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Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence
17 Nov 2005-
TL;DR: This chapter discusses single-species, Single-season Occupancy Models with Heterogeneous Detection Probabilities, and interspecific Relationships Between Species.
Abstract: Ch 1: Introduction Ch 2: Occupancy in Ecological Investigations Ch 3: Fundamental Principles of Statistical Inference Ch 4: Single-species, Single-season Occupancy Models Ch 5: Single-species, Single-season Models with Heterogeneous Detection Probabilities Ch 6: Design Issues for Single-species, Single-season Occupancy Models Ch 7: Single-species, Multiple-seasons Occupancy Models Ch 8: Examining the Local Species Pool Ch 9: Interspecific Relationships Between Species Ch10: Extensions and Future Work
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TL;DR: Citizen science, the involvement of volunteers in research, has increased the scale of ecological field studies with continent-wide, centralized monitoring efforts and tapping of volunteers to conduct large, coordinated, field experiments as mentioned in this paper.
Abstract: Citizen science, the involvement of volunteers in research, has increased the scale of ecological field studies with continent-wide, centralized monitoring efforts and, more rarely, tapping of volunteers to conduct large, coordinated, field experiments. The unique benefit for the field of ecology lies in understanding processes occurring at broad geographic scales and on private lands, which are impossible to sample extensively with traditional field research models. Citizen science produces large, longitudinal data sets, whose potential for error and bias is poorly understood. Because it does not usually aim to uncover mechanisms underlying ecological patterns, citizen science is best viewed as complementary to more localized, hypothesis-driven research. In the process of addressing the impacts of current, global “experiments” altering habitat and climate, large-scale citizen science has led to new, quantitative approaches to emerging questions about the distribution and abundance of organisms across spa...
1,490 citations
TL;DR: A novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water, using specific primers that amplify short mitochondrial DNA sequences to track the existence of a frog in controlled environments and natural wetlands.
Abstract: The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog (Rana catesbeiana) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.
1,226 citations
TL;DR: This paper comments on a number of general issues related to designing occupancy studies, including the need for clear objectives that are explicitly linked to science or management, selection of sampling units, timing of repeat surveys and allocation of survey effort, and found that an optimal removal design will generally be the most efficient.
Abstract: Summary
1
The fraction of sampling units in a landscape where a target species is present (occupancy) is an extensively used concept in ecology Yet in many applications the species will not always be detected in a sampling unit even when present, resulting in biased estimates of occupancy Given that sampling units are surveyed repeatedly within a relatively short timeframe, a number of similar methods have now been developed to provide unbiased occupancy estimates However, practical guidance on the efficient design of occupancy studies has been lacking
2
In this paper we comment on a number of general issues related to designing occupancy studies, including the need for clear objectives that are explicitly linked to science or management, selection of sampling units, timing of repeat surveys and allocation of survey effort Advice on the number of repeat surveys per sampling unit is considered in terms of the variance of the occupancy estimator, for three possible study designs
3
We recommend that sampling units should be surveyed a minimum of three times when detection probability is high (> 0·5 survey−1), unless a removal design is used
4
We found that an optimal removal design will generally be the most efficient, but we suggest it may be less robust to assumption violations than a standard design
5
Our results suggest that for a rare species it is more efficient to survey more sampling units less intensively, while for a common species fewer sampling units should be surveyed more intensively
6
Synthesis and applications Reliable inferences can only result from quality data To make the best use of logistical resources, study objectives must be clearly defined; sampling units must be selected, and repeated surveys timed appropriately; and a sufficient number of repeated surveys must be conducted Failure to do so may compromise the integrity of the study The guidance given here on study design issues is particularly applicable to studies of species occurrence and distribution, habitat selection and modelling, metapopulation studies and monitoring programmes
1,177 citations
Cites background from "Occupancy Estimation and Modeling: ..."
...…of the form: Cost = c 0 + s[c1 + c2(K − 1)] where c0 is a fixed overhead cost, c1 is the cost of conducting the first survey of a site, and c2 is the cost of conducting subsequent surveys, although other cost functions could be considered (Field, Tyre & Possingham 2005; MacKenzie et al. 2005)....
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...where c0 is a fixed overhead cost, c1 is the cost of conducting the first survey of a site, and c2 is the cost of conducting subsequent surveys, although other cost functions could be considered (Field, Tyre & Possingham 2005; MacKenzie et al. 2005)....
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TL;DR: Evaluating the consistency of CT protocols and sampling designs, the extent to which CT surveys considered sampling error, and the linkages between analytical assumptions and species ecology call for more explicit consideration of underlying processes of animal abundance, movement and detection by cameras, including more thorough reporting of methodological details and assumptions.
Abstract: Summary
Reliable assessment of animal populations is a long-standing challenge in wildlife ecology. Technological advances have led to widespread adoption of camera traps (CTs) to survey wildlife distribution, abundance and behaviour. As for any wildlife survey method, camera trapping must contend with sources of sampling error such as imperfect detection. Early applications focused on density estimation of naturally marked species, but there is growing interest in broad-scale CT surveys of unmarked populations and communities. Nevertheless, inferences based on detection indices are controversial, and the suitability of alternatives such as occupancy estimation is debatable.
We reviewed 266 CT studies published between 2008 and 2013. We recorded study objectives and methodologies, evaluating the consistency of CT protocols and sampling designs, the extent to which CT surveys considered sampling error, and the linkages between analytical assumptions and species ecology.
Nearly two-thirds of studies surveyed more than one species, and a majority used response variables that ignored imperfect detection (e.g. presence–absence, relative abundance). Many studies used opportunistic sampling and did not explicitly report details of sampling design and camera deployment that could affect conclusions.
Most studies estimating density used capture–recapture methods on marked species, with spatially explicit methods becoming more prominent. Few studies estimated density for unmarked species, focusing instead on occupancy modelling or measures of relative abundance. While occupancy studies estimated detectability, most did not explicitly define key components of the modelling framework (e.g. a site) or discuss potential violations of model assumptions (e.g. site closure). Studies using relative abundance relied on assumptions of equal detectability, and most did not explicitly define expected relationships between measured responses and underlying ecological processes (e.g. animal abundance and movement).
Synthesis and applications. The rapid adoption of camera traps represents an exciting transition in wildlife survey methodology. We remain optimistic about the technology's promise, but call for more explicit consideration of underlying processes of animal abundance, movement and detection by cameras, including more thorough reporting of methodological details and assumptions. Such transparency will facilitate efforts to evaluate and improve the reliability of camera trap surveys, ultimately leading to stronger inferences and helping to meet modern needs for effective ecological inquiry and biodiversity monitoring.
786 citations
TL;DR: The proximate causes of climate-change related extinctions and their empirical support are reviewed to support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change.
Abstract: Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. But what will actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change related extinctions and their empirical support. We find 136 case studies of climatic impacts that are potentially relevant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none show a straightforward relationship between local extinction and limited tolerances to high temperature. Instead, many studies implicate species interactions as an important proximate cause, especially decreases in food availability. We find very similar patterns in studies showing decreases in abundance associated with climate change, and in those studies showing impacts of climatic oscillations. Collectively, these results highlight our disturbingly limited knowledge of this crucial issue but also support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change. Finally, we briefly outline general research strategies for identifying these proximate causes in future studies.
703 citations