Mark-recapture validates the use of photo-identification for the widely distributed blue-spotted ribbontail ray, Taeniura lymma

The ability to identify individual animals can provide valuable insights into the behaviour, life history, survivorship, and demographics of wild populations. Photo-identification (photo-ID) uses unique natural markings to identify individuals and can be effective for scalable and non-invasive research on marine fauna. The successful application of photo-ID requires that chosen distinguishing markings are unique to individuals and persist over time. In this study, we validate the use of dorsal spot patterns for identifying individual blue-spotted ribbontail rays (Taeniura lymma) in conjunction with traditional tagging methods. Spot patterns were unique among T. lymma with 90.3% of individuals correctly identified using I3S photo-matching software from images taken up to 496 days apart. In comparison, traditional physical tagging methods showed a tag loss rate of 27% and a maximum tag retention period of only 356 days. Our findings demonstrate the effectiveness of photo-ID as a tool to monitor populations and better understand the ecology of the blue-spotted ribbontail ray without the need for physical tagging. The validation of photo-ID for this widespread species is important as it enables behavioural and demographic changes to be easily tracked in relation to coastal threats such as human development and habitat degradation.</p

The effects of elevated CO2 and eutrophication on surface elevation gain in a European salt marsh.

Salt marshes can play a vital role in mitigating the effects of global environmental change by dissipating incident storm wave energy and, through accretion, tracking increasing water depths consequent upon sea level rise. Atmospheric CO2 concentrations and nutrient availability are two key variables that can affect the biological processes that contribute to marsh surface elevation gain. We measured the effects of CO2 concentrations and nutrient availability on surface elevation change in intact mixed-species blocks of UK salt marsh using six open-top chambers receiving CO2 -enriched (800 ppm) or ambient (400 ppm) air. We found more rapid surface elevation gain in elevated CO2 conditions: an average increase of 3.4 mm over the growing season relative to ambient CO2 . Boosted regression analysis to determine the relative influence of different parameters on elevation change identified that a 10% reduction in microbial activity in elevated CO2 -grown blocks had a positive influence on elevation. The biomass of Puccinellia maritima also had a positive influence on elevation, while other salt marsh species (e.g. Suaeda maritima) had no influence or a negative impact on elevation. Reduced rates of water use by the vegetation in the high CO2 treatment could be contributing to elevation gain, either directly through reduced soil shrinkage or indirectly by decreasing microbial respiration rates due to lower redox levels in the soil. Eutrophication did not influence elevation change in either CO2 treatment despite doubling aboveground biomass. The role of belowground processes (transpiration, root growth and decomposition) in the vertical adjustment of European salt marshes, which are primarily minerogenic in composition, could increase as atmospheric CO2 concentrations rise and should be considered in future wetland models for the region. Elevated CO2 conditions could enhance resilience in vulnerable systems such as those with low mineral sediment supply or where migration upwards within the tidal frame is constrained.Marie Curie Incoming International Fellowship (Grant ID: FP7-PEOPLE-IIF 623720 STORM)This is the author accepted manuscript. The final version is available from Wiley via https://doi.org/10.1111/gcb.1339

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study

Introduction: The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. Methods: In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. Findings: Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2–6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p&lt;0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5–5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p&lt;0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4–10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p&lt;0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32–4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP &gt;5mg/L, OR 3·55 [1·23–11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. Interpretation: After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification

Freshwater crabs and the biodiversity crisis: Importance, threats, status, and conservation challenges

Freshwater ecosystems in the tropics host a diverse endemic fauna including freshwater crabs, but the rapid loss and deterioration of habitat means that many species are now under imminent threat. Studies on freshwater fish and amphibians suggest a third to half of the species in some tropical freshwaters is either extinct or endangered, but the status of the freshwater crabs is not known. Freshwater crabs, with 1280 species, represent one-fifth of all the World's brachyurans. We therefore undertook a comprehensive IUCN Red List assessment of the freshwater crabs, which was the first time that such a study had been attempted on a global scale for any group of freshwater invertebrates. The conservation status of all known species from the Americas, Africa, Europe, Asia, and Australasia revealed unexpectedly high threat levels. Here we show that about one-sixth of all freshwater crab species have an elevated risk of extinction, only one-third are not at-risk, and although none are actually extinct, almost half are too poorly known to assess. Out of 122 countries that have populations of freshwater crabs, 43 have species in need of protection. The majority of threatened species are restricted-range semi-terrestrial endemics living in habitats subjected to deforestation, alteration of drainage patterns, and pollution. This is illustrated with a case study of one such species found in Singapore. This underlines the need to prioritize and develop conservation measures before species decline to levels from which they cannot recover. The proportion of freshwater crabs threatened with extinction is equal to that of reef-building corals, and exceeds that of all other groups that have been assessed except for amphibians. These results represent a baseline that can be used to design strategies to save the World's threatened freshwater crab species. © 2009 Elsevier Ltd. All rights reserved

Distribution of Diatoms and Development of Diatom-Based Models for Inferring Salinity and Nutrient Concentrations in Florida Bay and Adjacent Coastal Wetlands of South Florida (USA)

The composition and distribution of diatom algae inhabiting estuaries and coasts of the subtropical Americas are poorly documented, especially relative to the central role diatoms play in coastal food webs and to their potential utility as sentinels of environmental change in these threatened ecosystems. Here, we document the distribution of diatoms among the diverse habitat types and long environmental gradients represented by the shallow topographic relief of the South Florida, USA, coastline. A total of 592 species were encountered from 38 freshwater, mangrove, and marine locations in the Everglades wetland and Florida Bay during two seasonal collections, with the highest diversity occurring at sites of high salinity and low water column organic carbon concentration (WTOC). Freshwater, mangrove, and estuarine assemblages were compositionally distinct, but seasonal differences were only detected in mangrove and estuarine sites where solute concentration differed greatly between wet and dry seasons. Epiphytic, planktonic, and sediment assemblages were compositionally similar, implying a high degree of mixing along the shallow, tidal, and storm-prone coast. The relationships between diatom taxa and salinity, water total phosphorus (WTP), water total nitrogen (WTN), and WTOC concentrations were determined and incorporated into weighted averaging partial least squares regression models. Salinity was the most influential variable, resulting in a highly predictive model (r apparent 2  = 0.97, r jackknife 2  = 0.95) that can be used in the future to infer changes in coastal freshwater delivery or sea-level rise in South Florida and compositionally similar environments. Models predicting WTN (r apparent 2  = 0.75, r jackknife 2  = 0.46), WTP (r apparent 2  = 0.75, r jackknife 2  = 0.49), and WTOC (r apparent 2  = 0.79, r jackknife 2  = 0.57) were also strong, suggesting that diatoms can provide reliable inferences of changes in solute delivery to the coastal ecosystem

The impact of conservation on the status of the world's vertebrates

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species