Misidentification errors in reencounters result in biased estimates of survival probability from CJS models: Evidence and a solution using the robust design

Misidentification of marked individuals is unavoidable in most studies of wild animal populations. Models commonly used for the estimation of survival from such capture–recapture data ignore misidentification errors potentially resulting in biased parameter estimates. With a simulation study, we show that ignoring misidentification in Cormack–Jolly–Seber (CJS) models results in systematic positive biases in the estimates of survival and in spurious declines of survival over time. We developed an extended robust design capture mark–resight (RDM) model that includes correct identification parameters to get unbiased survival estimates when resighting histories are prone to misidentification. The model assumes that resightings occur repeatedly within a season, which in practice is often the case when resightings of colour-marked individuals are collected. We implemented the RDM model in a state-space formulation and also an approximate, but computationally faster, model (RDMa) in JAGS and evaluated their performances using simulated and empirical capture–resight data on black-tailed godwits Limosa limosa. The CJS models applied to simulated data under an imperfect identification scenario data produced strongly positively biased estimates of survival. For a range of degrees of correct identification probabilities, the RDM model provided unbiased and accurate estimates of survival, reencounter and correct-identification probabilities. The RDMa model performed well for large datasets (>25 individuals), with high resighting (>0.3) and high correct identification (>0.7) probabilities. For the empirical data, the CJS model estimated average juvenile survival at 0.997% and adult survival at 0.939% and also detected a strong decline in adult survival over time at a rate of −0.14 ± 0.029. In contrast, the RDMa model estimated a probability of correct identification of 0.94, annual juvenile survival at 0.234%, adult at 0.834% and less strong decline over time (−0.046 ± 0.016). We conclude that estimates of survival probabilities obtained from data that include misidentification errors and analysed with standard CJS model are unlikely to be correct. The bias in survival increases with the magnitude of misidentification errors, which is inevitable as datasets become longer. Since misidentification due to tag misreads is common in empirical data, we recommend the use of the here presented RDM model to provide unbiased parameter estimates

A hidden Markov model for reconstructing animal paths from solar geolocation loggers using templates for light intensity

Background Solar archival tags (henceforth called geolocators) are tracking devices deployed on animals to reconstruct their long-distance movements on the basis of locations inferred post hoc with reference to the geographical and seasonal variations in the timing and speeds of sunrise and sunset. The increased use of geolocators has created a need for analytical tools to produce accurate and objective estimates of migration routes that are explicit in their uncertainty about the position estimates. Results We developed a hidden Markov chain model for the analysis of geolocator data. This model estimates tracks for animals with complex migratory behaviour by combining: (1) a shading-insensitive, template-fit physical model, (2) an uncorrelated random walk movement model that includes migratory and sedentary behavioural states, and (3) spatially explicit behavioural masks. The model is implemented in a specially developed open source R package FLightR. We used the particle filter (PF) algorithm to provide relatively fast model posterior computation. We illustrate our modelling approach with analysis of simulated data for stationary tags and of real tracks of both a tree swallow Tachycineta bicolor migrating along the east and a golden-crowned sparrow Zonotrichia atricapilla migrating along the west coast of North America. Conclusions We provide a model that increases accuracy in analyses of noisy data and movements of animals with complicated migration behaviour. It provides posterior distributions for the positions of animals, their behavioural states (e.g., migrating or sedentary), and distance and direction of movement. Our approach allows biologists to estimate locations of animals with complex migratory behaviour based on raw light data. This model advances the current methods for estimating migration tracks from solar geolocation, and will benefit a fast-growing number of tracking studies with this technology

Kronična opstruktivna plućna bolest i red: retrospektiva istraživanja provedenog na kohorti industrijskih radnika

The aim of this paper was to ascertain chronic obstructive pulmonary disease (COPD) prevalence among industrial workers in the Russian Federation and determine relative contribution of smoking and occupational factors to COPD. We recruited 1,375 workers aged 30 or over. Six hundred and twenty-four of them were occupationally exposed to vapours, gases, dust, and fumes (VGDF). Physical examination and baseline spirometry were performed for all the participants of the study. Those with airfl ow limitation of FEV1/FVC<0.70 were considered having COPD and those with presence of cough and sputum production for at least three months in each of two consecutive years were considered having chronic bronchitis (CB), with no overlapping between these 2 groups. Data on occupational history and VGDF levels in the working area were collected from all participants. In total, 105 cases of COPD and 170 cases of CB were diagnosed in the cohort of examined workers. Occupational exposure to VGDF was twice as often present among COPD patients than among both patients with CB and the control group of healthy workers (p<0.05). More than 40 % of COPD patients were occupationally exposed to VGDF above the value of 3.0 of the occupational exposure limit (OEL) and more than 20 % to 6.0 OEL and higher. Overall odds ratio for COPD development due to occupational VGDF exposure was 5.9 (95 % CI=3.6 to 9.8, p=0.0001). Both smoking and VGDF seem to be important for the development of COPD. Analysis of the combined effect of tobacco smoking and occupational noxious particles and gases on COPD development has shown the following order of risk factors based on the strength of their infl uence: VGDF levels, smoking index, age, and heating microclimate. There is a statistically signifi cant level of relationship and “dose-effect” dependence between occupational exposures to VGDF and the development of COPD. The effect of VGDF composition on the probability of COPD development was not found in the study. Results of this study were used to substantiate the inclusion of COPD into the National List of Occupational Diseases of the Russian Federation.Cilj ovog rada bio je potvrditi prevalenciju kronične opstruktivne plućne bolesti (engl. chronic obstructive pulmonary disease, COPD) među industrijskim radnicima u Ruskoj Federaciji i utvrditi relativni doprinos pušenja i profesionalnih čimbenika razvoju COPD-a. Odabrali smo 1.375 radnika u dobi od 30 godina i starijih. Šeststo dvadeset i četiri radnika bila su izložena parama, plinovima, prašini i dimovima (engl. vapours, gases, dust, and fumes – VGDF) na radu. Svi su radnici bili podvrgnuti fi zičkom pregledu i temeljnoj spirometriji. Za radnike koji su imali smanjen protok zraka (FEV1/FVC<0,70) smatralo se da imaju COPD, a za one koji su imali kašalj i pojačan sputum barem 3 mjeseca tijekom dvije uzastopne godine smatralo se da boluju od kroničnog bronhitisa (CB). Između ove dvije skupine nije bilo preklapanja. Od svih su sudionika prikupljeni podaci o radnoj anamnezi i razinama izloženosti VGDF-u na radu. Profesionalna izloženost VGDF-u bila je dvostruko češće prisutna kod radnika s COPD-om nego kod radnika s CB-om i kod kontrolne skupine zdravih radnika (p<0,05). Više od 40 % bolesnika s COPD-om bilo je profesionalno izloženo VGDF-u iznad 3,0 OEL (engl. occupational exposure limit – granica profesionalne izloženosti), a više od 20 % granici od 6,0 OEL i više. Ukupni omjer izgleda (engl. odds ratio – OR) za razvoj KOPB-a zbog izloženosti VGDF-u bio je 5,9 (95 %-tni CI=3,6 do 9,8; p=0,0001). Čini se da su i pušenje i VGDF važni za razvoj COPD-a. Analiza sjedinjenog učinka pušenja i profesionalne izloženosti štetnim česticama i plinovima na razvoj COPD-a pokazala je ovakav redoslijed čimbenika rizika prema jačini njihova utjecaja: razine VGDF-a, indeks pušenja, dob i mikroklima grijanja. Postoji statistički značajna veza i ovisnost „doza-učinak“ između profesionalne izloženosti VGDF-u i KOPB-a. Utjecaj sastava VGDF-a na vjerojatnost razvoja COPD-a nije utvrđen u istraživanju. Rezultati ovog rada potvrdili su potrebu uvrštavanja COPD-a u Nacionalni popis profesionalnih bolesti Ruske Federacije

Publisher Correction:Fuelling conditions at staging sites can mitigate Arctic warming effects in a migratory bird (Nature Communications, (2018), 9, 1, (4263), 10.1038/s41467-018-06673-5)

In the original HTML version of this Article, the order of authors within the author list was incorrect. The consortium VRS Castricum was incorrectly listed after Theunis Piersma and should have been listed after Cornelis J. Camphuysen. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication

Real and virtual photons in an external constant electromagnetic field of most general form

The photon behavior in an arbitrary superposition of constant magnetic and electric fields is considered on most general grounds basing on the first principles like Lorentz- gauge- charge- and parity-invariance. We make model- and approximation-independent, but still rather informative, statements about the behavior that the requirement of causal propagation prescribes to massive and massless branches of dispersion curves, and describe the way the eigenmodes are polarized. We find, as a consequence of Hermiticity in the transparency domain, that adding a smaller electric field to a strong magnetic field in parallel to the latter causes enhancement of birefringence. We find the magnetic field produced by a point electric charge far from it (a manifestation of magneto-electric phenomenon). We establish degeneracies of the polarization tensor that (under special kinematic conditions) occur due to space-time symmetries of the vacuum left after the external field is imposed.Comment: 30 pages, 1 figure, 57 equations, reference list of 38 item

Fuelling conditions at staging sites can mitigate Arctic warming effects in a migratory bird

Under climate warming, migratory birds should align reproduction dates with advancing plant and arthropod phenology. To arrive on the breeding grounds earlier, migrants may speed up spring migration by curtailing the time spent en route, possibly at the cost of decreased survival rates. Based on a decades-long series of observations along an entire flyway, we show that when refuelling time is limited, variation in food abundance in the spring staging area affects fitness. Bar-tailed godwits migrating from West Africa to the Siberian Arctic reduce refuelling time at their European staging site and thus maintain a close match between breeding and tundra phenology. Annual survival probability decreases with shorter refuelling times, but correlates positively with refuelling rate, which in turn is correlated with food abundance in the staging area. This chain of effects implies that conditions in the temperate zone determine the ability of godwits to cope with climate-related changes in the Arctic

FLightR:An R package for reconstructing animal paths from solar geolocation loggers

1. Solar geolocators are relatively cheap and simple tools which are widely used to study the migration of animals,especially birds. The methods to estimate the geographic positions from the light-intensity patterns collectedby these loggers, however, are still under development.2. The accurate reconstruction of the annual schedules and movement patterns of individual animals requiresanalytical methods which provide estimates of daily locations, distances between the locations and the directionsof movement, withmeasures of their uncertainty.3. The new R package FLIGHTRmeets all these requirements. It enables refined and statistically validated estimationsof movement patterns of birds. Here, we present main features of this advanced package

Advancing Agricultural Crop Recognition: The Application of LSTM Networks and Spatial Generalization in Satellite Data Analysis

This study addresses the challenge of accurate crop detection using satellite data, focusing on the application of Long Short-Term Memory (LSTM) networks. The research employs a “spatial generalization” approach, where a model trained on one geographic area is applied to another area with similar vegetation conditions during the growing season. LSTM networks, which are capable of learning long-term temporal dependencies, are used to overcome the limitations of traditional machine learning techniques. The results indicate that LSTM networks, although more computationally expensive, provide a more accurate solution for crop recognition compared with other methods such as Multilayer Perceptron (MLP) and Random Forest algorithms. The accuracy of LSTM networks was found to be 93.7%, which is significantly higher than the other methods. Furthermore, the study showed a high correlation between the real and model areas of arable land occupied by different crops in the municipalities of the study area. The main conclusion of this research is that LSTM networks, combined with a spatial generalization approach, hold great promise for future agricultural applications, providing a more efficient and accurate tool for crop recognition, even in the face of limited training data and complex environmental variables

Supplementary Materials to: Annual chronotypes functionally link life histories and life cycles in birds

Life‐history responses to ecological selection pressures can be described by a slow–fast life‐history axis. Along this axis, fast‐living animals usually invest in high breeding output, whereas slow‐living ones prioritize their own survival. Birds may solve the trade‐off between reproduction and survival by optimizing their seasonal schedules. Breeding early tends to facilitate reproductive success, whereas breeding late increases the chances to survive. On the basis of this argument, short‐ and long‐lived birds should benefit from initiating spring activities earlier and later, respectively. The timing of seasonal activities, all else being equal, depends on the architecture of endogenous circannual clocks. Particularly, the length of the circannual period relative to the 365‐day environmental year either facilitates the anticipation of seasonal activities (in case of periods shorter than 365 days) or represents a responsive mode (when periods are longer than 365 days). The two alternatives will be manifested by early or late annual chronotypes, respectively. We hypothesize that in birds, annual chronotype will correspond with position on the “pace‐of‐life scale.” Species with low survival probability, and thus a poor chance of breeding in a next season, should show early annual chronotypes facilitated by circannual‐clock periods shorter than 365 days. In contrast, species with high survival rates should benefit from relatively long circannual periods. We predicted that circannual‐period lengths should correlate positively with species‐specific adult annual survival rates. Using published data for 16 wild bird species, we confirmed the predicted correlation. In our analysis, we accounted for the possible metabolic nature of circannual clocks, a correlation between rate of metabolism and survival, and phylogenetic relationships. On the basis of our finding, we propose that evolutionary responsive circannual clocks help birds cope with temporal variation in the environment in ways that are most appropriate for their life‐history and life‐table attributes