Journals
Magazine:
SCIENCE OF THE TOTAL ENVIRONMENT
ISSN:
0048-9697
Year:
2023
Vol:
861
Ppgs:
160180
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 guide counts (mean of four Hirst-type traps), with R2 = 0.78. Counts from BAA500 were 1.92 times lower than with Hirst-type traps. The algorithm was then used to re-analyze the historical automatic pollen monitoring network (ePIN) dataset (2018-2022), which lacked Alternaria spore counts. Re-analysis of past data showed that Alternaria spore exposure in Bavaria was very variable, with the highest counts in the North (Marktheidenfeld, 154 m a.s.l.), and the lowest values close to the mountains in the South (Garmisch-Partenkirchen, 735 m a.s.l.). This approach shows that in our network future algorithms can be run on past datasets. Over time, the use of different algorithms could lead to misinterpretations as stemming from climate change or other phenological causes. Our approach enables consistent, homogeneous treatment of long-term series, thus preventing variability in particle counts due to changes in the algorithms.
Magazine:
FISHES
ISSN:
2410-3888
Year:
2022
Vol:
7
N°:
1
Pp:
2
Biodiversity loss is a global problem, accelerated by human-induced pressures. In the marine realm, one of the major threats to species conservation, together with climate change, is overfishing. In this context, having information on the conservation status of target commercial marine fish species becomes crucial for assuring safe standards. We put together fisheries statistics from the FAO, the IUCN network List, FishBase, and RAM Legacy databases to understand to what extent top commercial species¿ conservation status has been assessed. Levels of assessment for top-fished species were higher than those for general commercial or highly commercial species, but almost half of the species have outdated assessments. We found no relation between IUCN network List traits and FishBase Vulnerability Index, depreciating the latter value as a guidance for extinction threat. The RAM database suggests good management of more-threatened species in recent decades, but more data are required to assess whether the trend has reverted in recent years. Outdated IUCN network List assessments can benefit from reputed stock assessments for new reassessments. The future of IUCN network List assessments for commercial fish species relies on integrating new parameters from fisheries sources and improved collaboration with fisheries stakeholders and managers.
Magazine:
AMERICAN JOURNAL OF PUBLIC HEALTH
ISSN:
0090-0036
Year:
2022
Vol:
112
N°:
4
Pp:
570 - 573
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.
Magazine:
HYDROBIOLOGY
ISSN:
0018-8158
Year:
2022
Vol:
849
N°:
6
Pp:
1339 - 1349
IUCN network 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 network 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 network Lists are higher than their global counterparts, reinforcing the necessity of improving and maintaining up to date national network 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 updating their assessments constitute an excellent opportunity to use data obtained from eDNA to improve species monitoring practices and their conservation status.
Authors:
Picornell, A. (Corresponding author); Rojo, J.; Trigo, M. M.; et al.
Magazine:
SCIENCE OF THE TOTAL ENVIRONMENT
ISSN:
0048-9697
Year:
2022
Vol:
823
Ppgs:
153596
Alternaria conidia have high allergenic potential and they can trigger important respiratory diseases. Due to that and to their extensive detection period, airborne Alternaria spores are considered as a relevant airborne allergenic particle. Several studies have been developed in order to predict the human exposure to this aeroallergen and to prevent their negative effects on sensitive population. These studies revealed that some sampling locations usually have just one single Alternaria spore season while other locations generally have two seasons within the same year. However, the reasons of these two different seasonal patterns remain unclear. To understand them better, the present study was carried out in order to determine if there are any weather conditions that influence these different behaviours at different sampling locations. With this purpose, the airborne Alternaria spore concentrations of 18 sampling locations in a wide range of latitudinal, altitudinal and climate ranges of Spain were studied. The aerobiological samples were obtained by means of Hirst-Type volumetric pollen traps, and the seasonality of the airborne Alternaria spores were analysed. The optimal weather conditions for spore production were studied, and the main weather factor affectthat the temperature was the most relevant variable for the Alternaria spore dispersion and it influenced both the summer when the temperatures are extremely warm, what splits the favourable period for Alternaria spore production and dispersion into two separate ones, detected as two Alternaria spore seasons within the same year.
Magazine:
JOURNAL OF VETERINARY HEALTH SCIENCE
ISSN:
2831-3887
Year:
2022
Vol:
3
N°:
3
Pp:
223 - 249
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.
Authors:
Marcer, A. (Corresponding author); Chapman, A. D.; Wieczorek, J. R.; et al.
Magazine:
ECOGRAPHY
ISSN:
0906-7590
Year:
2022
Vol:
2022
N°:
9
Pp:
e06025
Natural history collections (NHCs) represent an enormous and largely untapped wealth of information on the Earth's biota, made available through GBIF as digitally preserved specimen records. Precise knowledge of where the specimens were collected is paramount to rigorous ecological studies, especially in the field of species distribution modelling. Here, we present a first comprehensive analysis of georeferencing quality for all preserved specimen records served by GBIF, and illustrate the impact that coordinate uncertainty may have on predicted potential distributions. We used all GBIF preserved specimen records to analyze the availability of coordinates and associated spatial uncertainty across geography, spatial resolution, taxonomy, publishing institutions and collection time. We used three plant species across their native ranges in different parts of the world to show the impact of uncertainty on predicted potential distributions. We found that 38% of the 180+ million records provide coordinates only and 18% coordinates and uncertainty. Georeferencing quality is determined more by country of collection and publishing than by taxonomic group. Distinct georeferencing practices are more determinant than implicit characteristics and georeferencing difficulty of specimens. Availability and quality of records contrasts across world regions. Uncertainty values are not normally distributed but peak at very distinct values, which can be traced back to specific regions of the world. Uncertainty leads to a wide spectrum of range sizes when modelling species distributions, potentially affecting conclusions in biogeographical and climate change studies. In summary, the digitised fraction of the world's NHCs are far from optimal in terms of georeferencing and quality mainly depends on where the collections are hosted. A collective effort between communities around NHC institutions, ecological research and data infrastructure is needed to bring the data on a par with its importance and relevance for ecological research.
Magazine:
CONSERVATION BIOLOGY
ISSN:
0888-8892
Year:
2021
Vol:
35
N°:
6
Pp:
1894 - 1902
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.
Authors:
Marcer, A. (Corresponding author); Haston, E.; Groom, Q.; et al.
Magazine:
DIVERSITY AND DISTRIBUTIONS
ISSN:
1366-9516
Year:
2021
Vol:
27
N°:
3
Pp:
564 - 567
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 organisation of a workshop which brought together key players in georeferencing of natural history collections. The discussion and outcomes of this workshop are here presented.
Magazine:
ECLINICALMEDICINE
ISSN:
2589-5370
Year:
2021
Vol:
37
Pgs:
100954
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. (c) 2021 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)
Magazine:
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
ISSN:
1052-7613
Year:
2020
Vol:
30
N°:
2
Pp:
225 - 236
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.
Magazine:
BIOLOGY LETTERS
ISSN:
1744-9561
Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (Epidalea calamita). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout their ontogeny, and that most attrition occurs during the first 1-2 years. We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.
Authors:
Rivas, E. (Corresponding author); Santiago, J. L.; Lechón, Y.; et al.
Magazine:
SCIENCE OF THE TOTAL ENVIRONMENT
ISSN:
0048-9697
Year:
2019
Vol:
649
Pgs:
1362 - 1380
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 pollutionmaps provided critical information for studying the traffic-related health effects ofNO2 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.
Magazine:
PLOS ONE
ISSN:
1932-6203
Year:
2019
Vol:
14
N°:
3: e0213542
Pgs:
1 - 16
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.
Authors:
Bal-Damerow J.E. (Corresponding author); Brenskelle L.; Barve N.; et al.
Magazine:
PLOS ONE
ISSN:
1932-6203
Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivalling 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. 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.
Magazine:
BIODIVERSITY INFORMATION SCIENCE AND STANDARDS
ISSN:
2535-0897
Year:
2018
Vol:
2
Pgs:
e25738
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 over time: what concepts/issues are pervasive, which taxon groups are mostly addressed, ...
Magazine:
SCIENTIFIC DATA
ISSN:
2052-4463
Year:
2018
Vol:
5
N°:
180108
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.
Magazine:
JOURNAL OF BIOGEOGRAPHY
ISSN:
0305-0270
Year:
2018
Vol:
45
N°:
2
Pp:
318 - 331
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-ST, 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-ST 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.
Magazine:
DATABASE
ISSN:
1758-0463
Year:
2018
Vol:
2018
N°:
bay033
Pgs:
1 - 6
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.
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 goal-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 recognise 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.
Magazine:
JOURNAL OF HEREDITY
ISSN:
0022-1503
Year:
2017
Vol:
108
N°:
5
Pgs:
535 - 543
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, FIS 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.
Magazine:
ECOLOGY AND EVOLUTION
ISSN:
2045-7758
Year:
2017
Vol:
7
N°:
23
Pp:
10301 - 10304
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.
Magazine:
PEERJ
ISSN:
2167-8359
Year:
2016
Vol:
4
N°:
e274
Pgs:
e274
Background. Primary biodiversity records (PBR) are essential in many areas of scientific research as they document the biodiversity through time and space. However, concerns about PBR quality and fitness-for-use have grown, especially as derived from taxonomical, geographical and sampling effort biases. Nonetheless, the temporal bias stemming from data ageing has received less attention. We examine the effect of changes in land use in the information currentness, and therefore data obsolescence, in biodiversity databases.
Methods. We created maps of land use changes for three periods (1956-1985, 1985-2000 and 2000-2012) at 5-kilometres resolution. For each cell we calculated the percentage of land use change within each period. We then overlaid distribution data about small mammals, and classified each data as 'non-obsolete or 'obsolete,' depending on both the amount of land use changes in the cell, and whether changes occurred at or after the data sampling's date.
Results. A total of 14,528 records out of the initial 59,677 turned out to be non-obsolete after taking into account the changes in the land uses in Navarra. These obsolete data existed in 115 of the 156 cells analysed. Furthermore, more than one half of the remaining cells holding non-obsolete records had not been visited at least for the last fifteen years.
Magazine:
SCIENTIFIC DATA
ISSN:
2052-4463
Year:
2016
Vol:
3
Pgs:
160085
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.
Magazine:
ZOOKEYS
ISSN:
1313-2989
Year:
2016
Vol:
634
Pgs.:
137 - 150
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.
Magazine:
BIODIVERSITY INFORMATICS
ISSN:
1546-9735
Year:
2015
Vol:
10
N°:
2
Pp:
45 - 55
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 digitally accessible knowledge and fieldwork, coupled with expert knowledge, to obtain a better picture of the completeness of the inventory in tropical ecosystems.
Magazine:
CONSERVATION BIOLOGY
ISSN:
0888-8892
Year:
2015
Vol:
29
N°:
2
Pp:
599 - 601
Magazine:
BIODIVERSITY AND CONSERVATION
ISSN:
0960-3115
Year:
2014
Vol:
23
N°:
9
Pp:
2239 - 2258
The knowledge of species occurrence within an area is crucial to develop proper conservation strategies to protect species diversity. Biosphere Reserves (BRs), established to preserve biodiversity and sustainably use their resources, should therefore have precise information of its biodiversity. We compared and evaluated information on threatened and non-threatened vertebrate species available for Spanish BRs from three sources: management documents (MDs), the Global Biodiversity Information Facility index (GBIF), and atlases and network books. Our results suggest that information from any one source was rather partial, to a degree that depended on which vertebrate group was considered. Management documents did list a high percentage of threatened species found in BRs, reaching up to the total number of species of birds and mammals. Species lists overlap between all three sources ranged from 59 % for fish to 84 % for mammals. In addition, there is an inconsistency between national and international threatened species categories and it should thus call for revisions. Even though the information of non-threatened and threatened species occurrence in MDs of Spanish BRs is good, it is necessary to pay attention to amphibian and fish species which are less recorded.
Magazine:
ZOOKEYS
ISSN:
1313-2989
Year:
2014
N°:
403
Pp:
67 - 109
The state of Hidalgo (Mexico) is an important region from the point of view of biodiversity. However, there exists a significant gap in accessible knowledge about species diversity and distribution, especially regarding to freshwater ecosystems. This dataset comprises the sampling records of two projects developed in Hidalgo between 2007 and 2009 about the freshwater fish communities of Tecocomulco lake and rivers belonging to the Metztitlan Canyon Biosphere Reserve. It contains the taxonomic identity (species level) and basic biometric data (total length and weight) as well as date of collection and coordinates of more than 9000 specimens. This dataset is the primary result of the first and unrepeated exhaustive freshwater fish's survey of Metztitlan Canyon Biosphere Reserve and Tecocomulco lake. It incorporates seven more species to the regional fish fauna, and new exclusive biometric data of ten species. This dataset can be used by studies dealing with, among other interests, North American freshwater fish diversity (species richness, distribution patterns) and biometric analyses, useful for the management and conservation of these areas. The complete dataset is also provided in Darwin Core Archive format.
Magazine:
BIOLOGICAL CONSERVATION
ISSN:
0006-3207
Year:
2014
Vol:
173
Pgs:
74 - 79
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.
Magazine:
PLoS One
ISSN:
1932-6203
Year:
2013
Vol:
8
N°:
1
Pp:
1 - 15
Magazine:
BIODIVERSITY INFORMATICS
ISSN:
1546-9735
Year:
2013
Vol:
8
N°:
2
Pp:
59 - 93
A Content Needs Assessment (CNA) survey has been conducted in order to determine what GBIF-mediated data users may be using, what they would be using if available, and what they need in terms of primary biodiversity data records. The survey was launched in 2009 in six languages, and collected more than 700 individual responses. Analysis of the responses showed some lack of awareness about the availability of accessible primary data, and pointed out some types of data in high demand for linking to distribution and taxonomic data now derived from the GBIF cache. A B example was linkages to molecular data. Also, the CNA survey uncovered some biases in the design of user needs surveys, by showing demographic and linguistic effects that may have influenced the distribution of responses received in analogous surveys conducted at the global scale.
Magazine:
BIODIVERSITY INFORMATICS
ISSN:
1546-9735
Year:
2013
Vol:
8
N°:
2
Pp:
41 - 58
Freely available high quality, data on species occurrence and associated variables are needed in order to track changes in biodiversity. One of the main issues surrounding the provision of such data is that sources vary in quality, scope, and accuracy. Publishers of such data must face the challenge of maximizing quality, utility and breadth of data coverage, in order to make such data useful to users. With the Global Biodiversity Information Facility (GBIF), we recently conducted a content needs assessment survey to consolidate and synthesize major user needs regarding biodiversity data. We find a broad range of recommendations from the survey respondents, principally concerning issues such as data quality, bias, and coverage, and ease of access. We recommend a candidate set of actions for the GBIF that fall into three classes: 1) addressing data gaps, data volume, and data quality, 2) aggregating data types that are relatively new to GBIF, to support emerging new applications, and 3) promoting ease-of-use and providing incentives for wider use. Addressing the challenge of providing high quality primary biodiversity data potentially can serve the needs of national and international biodiversity initiatives. These include the ¿flexible framework¿ for addressing the new 2020 biodiversity targets of the Convention on Biological Diversity, the global biodiversity observation network (GEO BON) and the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services.
Magazine:
BIODIVERSITY INFORMATICS
ISSN:
1546-9735
Year:
2013
Vol:
8
N°:
2
Pp:
94 - 172
With the establishment of the Global Biodiversity Information Facility (GBIF) in 2001 as an inter-governmental coordinating body, concerted efforts have been made during the past decade to establish a global research infrastructure to facilitate the publishing, discovery, and access to primary biodiversity data. The participants in GBIF have enabled the access to over 377 million records of such data as of August 2012. This is a remarkable achievement involving efforts at national, regional and global levels in multiple areas such as data digitization, standardization and exchange protocols. However concerns about the quality and `fitness for use¿ of the data mobilized in particular for the scientific communities have grown over the years and must now be carefully considered in future developments. This paper is the first comprehensive assessment of the content mobilised so far through GBIF, as well as a reflexion on possible strategies to improve its `fitness for use¿. The methodology builds on complementary approaches adopted by the GBIF Secretariat and the University of Navarra for the development of comprehensive content assessment methodologies. The outcome of this collaborative research demonstrates the immense value of the GBIF mobilized data and its potential for the scientific communities. Recommendations are provided to the GBIF community to improve the quality of the data published as well as priorities for future data mobilization.
Magazine:
BIODIVERSITY INFORMATICS
ISSN:
1546-9735
Year:
2013
Vol:
8
N°:
2
Pp:
173 - 184
There are more than 267 million primary biodiversity data records published by hundreds of data publishers through the GBIF network. Thus, GBIF network is the single most comprehensive index for this kind of data. Ensuring or, at least, assessing data quality is of capital importance for the reliability and usability of this data. While conducting a time data gap analysis on this mass of data, we have detected some issues with the way date information is processed and shared. Dates can be obscured or altered under certain circumstances, when a specific combination of publisher¿s error or date handling features, and faulty or inadequate date parsing and processing routines gets chained together. The extent of the date unreliability (either at the source or through GBIF portal) is not high, and further it is concentrated in a few data publishers. We analyse the types of errors and misprocessing in dates through the sources and the published records; assess their impact on the overall data quality of the published index, and suggest corrective measures.
Magazine:
BIOINFORMATICS
ISSN:
1367-4803
Year:
2012
Vol:
28
N°:
16
Pp:
2207-2208
In any data quality workflow, data publishers must become aware of issues in their data so these can be corrected. User feedback mechanisms provide one avenue, while global assessments of datasets provide another. To date, there is no publicly available tool to allow both biodiversity data institutions sharing their data through the Global Biodiversity Information Facility network and its potential users to assess datasets as a whole. Contributing to bridge this gap both for publishers and users, we introduce BIoDiversity DataSets Assessment Tool, an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.
Magazine:
ENVIRONMENTAL ENGINEERING AND MANAGEMENT JOURNAL
ISSN:
1582-9596
Year:
2012
Vol:
11
N°:
6
Pp:
1159 - 1169
Mites and springtails are important members of soil mesofauna and have been proven to be good bioindicators of airborne
pollutants. We studied the surrounding area of a steel mill located in a mountain valley of North Spain. Previous studies had
documented the existence of a pollution gradient in this area due to the emissions of the factory, thus providing an interesting site
to investigate the potential effects of pollutants (heavy metals and nitrogen) on soil biodiversity.
The density of Acari and Collembola significantly decreased with the increase in concentration of Cr, Mn, Zn, Cd and Pb. Mites
appeared to be more sensitive to heavy metal pollution than springtails. Likewise, the density of these microarthropoda was lower
in those soils exhibiting higher nitrogen content.
The species composition of the community of Acari and Collembola changed according to heavy metal pollution. Significant
differences in abundance, species richness and diversity were observed between the communities of the sampling sites. Some
species were exclusive of the less polluted sites, while others appeared in the most contaminated ones. This different response of
soil mesofauna to pollutants suggests that some mite or springtail species could be used as bioindicators of heavy metal pollution.
Magazine:
Environmental Engineering and Management Journal
ISSN:
1582-9596
Year:
2012
Vol:
11
N°:
6
Pp:
1059 - 1075
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.
Magazine:
Environmental Engineering and Management Journal
ISSN:
1582-9596
Year:
2012
Vol:
11
N°:
6
Pp:
1133 - 1140
The establishment of protected areas is one of the main tools used for biodiversity conservation, one of the components of environmental management. Although the theoretical framework for protected areas has been long known and discussed, there are few data about their practical effectiveness as a means to preserve biodiversity. Through the analysis of information from the Global Biodiversity Information Facility (GBIF), we have looked for any relationship between the protection status and the general species richness (i.e., number of all living species, taken as a surrogate for biodiversity) in the Spanish Pyrenees. We found that higher protection levels were associated to higher richness of non-endangered species. However, additional reliability tests have shown that for endangered species, the amount of currently available data may still be insufficient for effective management. To avoid this lack of reliability, enhancing public access to biodiversity data or improving sampling effort is mandatory.
Magazine:
ANALES DEL SISTEMA SANITARIO DE NAVARRA
ISSN:
1137-6627
Year:
2012
Vol:
35
N°:
1
Pp:
185 - 186
Magazine:
Environmental Engineering and Management Journal
ISSN:
1582-9596
Year:
2012
Vol:
11
N°:
6
Pp:
1171 - 1178
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 road-kill, while homogeneous agricultural and human landscapes increased road-kill rates.
Magazine:
Journal of Fish Biology
ISSN:
0022-1112
Year:
2011
Vol:
79
N°:
6
Pp:
1563 - 1591
Magazine:
THE FINNISH ENVIRONMENT
ISSN:
1238-7312
Year:
2011
N°:
18
Págs:
53 - 57
Magazine:
B M C Bioinformatics-(BioMed Central Ltd.)
ISSN:
1471-2105
Year:
2011
Vol:
12
N°:
Suppl 15
Pp:
S4
Magazine:
BIODIVERSITY INFORMATICS
ISSN:
1546-9735
Year:
2010
Vol:
7
N°:
2
Pp:
81 - 92
This contribution explores the problem of recognizing and measuring the universe of specimen-level data existing in natural history collections around the world, and in absence of a complete, world-wide census or register. Estimates of size seem necessary to plan for resource allocation for digitization or data capture, and may help to represent how many vouchered primary biodiversity data (in terms of collections, specimens or curatorial units) might remain to be mobilized. It further helps to set priorities, and assess certainties.
Three general approaches are proposed for further development, and initial estimates are given. Probabilistic models involve crossing data from a set of biodiversity datasets, finding commonalities and estimating the likelihood of totally obscure data from the fraction of known data missing from specific datasets in the set. Distribution models aim to find the underlying distribution of collections¿ compositions, estimating the hidden sector of the distributions. Finally, case studies seek to compare digitized data from collections known to the world to the amount of data known to exist in the collection but not generally available or not digitized.
Preliminary estimates of size range from 1.2 to 2.1 gigaunits (109) of which a mere 3% at most is currently web-accessible through GBIF¿s mobilization efforts. However, further data and analyses, along with other approaches relying more heavily on surveys, might change the picture and possibly help to narrow the estimate further. In particular, unknown collections not having emerged through literature are the major source of uncertainty.
Magazine:
Revista de Museologia
ISSN:
1134-0576
Year:
2010
Vol:
48
Ppgs:
94 - 105
