Methods to detect spatial biases in tracking studies caused by differential representativeness of individuals, populations and time

Este artículo contiene 20 páginas, 6 figuras, 4 tablas.Aim: Over the last decades, the study of movement through tracking data has grown exceeding the expectations of movement ecologists. This has posed new challenges, specifically when using individual tracking data to infer higher- level distributions (e.g. population and species). Sources of variability such as individual site fidelity (ISF), en-vironmental stochasticity over time, and space-use variability across species ranges must be considered, and their effects identified and corrected, to produce accurate estimates of spatial distribution using tracking data. Innovation: We developed R functions to detect the effect of these sources of vari-ability in the distribution of animal groups when inferred from individual tracking data. These procedures can be adapted for their use in most tracking datasets and tracking techniques. We demonstrated our procedures with simulated datasets and showed their applicability on a real-world dataset containing 1346 year- round migratory trips from 805 individuals of three closely related seabird species breeding in 34 colonies in the Mediterranean Sea and the Atlantic Ocean, spanning 10 years. We detected an effect of ISF in one of the colonies, but no effect of the environmental stochasticity on the distribution of birds for any of the species. We also identified among-colony variability in nonbreeding space use for one species, with significant effects of popu-lation size and longitude. Main conclusions: This work provides a useful, much- needed tool for researchers using animal tracking data to model species distributions or establish conservation measures. This methodology may be applied in studies using individual tracking data to accurately infer the distribution of a population or species and support the deline-ation of important areas for conservation based on tracking data. This step, designed to precede any analysis, has become increasingly relevant with the proliferation of studies using large tracking datasets that has accompanied the globalization process in science driving collaborations and tracking data sharing initiatives.We thank the following institutions for funding: EU H2020 pro-gramme through grant 634495; Seventh Framework Programme (Research Executive Agency) through Marie Curie Career Integration Grant 618841 (FP7-PEOPLE-2013- CIG); ESFRI LifeWatch Project; LIFE programme of the European Commission through projects LIFE10 NAT/MT090 and LIFE11 NAT/IT/000093; Ministerio de Ciencia e Innovación/Ministerio de Economia y Competitividad (Spain) through projects CGL2009- 11278/BOS, CGL2013-42585-P, C G L 2 0 1 3 - 4 2 2 0 3 - R , C G L 2 0 16 - 7 8 5 3 0 - R a n d C G L 2 0 17- 8 52 10 - P ; Organismo Autónomo de Parques Nacionales (Spain) through pro-ject 1248/2014; Fundação para a Ciência e a Tecnologia (MCTES, Portugal) through projects MARE-UID/MAR/04292/2019; IF/00502/2013/CP1186/CT0003, PTDC/BIA-ANM/3743/2014, PTDC/MAR-PRO/0929/2014, UID/AMB/50017/2019 and UIDP/50017/2020 + UIDB/50017/2020 (to CESAM); Office Français de la Biodiversité (France), through the Programme PACOMM, Natura2000 en mer; Hellenic Bird Ringing Centre; MSDEC (Malta). VMP was supported by pre-doctoral contract BES-2014- 068025 of the Spanish Ministerio de Industria, Economía y Competitividad; MM by grant SFRH/BPD/47047/2008 from the Portuguese Foundation for Science and Technology; JMRG by Ph.D. grant AP2009-2163 from the Spanish Ministerio de Educación; GDO and MMü by Ornis italica and by the Regione Siciliana and Assessorato Risorse Agricole e Alimentari thoriugh a grant to the Ringing Unit of Palermo; VHP by grant SFRH/BPD/85024/2012 from the Portuguese Foundation for Science and Technology; VN by grant SFRH/BPD/88914/2012 from the Portuguese Foundation for Science and Technology; and JN by the Spanish National Programme Ramón y Cajal (RYC-2015- 17809); GK and SX were partially funded by the Operational Program “Environment and Sustainable Development” (EPPERAA) of the National Strategic Reference Framework (NSRF) 2007-2013, co- financed by the ERDF and Greek EDP; FdF by a Ph.D. grant from the Coordination for the Improvement of Higher Education Personnel (CAPES—Brazilian government agency; Bex Process 1307/13-4); ZZ by a PhD grant from the University of Barcelona (APIF/2012); MCF by a PhD grant from the University of Barcelona; and RR by post-doctoral contracts of the PLEAMAR programme from MINECO and Fundación Biodiversidad (2017/2349), and Ministerio de Ciencia, in-novación y Universidades (RYC-2017- 22055). This publication is part of the project I+D+i/PID2020-117155GB-I00, funded by MCIN/ AEI/10.13039/501100011033.Peer reviewe

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Rising rural body-mass index is the main driver of the global obesity epidemic in adults

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities 1,2 . This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity 3�6 . Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary to the dominant paradigm, more than 55 of the global rise in mean BMI from 1985 to 2017�and more than 80 in some low- and middle-income regions�was due to increases in BMI in rural areas. This large contribution stems from the fact that, with the exception of women in sub-Saharan Africa, BMI is increasing at the same rate or faster in rural areas than in cities in low- and middle-income regions. These trends have in turn resulted in a closing�and in some countries reversal�of the gap in BMI between urban and rural areas in low- and middle-income countries, especially for women. In high-income and industrialized countries, we noted a persistently higher rural BMI, especially for women. There is an urgent need for an integrated approach to rural nutrition that enhances financial and physical access to healthy foods, to avoid replacing the rural undernutrition disadvantage in poor countries with a more general malnutrition disadvantage that entails excessive consumption of low-quality calories. © 2019, The Author(s)

A century of trends in adult human height

Being taller is associated with enhanced longevity, and higher education and earnings. We reanalysed 1472 population-based studies, with measurement of height on more than 18.6 million participants to estimate mean height for people born between 1896 and 1996 in 200 countries. The largest gain in adult height over the past century has occurred in South Korean women and Iranian men, who became 20.2 cm (95% credible interval 17.5-22.7) and 16.5 cm (13.3-19.7) taller, respectively. In contrast, there was little change in adult height in some sub-Saharan African countries and in South Asia over the century of analysis. The tallest people over these 100 years are men born in the Netherlands in the last quarter of 20th century, whose average heights surpassed 182.5 cm, and the shortest were women born in Guatemala in 1896 (140.3 cm; 135.8-144.8). The height differential between the tallest and shortest populations was 19-20 cm a century ago, and has remained the same for women and increased for men a century later despite substantial changes in the ranking of countries

Effects of feeding (omega-3) HUFA-enriched <i>Artemia</i> during a progressively increasing period on the larviculture of freshwater prawns

Larvae of the freshwater prawn (Macrobrachium rosenbergii) were reared to post-larvae in a closed recirculation system. Six treatments were designed where freshly-hatched Artemia nauplii were first given to the larvae for 3, 7, 11, 15, 17 and 25 days according to the treatment. After that (omega-3) HUFA-enriched Artemia were given until the 28th day at which time the test was terminated and evaluated. The requirement for (omega-3) Highly Unsaturated Fatty Acids (HUFA) for the larval stages of M. rosenbergii was confirmed by this experiment. Moreover, the longer the period of feeding on (omega-3) HUFA-enriched Artemia nauplii , the better the results in terms of growth, metamorphosis rate and stress resistance

First Observation of Microcystins in Tunisian inland waters: a threat to river mouths and lagoon ecosystems

1 - Microcystin pollution is known to affect different types of inland water bodies: river mouths and coastal lagoons may be affected by local production as well as by transportation through the freshwater network. Physicochemical and biological water quality, including the total microcystin concentration, was investigated from July to December 2003 in the reservoir Hjar, Tunisia. 2 - Microcystin levels and characterization of the different microcystin variants present were measured by protein phosphatase inhibition assays (PP2A) and by high performance liquid chromatography coupled to diode array detector and tandem mass spectrometry, respectively. The microscopic examination of the phytoplankton samples showed the dominance of the Oscillatoria and Pseudoanabaena genera. The total (particulate and dissolved) microcystin concentrations in the reservoir water varied between 23.4 and 7455.2 ng/l microcystin-LR equivalent per liter. 3 - The highest MCYST concentration was observed in November 2003. The analysis of the field bloom extract from this month by HPLC coupled to photodiode-array detector revealed the presence of five peaks having characteristic spectra of microcystins with a maximum of absorbance at 238 nm. HPLC/MS/MS analysis of this sample demonstrated the presence of three variants of microcystins: microcystin-LR (MCYST-LR), microcystin- (MCYST-RR), microcystin- (MCYST-YR). Therefore, estuaries of rivers contaminated by cyanobacteria toxins may play an important role on the transfer of these cyanotoxins through food chains

Live-food mediated drug delivery as a tool for disease treatment in larviculture: 2. A case study with European seabass

The purpose of this study is to investigate the possibility of oral delivery of the antibiotics Trimethoprim (TMP) and Sulfamethoxazole (SMX) to marine fish larvae through incorporation of these antibiotics into the live food organism Artemia. SMX and TMP were selected for their wide range action against gram negative pathogenic bacteria and because of their limited solubility in seawater. Ormetoprim-Sulfadimethoxine (brand name Romet-30) is a new combination of a similar antimicrobial drug used in aquaculture. Diseased penaeid larvae fed Romet-30 through the food chain exhibited greater survival than the untreated ones. In an earlier study Verpraet have described a technique for bioencapsulating high doses of more than 500 mu g TMP + SMX per gram dry weight (DW) Artemia nauplii. In this study we have used 2-month-old European seabass (Dicentrarchus labrax) larvae that were fed with TMP + SMX - bioencapsulated Artemia nauplii

A trophodynamic approach for the evaluation of Fishery Management Plans in the gulf of Gabes (Southern Tunisia)

An Ecopath with Ecosim food web model of the Gulf of Gabes (southern Tunisia) was constructed in order to describe its trophic structure and functioning. To assess the impacts of fisheries, an Ecosim routine was applied to predict temporal variation of catches. The model was fitted with time series data of landings for the period 1995-2008. Then, several fishery management plans were simulated by implementing different biological rest-periods. To a better evaluation of each management plan, ecological and socio-economic indicators were calculated. These indicators were used to i) establish a ranking between the fishery management plans, ii) study the effects of conservation measures on the ecosystem

Genetic responses to metal contamination in two clams: Ruditapes decussatus and Ruditapes philippinarum

International audienc

Fishing impact in Mediterranean ecosystems : an EcoTroph modeling approach

The EcoTroph modeling approach was applied to five Mediterranean marine ecosystems to characterize their food webs and investigate their responses to several simulated fishing scenarios. First, EcoTroph was used to synthesize the outputs of five pre-existing heterogeneous Ecopath models in a common framework, and thus to compare different ecosystems through their trophic spectra of biomass, catch, and fishing mortalities. This approach contributes to our understanding of ecosystem functioning, from both ecological and fisheries perspectives. Then, we assessed the sensitivity of each ecosystem to fishery, using EcoTroph simulations. For the five ecosystems considered, we simulated the effects of increasing or decreasing fishing mortalities on both the biomass and the catch per trophic class. Our results emphasize that the Mediterranean Sea is strongly affected by the depletion of high trophic level organisms. Results also show that fisheries impacts, at the trophic level scale, differ between ecosystems according to their trophic structure and exploitation patterns. A top-down compensation effect is observed in some simulations where a fishing-induced decrease in the biomass of predators impacts their prey, leading to an increase in the biomass at lower trophic levels. The results of this comparative analysis highlight that ecosystems where top-down controls are observed are less sensitive to variations in fishing mortality in terms of total ecosystem biomass. This suggests that the magnitude of topdown control present in a system can affect its stability