland

BACKGROUND: Explanations for patterns observed in the structure of local assemblages are frequently sought with reference to interactions between species, and between species and their local environment. However, analyses of null models, where non-interactive local communities are assembled from regional species pools, have demonstrated that much of the structure of local assemblages remains in simulated assemblages where local interactions have been excluded. Here we compare the ability of two null models to reproduce the breeding bird community of Eastern Wood, a 16-hectare woodland in England, UK. A random draw model, in which there is complete annual replacement of the community by immigrants from the regional pool, is compared to a locally neutral community model, in which there are two additional parameters describing the proportion of the community replaced annually (per capita death rate) and the proportion of individuals recruited locally rather than as immigrants from the regional pool. RESULTS: Both the random draw and locally neutral model are capable of reproducing with significant accuracy several features of the observed structure of the annual Eastern Wood breeding bird community, including species relative abundances, species richness and species composition. The two additional parameters present in the neutral model result in a qualitatively more realistic representation of the Eastern Wood breeding bird community, particularly of its dynamics through time. The fact that these parameters can be varied, allows for a close quantitative fit between model and observed communities to be achieved, particularly with respect to annual species richness and species accumulation through time. CONCLUSION: The presence of additional free parameters does not detract from the qualitative improvement in the model and the neutral model remains a model of local community structure that is null with respect to species differences at the local scale. The ability of this locally neutral model to describe a larger number of woodland bird communities with either little variation in its parameters or with variation explained by features local to the woods themselves (such as the area and isolation of a wood) will be a key subsequent test of its relevance

A spectral approach to estimating the timescale-dependent uncertainty of paleoclimate records – Part 1: Theoretical concept

Proxy records represent an invaluable source of information for reconstructing past climatic variations, but they are associated with considerable uncertainties. For a systematic quantification of these reconstruction errors, however, knowledge is required not only of their individual sources but also of their auto-correlation structure as this determines the timescale dependence of their magnitude, an issue that has been often ignored until now. Here a spectral approach to uncertainty analysis is provided for paleoclimate reconstructions obtained from single sediment proxy records. The formulation in the spectral domain rather than the time domain allows for an explicit demonstration and quantification of the timescale dependence that is inherent in any proxy-based reconstruction uncertainty. This study is published in two parts. In this first part, the theoretical concept is presented, and analytic expressions are derived for the power spectral density of the reconstruction error of sediment proxy records. The underlying model takes into account the spectral structure of the climate signal, seasonal and orbital variations, bioturbation, sampling of a finite number of signal carriers, and uncorrelated measurement noise, and it includes the effects of spectral aliasing and leakage. The uncertainty estimation method, based upon this model, is illustrated by simple examples. In the second part of this study, published separately, the method is implemented in an application-oriented context, and more detailed examples are presented

A spectral approach to estimating the timescale-dependent uncertainty of paleoclimate records – Part 2: Application and interpretation

Proxy climate records are an invaluable source of information about the earth's climate prior to the instrumental record. The temporal and spatial coverage of records continues to increase; however, these records of past climate are associated with significant uncertainties due to non-climate processes that influence the recorded and measured proxy values. Generally, these uncertainties are timescale dependent and correlated in time. Accounting for structure in the errors is essential for providing realistic error estimates for smoothed or stacked records, detecting anomalies, and identifying trends, but this structure is seldom accounted for. In the first of these companion articles, we outlined a theoretical framework for handling proxy uncertainties by deriving the power spectrum of proxy error components from which it is possible to obtain timescale-dependent error estimates. Here in Part 2, we demonstrate the practical application of this theoretical framework using the example of marine sediment cores. We consider how to obtain estimates for the required parameters and give examples of the application of this approach for typical marine sediment proxy records. Our new approach of estimating and providing timescale-dependent proxy errors overcomes the limitations of simplistic single-value error estimates. We aim to provide the conceptual basis for a more quantitative use of paleo-records for applications such as model–data comparison, regional and global synthesis of past climate states, and data assimilation

Challenges and potential in the interpretation of global temperature proxy data compilations

As the availability of high-resolution proxy records increases, the number of large-scale compilations that are built and analyzed continues to grow. Such datasets allow us to disentangle regional and global climate changes from local and proxy specific effects, to better bridge the spatial scales of local proxy recorders vs. global climate models and they support more objective statistical analyses. However, compilations also often combine data for multiple proxy types and which may record different climate variables (e.g. different seasonal or atmospheric vs. water temperatures). Datasets may also vary in quality, and compilations often ignore the expert knowledge of the authors of the original individual paleoclimate datasets as well as site-specific and proxy-specific effects. Here I review current and recent studies that have used global compilations of temperature related proxy data to infer the glacial and Holocene climate evolution and the temporal and spatial structures of climate variability. I demonstrate how the analysis of large-scale compilations can not only improve our knowledge of the evolution of past climate but also provide insight into the potential and limitations of specific paleoclimate proxies and emphasize the importance of realistic uncertainty estimates

Age-Heterogeneity in Marine Sediments Revealed by Three-Dimensional High-Resolution Radiocarbon Measurements

Marine sedimentary archives are routinely used to reconstruct past environmental changes. In many cases, bioturbation and sedimentary mixing affect the proxy time-series and the age-depth relationship. While idealized models of bioturbation exist, they usually assume homogeneous mixing, thus that a single sample is representative for the sediment layer it is sampled from. However, it is largely unknown to which extent this assumption holds for sediments used for paleoclimate reconstructions. To shed light on 1) the age-depth relationship and its full uncertainty, 2) the magnitude of mixing processes affecting the downcore proxy variations, and 3) the representativity of the discrete sample for the sediment layer, we designed and performed a case study on South China Sea sediment material which was collected using a box corer and which covers the last glacial cycle. Using the radiocarbon content of foraminiferal tests as a tracer of time, we characterize the spatial age-heterogeneity of sediments in a three-dimensional setup. In total, 118 radiocarbon measurements were performed on defined small- and large-volume bulk samples ( ∼ 200 specimens each) to investigate the horizontal heterogeneity of the sediment. Additionally, replicated measurements on small numbers of specimens (10 × 5 specimens) were performed to assess the heterogeneity within a sample volume. Visual assessment of X-ray images and a quantitative assessment of the mixing strength show typical mixing from bioturbation corresponding to around 10 cm mixing depth. Notably, our 3D radiocarbon distribution reveals that the horizontal heterogeneity (up to 1,250 years), contributing to the age uncertainty, is several times larger than the typically assumed radiocarbon based age-model error (single errors up to 250 years). Furthermore, the assumption of a perfectly bioturbated layer with no mixing underneath is not met. Our analysis further demonstrates that the age-heterogeneity might be a function of sample size; smaller samples might contain single features from the incomplete mixing and are thus less representative than larger samples. We provide suggestions for future studies, optimal sampling strategies for quantitative paleoclimate reconstructions and realistic uncertainty in age models, as well as discuss possible implications for the interpretation of paleoclimate records

Marine Noise Pollution - Increasing Recognition But Need for More Practical Action

Over the last two decades, marine noise pollution has become increasingly recognized as an issue of major significance. The issue has become a primary focus of marine mammal research, but is also of concern to the public and policy makers. The result has been efforts involving a variety of disciplines, and relevant legislation and associated guidance are now in place in many parts of the world. Most current mitigation efforts are directed at reducing the risk of injury from exposure to intense noise, although the effectiveness of such mitigation measures in terms of risk reduction has rarely been quantified. Longer-term chronic impacts of noise including disturbance or masking of sounds critical for feeding and reproduction have received substantially less attention in management. New technologies are being developed for a number of activities which can substantially reduce noise inputs into the marine environment. As with other forms of pollution, reducing input at source is likely to be the most effective way of reducing impacts. We recommend as a priority the implementation of noise quieting technologies and the spatial and temporal exclusion of noise to minimize contact with marine life

Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0)

Although numerous pollen records are available worldwide in various databases, their use for synthesis works is limited as the chronologies are, as yet, not harmonized globally, and temporal uncertainties are unknown. We present a chronology framework named LegacyAge 1.0 that includes harmonized chronologies of 2831 palynological records (out of 3471 available records), downloaded from the Neotoma Paleoecology Database (last access: April 2021) and 324 additional Asian records. All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, thickness) were identified based on previous experiences or iteratively after preliminary model inspection. The most common control points for the chronologies are radiocarbon dates (86.1 %), calibrated by the latest calibration curves (IntCal20 and SHcal20 for the terrestrial radiocarbon dates in the northern and southern hemispheres; Marine20 for marine materials). The original literature was consulted when dealing with obvious outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8 % of records), reservoir effect (4.9 %), and sediment deposition discontinuity (4.4 %). Finally, we numerically compare the LegacyAge 1.0 chronologies to the original ones and show that the chronologies of 95.4 % of records could be improved according to our assessment. Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. The LegacyAge 1.0 dataset and R code used are open-access and available at PANGAEA (https://doi.pangaea.de/10.1594/PANGAEA.933132) and Github (https://github.com/LongtermEcology/LegacyAge-1.0), respectively

Effectiveness and cost-effectiveness of psychiatric mother and baby units: quasi-experimental study

BACKGROUND: Psychiatric mother and baby units (MBUs) are recommended for severe perinatal mental illness, but effectiveness compared with other forms of acute care remains unknown. AIMS: We hypothesised that women admitted to MBUs would be less likely to be readmitted to acute care in the 12 months following discharge, compared with women admitted to non-MBU acute care (generic psychiatric wards or crisis resolution teams (CRTs)). METHOD: Quasi-experimental cohort study of women accessing acute psychiatric care up to 1 year postpartum in 42 healthcare organisations across England and Wales. Primary outcome was readmission within 12 months post-discharge. Propensity scores were used to account for systematic differences between MBU and non-MBU participants. Secondary outcomes included assessment of cost-effectiveness, experience of services, unmet needs, perceived bonding, observed mother-infant interaction quality and safeguarding outcome. RESULTS: Of 279 women, 108 (39%) received MBU care, 62 (22%) generic ward care and 109 (39%) CRT care only. The MBU group (n = 105) had similar readmission rates to the non-MBU group (n = 158) (aOR = 0.95, 95% CI 0.86-1.04, P = 0.29; an absolute difference of -5%, 95% CI -14 to 4%). Service satisfaction was significantly higher among women accessing MBUs compared with non-MBUs; no significant differences were observed for any other secondary outcomes. CONCLUSIONS: We found no significant differences in rates of readmission, but MBU advantage might have been masked by residual confounders; readmission will also depend on quality of care after discharge and type of illness. Future studies should attempt to identify the effective ingredients of specialist perinatal in-patient and community care to improve outcomes

SOX9 predicts progression towards cirrhosis in patients while its loss protects against liver fibrosis

Fibrosis and organ failure is a common endpoint for many chronic liver diseases. Much is known about the upstream inflammatory mechanisms provoking fibrosis and downstream potential for tissue remodeling. However, less is known about the transcriptional regulation in vivo governing fibrotic matrix deposition by liver myofibroblasts. This gap in understanding has hampered molecular predictions of disease severity and clinical progression and restricted targets for antifibrotic drug development. In this study we show the prevalence of SOX9 in biopsies from patients with chronic liver disease correlated with fibrosis severity and accurately predicted disease progression towards cirrhosis. Inactivation of Sox9 in mice protected against both parenchymal and biliary fibrosis, improved liver function and ameliorated chronic inflammation. SOX9 was downstream of mechanosignaling factor, YAP1. These data demonstrate a role for SOX9 in liver fibrosis and open the way for the transcription factor and its dependent pathways as new diagnostic, prognostic and therapeutic targets in patients with liver fibrosis

European anthropogenic AFOLU emissions and their uncertainties: a review and benchmark data

Emission of greenhouse gases (GHG) and removals from land, including both anthropogenic and natural fluxes, require reliable quantification, along with estimates of their inherent uncertainties, in order to support credible mitigation action under the Paris Agreement. This study provides a state-of-the-art scientific overview of bottom-up anthropogenic emissions data from agriculture, forestry and other land use (AFOLU) in Europe. The data integrates recent AFOLU emission inventories with ecosystem data and land carbon models, covering the European Union (EU28) and summarizes GHG emissions and removals over the period 1990–2016, of relevance for UNFCCC. This compilation of bottom-up estimates of the AFOLU GHG emissions of European national greenhouse gas inventories (NGHGI) with those of land carbon models and observation-based estimates of large-scale GHG fluxes, aims at improving the overall estimates of the GHG balance in Europe with respect to land GHG emissions and removals. Particular effort is devoted to the estimation of uncertainty, its propagation and role in the comparison of different estimates. While NGHGI data for EU28 provides consistent quantification of uncertainty following the established IPCC guidelines, uncertainty in the estimates produced with other methods will need to account for both within model uncertainty and the spread from different model results. At EU28 level, the largest inconsistencies between estimates are mainly due to different sources of data related to human activity which result in emissions or removals taking place during a given period of time (IPCC 2006) referred here as activity data (AD) and methodologies (Tiers) used for calculating emissions/removals from AFOLU sectors. The referenced datasets related to figures are visualised at https://doi.org/10.5281/zenodo.3460311, Petrescu et al., 2019