Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN examines the Bayesian and frequentist methods of conducting data analyses. The book provides the theoretical background in ...an easy-to-understand approach, encouraging readers to examine the processes that generated their data. Including discussions of model selection, model checking, and multi-model inference, the book also uses effect plots that allow a natural interpretation of data. Bayesian Data Analysis in Ecology Using Linear Models with R, BUGS, and STAN introduces Bayesian software, using R for the simple modes, and flexible Bayesian software (BUGS and Stan) for the more complicated ones. Guiding the ready from easy toward more complex (real) data analyses ina step-by-step manner, the book presents problems and solutions-including all R codes-that are most often applicable to other data and questions, making it an invaluable resource for analyzing a variety of data types.
To track peaks in resource abundance, temperate-zone animals use predictive environmental cues to rear their offspring when conditions are most favourable. However, climate change threatens the ...reliability of such cues when an animal and its resource respond differently to a changing environment. This is especially problematic in alpine environments, where climate warming exceeds the Holarctic trend and may thus lead to rapid asynchrony between peaks in resource abundance and periods of increased resource requirements such as reproductive period of high-alpine specialists. We therefore investigated interannual variation and long-term trends in the breeding phenology of a high-alpine specialist, the white-winged snowfinch, Montifringilla nivalis, using a 20-year dataset from Switzerland. We found that two thirds of broods hatched during snowmelt. Hatching dates positively correlated with April and May precipitation, but changes in mean hatching dates did not coincide with earlier snowmelt in recent years. Our results offer a potential explanation for recently observed population declines already recognisable at lower elevations. We discuss non-adaptive phenotypic plasticity as a potential cause for the asynchrony between changes in snowmelt and hatching dates of snowfinches, but the underlying causes are subject to further research.
1. Populations of migratory birds often mix to a considerable extent in their wintering areas. Knowledge about the composition of wintering populations is highly relevant to management, not least for ...species such as the great cormorant Phalacrocorax carbo sinensis, prone to conflicts with human interests. However, few studies have been able to estimate long-term changes in winter population composition. 2. We use 30 years of ringing and recovery data (1983-2013) from all major breeding populations of cormorants in continental Europe (except the Black Sea region) to estimate partitioning probabilities (i.e. the probabilities of moving to specific wintering areas) using a Bayesian capture-mark-recovery model. Combining these results with information on breeding numbers and reproductive output in a population model, we estimate the size and composition of wintering populations in Europe and North Africa. 3. Partitioning probabilities showed some variation over time, but were similar for first-winter and older birds. Cormorants from the western part of the breeding range tended to winter progressively further west over time. This may be a density-dependent response to the recent growth of more easterly breeding populations. 4. All wintering populations grew rapidly over the study period, and their composition showed pronounced changes. All wintering populations were composed of birds from many different breeding populations, but the proportion of cormorants of more easterly origin increased markedly over time in most wintering areas. 5. Policy implications. Cormorant wintering populations in Europe consist of mixtures of birds of different breeding origins. These mixtures are also highly variable over time. These factors reduce the chances of successfully limiting conflicts in specific wintering areas through, for example, regulation of breeding numbers in one breeding area. The dynamic nature of cormorant winter populations means that conflicts are best addressed when and where the conflict occurs, or on the scale of the entire continental population. It is unlikely that the latter will be cost-effective and politically realistic.
Summary
1. Geolocation by light allows for tracking animal movements, based on measurements of light intensity over time by a data‐logging device (‘geolocator’). Recent developments of ultra‐light ...devices (<2 g) broadened the range of target species and boosted the number of studies using geolocators. However, an inherent problem of geolocators is that any factor or process that changes the natural light intensity pattern also affects the positions calculated from these light patterns. Although the most important factors have been identified, estimation of their effect on the accuracy and precision of positions estimated has been lacking but is very important for the analyses and interpretation of geolocator data.
2. The ‘threshold method’ is mainly used to derive positions by defining sunrise and sunset times from the light intensity pattern for each recorded day. This method requires calibration: a predefined sun elevation angle for estimating latitude by fitting the recorded day/night lengths to theoretical values across latitudes. Therewith, almost constant shading can be corrected for by finding the appropriate sun elevation angle.
3. Weather, topography and vegetation are the most important factors that influence light intensities. We demonstrated their effect on the measurement of day/night length, time of solar midnight/noon and the resulting position estimates using light measurements from stationary geolocators at known places and from geolocators mounted on birds. Furthermore, we investigated the influence of different calibration methods on the accuracy of the latitudinal positions.
4. All three environmental factors can influence the light intensity pattern significantly. Weather and an animal’s behaviour result in increased noise in positioning, whereas topography and vegetation result in systematic shading and biased positions. Calibration can significantly shift the estimated latitudes and potentially increase the accuracy, but detailed knowledge about the particular confounding factors and the behaviour of the studied animal is crucial for the choice of the most appropriate calibration method.
The formation of an upper distributional range limit for species breeding along mountain slopes is often based on environmental gradients resulting in changing demographic rates towards high ...elevations. However, we still lack an empirical understanding of how the interplay of demographic parameters forms the upper range limit in highly mobile species. Here, we study apparent survival and within-study area dispersal over a 700 m elevational gradient in barn swallows (Hirundo rustica) by using 15 years of capture-mark-recapture data. Annual apparent survival of adult breeding birds decreased while breeding dispersal probability of adult females, but not males increased towards the upper range limit. Individuals at high elevations dispersed to farms situated at elevations lower than would be expected by random dispersal. These results suggest higher turn-over rates of breeding individuals at high elevations, an elevational increase in immigration and thus, within-population source-sink dynamics between low and high elevations. The formation of the upper range limit therefore is based on preference for low-elevation breeding sites and immigration to high elevations. Thus, shifts of the upper range limit are not only affected by changes in the quality of high-elevation habitats but also by factors affecting the number of immigrants produced at low elevations.
Summary
N‐mixture and occupancy models are often used to account for non‐detections in population surveys. The consensus has been that the methods require data that are replicated in space, as well ...as within a short period of time while the population at each site remains closed, in order for parameters such as detection probabilities and expected abundances to be identifiable. The requirement of replication prohibits the use of N‐mixture and occupancy models for many surveys in practice. Recently, some studies have argued that N‐mixture and occupancy models for surveys with only one visit at each site are identifiable when covariates for both detection probabilities and expected abundances, with at least one distinct covariate for each, are available (Journal of Plant Ecology, 5, 2012, 22; Environmetrics, 23, 2012, 197).
We investigate the reasons for why detection probabilities have traditionally been considered unestimable from non‐replicated counts and how the new methods sidestep these issues. We further use simulations to investigate properties of the new estimators.
We show that detection probabilities of the single‐visit models with covariates are non‐identifiable and that absolute abundances cannot be estimated when particular link functions are employed (log links for both expected abundance and detection probability). Further, assumptions about the range within which detection probabilities vary are necessary to render estimability. The possibility of estimating abundance from single‐visit surveys therefore implicitly hinges on knowledge about the link functions. Simulations show that estimates of abundance can be highly variable and sensitive to the choice of link function. We further show how a reduced parameterization of an N‐mixture model for surveys repeated over time, without replication under closure but where detection probabilities are constant over time, corresponds to a Poisson model.
Non‐robust estimation can result in misleading conclusions about population abundance. When estimating abundance from count data that are not replicated, it is therefore important to be aware of how imprecise estimators may be and how sensitive they are to model assumptions.
The Alpine Rock Ptarmigan Lagopus muta helvetica is considered to be particularly vulnerable to climate change because it lives exclusively above the treeline in alpine habitats and is adapted to ...cold climates. Its Swiss population index has decreased over the last two decades. A considerable shrinkage in distributional area is predicted with further climate change. We assess whether the Alpine Rock Ptarmigan has moved to higher elevations in recent years in the Swiss Alps, and whether such elevational shifts have differed between regions and seasons, using observations recorded by volunteers over a 29‐year period. The elevational shifts differed greatly between regions. In the Eastern and Southern Alps, Ptarmigans were increasingly recorded at higher elevations, with a mean uphill shift of 6.4–9.4 m/year over the last three decades, a pattern that could not be explained by the yearly variation in weather conditions, whereas there was only a moderate upward shift (1.5–3.2 m/year) in the Northern Alps and almost no shift in the Western Alps. Elevational changes were generally greater than those observed in other bird species. The observed upward shift in the Eastern and Southern Alps is among the fastest observed in animals and plants, and may be caused by an upward shift of the treeline and reforestation of formerly cut or unforested areas. The observed elevational shift of the distribution of the Alpine Rock Ptarmigan has led to a reduction in the range of this subspecies, which is restricted to the Alps and isolated from other populations.
Summary
Count data of animals observed from multiple sites are commonly used to study variation in abundance across space and time. Because some individuals typically go undetected in such surveys, ...count data alone have traditionally been thought to not contain information about absolute abundance. In a recent paper, we showed that estimates of absolute abundance using single‐visit methods with covariates (Sólymos, et al. Environmetrics, 2012, 23, 197 ) can be biased arbitrarily low if the link function used for detection probability is mis‐specified. Sólymos & Lele (Methods in Ecology and Evolution, 2015, in press) argue that this is not a relevant issue in practice.
We discuss the implications of the assumptions necessary for estimating abundance from the single‐visit model and clarify and extend results in Knape & Korner‐Nievergelt (Methods in Ecology and Evolution, 2015, 6, 298). We also discuss assumptions of the Dail‐Madsen model.
We show that for the single‐visit model a partially scaled link function which covers the full range from 0 to 1 leads to the same scaling issue as the scaled link function used in Knape & Korner‐Nievergelt (2015) which only covers a restricted range.
We argue that there is essentially no information about absolute abundance contained in single‐visit count data. Additional more direct data on detection probabilities is required to robustly estimate absolute abundances.
We investigated sex‐ and year‐dependent variation in the temporal and spatial movement pattern of barn swallows Hirundo rustica during the non‐breeding period. Hundred and three individuals equipped ...with miniaturized light‐level geolocators at three different breeding areas in southern Switzerland and northern Italy provided data for the analysis. We identified a region 1000 km in radius centred in Cameroon as the main non‐breeding residence area of these three geographical populations. Five residence areas of males only were in southern Africa, south of 19°S. Most individuals occupied a single site during their stay south of the Sahara. The timing of migration broadly overlapped between sexes and all geographical breeding populations. Between the two study years there was a distinct difference of 5 to 10 d in departure dates from and arrival at the breeding sites. Remarkably, the period of residence in sub‐Saharan Africa was very similar (157 d) in the two study years, but their positions in the first year (2010–2011) were about 400 km more to the north than in the second (2011–2012). Independent of the year, individuals with sub‐Saharan residence areas further north and east had a shorter pre‐breeding migration and arrived earlier than those staying further south and west. In addition, birds breeding in southern Switzerland arrived at their breeding colony 7–10 d later than those breeding only 100 km south, in the Po river plain. Our study provides new information on the variance in migration phenology and the distribution of residence areas in sub‐Saharan Africa in relation to sex, population and year. It supports the usefulness of light‐level geolocators for the study of annual routines of large samples of small birds.
Voigt et al. (2021) provide a thorough analysis of the restrictions inherent to the estimation of bat abundance from acoustic surveys, and conclude that limitations of acoustic monitoring impede the ...reliable evaluation of bat fatalities at wind turbines. We argue that acoustic data recorded at the nacelle of wind turbines have been experimentally validated as a useful and appropriate measure of bat collisions. Therefore, acoustic data can be used to estimate bat fatalities at wind turbines, provided a referenced and standardised protocol for data acquisition and analysis is used.
Zusammenfassung in Deutsch
Voigt et al. (2021) zeigen in einer detaillierten Analyse Einschränkungen auf, die sich für die Bestimmung von Fledermausabundanz auf der Grundlage akustischer Erfassungen ergeben, und kommen zu dem Schluss, dass diese Einschränkungen keine zuverlässige Bewertung der an Windkraftanlagen versterbenden Fledermäuse erlauben. Wir argumentieren, dass in Experimenten validiert wurde, dass an der Gondel von Windenergieanlagen aufgezeichnete akustische Daten ein nützliches und geeignetes Maß für Fledermausschlagopfer sind. Daher können akustische Daten zur Abschätzung an Windenergieanlagen zu Tode kommender Fledermäuse verwendet werden, vorausgesetzt, es wird ein referenziertes und standardisiertes Protokoll für die Datenerfassung und ‐analyse verwendet.
Wind turbines cause bat mortality all over the world, thus effective curtailment strategies are crucial for bat conservation. A recent perspective suggested that technical, physical, and biological factors severely limit acoustic monitoring at wind turbines for evaluating fatalities of bats. We argue that standardised and referenced acoustic monitoring can reliably estimate fatalities of bats at wind turbines. Biases can be accounted for by correlating bat fatalities to the number of acoustic recordings in a large dataset from many turbines. Standardised detector measurements are then used to assess the level of bat activity and the resulting collisions, and to model relationships between environmental factors and bat activity at a specific turbine in order to predict future bat activity and to adapt wind turbine curtailment accordingly.
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