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The “Safe Campus Program,” implemented in 2020 through 2021 at the University of Navarra (Spain), aimed to guarantee a safe return to university campus and prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, avoiding university-wide lockdown. It included COVID-19 education, campus adaptation, and polymerase chain reaction (PCR) testing. We describe the main characteristics of the program and analyze the SARS-CoV-2 cumulative incidence among 14 496 university members. The 14-day cumulative incidence in the university was 415.2 versus 447.7 in the region. The program, sustainable in the long term, achieved low SARS-CoV-2 in-campus rates. (Am J Public Health. 2022;112(4):570–573. https://doi.org/10.2105/AJPH.2021.306682

The aim of this study is to analyze the life habits and personal factors associated with an increased SARS-CoV-2 risk in a university environment with in-person lectures during the COVID-19 pandemic. There are no previous longitudinal studies that have analyzed behavioral and personal factors with the risk of SARS-CoV-2 infection on an entire university population. A cohort study was conducted in the three campuses of the University of Navarra between August 24th 2020 and May 30th 2021, including 14,496 students and employees. 10,959 participants were finally included. Descriptive and multivariate adjusted models were performed using Cox regression. A total of 1,032 (9.4%) participants were diagnosed with COVID-19 (879 students, 153 employees), almost 50% living with their family. COVID-19 was associated with living in college or residence (HR:1.96 CI 95% 1.45 to 2.63), motor transportation (HR:1.36 CI 95% 1.14 to 1.62), South American origin (HR:1.41 CI 95% 1.17 to 1.69) and belonging to Madrid’s campus (HR:3.15 CI 95% 2.50 to 3.97). In conclusion, international students, especially from Latin America, mostly lived in university apartments or shared flats and cohabited with 4-11 people. Living in a big city (Madrid), was a significant risk factor.

It is known that indoor air is affected by outdoor air, thanks to the various studies that have been conducted in this area, the causes can be varied, from infiltration of buildings, natural or mechanical ventilation. Although it is known that transportation is one of the major contributors to this problem, studies have concluded that there is a proportion of pollutants coming from 'non-specific sources of human origin', all this emphasizes the importance of identifying and quantifying the sources of air pollution.The intention of this research project, is to characterize and quantify the pollutants that are emitted from residential buildings through their ventilation systems, and how such exhalation affects urban air quality both outdoors and, through recapture, indoors.The design of a viable methodology for monitoring two residential buildings in Pamplona (Spain) has been proposed, involving aspects such as the extension of the city where the buildings selected for the project are located, their typology, the areas destined for the ventilation systems, the equipment chosen for the quantification of pollutants and the procedure to be followed. All this procedure represents the core of the monitoring process.Thanks to this methodology, the researchers intend to present results of the quantification of pollutants such as Carbon Dioxide (CO2), Carbon Monoxide (CO), Methane (CH4), Particulate Matter (PM), Volatile Organic Compounds (VOC), resulting from the exhalation of residential buildings. These results are the foundation for demonstrating how residential buildings can become another source of pollution for urban environments.

IUCN Red List assessments for fish species can quickly become out of date. In recent years molecular techniques have added new ways of obtaining information about species distribution or populations. In this work, we propose the Iberian Peninsula as an example of reassessment needs in its endangered freshwater fish fauna. We compiled the list of freshwater fish species occurring in continental Spain and Portugal and examined their conservation status in global and national Red Lists. We retrieved records for these species in the Iberian Peninsula and calculated several biological indexes (richness and vulnerability indexes). Our results showed a patchy data coverage of fish records in the Iberian Peninsula. Threat levels reported within national Red Lists are higher than their global counterparts, reinforcing the necessity of improving and maintaining up to date national Red Lists. Iberian watersheds have moderate levels of threat and high levels of out of date assessments. The nearly fully completed genetic databases for Iberian fish species, along with the limited distribution of many endangered species and the necessity of update their assessments constitute an excellent opportunity to use data obtained from eDNA to improve species monitoring practices and their conservation status.

The issue of air pollutants from livestock buildings is prevalent in the literature. Because they and their emissions impact both animal production and livestock building users as well as the outdoor environment. This paper aims to compile and review data available in the scientific literature on the types of pollutants for a better understanding of their generation form, their distribution according to the kind of animal, and the main factors affecting their generation and concentration, i.e., the rearing system, the indoor microclimate, and the manure management. The elevated generation of pollutants in animal buildings is tied to the dense occupancy in this industrial activity. The indoor air quality is defined according to the type of livestock in animal housing, considering its welfare needs, and the types and concentrations of pollutants generated as a function of the family of animal and the management used in production. The main gases generated are CH4, CO2, H2S, NH3, N2O, in addition to particulate matter and airborne microorganisms such as fungi and bacteria that very negatively affect the health of animals and users of the animal buildings. Furthermore, knowledge about the main contaminants generated, the form of generation, their origin, their concentrations, and their distribution throughout the shed is essential to achieve a permanent and adequate indoor air quality and, with that, a high-quality product that will lead to high production yield without neglecting animal welfare.

The identity of a biological specimen can be considered the most basic type of trait: the species (or higher taxon) the specimen belongs to, one of the three most fundamental data elements (along with location and time) that configure the primary biodiversity data record whose quantification may underpin biological monitoring programs. A general image containing specimens (for example, a photo from a surveillance camera), where individual organisms are to be identified, is akin to an image of a single organism where traits are to be recognized: the individual, often distinct organisms in the image, become the traits of the image. In many cases, automated segmentation and classification/identification and counting of individuals captured within general images containing multiple organisms is most desirable—provided precision and recall exceed a reasonable threshold: that which minimizes the false-positive error rate, as compared to human identification in images. When this occurs, quantitative monitoring data are amenable to good automation, saving much time and human effort. One particularly well-suited case is that of airborne pollen and spore monitoring, hitherto done manually in most of the world. However, systems are being developed that can recognize atmospheric pollen content from images. Two main approaches are possible: either fully automated systems, or recognition from captured field images. In both cases, some instance of artificial intelligence, most often a convolutional neural network, is tasked with the recognition of pollen and spore types, after proper training, from microscopic images. Several problems exist for the wider adoption of such approaches. Among them, the workflow order of segmentation and identification, the portability of the neural network training for different locations, the differences in performance for distinct particle types, and the generation and archival of images: field images vs. individual (segmented) detected specimens, which call for wholly different approaches to metadata. In this presentation we review the general outlook of automated airborne pollen and spore monitoring data, and compare performance data in some specific deep learning settings and workflows, based on actual monitoring work, training and tests with real images.

Although Alternaria spores are well-known allergenic fungal spores, automatic bioaerosol recognition systems have not been trained to recognize these particles until now. Here we report the development of a new algorithm able to classify Alternaria spores with BAA500 automatic bioaerosol monitors. The best validation score was obtained when the model was trained on both data from the original dataset and artificially generated images, with a validation unweighted mean Intersection over Union (IoU), also called Jaccard Index, of 0.95. Data augmentation techniques were applied to the training set. While some particles were not recognized (false negatives), false positives were few. The results correlated well with manual counts (mean of four Hirst-type traps), with R

More than 33,500 fish species inhabit freshwater and marine environments, according to FishBase database records. The International Union for the Conservation of Nature (IUCN) has assessed the conservation status of approximately half of them, the lowest percentage in any vertebrate group. In order to identify what factors may underlie this assessment gap, several traits were examined related to distribution, life‐history, taxonomy, conservation, and the economic relevance of species according to their assessment status. IUCN assessment patterns were explored and separate analyses were included for freshwater and marine species. The results showed that IUCN assessments were biased towards economically developed regions, species with early description dates and species covered by current IUCN specialist groups. Species living in remote areas or habitats were more likely to be unassessed. In particular, South America had low assessment levels. Other traits such as commercial importance did not influence the assessment status of fish species. We therefore encourage assessment in poorly assessed areas and taxonomic subgroups to prompt timely conservation action to prevent species extinctions.

Zoos and aquaria, often regarded as preservation-cum-entertainment enterprises, are also actors in the effort to curb the biodiversity crisis: raising awareness, supporting conservation, and conducting research. We assessed trends in zoo and aquaria research topics and study organisms over time worldwide. For the zoos and aquaria registered in the Species360's Zoological Information Management System and the World Association of Zoos and Aquariums, we compiled metadata on their research published in the peer-reviewed literature indexed in Scopus and carried out a keyword frequency analysis. The production of scientific papers by zoos increased at a much faster rate than the average accrual of scientific papers in the literature. Evolution of research themes ran parallel to that of biological sciences (e.g., development of molecular genetics or increased awareness about conservation). The focus of 48.5% of zoo-led research was on vertebrates, of which mammal research was 33.7%. Whether zoos are effectively contributing to conservation may still be debatable, but our results highlight their institutional efforts to increase knowledge about the species in their care.Tendencias Mundiales en la Producción Investigativa de los Zoológicos y Acuarios Resumen Los zoológicos y los acuarios, con frecuencia considerados empresas de conservación y entretenimiento, también son actores en el esfuerzo por reducir la crisis de la biodiversidad al crear conciencia, apoyar a la conservación y llevar a cabo investigaciones. Evaluamos las tendencias en los temas de investigación y los organismos de estudios en los zoológicos y los acuarios en todo el mundo a través del tiempo. Compilamos los metadatos de las investigaciones realizadas en los zoológicos y acuarios registrados en el Sistema de Manejo de Información Zoológica de Species360 y en la Asociación Mundial de Zoológicos y Acuarios que han sido publicadas en la literatura revisada por pares indexada en Scopus y realizamos un análisis de frecuencias de palabras clave. La producción de artículos científicos por zoológicos se incrementó a una tasa mucho más rápida que la acumulación promedio de artículos científicos en la literatura. La evolución de los temas de investigación fue paralela a la de las ciencias biológicas (p. ej.: desarrollo de la genética molecular o incremento en la conciencia por la conservación). El enfoque del 48.5% de las investigaciones conducidas por los zoológicos estuvo sobre los vertebrados. De este 48.5%, el 33.7% fueron investigaciones sobre mamíferos. Todavía puede debatirse si los zoológicos están contribuyendo efectivamente a la conservación, pero nuestros resultados resaltan sus esfuerzos institucionales por incrementar el conocimiento sobre las especies bajo su cuidado.

Natural history collections constitute an enormous wealth of information of Life on Earth. It is estimated that over 2 billion specimens are preserved at institutions worldwide, of which less than 10% are accessible via biodiversity data aggregators such as GBIF. Moreover, they are a very important resource for eco-evolutionary research, which greatly depends on knowing the precise location where the specimens were collected in order to characterize the environment in which they lived. Yet, only about 55% of the accessible records are georeferenced and only 31% have coordinate uncertainty information, which is critical for conducting rigorous studies. The awareness of this gap of knowledge which hinders the enormous potential of such data in research led to the organization of a workshop which brought together key players in georeferencing of natural history collections. The discussion and outcomes of this workshop are here presented., This work has been possible thanks to the EU Cost Action CA17106: “MOBILISE. Mobilizing Data, Experts and Policies in Scientific Collections.”

Background Early diagnosis of SARS-CoV-2 infection is essential to reduce disease spread. Rapid antigen tests have not been sufficiently evaluated in asymptomatic patients to be used as massive population screening tools. Methods Head-to-head evaluation of Roche SARS-CoV-2 Rapid Antigen Test and real-time reverse transcription polymerase chain reaction (RT-PCR) as SARS-CoV-2 screening tools performed in asymptomatic adults from a semi-closed community in University of Navarra (Spain) from November 2020 to January 2021. Sensitivity, specificity and predictive values were calculated using RT-PCR as reference method. Findings Roche SARS-CoV-2 Rapid Antigen Test was performed on 2542 asymptomatic adults in a community with a SARS-CoV-2 incidence of 1·93%. It showed a sensitivity of 71·43% (CI 95%: 56·74 – 83·42) and a specificity of 99·68% (CI 95%: 99·37 - 99·86). Positive Predictive Value was 81·4 (CI 95% 66·6 – 91·61) and Negative Predictive Value was 99·44 (CI 95% 99·06 – 99·69). Test sensitivity was related to viral load, with higher sensitivity in RT-PCR cycle threshold (Ct) values under 25 (93·75%, CI 95%: 71·96 – 98·93), that dropped to 29·41% (CI 95%: 10·31- 55·96) in RT-PCR Ct values above 25. Interpretation This study suggests that rapid antigen tests are less effective in asymptomatic population, when compared with RT-PCR. Further studies are needed to evaluate different options to improve screenings based on rapid antigen test, such as the use of clinical questionnaires to select higher risk-participants, the confirmation of negative results with RT-PCR or the use of repetitive sequential testing. Funding This research received no external funding.

Pollen exposure weakens the immunity against certain seasonal respiratory viruses by diminishing the antiviral interferon response. Here we investigate whether the same applies to the pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is sensitive to antiviral interferons, if infection waves coincide with high airborne pollen concentrations. Our original hypothesis was that more airborne pollen would lead to increases in infection rates. To examine this, we performed a cross-sectional and longitudinal data analysis on SARS-CoV-2 infection, airborne pollen, and meteorological factors. Our dataset is the most comprehensive, largest possible worldwide from 130 stations, across 31 countries and five continents. To explicitly investigate the effects of social contact, we additionally considered population density of each study area, as well as lockdown effects, in all possible combinations: without any lockdown, with mixed lockdown?no lockdown regime, and under complete lockdown. We found that airborne pollen, sometimes in synergy with humidity and temperature, explained, on average, 44% of the infection rate variability. Infection rates increased after higher pollen concentrations most frequently during the four previous days. Without lockdown, an increase of pollen abundance by 100 pollen/m3 resulted in a 4% average increase of infection rates. Lockdown halved infection rates under similar pollen concentrations. As there can be no preventive measures against airborne pollen exposure, we suggest wide dissemination of pollen?virus coexposure dire effect information to encourage high-risk individuals to wear particle filter masks during high springtime pollen concentrations. © 2021 National Academy of Sciences. All rights reserved., 1.1.1.2/VIAA/2/18/283; European Cooperation in Science and Technology, COST: CA18226; Academy of Finland, AKA: 318194, PS4A; Ministerio de Educación, Cultura y Deporte, MECD: FPU15/01668; Department of the Environment, Australian Government; Lietuvos Mokslo Taryba; Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja, MPNTR: 451-03-68/2020-14/200358; European Social Fund, ESF: 09.3.3-LMT-K-712-01-0066; Helmholtz Association; Christine Kühne – Center for Allergy Research and Education, CK-CARE, ACKNOWLEDGMENTS. We thank Mr. Luis-Leopold Moelter and Mr. Mehmet Gökkaya for assistance in overall data curation. The study was partly implemented in the frame of the European Cooperation in Science and Technology (EU-COST) program, "New approaches in detection of pathogens and aeroallergens (ADOPT)," Grant CA18226 (EU Framework Program Horizon 2020). D.B. and C.T.-H. were supported by the Helmholtz Climate Initiative (HI-CAM), Mitigation and Adaptation. A.Ch. and D.V. were supported by the Municipality of Thessaloniki, Greece (Directorate for the Management of the Urban Environment, Department of Environment). This research has been partly supported by the European Social Fund (Project 09.3.3-LMT-K-712-01-0066) under grant agreement with the Research Council of Lithuania (LMTLT). The study was also partly conducted within the frame of the project of the European Community European Regional Development Fund (EC ERDF) and PostDoc Latvia (Grant 1.1.1.2/VIAA/2/18/283). M.S. acknowledges the Academy of Finland (Project PS4A, Grant 318194). We thank the Department of Health and Rehabilitation of Vinnytsia Regional Council, Ukraine, for providing the numbers of COVID-19 cases. A.H.A. acknowledges Angel Chaves and the Government of Navarra: Institute of Public and Labor Health of Navarra, within LIFE-IP NAdatpa-CC (LIFE16 IPC/ES/000001). A.P. was supported by a predoctoral grant financed by the Ministry of Education, Culture and Sports of Spain, in the Program for the Promotion of Talent and its Employability (Grant FPU15/01668). B.S. acknowledges the Ministry of Education, Science, and Technological Development of the Republic of Serbia (Grant 451-03-68/2020-14/200358). C.T.H. acknowledges the Christine Kühne–Center for Allergy Research and Education (CK-CARE), and The Initiative and Networking Fund of the Helmholtz Association (Immunology & Inflammation). We thank Jan Bumberger, Marcus Karsten, Paul Remmler, Jan C. Simon, and Regina Treudler for data provision and curation from Leipzig, Germany. We thank Claudia Langford Brown and Dana Flanders for statistical advice and scientific discussions. We thank Penelope Jones, Edith Bucher, Reyhan Gumusburun, Haydar Soydaner Karakus, Su Ozgur, and Asli Tetik Vardarli for data curation.

A methodology based on CFD-RANS simulations (WA CFD-RANS, Weighted Averaged Computational Fluid Dynamic-Reynolds-Averaged Navier-Stokes simulations) which includes appropriate modifications, has been applied to compute the annual, seasonal, and hourly average concentration of NO2 and NOX throughout the city of Pamplona (Spain) at pedestrian level during 2016. The results have been evaluated using measurements provided both by the city's network of air quality monitoring stations and by a network of mobile microsensors carried around by cyclists during their daily commutes, obtaining a maximum relative error lower than 30% when computing NO2 annual average concentrations. The model has taken into account the actual city layout in three dimensions, as well as the traffic emissions. The resulting air pollution maps provided information critical for studying the traffic-related health effects of NO2 and their associated external costs in the city of Pamplona and the spatial representativeness of the current network of air quality monitoring stations (it has not been carried out for an entire city to date). The developed methodology can be applied to similar cities, providing useful information for the decision-makers.

Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Epidalea calamita, and Pelophylax perezi. We studied 17-21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77-96 individuals). As expected, F IS and tests for Hardy-Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses., This work was supported by Ministerio de Ciencia e Innovación, Spain, and FEDER (CGL2008-04271-C02-01/BOS); and Ministerio de Economía y Competitividad, Spain, and FEDER (CGL2011-28300) to I.M.S., who was also supported by funding from the Spanish Ramón y Cajal (RYC-2007-1668) and Severo Ochoa (SEV-2012-0262) programs. G. S.M. was funded by a predoctoral grant provided by the Asociación de Amigos de la Universidad de Navarra and benefited from funding from the Programa de ayudas de movilidad de la Asociación de Amigos de la Universidad de Navarra.

Telomere shortening with age has been documented in many organisms, butfew studies have reported telomere length measurements in amphibians, andno information is available for growth after metamorphosis, nor in wild popu-lations. We provide both cross-sectional and longitudinal evidence of nettelomere attrition with age in a wild amphibian population of natterjacktoads (Epidalea calamita). Based on age-estimation by skeletochronology andqPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recapturedmales. Our results support that toads experience telomere attrition throughouttheir ontogeny, and that most attrition occurs during the first 1–2 years. We didnot find associations between telomere length and inbreeding or body con-dition. Our results on telomere length dynamics under natural conditionsconfirm telomere shortening with age in amphibians and provide quantifi-cation of wide telomere length variation within and among age-classes in awild breeding population., This work was supported by FEDER/Ministerio de Ciencia, Innovación y Universidades, Spain (grant nos CGL2017-83131-P, CGL2017-83407-P) and Asociación de Amigos de la Universidad de Navarra (predoctoral grant to G.S.-M.).

Building on the development of Biodiversity Informatics, the Global Biodiversity Information Facility (GBIF) undertook the task of enabling access to the world’s wealth of biodiversity data via the Internet. To date, GBIF has become, in many respects, the most extensive biodiversity information exchange infrastructure in the world, opening up a full range of possibilities for science. Science has benefited from such access to biodiversity data in research areas ranging from the effects of environmental change on biodiversity to the spread of invasive species, among many others. As of this writing, more than 7,000 published items (scientific papers, reviews, conference proceedings) have been indexed in the GBIF Secretariat’s literature tracking programme. On the basis on this database, we will represent trends in GBIF in the users’ behaviour over time regarding openness, social structure, and other features associated to such scientific production: what is the measurable impact of research using GBIF data? How is the GBIF community of users growing? Is the science made with, and enabled by, open data, actually open? Mapping GBIF users’ choices will show how biodiversity research is evolving through time, synthesising past and current priorities of this community in an attempt to forecast whether summer—or winter—is coming.

Critical as they are for humans and nature, freshwater ecosystems are threatened—but the extent and depth of these threats are not well understood, especially if essential biodiversity data are lacking. Any policy aimed at protecting such ecosystems must first assess the threat factors and the potential harm, well before proposing conservation measures such as the creation and development of Protected Areas (PAs). These assessments must be done using a deep and sound knowledge of the actual and potential biodiversity variables. Freshwater ecosystems have been largely neglected in traditional PA design and management (Abell et al. 2007), be it for scarcity of biodiversity data, or for more perception-related reasons such as visibility and accessibility driving the allocation of conservation resources to more data-rich environments. In an effort to contribute to shifting this state of affairs, we have developed an irreplaceability index to identify the most relevant places to achieve conservation aims for freshwater fish, based on the International Union for the Conservation of Nature (IUCN) Red List, which, in turn, should be founded on available biodiversity data upon which expert knowledge is based (Le Saout 2013). However, we found large assessment gaps in the IUCN Red List for freshwater fish. These gaps may result from the non-systematic acquisition of primary biodiversity data, which could eventually be alleviated by coordinated policies promoting ecosystem surveys tailored at increasing the availability and spread of such data, while identifying, targeting and prioritizing hotspots. Obtaining valid conclusions from low-assessment areas such as South America, which are simultaneously biodiversity and endangerment hotspots (Collen 2014), is particularly troublesome. Building an irreplaceability index requires access to abundant, fine-scale biodiversity data. When combined with the assessment information available in the IUCN Red List, we can identify those areas where low assessment rates for highly irreplaceable rivers become keystones to protect freshwater biodiversity, and can therefore suggest actions for policy makers to take at both regional and local scales. In particular, we have thus identified those irreplaceable rivers that fall outside the current net of PAs. In a context of inadequate investment in biodiversity conservation (Juffe-Bignoli et al. 2016), our findings and the informatics-powered methods we propose, will hopefully help decision makers establish conservation priorities and allocate funds to preserve irreplaceable rivers and their fish fauna. Furthermore, the necessity of improving the IUCN Red List in low-assessed areas, requires synergies among IUCN, Global Biodiversity Information Facility (GBIF) and conservation scientists to achieve accurate and reliable assessments.

We are in the midst of unprecedented change—climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences and genetic barcodes. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing world.

In business, the “long-tail economy” refers to a market strategy where the gravity center shifts from a few high-demand products to many, varied products focused on small niches. Commercialization of individually low-demand products can be profitable as long as their production cost is low and, all taken together, they aggregate into a big chunk of the market. Similarly, in the “business” of biodiversity data acquisition, we can find several mainstream products that produce zillions of bits of information every year and account for most of the budget allocated to increase our primary data-based knowledge about Earth’s biological diversity. These products play a crucial role in biodiversity research. However, along with these large global projects, there is a constellation of small-scale institutions that work locally, but whose contribution to our understanding of natural processes should not be dismissed. These information datasets can be collectively referred to as the “long-tail biodiversity data”. Here we present the case of the Museum of Sciences University of Navarra, which harbors the research activity of the Museum of Zoology (MZNA) and herbarium (PAMP) of the University of Navarra in Spain. For the last 40 years, its members have been involved in hundreds of research projects, from local to international level—but quantitatively, the vast majority of its biodiversity records come from Navarra, a smallish (10,000 sq. km) administrative region in the north of Spain. Despite its modest area, the available information about the region in the Museum database approaches one million records of thousands of species, including dozens of type series. Fifteen years ago, a series of national research grants enabled boosting digitization and public access to the database records through the Global Biodiversity Information Facility (GBIF). Although those grants were never renewed, the Museum continued its digitizing and standardizing program on vouchered collections, as well as sampling additional raw biodiversity data through long term ecological sites using the Museum’s resources, which annually provide thousands of new records at the local level. Currently, the Museum has already published through GBIF’s IPT (Integrated Publishing Toolkit) 30 datasets, containing more than half-million records of about 5700 taxa. Its records have contributed to more than 60 peer-reviewed publications over the last five years. Institutions that basically harvest biodiversity data at a local scale usually show a high degree of specialization, gathering researchers with strong (albeit often narrow) expertise in the taxonomy and ecology of nearby ecosystems. They are thus an extremely valuable tool when dealing with processes resulting in diversity changes that can be identified rather precisely, especially when their work can be traced back many decades. Making all this fine-scale information accessible and actionable requires, in most of the cases, a rather modest investment in staff training on data management (e.g., standards, database interoperability) or museum curation procedures, and on informatics infrastructure. As in the case of business, it is not a matter of choosing between producing blockbusters or independent cinema--but of leveraging available resources and maximizing output.

With more than one billion primary biodiversity data records (PBR), the Global Biodiversity Information Facility (GBIF) is the largest and, arguably, most comprehensive and accurate resource about the biodiversity data on the planet. Yet, its gaps (taxonomical, geographical or chronological, among others) have often been brought to attention (Gaijy et al. 2013) and efforts are continuously made to ensure more uniform coverage. Especially as data obtained through this resource are increasingly being used for science, policy, and conservation (Ariño et al. 2018), drawing on every possible source of information to complement already existing data opens new opportunities for supplying the integrative knowledge required for global endeavors, such as understanding the global patterns of ecosystem and environment changes. One such potential source that exists, but so far has experienced little integration, is the vast body of data acquired through airborne particle monitoring systems (for example, the European Aeroallergen Network, EAN). A large portion of pollen data is comprised of quantitative sampling of airborne pollen collected through semi-automated spore traps throughout the world. Its main use is clinical, as it forms the basis of the widespread allergen forecast bulletins. While geolocating the source of airborne pollen is fraught with obviously large uncertainty radii, the time and taxon components of the PBR remain highly precise and are therefore fit for many other uses (Hill et al. 2010). Presence data, and under certain circumstances, frequency data inferred from pollen counts have been often proposed as an excellent proxy for past climate change assessments as far back as the start of the Holocene (Mauri et al. 2015) and might therefore also be possibly used for current climate change detection. We call for a concerted effort throughout the palynological community to first increase harmonizing, and then eventually standardizing, pollen data acquisition through the adoption of Darwin Core (DwC) and, eventually, DwC extensions to mine current data and pipeline future airborne pollen data as PBR. mine current data and pipeline future airborne pollen data as PBR. Success in this endeavor may contribute to a better understanding of global change.

The advent of online data aggregator infrastructures has facilitated the accumulation of Digital Accessible Knowledge (DAK) about biodiversity. Despite the vast amount of freely available data records, their usefulness for research depends on completeness of each body of data regarding their spatial, temporal and taxonomic coverage. In this paper, we assess the completeness of DAK about terrestrial mammals distributed across the Iberian Peninsula. We compiled a dataset with all records about mammals occurring in the Iberian Peninsula available in the Global Biodiversity Information Facility and in the national atlases from Portugal and Spain. After cleaning the dataset of errors as well as records lacking collection dates or not determined to species level, we assigned all occurrences to a 10-km grid. We assessed inventory completeness by calculating the ratio between observed and expected richness (based on the Chao2 richness index) in each grid cell and classified cells as well-sampled or under-sampled. We evaluated survey coverage of well-sampled cells along four environmental gradients and temporal coverage. Out of 796,283 retrieved records, quality issues led us to remove 616,141 records unfit for this use. The main reason for discarding records was missing collection dates. Only 25.95% cells contained enough records to robustly estimate completeness. The DAK about terrestrial mammals from the Iberian Peninsula was low, and spatially and temporally biased. Out of 5,874 cells holding data, only 620 (9.95%) were classified as well-sampled. Moreover, well-sampled cells were geographically aggregated and reached inventory completeness over the same temporal range. Despite the increasing availability of DAK, its usefulness is still compromised by quality issues and gaps in data. Future work should therefore focus on increasing data quality, in addition to mobilizing unpublished data.

This dataset gathers information about the macroinvertatebrate samples and environmental variables collected on rivers of the Ebro River Basin (NE Iberian Peninsula), the second largest catchment in the Iberian Peninsula. The collection is composed of 1,776 sampling events carried out between 2005 and 2015 at more than 400 sampling sites. This dataset is part of a monitoring network set up by the Ebro Hydrographic Confederation, the official body entrusted with the care of the basin, to fulfill the requirements of the European Water Framework Directive. Biological indices based on the freshwater macroinvertebrate communities were used to evaluate the ecological status of the water bodies within the basin. Samples were qualitatively screened for all occurring taxa. Then, all individuals from all taxa in a quantitative subsample of each sample were counted. Biological indices were calculated to estimate water quality at each sampling site. All samples are kept at the Museum of Zoology of the University of Navarra. Machine-accessible metadata file describing the reported data (ISA-Tab format)

Standards set up by Biodiversity Information Standards-Taxonomic Databases Working Group (TDWG), initially developed as a way to share taxonomical data, greatly facilitated the establishment of the Global Biodiversity Information Facility (GBIF) as the largest index to digitally-accessible primary biodiversity information records (PBR) held by many institutions around the world. The level of detail and coverage of the body of standards that later became the Darwin Core terms enabled increasingly precise retrieval of relevant records useful for increased digitally-accessible knowledge (DAK) which, in turn, may have helped to solve ecologically-relevant questions. After more than a decade of data accrual and release, an increasing number of papers and reports are citing GBIF either as a source of data or as a pointer to the original datasets. GBIF has curated a list of over 5,000 citations that were examined for contents, and to which tags were applied describing such contents as additional keywords. The list now provides a window on what users want to accomplish using such DAK. We performed a preliminary word frequency analysis of this literature, starting at titles, which refers to GBIF as a resource. Through a standardization and mapping of terms, we examined how the facility-enabled data seem to have been used by scientists and other practitioners through time: what concepts/issues are pervasive, which taxon groups are mostly addressed, and whether data concentrate around specific geographical or biogeographical regions. We hoped to cast light on which types of ecological problems the community believes are amenable to study through the judicious use of this data commons and found that, indeed, a few themes were distinctly more frequently mentioned than others. Among those, generally-perceived issues such as climate change and its effect on biodiversity at global and regional scales seemed prevalent. The taxonomic groups were also unevenly mentioned, with birds and plants being the most frequently named. However, the entire list of potential subjects that might have used GBIF-enabled data is now quite wide, showing that the availability of well-structured data has spawned a widening spectrum of possible use cases. Among them, some enjoy early and continuous presence (e.g. species, biodiversity, climate) while others have started to show up only later, once a critical mass of data seemed to have been attained (e.g. ecosystems, suitability, endemism). Biodiversity information in the form of standards-compliant DAK may thus already have become a commodity enabling insight into an increasingly more complex and diverse body of science. Paraphrasing Tennyson, more things were wrought by data than TDWG dreamt of.

[Aim]: To test the role of mountains as barriers to gene flow in co-distributed taxa with different life history traits. [Location]: Sierra de Guadarrama, Central Spain. [Methods]: We used larval genotypes of four amphibian species (Epidalea calamita, Hyla molleri, Pelophylax perezi and Pelobates cultripes) sampled on northern and southern slopes of Sierra de Guadarrama to describe genetic structure with F, migration rates per generation, clustering algorithms and resistance by elevation surfaces. We also recorded individual displacement events as a proxy of dispersal potential during a seven-year monitoring project based on capture–mark–recapture (CMR). [Results]: All species travelled longer cumulative distances than those reported in the study area for P. cultripes (0.71 km). Individuals of E. calamita travelled up to 3.55 km, followed by H. molleri (2.84 km) and P. perezi (1.51 km). Pairwise F estimates showed lower overall connectivity in P. cultripes. Average migration rates per generation were low in all species, with exceptions in same-slope populations of H. molleri and P. cultripes. Clustering algorithms consistently recovered well-differentiated population groups of P. cultripes in northern versus southern slopes, but widely admixed areas were observed in the other species, especially near mountain passes. Resistance by elevation surfaces showed a strong barrier effect of Sierra de Guadarrama in P. cultripes and suggested a potential role of topography in the genetic structure of E. calamita and H. molleri. [Main conclusions]: Sierra de Guadarrama currently acts as a strong barrier to gene flow for P. cultripes and, to a lesser extent, for E. calamita, H. molleri and P. perezi. This differential effect can be partly explained by differences in life history traits, including dispersal potential. Our findings support the general role of the Central System as a key feature shaping population connectivity and genetic variation in amphibian communities., G.S.M. was funded by Asociación de Amigos de la Universidad de Navarra. This research was funded by grants CGL2008-04271-C02-01/BOS and CGL2011-28300 (Ministerio de Ciencia e Innovación, Ministerio de Economía y Competitividad, Spain, and FEDER) toI.M.S., who was supported by funding from the Spanish ‘Ramón yCajal’(RYC-2007-01668) and ‘Severo Ochoa’ (SEV-2012-0262) programmes

Researchers are embracing the open access movement to facilitate unrestricted availability of scientific results. One sign of this willingness is the steady increase in data freely shared online, which has prompted a corresponding increase in the number of papers using such data. Publishing datasets is a time-consuming process that is often seen as a courtesy, rather than a necessary step in the research process. Making data accessible allows further research, provides basic information for decision-making and contributes to transparency in science. Nevertheless, the ease of access to heaps of data carries a perception of `free lunch for all¿, and the work of data publishers is largely going unnoticed. Acknowledging such a significant effort involving the creation, management and publication of a dataset remains a flimsy, not well established practice in the scientific community. In a meta-analysis of published literature, we have observed various dataset citation practices, but mostly (92%) consisting of merely citing the data repository rather than the data publisher. Failing to recognize the work of data publishers might lead to a decrease in the number of quality datasets shared online, compromising potential research that is dependent on the availability of such data. We make an urgent appeal to raise awareness about this issue.

The knowledge of biodiversity within an area is vital if we want to develop adequate conservation strategies. Biosphere Reserves are purposefully established for the sustainable use of their resources, and therefore their biodiversity should be well known. We compared and evaluated information available for Mexican Biosphere Reserves on threatened and non-threatened vertebrate species records from three different sources – the corresponding Biosphere Reserves management plans (MPs), the Global Biodiversity Information Facility index (GBIF), and scientific literature, in order to find potential knowledge gaps. Our results suggest that there were varying gaps in information among sources according to vertebrate group. For each group of vertebrate species, management plans held the largest subsets of information but were not complete, ranging from 89.6% of the combined known species of birds to 70% for amphibians and freshwater fishes. However, both GBIF and literature included data absent from MPs, and GBIF included data not otherwise available, proving it as important as literature or other data sources (e.g. field data) used for crafting such plans. Moreover, we found references to threatened species that were not listed in the MPs, reaching to as many as 50% of the total known species of fish. Species information shared by all three sources ranged from 28% for amphibians to 72.5% for birds. Conservation efforts should therefore take into account that possibly less charismatic taxa such as amphibians, reptiles and freshwater fish lack more information than birds or mammals. The disparity observed in the vertebrate species information constitutes an information gap that could (or should) be solved by scientists and managers alike.

The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales, and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging. The sibship frequency (SF) method is adequate for reliable Nb estimation because it is based on sibship and parentage reconstruction from genetic marker data, thereby providing demographic inferences that can be compared with field-based information. In addition, capture–mark–recapture (CMR) robust design methods are well suited for Na estimation in seasonal-breeding species. We used tadpole genotypes of three pond-breeding amphibian species (Epidalea calamita, Hyla molleri, and Pelophylax perezi, n = 73–96 single-cohort tadpoles/species genotyped at 15–17 microsatellite loci) and candidate parental genotypes (n = 94–300 adults/species) to estimate Nb by the SF method. To assess the reliability of Nb estimates, we compared sibship and parentage inferences with field-based information and checked for the convergence of results in replicated subsampled analyses. Finally, we used CMR data from a 6-year monitoring program to estimate annual Na in the three species and calculate the Nb/Na ratio. Reliable ratios were obtained for E. calamita (Nb/Na = 0.18–0.28) and P. perezi (0.5), but in H. molleri, Na could not be estimated and genetic information proved insufficient for reliable Nb estimation. Integrative demographic studies taking full advantage of SF and CMR methods can provide accurate estimates of the Nb/Na ratio in seasonal-breeding species. Importantly, the SF method provides results that can be readily evaluated for reliability. This represents a good opportunity for obtaining robust demographic inferences with wide applications for evolutionary and conservation research., This research was funded by grants CGL2008‐04271‐C02‐01/BOS, and CGL2011‐28300 (Ministerio de Ciencia e Innovación ‐MICINN‐, Ministerio de Economía y Competitividad ‐MEC‐, Spain, and FEDER) to IMS, who was also supported by funding from the Spanish “Ramón y Cajal” (RYC‐2007‐01668) and “Severo Ochoa” (SEV‐2012‐0262) programs.

In this paper five datasets are described that provide information about records of mammals in the Vertebrate Collection of the Museum of Zoology of the University of Navarra (MZNA-VERT). The datasets contain 3,466 records belonging to 20 species of mammals sampled across the transition zone between the Atlantic and Mediterranean biogeographical regions (north Iberian Peninsula). The datasets include both distributional data (georeferenced records) and basic biometric data of most of the vouchered specimens stored in the museum facilities. The samples originated mainly within research projects and PhD theses carried out in the former department of Zoology and Ecology of the University of Navarra between 1982 and 2011. The Darwin Core Archive Format datasets are accessible through GBIF.

We describe the pellet sampling data set from the Vertebrate Collection of the Museum of Zoology of the University of Navarra. This data set compiles all information about small mammals obtained from the analysis of owl pellets. The collection consists on skulls, mandibles, and some skeletons of 36 species of more than 72,000 georeferenced specimens. These specimens come from the Iberian Peninsula although most samples were collected in Navarra, a highly diverse transitional area of 10,000 kilometre square sitting across three biogeographical regions. The collection spans more than forty years and is still growing as a result of the establishment of a barn owl pellet monitoring network in 2015. The program will provide critical information about the evolution of the small mammals’ community in this transition zone as it changes over time. Machine-accessible metadata file describing the reported data (ISA-Tab format)

A research on wildlife road-kills, mostly medium-sized mammals, has been conducted for two years along two highways (namely A-15 and A-10) in the Euro Siberian area of northwest Navarre (Northern Spain) between the westernmost side of the Pyrenees and the Basque Mountains. The study intended to find out a link between their distribution and the structure of the landscape surrounding it. The roads were segmented into 100-m stretches, and inspected weekly for roadkill by research staff with the collaboration of the maintenance service of both freeways. The data of the 539 animals recorded and geolocated in the segments were analysed spatially and matched to the surrounding landscape and presence of crossing structures. Results showed that the spatial distribution of wild medium-sized mammal road-kills along these freeways was not random, and that the surrounding landscape and the potential permeability of these roads did affect the road-kill rates. Existence of permeable crossings and heterogeneous landscape units reduced roadkill, while homogeneous agricultural and human landscapes increased roadkill rates.

We characterize the primary biodiversity data records that have been made public for retrieval for the Pyrenean region. Such data, spanning more than a hundred years, have been collected by many institutions and individual researchers and digitized in databases, some of which have been shared through the Global Biodiversity Information Facility platform by using a standard format, Darwin Core. The datasets are not homogeneous in extent, coverage, taxonomy, or accuracy. Differences arising from taxonomic depth or group, georeferencing precision, age of collection, and other features result in biases and gaps that may influence the fitness for use of such data. Knowledge of patterns found in the data may help researchers and managers operating in the Pyrenees to estimate the reliability of available information and to assess what uses for the data are acceptable.

Over the past decades, digitization endeavors across many institutions holding natural history collections (NHCs) have multiplied with three broad aims: first, to facilitate collection management by moving existing analog catalogues into digital form; second, to efficiently document and inventory specimens in collections, including imaging them as taxonomical surrogates; and third, to enable discovery of, and access to, the resulting collection data. NHCs contain a unique wealth of potential knowledge in the form of primary biodiversity data records (PBR): at its most basic level, the “what, where and when” of occurrences of the specimens in the collections. But as T.S. Eliot famously said, “knowledge is invariably a matter of degree”. For such data to be transformed into digitally accessible knowledge (DAK) that is conducive to an understanding about how the natural world works, release of digitized data (the “this we know”) is necessary. At least two billion specimens are estimated to exist in NHCs already, but only a small fraction can be considered properly DAK: most have either not been digitized yet, or not released through a discovery facility. Digitizing is relatively costly as it often entails manually processing each specimen unit (e.g. a herbarium sheet, a pinned insect, or a vial full of invertebrates). How long could it take us to transform all NHCs into DAK? Can we keep up with the natural growth in collections? The Global Biodiversity Information Facility (GBIF) has become the de facto main index of PBR, both originated in NHCs or as field observations. Digitized NHC that are standards-compliant and can be connected to, or harvested by, GBIF, effectively become DAK. I have examined GBIF growth data looking for a pattern of DAK generation. I found that the rate of NHC-based PBR accrual is remarkably constant: the total DAK shows a strongly linear growth, as opposed to the exponential growth exhibited by cumulative observation data. Projecting the trend to the estimated holdings shoots the completion many decades ahead. In addition, digitized data appear to be taxonomically biased. Digitization efforts must therefore step up qualitatively in order to enable processing the backlog, let alone newly-acquired accessions, within one generation. Among several possible solutions, emerging, industrial-scale mass-digitization techniques may help harnessing this otherwise daunting task—but there’s also a risk that DAK becomes even more uneven across taxon groups because of the narrow application specificity of such techniques, thus potentially biasing our knowledge of nature.

The present work aims to analyze the spatio-temporal variability in benthic macroinvertebrate assemblages and biotic indices in an undisturbed and unpolluted Pyrenean river. Samples were collected seasonally over 2 year-cycles (2001–2002) at fifteen sampling sites along the Erro River (Ebro River Basin, Spain) during a exhaustive biomonitoring program following the IBMWP–IASPT scoring system protocol routinely applied in Iberia. Despite absolute values of the biotic indices showed high spatio-temporal variation, the IBMWP–IASPT scoring system proved useful because water quality classes were consistent throughout seasons and years as well as along-river. The original macroinvertebrate families’ presence/absence data matrix was reduced in a number of ways to conduct different statistical procedures in order to detect and separate the underlying near-natural spatial and temporal gradients of the assemblage composition in the Erro River. Along-river, spatial variation of the macroinvertebrate community composition was well assessed by similarity analysis, which clearly detected physical features on the river (drought-affected reach, gorge, towns and flow gauging weirs). Categorical principal component analysis (CATPCA) synthesized and jointly ordered macroinvertebrate samples in a spatio-temporal gradient in the factorial map defined by the first two principal components providing a parsimonious way to assess the assemblages’ variation. These two variation gradients throughout the macroinvertebrate families’ occurrence data were subsequently confirmed separately by several correspondence analyses and revealed additional information, as the representative families for each sampling site group and season could be identified. Furthermore, these spatio-temporal gradients were discussed and put in relation with changes in the aquatic habitat (water temperature, conductivity, total dissolved solids, water velocity, channel width, canopy cover, etc.). The near-natural functioning of the Erro River promoted us to emphasize that conservation efforts should aim to maintain the free-flowing as a permanent source of variability.

Despite many efforts by researchers worldwide to assess the biodiversity of plant groups, many locations on Earth remain not well surveyed and data-deprivation biases often occur. Robust estimates of inventory completeness could help alleviate the problem. This study aimed at identifying areas representing gaps in current knowledge of African palms, with a focus on Benin (West Africa). We assessed the completeness of knowledge of African palms targeting geographical distance and climatic difference from well-known sites. Data derived from intensive fieldwork were combined with independent data available online. Completeness inventory indices were calculated and coupled with other criteria to decide on the extent of knowledge. Results showed a high overall value for inventory completeness, as well as an even distribution of well-known areas across the country. However, poorly-known areas were distinctly identified and correlated to remote locations with low accessibility. This study illustrates how biodiversity survey and inventory efforts can be guided by existing knowledge. We strongly recommend the combination of digital accessible knowledge and fieldwork, coupled with expert knowledge, to obtain a better picture of the completeness of the inventory in tropical ecosystems.

As an indicator of ecological maturity, we have analyzed the nematode community of an erosion-prone Mediterranean macchia and a pine stand within it. Species richness, abundance, diversity and maturity indexes have been measured from a number of standardized soil samples taken along parallel transects laid across the boundary between the pine stand and the macchia. Results of multifactor analysis on these data show three distinct nematode communities of different species composition. The intermediate nematode community (ecotone) is not a mixture of elements of adjacent communities (pine stand and macchia), thus suggesting the existence of an ecotone-specific community beyond the expected boundary effect.