Marc Kéry's research while affiliated with Swiss Ornithological Institute and other places

Publications (230)

Article
The global biodiversity crisis is escalating rapidly, with nearly a million species facing extinction risk in the near future. Monitoring of Essential Biodiversity Variables (EBV; key variables measured to detect changes in biodiversity) over time is important for biodiversity conservation, which in turn necessitates baseline estimates of EBVs. Usi...
Preprint
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Point counts (PCs) are widely used in biodiversity surveys, but despite numerous advantages, simple PCs suffer from several problems: detectability, and therefore abundance, is unknown; systematic spatiotemporal variation in detectability produces biased inferences, and unknown survey area prevents formal density estimation and scaling-up to the la...
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Generating spatial predictions of species distribution is a central task for research and policy. Among the currently most widely used tools for this purpose are correlative species distribution models (cSDMs). Their basic assumption of a species distribution in equilibrium with its environment, however, is rarely met in real data and prevents dyna...
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Species responses to climate change are widely detected as range and abundance changes. To better explain and predict them, we need a mechanistic understanding of how the underlying demographic processes are shaped by climatic conditions. We built spatially-explicit, process-based models for eight Swiss breeding bird populations. They jointly consi...
Article
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Global change in climate and land use has profound effects on species' geographic and elevational distributions. In European birds, while species are predicted to track their climatic niches upslope, lowland agricultural intensification and high‐elevation land abandonment can drive elevational shifts. Species traits that can predict response to cha...
Article
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Occupancy modeling is a common approach to assess species distribution patterns, while explicitly accounting for false absences in detection‐nondetection data. Numerous extensions of the basic single‐species occupancy model exist to model multiple species, spatial autocorrelation, and to integrate multiple data types. However, development of specia...
Article
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In biodiversity monitoring, observational data are often collected in multiple, disparate schemes with greatly varying degrees of standardization and possibly at different spatial and temporal scales. Technical advances also change the type of data over time. The resulting heterogeneous datasets are often deemed to be incompatible. Consequently, ma...
Article
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The capercaillie Tetrao urogallus - the world's largest grouse- is a circumboreal forest species, which only two remaining populations in Spain: one in the Cantabrian mountains in the west and the other in the Pyrenees further east. Both have shown severe declines, especially in the Cantabrian population, which has recently been classified as “Crit...
Chapter
The focus of this chapter is the presentation of demographic population analyses that look backward in time and attempt to understand why a population has shown the observed trajectory. Such analyses are called retrospective population analyses and allow a fundamental understanding about demographic drivers of population dynamics. There are several...
Chapter
We develop an integrated population model on greater horseshoe bats (Rhinolophus ferrumequinum) to estimate demographic rates and population composition. We combine three different data sets from a nursery colony of this bat in a small church in the Swiss Alps: counts of free-flying adults emerging from the colony at dusk, counts of newborns, and c...
Chapter
We develop an IPM for a small population of woodchat shrikes (Lanius senator) that combines three types of data: capture-recapture data, and counts of the number of fledglings and of breeding pairs (the latter being interpreted as the population counts). The model accounts for environmental variability and demographic stochasticity, and adopts a Po...
Chapter
We introduce integrated population models (IPMs) in two different ways. First, we start from a matrix population model and progressively add more data sets along with likelihoods for estimating certain parameters from them as part of a single model fit with the JAGS program. We emphasize that the inclusion of population count (or similarly, populat...
Chapter
As with any statistical model, an integrated population model (IPM) makes simplifying assumptions about Nature. Accurate parameter estimates are only obtained when these assumptions have been sufficiently met. The main assumptions of an IPM are classified as two types. The first comprises the assumptions made by each component model; the second is...
Chapter
Density dependence is a crucial regulation mechanism in population dynamics but is challenging to study empirically. We illustrate the use of integrated population models (IPMs) to study density dependence while offering a number of interesting possibilities to overcome some of these challenges. As IPMs include both individual and population levels...
Chapter
We develop an integrated population model (IPM) for the hoopoe (Upupa epops) data set consisting of the classical combination of population count, capture-recapture, and individual productivity data to estimate latent individual quality. In the model for productivity, we use a finite-mixture model with two latent groups to define individual quality...
Chapter
We develop an integrated population model (IPM) to study the demographic causes of synchrony in population dynamics, i.e., coincidence in the changes in demographic rates and of population growth in multiple populations. The model requires that component data sets are sampled at different sites and during time periods that must overlap at least par...
Chapter
In this chapter, we extend the previous case study to a continuous representation of space. Rather than dividing up a large region into a few discrete strata, we model spatial variation in the initial abundance, apparent survival, and recruitment rate of kestrels (Falco tinnunculus) in the northwestern corner of Switzerland in an essentially contin...
Chapter
We give an overview of the data types and associated models typically combined in an integrated population model (IPM). These models are the components or “ingredients” of an IPM. We focus on key models for surveys of population counts, productivity, and capture-recapture. We start with an overview of the main features of these data types that focu...
Chapter
We develop an individual-based spatial integrated population model (IPM) to jointly analyze spatial capture-recapture and occupancy data of black bears (Ursus americanus luteolus) collected from 2007 to 2012 in Louisiana, USA. The process model of this IPM does not aggregate individuals into stage or age classes as do traditional IPMs, but instead,...
Chapter
The core of most integrated population models is a stage-structured (or matrix) population model, which provides the linkage between the demography of individuals and the trajectory of a population. We give a concise summary of the traditional analysis of matrix population models and emphasize the connection between matrix and integrated population...
Chapter
We provide a largely nonmathematical introduction to the using of probability in statistical modeling and parametric statistical inference by the two dominant estimation methods, maximum likelihood and Bayesian posterior inference. We explain and illustrate the simulation method concepts collectively known as Markov chain Monte Carlo (MCMC), which...
Chapter
A population viability analysis (PVA) is an important technique in the population assessment applied to rare, harvested, and pest species alike. In a broad sense, it aims to project the future size of a population and possibly incorporate the effects of predicted changes in the environment or in some management action. We illustrate the use of an i...
Chapter
We develop a multisite integrated population model (IPM) for great cormorants (Phalacrocorax carbo) to analyze count and capture-recapture data sampled in three Danish breeding colonies. The goal is the estimation of colony-specific survival and productivity as well as natal and breeding dispersal among the three colonies. The population model beco...
Chapter
The joint analysis of data sets from population and individual levels through an integrated population model provides a number of benefits highlighted here. Key benefits of integrated population models (IPMs) are the increased precision of parameter estimates and the ability to estimate parameters without explicit data—the so-called hidden paramete...
Chapter
We develop an integrated population model based on data collected over large spatial scales for monitoring populations and demography. Specifically, we analyze data from the North American Breeding Bird Survey and Monitoring Avian Productivity and Survivorship programs for gray catbirds (Dumetella carolinensis) in the New England/Mid-Atlantic regio...
Chapter
In this case study, we develop a seasonal, two-sex integrated population model (IPM) for a population of black grouse (Lyrurus tetrix) in the Italian Alps. Three different data sets are entered in this model: a lek survey in spring to count displaying males, a survey in late summer to count males, females, and chicks, and radio tracking data. The m...
Chapter
In this case study, we fit two integrated population models to population counts, productivity counts, and dead-recovery data in a population of the Peregrine Falcon (Falco peregrinus) in the Jura mountains over 43 years (1965–2007). The main objectives are to investigate whether the much-publicized population crash caused by the effects of pestici...
Article
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• The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously mo...
Preprint
Full-text available
Occupancy modeling is a common approach to assess spatial and temporal species distribution patterns, while explicitly accounting for measurement errors common in detection-nondetection data. Numerous extensions of the basic single species occupancy model exist to address dynamics, multiple species or states, interactions, false positive errors, au...
Article
Full-text available
Effective conservation of animal populations depends on the availability of reliable data derived from rigorous monitoring protocols, which allows us to assess trends and understand the processes they are governed by. Nevertheless, population monitoring schemes are hampered by multiple sources of errors resulting from specific logistical and survey...
Article
After spectacular population crashes in the 1960-70s, Peregrine Falcons Falco peregrinus recovered worldwide, and in the 2000s many study populations were back to normal. However, post-recovery trends have not been documented. We combined three long-term population studies covering the entire Jura mountains (16,304 km²) to examine spatio-temporal v...
Article
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Illegal hunting represents a major threat to the conservation of predators, but its impact remains difficult to assess as there are strong incentives to conceal this criminal activity. Attributing declines of carnivores to poaching is therefore an important conservation challenge. We present a case study of the Eurasian lynx (Lynx lynx) in the Swis...
Article
Predictions of species' current and future ranges are needed to effectively manage species under environmental change. Species ranges are typically estimated using correlative species distribution models (SDMs), which have been criticized for their static nature. In contrast, dynamic occupancy models (DOMs) explicitily describe temporal changes in...
Article
Full-text available
Effective conservation of animal populations depends on the availability of reliable data derived from rigorous monitoring protocols, which allows us to assess trends and understand the processes they are governed by. Nevertheless, population monitoring schemes are hampered by multiple sources of errors resulting from specific logistical and survey...
Article
Full-text available
Dry deciduous dipterocarp forests (DDF) cover about 15%–20% of Southeast Asia and are the most threatened forest type in the region. The jungle cat (Felis chaus) is a DDF specialist that occurs only in small isolated populations in Southeast Asia. Despite being one of the rarest felids in the region, almost nothing is known about its ecology. We in...
Article
1. Many studies in ecology and management aim at quantifying absolute abundance based on counts at a set of surveyed sites. As time for data collection is typically limited, methods for reliable estimation of occupancy or abundance from low‐cost data are desirable. Time‐to‐detection (TTD) models have shown promise for the estimation of occupancy. H...
Article
Population size of species with birth-pulse life-cycles varies both within and between seasons, but most population dynamics models assume that a population can be characterised adequately by a single number within a season. However, within-season dynamics can sometimes be too substantial to be ignored when modelling dynamics between seasons. Typic...
Article
Managers often rely on species surveys and distribution models to evaluate species occurrence and develop management and conservation plans. However, these tools are rarely used in concert. We used a three-step framework to evaluate the distribution of a declining and elusive freshwater amphibian species, the hellbender salamander (Cryptobranchus a...
Preprint
1. Illegal hunting (poaching) represents a major threat to the conservation of large predators. Yet, its impact remains difficult to quantify as there are strong incentives to conceal this criminal activity. Attributing changes in the population status of large carnivores in part to poaching is therefore an important conservation challenge. 2. We p...
Article
Population size is a key predictor of extinction risk and is critical to listing species in IUCN threat categories. Assessing population size can be particularly difficult for gregarious species, such as parrots—one of the most threatened bird families—whose ecology and behavior generate multiple sources of uncertainty that need to be addressed in...
Article
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The Peregrine Falcon (Falco peregrinus) is the most widely distributed bird species in the world, but very little is known about its tropical populations, where even very basic information (e.g. about population density) is mostly lacking. In January 2017, 2018 and 2019, we conducted three intensive surveys amounting to 27 days and 5,400 km driven...
Article
Full-text available
Migratory species form an important component of biodiversity; they link ecosystems across the globe, but are increasingly threatened by global environmental change. Understanding and mitigating threats requires knowledge of how demographic processes operate throughout the annual cycle, but this can be difficult to achieve when breeding and non‐bre...
Article
The return of top carnivores to their historical range triggers conflicts with the interests of different stakeholder groups. Anticipating such conflicts is key to appropriate conservation management, which calls for reliable spatial predictions of future carnivore occurrence. Previous models have assessed general habitat suitability for wolves, bu...
Article
Full-text available
Capsule: We used data from different sources, developed and applied several estimation methods, and confronted the resulting estimates with species experts to achieve breeding size population estimates for all bird species currently breeding in Switzerland. Aims: Population size estimates of birds have a wide range of practical conservation uses. A...
Article
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Wildlife demography is typically studied at a single point in time within a year when species, often during the reproductive season, are more active and therefore easier to find. However, this provides only a low-resolution glimpse into demographic temporal patterns over time and may hamper a more complete understanding of the population dynamics o...
Article
Assessing and modelling abundance from animal count data is a very common task in ecology and management. Detection is arguably never perfect, but modern hierarchical models can incorporate detection probability and yield abundance estimates that are corrected for imperfect detection. Two variants of these models rely on counts of unmarked individu...
Article
Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Here, we develop an open population spatial capture–recapture (SCR) model with sex‐specific detection and population dynamics parameters...
Preprint
Full-text available
Demography is usually studied at a single point in time within a year when species, mostly long-distance migrants, are more active and easier to find. However, this provides only a low-resolution glimpse into demographic temporal patterns, compromising a complete understanding of species' population dynamics over full annual cycles. The full annual...
Article
Full-text available
The Nam Et - Phou Louey National Protected Area (NEPL) is known for its diverse community of carnivores, and a decade ago was identified as an important source site for tiger conservation in Southeast Asia. However, there are reasons for concern that the status of this high priority diverse community has deteriorated, making the need for updated in...
Article
Spatiotemporal patterns in biological communities are typically driven by environmental factors and species interactions. Spatial data from communities are naturally described by stacking models for all species in the community. Two important considerations in such multi‐species or joint species distribution models (JSDMs) are measurement errors an...
Data
Monitoring dates since monitoring is conducted, with transect details. (DOCX)
Data
List of all species found in our study sites in all years with Swiss Red list category and Swiss priority status. Species highlighted in bold were used for species-specific analyses, while all species were used for community analyses (LC = least concern, NT = near-threatened, VU = vulnerable). (DOCX)
Article
Full-text available
As major disturbance agents, natural catastrophes impact habitats, thereby maintaining the dynamics of ecological communities. Such discrete events are expected to positively affect biodiversity because they generate high habitat heterogeneity and thus numerous ecological niche opportunities. Species typical of open and semi-open habitats, which ar...
Data
Species-specific best models calculated with the dredge function, for species with competing best models in terms of AIC. Numbers following a species name distinguish different but equivalent models in terms of AIC. (DOCX)
Data
Map of Leuk (a) and Visp (b) with transects walked in all years for SOI data collection. One square is 1 km2. Reprinted from map.geo.admin.ch under a CC BY license, with permission from swisstopo (BA18049), original copyright 2018. (TIF)
Data
Map with predefined transect lines of Leuk (a) and Visp (b) walked by the first author in 2014. One square is 1 km2. Red = subtransect within the burnt forest, blue = subtransects within control forests. Note that transects are surrounded by the 100 m buffer. Reprinted from map.geo.admin.ch under a CC BY license, with permission from swisstopo (BA1...
Data
Model selection tables for analyses, where competing best models were found. Model selection table for species richness. (DOCX)
Data
List of excluded species in all years with Swiss Red list category and Swiss priority status. Several corvid species and all birds of prey were excluded from the analysis. LC = least concern, NT = near-threatened, VU = vulnerable, EN = endangered. (DOCX)
Data
Averaged best models for Red list and priority analyses, calculated only for analyses with competing best models from Tables 2–4. a Best model for Red list analysis with index after model averaging. b Best model for Red list analysis with territories after model averaging. c Best model for priority analysis with territories after model averaging. (...
Data
Model selection tables for analyses, where no competing best models were found. a Model selection table for species abundance. b Model selection table for priority analysis with index. (DOCX)
Preprint
Full-text available
Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Open population spatial capture-recapture (SCR) models are ideally suited to quantify population trends, but have seen only limited use...
Preprint
Full-text available
1. Modeling the population dynamics of patchily distributed species is a challenge, particularly when inference must be based on incomplete and small data sets such as those from most species of conservation concern. Open population spatial capture-recapture (SCR) models are ideally suited to quantify population trends, but have seen only limited u...
Article
Full-text available
Population dynamics models have long assumed that populations are composed of a restricted number of groups, where individuals in each group have identical demographic rates and where all groups are similarly affected by density‐dependent and ‐independent effects. However, individuals usually vary tremendously in performance and in their sensitivit...
Article
Full-text available
Multispecies occupancy models can estimate species richness from spatially replicated multispecies detection/non-detection survey data, while accounting for imperfect detection. A model extension using data augmentation allows inferring the total number of species in the community, including those completely missed by sampling (i.e., not detected i...