Georeferenced biological data of species distributions, abundances or traits are critical for ecological and evolutionary research. However, the accuracy (true vs. false records) and biogeographical ...status (native vs. alien) of individual georeferenced records are often unclear, which limits their use in species distribution modelling, analyses of biodiversity change and other applications.
Here, we introduced bRacatus, a new method and R package to estimate a given georeferenced record's probability of being true or false and of corresponding to a native or an alien occurrence. Our framework avoided artificial thresholds of data filtering and instead implemented a probabilistic framework which allowed propagating uncertainties in subsequent analyses. We trained and tested our method on 400 terrestrial species of amphibians, birds, terrestrial mammals and vascular plants from four continents.
bRacatus showed good predictive power (mean AUC higher than 0.9; mean RMSE lower than 0.3) for both the accuracy and biogeographical status. Model performance was similar among continents, range sizes and taxa not used in the training. Tests were robust using either range maps or regional checklists of differing levels of data completeness as reference regions.
bRacatus was implemented as a user‐friendly R package that enabled researchers to assess the accuracy and biogeographical status of species occurrences, population abundances, community composition or any other type of georeferenced biodiversity records. We proposed this method as a routine step in addressing the inherent uncertainty of point observations to promote more accurate ecological inference and predictions.
Resumo
Dados biológicos georreferenciados de distribuições, abundâncias ou características das espécies são fundamentais para pesquisas em ecologia e evolução. No entanto, a acurácia (registros verdadeiros vs. falsos) e o status biogeográfico (nativo vs. exótico) de registros individuais georreferenciados são frequentemente obscuros, o que limita seu uso em modelagem de distribuição de espécies, análises de mudança de biodiversidade e outras aplicações.
Neste trabalho, apresentamos bRacatus, um novo método e pacote R para estimar a probabilidade de um dado registro georreferenciado de ser verdadeiro ou falso e de corresponder a uma ocorrência nativa ou exótica. Nossa estrutura evita limiares artificiais de filtragem de dados e, alternativamente, implementa uma estrutura probabilística que permite a propagação de incertezas em análises subsequentes. Treinamos e testamos nosso método em 400 espécies terrestres de anfíbios, pássaros, mamíferos terrestres e plantas vasculares de quatro continentes.
bRacatus mostrou bom poder preditivo (AUC média superior a 0,9; RMSE médio inferior a 0,3) para acurácia e status biogeográfico. O desempenho do modelo foi semelhante entre os continentes, tamanhos de área de distribuição, e taxa não usados no treinamento. Os testes foram robustos usando mapas de distribuição ou checklists regionais em diferentes níveis de completude de dados como regiões de referência.
bRacatus está implementado em um pacote R acessível que permite aos pesquisadores avaliar a acurácia e o status biogeográfico de ocorrências de espécies, abundâncias populacionais, composição de comunidades ou qualquer outro tipo de registro de biodiversidade georreferenciado. Propomos este método como uma etapa de rotina para abordar a incerteza inerente a observações de pontos para promover inferência ecológica e predições mais precisas.
Ecological Niche Models (ENMs) are often used to project species distributions within alien ranges and in future climatic scenarios. However, ENMs depend on species‐environment equilibrium, which may ...be absent for actively expanding species. We present a novel framework to estimate whether species have reached environmental equilibrium in their native and alien ranges. The method is based on the estimation of niche breadth with the accumulation of species occurrences. An asymptote will indicate exhaustive knowledge of the realised niches. We demonstrate the CNA framework for 26 species of mammals, amphibians, and birds. Possible outcomes of the framework include: (1) There is enough data to quantify the native and alien realised niches, allowing us to calculate niche expansion between the native and alien ranges, also indicating that ENMs can be reliably projected to new environmental conditions. (2) The data in the native range is not adequate but an asymptote is reached in the alien realised niche, indicating low confidence in our ability to evaluate niche expansion in the alien range but high confidence in model projections to new environmental conditions within the alien range. (3) There is enough data to quantify the native realised niche, but not enough knowledge about the alien realised niche, hindering the reliability of projections beyond sampled conditions. (4) Both the native and alien ranges do not reach an asymptote, and thus few robust conclusions about the species’ niche or future projections can be made. Our framework can be used to detect species’ environmental equilibrium in both the native and alien ranges, to quantify changes in the realised niche during the invasion processes, and to estimate the likely accuracy of model projections to new environmental conditions.
The Cumulative Niche Approach: a novel framework to estimate the predictive power of Ecological Niche Model projections. Our theoretical framework allows to quantify changes in the realised niche during invasion processes and to estimate the likely accuracy of model projections to new environmental conditions.
Bird ring‐recovery data have been widely used to estimate demographic parameters such as survival probabilities since the mid‐20th century. However, while the total number of birds ringed each year ...is usually known, historical information on age at ringing is often not available. A standard ring‐recovery model, for which information on age at ringing is required, cannot be used when historical data are incomplete. We develop a new model to estimate age‐dependent survival probabilities from such historical data when age at ringing is not recorded; we call this the historical data model. This new model provides an extension to the model of Robinson, 2010, Ibis, 152, 651–795 by estimating the proportion of the ringed birds marked as juveniles as an additional parameter. We conduct a simulation study to examine the performance of the historical data model and compare it with other models including the standard and conditional ring‐recovery models. Simulation studies show that the approach of Robinson, 2010, Ibis, 152, 651–795 can cause bias in parameter estimates. In contrast, the historical data model yields similar parameter estimates to the standard model. Parameter redundancy results show that the newly developed historical data model is comparable to the standard ring‐recovery model, in terms of which parameters can be estimated, and has fewer identifiability issues than the conditional model. We illustrate the new proposed model using Blackbird and Sandwich Tern data. The new historical data model allows us to make full use of historical data and estimate the same parameters as the standard model with incomplete data, and in doing so, detect potential changes in demographic parameters further back in time.
A method to estimate age‐specific survival of fledged birds when age at ringing is known only for birds later recovered.
This study investigated the impact of struvite as a sustainable phosphorus source on the growth and phycocyanin production by the blue-green alga
Arthrospira platensis
. Three modified growth media ...were compared to the typical SAG-spirul culture media. CS(+) refers to the completely recycled struvite from bovine urine as a phosphate source, while S(-) and S(+) refer to commercially available struvite as a phosphate source. On media with (+), a pre-treatment was conducted to evaporate NH
4
, as it negatively affects cell growth and functions of the photosynthetic apparatus at high concentrations, and to release phosphate due to the low solubility of struvite in water. For each medium, three cultures were cultivated in Erlenmeyer flasks for a duration of 42 days. Results showed that no statistically significant negative effect of struvite was found on the growth rates. However, C-phycocyanin (CPC-P) in CS(+) and S(+) was significantly higher compared to CPC-P in untreated growth media. The study hypothesized that low concentrations of NH
3
remaining after the pre-treatment of struvite could have a positive impact on phycocyanin accumulation, as an energy efficient and quick nitrogen source for
A. platensis
.
Desertion of offspring before its independence by one of the parents is observed in a number of avian species with bi-parental care but reasons for this strategy are not fully understood. This ...behaviour is particularly intriguing in species where bi-parental care is crucial to raise the brood successfully. Here, we focus on the little auk, Alle alle, a small seabird with intensive bi-parental care, where the female deserts the brood at the end of the chick rearing period. The little auk example is interesting as most hypotheses to explain desertion of the brood by females (e.g. “re-mating hypothesis”, “body condition hypothesis”) havebeenrejectedfor this species. Here, we analysed a possible relationship between the duration of female parental care over the chick and her chances to survive to the next breeding season. We performed the study in two breeding colonies on Spitsbergen with different foraging conditions – more favourable in Hornsund and less favourable in Magdalenefjorden. We predicted that in Hornsund females would stay for shorter periods of time with the brood and would have higher survival rates in comparison with birds from Magdalenefjorden. We found that indeed in less favourable conditions of Magdalenefjorden, females stay longer with the brood than in the more favourable conditions of Hornsund. Moreover, female survival was negatively affected by the length of stay in the brood. Nevertheless, duration of female parental care over the chick was not related to their parental efforts, earlier in the chick rearing period, and survival of males and females was similar. Thus, although females brood desertion and winter survival are linked, the relationship is not straightforward.
To mitigate biodiversity loss, we need to understand the environmental and demographic causes of changes in the distributions and abundances of species. Bird populations are in a continual state of ...flux; these fluctuations can be explained by changes in vital rates, such as survival and productivity (breeding success).This thesis is the result of three different ecological projects for which we have developed statistical methods that combine different types of data together. In particular, in this thesis we describe, implement, and develop statistical models that can be applied to different types of ecological data such as census, ring-recovery, and capture-recapture data.In the first project we use data from the British Trust for Ornithology (BTO), which has developed an extensive historical data set of the total number of birds ringed in Britain and Ireland, dating back to 1909. However, until 2000 the data were submitted by ringers in paper form. The way in which such archival data were collected and stored means that the total number of birds ringed in different age categories is difficult to obtain. Bird survival changes with age, with younger birds being more vulnerable. Missing information on the age at ringing compromises our ability to understand historic variation in survival rates. We examine suitable methods and propose a new model for enhancing the use of such data. Using blackbird (Turdus merula) and sandwich tern (Thalasseus sandvicensis) data we show the rigour of our model in estimating unknown age proportions for different species, allowing the BTO and other European institutions to fully utilise their historical data.Bi-parental care is crucial in the reproduction success of the little auk (Alle alle) which we study in the second project. For this species, typically, the female deserts the brood before the male does. Hypotheses which considered that females left the nest earlier in order to increase their remating success or to secure their good body conditions have been rejected. As a result, a biological explanation for this unusual trait has not been found yet. We investigate whether the length of time that females stay in the nest in a given breeding season may have an impact on their survival probability in the period following breeding. We combine capture-recapture data from two sites and use sparse continuous covariates data to study if the survival of the female little auk is affected by the time spent in the brood guarding the chicks.Animals are affected by local environmental conditions that vary with space. In the third project, we incorporate detailed local spatial information, such as geographical coordinates and land cover type data, into an spatially-explicit integrated population model. This involves supplementing census data with ring-recovery data to study demographic rates, while also incorporating detailed local spatial information into integrated population models. Bird count data are typically modelled at large scales using state-space models. In classical analysis, the time-series likelihood component has traditionally been approximated using a Kalman filter methodology, which is computationally efficient but relies on the assumption of the suitability of Gaussian approximations.Rather than one single nation-wide time-series of counts, spatial census data consist of multiple time-series associated to specific locations. These data are particularly challenging to model because of the presence of very small counts at some locations, which violates the Gaussian assumption of the Kalman filter. To address this issue, we consider hidden Markov models, which are ideally suited to the analysis of very small counts, as their validity does not rely on Gaussian approximations. Both methodologies, the Kalman filter and hidden Markov models, are combined in a flexible algorithm which adapts to the varying sample sizes at different locations-it is therefore able to accommodate data sets of different sizes for many bird species. We illustrate our methods using starling (Sturnus vulgaris) data.
The olive moth, Prays oleae, is one of the most common insects that damages olives in the Mediterranean region. The establishment of ground cover within olive orchards has been promoted in this ...region in recent years to avoid erosion and soil degradation. Nevertheless, its role as a shelter for natural enemies of pests has been controversial. In this study, we have investigated the effectiveness of the biological control of P. oleae in organic olive orchards with ground cover (mowed) and without ground cover (tilled). For this, (1) we assessed the relationship between predated eggs and the abundance of natural enemies in both types of orchards; (2) we compared both the potential damage of the pest and the egg hatching in the two types of orchards; and (3) we examined the interaction amongst families of natural enemies and P. oleae (as adults and as predated eggs). The results showed that there is a high rate of predation in the studied olive orchards, 81% of the eggs were predated, 12.2% hatched, and 6.9% were live eggs. However, mowed orchards were more effective for controlling P. oleae by means of egg predation rather than tilled orchards, i.e., in mowed orchards, whilst the potential damage of the pest was higher, egg hatching was rather low. The structure of the adult arthropod community, i.e., the composition and abundance of families of natural enemies did not differ between the orchards, but the abundance of the families Anthocoridae, Miridae and Scelionidae was significantly higher in the mowed orchards. Finally, the interaction amongst natural enemies and P. oleae showed that the families that better explained the effects on egg predation were Aeolothripidae, Anthocoridae, Miridae, Chrysopidae (predators), and Formicidae (omnivore). We discuss the results in terms of ecological interactions of trophic guilds and we conclude that the establishment and maintenance of ground cover in organic olive orchards, at least in June and July, is of great significance because it positively affects the egg predation of P. oleae. This effect is especially significant when there is a low abundance of natural enemies in the olive orchards.
•Ground cover positively affects the egg predation of Prays oleae.•The relationship amongst natural enemy and egg predation of P. oleae is enhanced in mowed orchards.•Natural enemies do not tend to differ between mowed and tilled organic orchards.•Ground cover could produce more active and voracious predators rather than their high abundance.
To provide an overview on the current use of belimumab (BLM) in SLE patients in clinical practice and to examine its efficacy in terms of standardized outcomes, drug survival, as well as patient and ...safety profiles.
A longitudinal retrospective multicentre cohort including SLE patients treated with BLM at 18 Spanish centers. Data was collected upon initiation of BLM, at 6 and 12 months after initiation, and at the last recorded visit. Changes in SLEDAI-2K, the proportion of patients who achieved LLDAS and DORIS 2021, and number of flares were compared between visits. Changes in damage, glucocorticoids use and employment status pre-BLM and post-BLM were also assessed.
A total of 324 patients were included with a mean follow-up of 3.8 (±2.7) years. LLDAS was attained by 45.8%, 62% and 71% of patients, and DORIS by 24%, 36.2% and 52.5% on successive visits, respectively. Twenty-seven-point two percent of patients were in DORIS ≥ 50% of the visits and a 46% in LLDAS-50. Flares and number of flares were significantly lower one year after treatment with BLM and no changes in damage accrual were observed. Mean (±SD) prednisone dose was significantly reduced over time, with 70 (24%) patients discontinuing GC.
Our study not only demonstrates belimumab´s efficacy in attaining treat-to-target goals in SLE patients, but also confirms its GC-sparing effect, and its prevention of flares and organ damage accrual.
Fluoropyrimidine-radiosensitizing agents in conjunction with preoperative radiotherapy have proven to induce tumor and nodal downstaging effects, sphincter preservation promotion, and mid-term ...favorable survival rates. Intraoperative electron beam radiation therapy may improve pelvic control in patients with locally advanced rectal cancer stages. Potential predictive factors for response and disease-free survival, with intense local multidisciplinary approach, are analyzed.
One hundred fifteen patients with rectal cancer were treated with oral 5-fluorouracil or Tegafur with preoperative radiotherapy, surgery, and intraoperative electron beam radiation therapy to identify potential pre- and on-treatment characteristics that might be of prognostic value for disease outcome. Univariate and multivariate analyses were performed.
Older patients and those treated with Tegafur were more likely to achieve a major histologic response, categorized as persistence of minimal residual microscopic disease foci in the surgical specimen ("mic" response). Factors unfavorably associated with disease-free survival in the multivariate model were male gender and persistence of macroscopic disease in the rectal wall ("mac" response). Accordingly, 3-year disease-free survival rates in the groups of patients with 0, 1, or 2 of these risk factors were 100%, 81%, and 53%, respectively (p < 0.001).
Females with an intense pathologic response (pT(mic) residue) to preoperative chemoradiotherapy have an excellent 3-year disease-free survival. This information might be of interest for stratification of patients in the development of adjuvant treatment trials.
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