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Chadwick FJ, Haydon DT, Husmeier D, Ovaskainen O, Matthiopoulos J. LIES of omission: complex observation processes in ecology. Trends Ecol Evol 2024; 39:368-380. [PMID: 37949794 DOI: 10.1016/j.tree.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Advances in statistics mean that it is now possible to tackle increasingly sophisticated observation processes. The intricacies and ambitious scale of modern data collection techniques mean that this is now essential. Methodological research to make inference about the biological process while accounting for the observation process has expanded dramatically, but solutions are often presented in field-specific terms, limiting our ability to identify commonalities between methods. We suggest a typology of observation processes that could improve translation between fields and aid methodological synthesis. We propose the LIES framework (defining observation processes in terms of issues of Latency, Identifiability, Effort and Scale) and illustrate its use with both simple examples and more complex case studies.
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Affiliation(s)
- Fergus J Chadwick
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK; Centre for Research Into Ecological and Environmental Monitoring, School of Mathematics and Statistics, University of St Andrews, St. Andrews, Scotland, UK.
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Dirk Husmeier
- School of Mathematics and Statistics, University of Glasgow, Glasgow, G12 8TA, UK
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, P.O. Box 35 FI-40014, University of Jyväskylä, Jyväskylä, Finland
| | - Jason Matthiopoulos
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
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Benhamou S, Courbin N. Accounting for central place foraging constraints in habitat selection studies. Ecology 2023; 104:e4134. [PMID: 37386731 DOI: 10.1002/ecy.4134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/25/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Habitat selection studies contrast actual space use with the expected use under the null hypothesis of no selection (hereafter neutral use). Neutral use is most often equated to the relative frequencies with which environmental features occur. This generates a considerable bias when studying habitat selection by foragers that perform numerous trips back and forth to a central place (CP). Indeed, the increased space use close to the CP with respect to distant places reflects a mechanical effect, rather than a true selection for the closest habitats. Yet, correctly estimating habitat selection by CP foragers is of paramount importance for a better understanding of their ecology and to properly plan conservation actions. We show that including the distance to the CP as a covariate in unconditional Resource Selection Functions, as applied in several studies, is ineffective to correct for the bias. This bias can be eliminated only by contrasting the actual use to an appropriate neutral use that considers the CP forager behavior. We also show that the need to specify an appropriate neutral use overall distribution can be bypassed by relying on a conditional approach, where the neutral use is assessed locally regardless of the distance to the CP.
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Affiliation(s)
- Simon Benhamou
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Montpellier, France
| | - Nicolas Courbin
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Montpellier, France
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Aldossari S, Husmeier D, Matthiopoulos J. Transferable species distribution modelling: Comparative performance of Generalised Functional Response models. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Matthiopoulos J. Defining, estimating, and understanding the fundamental niches of complex animals in heterogeneous environments. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jason Matthiopoulos
- Institute of Biodiversity Animal Health and Comparative Medicine. University of Glasgow. Glasgow. G12 8QQ Scotland
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Crabb ML, Clement MJ, Jones AS, Bristow KD, Harding LE. Black bear spatial responses to the Wallow Wildfire in Arizona. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michelle L. Crabb
- Arizona Game and Fish Department Research Branch 5000 W. Carefree Hwy Phoenix AZ 85068 USA
| | - Matthew J. Clement
- Arizona Game and Fish Department Research Branch 5000 W. Carefree Hwy Phoenix AZ 85068 USA
| | - Andrew S. Jones
- Arizona Game and Fish Department Research Branch 5000 W. Carefree Hwy Phoenix AZ 85068 USA
| | - Kirby D. Bristow
- Arizona Game and Fish Department Field Operations Division 555 N. Greasewood Road Tucson AZ 85745 USA
| | - Larisa E. Harding
- Arizona Game and Fish Department Terrestrial Wildlife Branch 5000 W. Carefree Hwy Phoenix AZ 85068 USA
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Pérez-Girón JC, Díaz-Varela ER, Álvarez-Álvarez P, Hernández Palacios O, Ballesteros F, López-Bao JV. Linking landscape structure and vegetation productivity with nut consumption by the Cantabrian brown bear during hyperphagia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152610. [PMID: 34963596 DOI: 10.1016/j.scitotenv.2021.152610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/18/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
In bears, reproduction is dependent on the body reserves accumulated during hyperphagia. The Cantabrian brown bear mainly feeds on nuts during the hyperphagia period. Understanding how landscape heterogeneity and vegetation productivity in human-dominated landscapes influence the feeding habits of bears may therefore be important for disentangling species-habitat relationships of conservation interest. We determined the spatial patterns of nut consumption by brown bears during the hyperphagia period in relation to landscape structure, characteristics of fruit-producing patches and vegetation productivity. For this purpose, we constructed foraging models based on nut consumption data (obtained by scat analysis), by combining vegetation productivity data, topographical variables and landscape metrics to identify nut foraging patterns during this critical period for bears. The average wooded area of patches where scats were collected and where the nuts that the bears had consumed were produced was larger than that of the corresponding patches where nuts were not produced. For scats collected outside of nut-producing patches, the distance between the scats and the patches was greatest for chestnut-producing patches. Elevation, Gross Primary Production (GPP) and the Aggregation Index (AI) were good predictors of acorn consumption in the models. Good model fits were not obtained for data on chestnut consumption in bears. The findings confirm that brown bears feeding on nuts show a preference for relatively large, highly aggregated patches with a high degree of diversity in the landscape pattern, which may help the bears to remain undetected. The nut prediction model highlights areas of particular importance for brown bears during hyperphagia. The human presence associated with sweet chestnut forest stands or orchards may make bears feel more vulnerable when feeding.
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Affiliation(s)
- José Carlos Pérez-Girón
- Department of Organisms and Systems Biology, Polytechnic School of Mieres, University of Oviedo, E-33600, Mieres, Asturias, Spain.
| | - Emilio Rafael Díaz-Varela
- Research Group on Planning and Management in Complex Adaptive Socio-Ecological Systems (COMPASSES), School of Engineering, University of Santiago de Compostela, E-27002 Lugo, Spain
| | - Pedro Álvarez-Álvarez
- Department of Organisms and Systems Biology, Polytechnic School of Mieres, University of Oviedo, E-33600, Mieres, Asturias, Spain
| | - Orencio Hernández Palacios
- Dirección General del Medio Natural y Planificación Rural, Gobierno del Principado de Asturias, E-33005 Oviedo, Spain
| | | | - José Vicente López-Bao
- Biodiversity Research Institute (CSIC - Oviedo University - Principality of Asturias), University of Oviedo, E-33600 Mieres, Spain
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Matthiopoulos J, Wakefield E, Jeglinski JWE, Furness RW, Trinder M, Tyler G, Mccluskie A, Allen S, Braithwaite J, Evans T. Integrated modelling of seabird‐habitat associations from multi‐platform data: A review. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jason Matthiopoulos
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow Glasgow Scotland
- MacArthur Green Glasgow Scotland
| | - Ewan Wakefield
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow Glasgow Scotland
| | - Jana W. E. Jeglinski
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences, Graham Kerr Building, University of Glasgow Glasgow Scotland
| | | | | | | | - Aly Mccluskie
- RSPB Centre for Conservation Science RSPB, Etive House, Beechwood Park Inverness Scotland
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Fieberg J, Signer J, Smith B, Avgar T. A 'How to' guide for interpreting parameters in habitat-selection analyses. J Anim Ecol 2021; 90:1027-1043. [PMID: 33583036 PMCID: PMC8251592 DOI: 10.1111/1365-2656.13441] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/02/2021] [Indexed: 11/29/2022]
Abstract
Habitat‐selection analyses allow researchers to link animals to their environment via habitat‐selection or step‐selection functions, and are commonly used to address questions related to wildlife management and conservation efforts. Habitat‐selection analyses that incorporate movement characteristics, referred to as integrated step‐selection analyses, are particularly appealing because they allow modelling of both movement and habitat‐selection processes. Despite their popularity, many users struggle with interpreting parameters in habitat‐selection and step‐selection functions. Integrated step‐selection analyses also require several additional steps to translate model parameters into a full‐fledged movement model, and the mathematics supporting this approach can be challenging for many to understand. Using simple examples, we demonstrate how weighted distribution theory and the inhomogeneous Poisson point process can facilitate parameter interpretation in habitat‐selection analyses. Furthermore, we provide a ‘how to’ guide illustrating the steps required to implement integrated step‐selection analyses using the amt package By providing clear examples with open‐source code, we hope to make habitat‐selection analyses more understandable and accessible to end users.
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Affiliation(s)
- John Fieberg
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN, USA
| | - Johannes Signer
- Wildlife Science, Faculty of Forestry and Forest Ecology, University of Goettingen, Göttingen, Germany
| | - Brian Smith
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, USA
| | - Tal Avgar
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT, USA
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Avgar T, Betini GS, Fryxell JM. Habitat selection patterns are density dependent under the ideal free distribution. J Anim Ecol 2020; 89:2777-2787. [PMID: 32961607 PMCID: PMC7756284 DOI: 10.1111/1365-2656.13352] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 08/07/2020] [Indexed: 11/27/2022]
Abstract
Despite being widely used, habitat selection models are rarely reliable and informative when applied across different ecosystems or over time. One possible explanation is that habitat selection is context-dependent due to variation in consumer density and/or resource availability. The goal of this paper is to provide a general theoretical perspective on the contributory mechanisms of consumer and resource density-dependent habitat selection, as well as on our capacity to account for their effects. Towards this goal we revisit the ideal free distribution (IFD), where consumers are assumed to be omniscient, equally competitive and freely moving, and are hence expected to instantaneously distribute themselves across a heterogeneous landscape such that fitness is equalised across the population. Although these assumptions are clearly unrealistic to some degree, the simplicity of the structure in IFD provides a useful theoretical vantage point to help clarify our understanding of more complex spatial processes. Of equal importance, IFD assumptions are compatible with the assumptions underlying common habitat selection models. Here we show how a fitness-maximising space use model, based on IFD, gives rise to resource and consumer density-dependent shifts in consumer distribution, providing a mechanistic explanation for the context-dependent outcomes often reported in habitat selection analysis. Our model suggests that adaptive shifts in consumer distribution patterns would be expected to lead to nonlinear and often non-monotonic patterns of habitat selection. These results indicate that even under the simplest of assumptions about adaptive organismal behaviour, habitat selection strength should critically depend on system-wide characteristics. Clarifying the impact of adaptive behavioural responses may be pivotal in making meaningful ecological inferences about observed patterns of habitat selection and allow reliable transferability of habitat selection predictions across time and space.
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Affiliation(s)
- Tal Avgar
- Department of Wildland ResourcesUtah State UniversityLoganUTUSA
| | | | - John M. Fryxell
- Department of Integrative BiologyUniversity of GuelphGuelphCanada
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