1
|
Meunier ZD, Hacker SD, Menge BA. Regime shifts in rocky intertidal communities associated with a marine heatwave and disease outbreak. Nat Ecol Evol 2024; 8:1285-1297. [PMID: 38831017 DOI: 10.1038/s41559-024-02425-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Abstract
Long-term, large-scale experimental studies provide critical information about how global change influences communities. When environmental changes are severe, they can trigger abrupt transitions from one community type to another leading to a regime shift. From 2014 to 2016, rocky intertidal habitats in the northeast Pacific Ocean experienced extreme temperatures during a multi-year marine heatwave (MHW) and sharp population declines of the keystone predator Pisaster ochraceus due to sea star wasting disease (SSWD). Here we measured the community structure before, during and after the MHW onset and SSWD outbreak in a 15-year succession experiment conducted in a rocky intertidal meta-ecosystem spanning 13 sites on four capes in Oregon and northern California, United States. Kelp abundance declined during the MHW due to extreme temperatures, while gooseneck barnacle and mussel abundances increased due to reduced predation pressure after the loss of Pisaster from SSWD. Using several methods, we detected regime shifts from substrate- or algae-dominated to invertebrate-dominated alternative states at two capes. After water temperatures cooled and Pisaster population densities recovered, community structure differed from pre-disturbance conditions, suggesting low resilience. Consequently, thermal stress and predator loss can result in regime shifts that fundamentally alter community structure even after restoration of baseline conditions.
Collapse
Affiliation(s)
- Zechariah D Meunier
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA.
| | - Sally D Hacker
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Bruce A Menge
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
McPartland MY. Decadal-scale variability and warming affect spring timing and forest growth across the western Great Lakes region. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2024; 68:701-717. [PMID: 38236422 DOI: 10.1007/s00484-023-02616-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
The Great Lakes region of North America has warmed by 1-2 °C on average since pre-industrial times, with the most pronounced changes observable during winter and spring. Interannual variability in temperatures remains high, however, due to the influence of ocean-atmosphere circulation patterns that modulate the warming trend across years. Variations in spring temperatures determine growing season length and plant phenology, with implications for whole ecosystem function. Studying how both internal climate variability and the "secular" warming trend interact to produce trends in temperature is necessary to estimate potential ecological responses to future warming scenarios. This study examines how external anthropogenic forcing and decadal-scale variability influence spring temperatures across the western Great Lakes region and estimates the sensitivity of regional forests to temperature using long-term growth records from tree-rings and satellite data. Using a modeling approach designed to test for regime shifts in dynamic time series, this work shows that mid-continent spring climatology was strongly influenced by the 1976/1977 phase change in North Pacific atmospheric circulation, and that regional forests show a strengthening response to spring temperatures during the last half-century.
Collapse
Affiliation(s)
- Mara Y McPartland
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Potsdam, Germany.
- Department of Geography, Environment & Society, University of Minnesota, Minneapolis, MN, USA.
| |
Collapse
|
4
|
Pohle J, Signer J, Eccard JA, Dammhahn M, Schlägel UE. How to account for behavioral states in step-selection analysis: a model comparison. PeerJ 2024; 12:e16509. [PMID: 38426131 PMCID: PMC10903358 DOI: 10.7717/peerj.16509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/01/2023] [Indexed: 03/02/2024] Open
Abstract
Step-selection models are widely used to study animals' fine-scale habitat selection based on movement data. Resource preferences and movement patterns, however, often depend on the animal's unobserved behavioral states, such as resting or foraging. As this is ignored in standard (integrated) step-selection analyses (SSA, iSSA), different approaches have emerged to account for such states in the analysis. The performance of these approaches and the consequences of ignoring the states in step-selection analysis, however, have rarely been quantified. We evaluate the recent idea of combining iSSAs with hidden Markov models (HMMs), which allows for a joint estimation of the unobserved behavioral states and the associated state-dependent habitat selection. Besides theoretical considerations, we use an extensive simulation study and a case study on fine-scale interactions of simultaneously tracked bank voles (Myodes glareolus) to compare this HMM-iSSA empirically to both the standard and a widely used classification-based iSSA (i.e., a two-step approach based on a separate prior state classification). Moreover, to facilitate its use, we implemented the basic HMM-iSSA approach in the R package HMMiSSA available on GitHub.
Collapse
Affiliation(s)
- Jennifer Pohle
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Signer
- Wildlife Sciences, Faculty of Forest Sciences and Forest Ecology, University of Goettingen, Göttingen, Germany
| | - Jana A. Eccard
- Animal Ecology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Melanie Dammhahn
- Department of Behavioural Biology, University of Münster, Münster, Germany
| | - Ulrike E. Schlägel
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| |
Collapse
|
5
|
Labuzzetta CJ, Coulter AA, Erickson RA. Comparing maximum likelihood and Bayesian methods for fitting hidden Markov models to multi-state capture-recapture data of invasive carp in the Illinois River. MOVEMENT ECOLOGY 2024; 12:2. [PMID: 38191559 PMCID: PMC10775585 DOI: 10.1186/s40462-023-00434-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/23/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Hidden Markov Models (HMMs) are often used to model multi-state capture-recapture data in ecology. However, a variety of HMM modeling approaches and software exist, including both maximum likelihood and Bayesian methods. The diversity of these methods obscures the underlying HMM and can exaggerate minor differences in parameterization. METHODS In this paper, we describe a general framework for modelling multi-state capture-recapture data via HMMs using both maximum likelihood and Bayesian methods. We then apply an HMM to invasive silver carp telemetry data from the Illinois River and compare the results estimated by both methods. RESULTS Our analysis demonstrates disadvantages of relying on a single approach and highlights insights obtained from implementing both methods together. While both methods often struggled to converge, our results show biologically informative priors for Bayesian methods and initial values for maximum likelihood methods can guide convergence toward realistic solutions. Incorporating prior knowledge of the system can successfully constrain estimation to biologically realistic movement and detection probabilities when dealing with sparse data. CONCLUSIONS Biologically unrealistic estimates may be a sign of poor model convergence. In contrast, consistent convergence behavior across approaches can increase the credibility of a model. Estimates of movement probabilities can strongly influence the predicted population dynamics of a system. Therefore, thoroughly assessing results from HMMs is important when evaluating potential management strategies, particularly for invasive species.
Collapse
Affiliation(s)
- Charles J Labuzzetta
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, WI, 54603, USA.
| | - Alison A Coulter
- South Dakota State University, McFadden Biostress Laboratory 138, Box 2140B, Brookings, SD, 57007, USA
| | - Richard A Erickson
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Road, La Crosse, WI, 54603, USA
| |
Collapse
|
6
|
McClintock BT, Lander ME. A multistate Langevin diffusion for inferring behavior-specific habitat selection and utilization distributions. Ecology 2024; 105:e4186. [PMID: 37794831 DOI: 10.1002/ecy.4186] [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: 12/15/2022] [Revised: 06/29/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The identification of important habitat and the behavior(s) associated with it is critical to conservation and place-based management decisions. Behavior also links life-history requirements and habitat use, which are key to understanding why animals use certain habitats. Animal population studies often use tracking data to quantify space use and habitat selection, but they typically either ignore movement behavior (e.g., foraging, migrating, nesting) or adopt a two-stage approach that can induce bias and fail to propagate uncertainty. We develop a habitat-driven Langevin diffusion for animals that exhibit distinct movement behavior states, thereby providing a novel single-stage statistical method for inferring behavior-specific habitat selection and utilization distributions in continuous time. Practitioners can customize, fit, assess, and simulate our integrated model using the provided R package. Simulation experiments demonstrated that the model worked well under a range of sampling scenarios as long as observations were of sufficient temporal resolution. Our simulations also demonstrated the importance of accounting for different behaviors and the misleading inferences that can result when these are ignored. We provide case studies using plains zebra (Equus quagga) and Steller sea lion (Eumetopias jubatus) telemetry data. In the zebra example, our model identified distinct "encamped" and "exploratory" states, where the encamped state was characterized by strong selection for grassland and avoidance of other vegetation types, which may represent selection for foraging resources. In the sea lion example, our model identified distinct movement behavior modes typically associated with this marine central-place forager and, unlike previous analyses, found foraging-type movements to be associated with steeper offshore slopes characteristic of the continental shelf, submarine canyons, and seamounts that are believed to enhance prey concentrations. This is the first single-stage approach for inferring behavior-specific habitat selection and utilization distributions from tracking data that can be readily implemented with user-friendly software. As certain behaviors are often more relevant to specific conservation or management objectives, practitioners can use our model to help inform the identification and prioritization of important habitats. Moreover, by linking individual-level movement behaviors to population-level spatial processes, the multistate Langevin diffusion can advance inferences at the intersection of population, movement, and landscape ecology.
Collapse
Affiliation(s)
- Brett T McClintock
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA, National Marine Fisheries Service, Seattle, Washington, USA
| | - Michelle E Lander
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NOAA, National Marine Fisheries Service, Seattle, Washington, USA
| |
Collapse
|
7
|
Mildiner Moraga S, Aarts E. Go Multivariate: Recommendations on Bayesian Multilevel Hidden Markov Models with Categorical Data. MULTIVARIATE BEHAVIORAL RESEARCH 2024; 59:17-45. [PMID: 37195880 DOI: 10.1080/00273171.2023.2205392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The multilevel hidden Markov model (MHMM) is a promising method to investigate intense longitudinal data obtained within the social and behavioral sciences. The MHMM quantifies information on the latent dynamics of behavior over time. In addition, heterogeneity between individuals is accommodated with the inclusion of individual-specific random effects, facilitating the study of individual differences in dynamics. However, the performance of the MHMM has not been sufficiently explored. We performed an extensive simulation to assess the effect of the number of dependent variables (1-8), number of individuals (5-90), and number of observations per individual (100-1600) on the estimation performance of a Bayesian MHMM with categorical data including various levels of state distinctiveness and separation. We found that using multivariate data generally alleviates the sample size needed and improves the stability of the results. Moreover, including variables only consisting of random noise was generally not detrimental to model performance. Regarding the estimation of group-level parameters, the number of individuals and observations largely compensate for each other. However, only the former drives the estimation of between-individual variability. We conclude with guidelines on the sample size necessary based on the level of state distinctiveness and separation and study objectives of the researcher.
Collapse
Affiliation(s)
- Sebastian Mildiner Moraga
- Department of Methodology and Statistics, Faculty of Social and Behavioural Sciences, Utrecht University
| | - Emmeke Aarts
- Department of Methodology and Statistics, Faculty of Social and Behavioural Sciences, Utrecht University
| |
Collapse
|
8
|
Russo NJ, Davies AB, Blakey RV, Ordway EM, Smith TB. Feedback loops between 3D vegetation structure and ecological functions of animals. Ecol Lett 2023; 26:1597-1613. [PMID: 37419868 DOI: 10.1111/ele.14272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 07/09/2023]
Abstract
Ecosystems function in a series of feedback loops that can change or maintain vegetation structure. Vegetation structure influences the ecological niche space available to animals, shaping many aspects of behaviour and reproduction. In turn, animals perform ecological functions that shape vegetation structure. However, most studies concerning three-dimensional vegetation structure and animal ecology consider only a single direction of this relationship. Here, we review these separate lines of research and integrate them into a unified concept that describes a feedback mechanism. We also show how remote sensing and animal tracking technologies are now available at the global scale to describe feedback loops and their consequences for ecosystem functioning. An improved understanding of how animals interact with vegetation structure in feedback loops is needed to conserve ecosystems that face major disruptions in response to climate and land-use change.
Collapse
Affiliation(s)
- Nicholas J Russo
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Andrew B Davies
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Rachel V Blakey
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, California, USA
- Biological Sciences Department, California State Polytechnic University, Pomona, California, USA
| | - Elsa M Ordway
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, California, USA
| | - Thomas B Smith
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, California, USA
| |
Collapse
|
9
|
Raboin M, Plumb JM, Sholtis MD, Smith DL, Jackson PR, Rivera JM, Suski CD, Cupp AR. Movement and behavioral states of common carp (Cyprinus carpio) in response to a behavioral deterrent in a navigational lock. MOVEMENT ECOLOGY 2023; 11:42. [PMID: 37496021 PMCID: PMC10373248 DOI: 10.1186/s40462-023-00396-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 05/30/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Freshwater ecosystems are some of the most affected by biological invasions due, in part, to the introduction of invasive carp worldwide. Where carp have become established, management programs often seek to limit further range expansion into new areas by reducing their movement through interconnected rivers and waterways. Lock and dams are important locations for non-physical deterrents, such as carbon dioxide (CO2), to reduce unwanted fish passage without disrupting human use. The purpose of this study was to evaluate the behavioral responses of common carp (Cyprinus carpio) to non-physical deterrents within a navigation structure on the Fox River, Wisconsin. Acoustic telemetry combined with hidden Markov models (HMMs) was used to analyze variation in carp responses to treatments. Outcomes may inform CO2 effectiveness at preventing invasive carp movement through movement pinch-points. METHODS Carbon dioxide (CO2) was recently registered as a pesticide in the United States for use as a deterrent to invasive carp movement. As a part of a multi-component study to test a large-scale CO2 delivery system within a navigation lock, we characterized the influence of elevated CO2 and forced water circulation in the lock chamber on carp movements and behavior. Through time-to-event analyses, we described the responses of acoustic-tagged carp to experimental treatments including (1) CO2 injection in water with forced water circulation, (2) forced water circulation without CO2 and (3) no forced water circulation or CO2. We then used hidden Markov models (HMMs) to define fine-scale carp movement and evaluate the relationships between carp behavioral states and CO2 concentration, forced water circulation, and temperature. RESULTS Forced water circulation with and without CO2 injection were effective at expelling carp from the lock chamber relative to null treatments where no stimulus was applied. A portion of carp exposed to forced water circulation with CO2 transitioned from an exploratory to an encamped behavioral state with shorter step-lengths and a unimodal distribution in turning angles, resulting in some carp remaining in the lock chamber. Whereas carp exposed to forced water circulation only remained primarily in an exploratory behavioral state, resulting in all carp exiting the lock chamber. CONCLUSION Our findings illustrate the potential of forced water circulation, alone, as a non-physical deterrent and the efficacy of CO2 injection with forced water circulation in expelling carp from a navigation lock. Results demonstrate how acoustic telemetry and HMMs in an experimental context can describe fish behavior and inform management strategies.
Collapse
Affiliation(s)
- Maggie Raboin
- Contractor to U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Rd, La Crosse, WI, 54603, USA.
| | - John M Plumb
- U.S. Geological Survey, Columbia River Research Laboratory, 5501A Cook-Underwood Rd., Cook, WA, 98605, USA
| | - Matthew D Sholtis
- U.S. Geological Survey, Columbia River Research Laboratory, 5501A Cook-Underwood Rd., Cook, WA, 98605, USA
| | - David L Smith
- Engineer Research and Development Center, U.S. Army Corps of Engineers, 3909 Halls Ferry Rd., Vicksburg, MS, 39180, USA
| | - P Ryan Jackson
- U.S. Geological Survey Central Midwest Water Science Center, 405 N Goodwin Ave, Urbana, IL, 61801, USA
| | - Jose M Rivera
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Rd., La Crosse, WI, 54603, USA
| | - Cory D Suski
- Department of Natural Resources and Environmental Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Aaron R Cupp
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, 2630 Fanta Reed Rd., La Crosse, WI, 54603, USA
| |
Collapse
|
10
|
Gonçalves BP, Poyraz O, Paul P, Lawn JE. Inferring longitudinal patterns of group B Streptococcus colonization during pregnancy. iScience 2023; 26:107023. [PMID: 37534153 PMCID: PMC10391671 DOI: 10.1016/j.isci.2023.107023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 08/04/2023] Open
Abstract
Maternal colonization by Group B Streptococcus (GBS) can lead to severe infection in neonates and has also been associated with prematurity and stillbirth. Better quantitative understanding of the trajectories of GBS carriage during pregnancy is essential for the design of informative epidemiological studies. Here, we describe analyses of published longitudinal data using Bayesian hidden Markov models, which involve the estimation of parameters related to the succession of latent states (infection status) and observations (culture positivity). In addition to quantifying infection acquisition and clearance probabilities, the statistical approach also suggests that for some longitudinal patterns of culture results, pregnant women were likely to have been GBS-colonized despite a negative diagnostic result. We believe this method, if used in future longitudinal studies of maternal GBS colonization, would improve our understanding of the pathologies linked to this bacterium and could also inform maternal GBS vaccine trial design.
Collapse
Affiliation(s)
- Bronner P. Gonçalves
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Maternal, Adolescent, Reproductive & Child Health Centre, London School of Hygiene & Tropical Medicine, London, UK
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Onur Poyraz
- Department of Computer Science, Aalto University School of Science, Aalto, Finland
| | - Proma Paul
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Maternal, Adolescent, Reproductive & Child Health Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Joy E. Lawn
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Maternal, Adolescent, Reproductive & Child Health Centre, London School of Hygiene & Tropical Medicine, London, UK
| |
Collapse
|
11
|
Paterson JT, Johnston AN, Ortega AC, Wallace C, Kauffman M. Hidden Markov movement models reveal diverse seasonal movement patterns in two North American ungulates. Ecol Evol 2023; 13:e10282. [PMID: 37484933 PMCID: PMC10361361 DOI: 10.1002/ece3.10282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Animal movement is the mechanism connecting landscapes to fitness, and understanding variation in seasonal animal movements has benefited from the analysis and categorization of animal displacement. However, seasonal movement patterns can defy classification when movements are highly variable. Hidden Markov movement models (HMMs) are a class of latent-state models well-suited to modeling movement data. Here, we used HMMs to assess seasonal patterns of variation in the movement of pronghorn (Antilocapra americana), a species known for variable seasonal movements that challenge analytical approaches, while using a population of mule deer (Odocoileus hemionus), for whom seasonal movements are well-documented, as a comparison. We used population-level HMMs in a Bayesian framework to estimate a seasonal trend in the daily probability of transitioning between a short-distance local movement state and a long-distance movement state. The estimated seasonal patterns of movements in mule deer closely aligned with prior work based on indices of animal displacement: a short period of long-distance movements in the fall season and again in the spring, consistent with migrations to and from seasonal ranges. We found seasonal movement patterns for pronghorn were more variable, as a period of long-distance movements in the fall was followed by a winter period in which pronghorn were much more likely to further initiate and remain in a long-distance movement pattern compared with the movement patterns of mule deer. Overall, pronghorn were simply more likely to be in a long-distance movement pattern throughout the year. Hidden Markov movement models provide inference on seasonal movements similar to other methods, while providing a robust framework to understand movement patterns on shorter timescales and for more challenging movement patterns. Hidden Markov movement models can allow a rigorous assessment of the drivers of changes in movement patterns such as extreme weather events and land development, important for management and conservation.
Collapse
Affiliation(s)
| | - Aaron N. Johnston
- U.S. Geological SurveyNorthern Rocky Mountain Science CenterBozemanMontanaUSA
| | - Anna C. Ortega
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWyomingUSA
| | - Cody Wallace
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWyomingUSA
| | - Matthew Kauffman
- Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWyomingUSA
- U.S. Geological Survey, Wyoming Cooperative Fish and Wildlife Research Unit, Department of Zoology and PhysiologyUniversity of WyomingLaramieWyomingUSA
| |
Collapse
|
12
|
True MC, Gorman KM, Taylor H, Reynolds RJ, Ford WM. Fall migration, oceanic movement, and site residency patterns of eastern red bats (Lasiurus borealis) on the mid-Atlantic Coast. MOVEMENT ECOLOGY 2023; 11:35. [PMID: 37316899 DOI: 10.1186/s40462-023-00398-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
Along the mid-Atlantic coast of the United States, eastern red bats (Lasiurus borealis) are present during fall mating and migration, though little is currently known about most aspects of bat migration. To reveal migration patterns, and understand drivers of over-water flight, we captured and radio-tagged 115 eastern red bats using novel technology, and subsequently tracked and described their movements throughout the region. We compared over-water flight movements to randomly generated patterns using a use-availability framework, and subsequently used a generalized linear mixed effects model to assess the relationship of over-water flight to atmospheric variables. We used hidden Markov models to assess daily activity patterns and site residency. Most bats with long-distance movements traveled in a southwesterly direction, however path vectors were often oriented interior toward the continental landmass rather than along the coastline. We observed that some bats transited wide sections of the Chesapeake and Delaware bays, confirming their ability to travel across large water bodies. This over-water flight typically occurred in the early hours of the night and during favorable flying conditions. If flight over large water bodies is a proxy for over-ocean flight, then collision risk at offshore wind turbines - a major source of migratory bat fatalities - may be linked nightly to warm temperatures that occur early in the fall season. Risk, then, may be somewhat predictable and manageable with mitigation options linking wind-energy operation to weather conditions and seasonality.
Collapse
Affiliation(s)
- Michael C True
- Western EcoSystems Technology, Inc., 2121 Midpoint Drive, Suite 201, Fort Collins, CO, 80525, USA
| | - Katherine M Gorman
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, 149 Cheatham Hall, 310 West Campus Drive, Blacksburg, VA, 24061-0321, USA.
| | - Hila Taylor
- Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State University, 149 Cheatham Hall, 310 West Campus Drive, Blacksburg, VA, 24061-0321, USA
| | - Richard J Reynolds
- Virginia Department of Wildlife Resources, 517 Lee Hwy, Verona, VA, 24482, USA
| | - W Mark Ford
- U.S. Geological Survey, Virginia Cooperative Fish and Wildlife Research Unit, Virginia Polytechnic Institute and State University, 106 Cheatham Hall, 310 West Campus Drive, Blacksburg, VA, 24061-0321, USA
| |
Collapse
|
13
|
Silk MJ, Gimenez O. Generation and applications of simulated datasets to integrate social network and demographic analyses. Ecol Evol 2023; 13:e9871. [PMID: 37200911 PMCID: PMC10185435 DOI: 10.1002/ece3.9871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/15/2022] [Accepted: 02/09/2023] [Indexed: 05/20/2023] Open
Abstract
Social networks are tied to population dynamics; interactions are driven by population density and demographic structure, while social relationships can be key determinants of survival and reproductive success. However, difficulties integrating models used in demography and network analysis have limited research at this interface. We introduce the R package genNetDem for simulating integrated network-demographic datasets. It can be used to create longitudinal social network and/or capture-recapture datasets with known properties. It incorporates the ability to generate populations and their social networks, generate grouping events using these networks, simulate social network effects on individual survival, and flexibly sample these longitudinal datasets of social associations. By generating co-capture data with known statistical relationships, it provides functionality for methodological research. We demonstrate its use with case studies testing how imputation and sampling design influence the success of adding network traits to conventional Cormack-Jolly-Seber (CJS) models. We show that incorporating social network effects into CJS models generates qualitatively accurate results, but with downward-biased parameter estimates when network position influences survival. Biases are greater when fewer interactions are sampled or fewer individuals observed in each interaction. While our results indicate the potential of incorporating social effects within demographic models, they show that imputing missing network measures alone is insufficient to accurately estimate social effects on survival, pointing to the importance of incorporating network imputation approaches. genNetDem provides a flexible tool to aid these methodological advancements and help researchers testing other sampling considerations in social network studies.
Collapse
|
14
|
Hewitt DE, Johnson DD, Suthers IM, Taylor MD. Crabs ride the tide: incoming tides promote foraging of Giant Mud Crab (Scylla serrata). MOVEMENT ECOLOGY 2023; 11:21. [PMID: 37069648 PMCID: PMC10108527 DOI: 10.1186/s40462-023-00384-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Effective fisheries management of mobile species relies on robust knowledge of animal behaviour and habitat-use. Indices of behaviour can be useful for interpreting catch-per-unit-effort data which acts as a proxy for relative abundance. Information about habitat-use can inform stocking release strategies or the design of marine protected areas. The Giant Mud Crab (Scylla serrata; Family: Portunidae) is a swimming estuarine crab that supports significant fisheries harvest throughout the Indo-West Pacific, but little is known about the fine-scale movement and behaviour of this species. METHODS We tagged 18 adult Giant Mud Crab with accelerometer-equipped acoustic tags to track their fine-scale movement using a hyperbolic positioning system, alongside high temporal resolution environmental data (e.g., water temperature), in a temperate south-east Australian estuary. A hidden Markov model was used to classify movement (i.e., step length, turning angle) and acceleration data into discrete behaviours, while also considering the possibility of individual variation in behavioural dynamics. We then investigated the influence of environmental covariates on these behaviours based on previously published observations. RESULTS We fitted a model with two well-distinguished behavioural states describing periods of inactivity and foraging, and found no evidence of individual variation in behavioural dynamics. Inactive periods were most common (79% of time), and foraging was most likely during low, incoming tides; while inactivity was more likely as the high tide receded. Model selection removed time (hour) of day and water temperature (°C) as covariates, suggesting that they do not influence Giant Mud Crab behavioural dynamics at the temporal scale investigated. CONCLUSIONS Our study is the first to quantitatively link fine-scale movement and behaviour of Giant Mud Crab to environmental variation. Our results suggest Giant Mud Crab are a predominantly sessile species, and support their status as an opportunistic scavenger. We demonstrate a relationship between the tidal cycle and foraging that is likely to minimize predation risk while maximizing energetic efficiency. These results may explain why tidal covariates influence catch rates in swimming crabs, and provide a foundation for standardisation and interpretation of catch-per-unit-effort data-a commonly used metric in fisheries science.
Collapse
Affiliation(s)
- Daniel E Hewitt
- Fisheries and Marine Environmental Research Lab, Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, University of New South Wales, NSW, Sydney, 2052, Australia.
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, NSW, Locked Bag 1, Nelson Bay, 2315, Australia.
| | - Daniel D Johnson
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, NSW, Locked Bag 1, Nelson Bay, 2315, Australia
| | - Iain M Suthers
- Fisheries and Marine Environmental Research Lab, Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, University of New South Wales, NSW, Sydney, 2052, Australia
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Matthew D Taylor
- Fisheries and Marine Environmental Research Lab, Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Science, University of New South Wales, NSW, Sydney, 2052, Australia
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, NSW, Locked Bag 1, Nelson Bay, 2315, Australia
| |
Collapse
|
15
|
Gilbert NA, McGinn KA, Nunes LA, Shipley AA, Bernath-Plaisted J, Clare JDJ, Murphy PW, Keyser SR, Thompson KL, Maresh Nelson SB, Cohen JM, Widick IV, Bartel SL, Orrock JL, Zuckerberg B. Daily activity timing in the Anthropocene. Trends Ecol Evol 2023; 38:324-336. [PMID: 36402653 DOI: 10.1016/j.tree.2022.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/12/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022]
Abstract
Animals are facing novel 'timescapes' in which the stimuli entraining their daily activity patterns no longer match historical conditions due to anthropogenic disturbance. However, the ecological effects (e.g., altered physiology, species interactions) of novel activity timing are virtually unknown. We reviewed 1328 studies and found relatively few focusing on anthropogenic effects on activity timing. We suggest three hypotheses to stimulate future research: (i) activity-timing mismatches determine ecological effects, (ii) duration and timing of timescape modification influence effects, and (iii) consequences of altered activity timing vary biogeographically due to broad-scale variation in factors compressing timescapes. The continued growth of sampling technologies promises to facilitate the study of the consequences of altered activity timing, with emerging applications for biodiversity conservation.
Collapse
Affiliation(s)
- Neil A Gilbert
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kate A McGinn
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laura A Nunes
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy A Shipley
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA; School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Jacy Bernath-Plaisted
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John D J Clare
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA; Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Penelope W Murphy
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer R Keyser
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kimberly L Thompson
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA; German Centre for Integrative Biodiversity Research (iDiv), 04103 Halle-Jena-Leipzig, Germany
| | - Scott B Maresh Nelson
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jeremy M Cohen
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Ivy V Widick
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Savannah L Bartel
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John L Orrock
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benjamin Zuckerberg
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
16
|
Nussbaumer R, Gravey M, Briedis M, Liechti F, Sheldon D. Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Affiliation(s)
- Raphaël Nussbaumer
- Cornell Lab of Ornithology Ithaca New York USA
- Swiss Ornithological Institute Sempach Switzerland
| | - Mathieu Gravey
- Department of Physical Geography, Faculty of Geosciences Utrecht University Utrecht Netherlands
| | - Martins Briedis
- Swiss Ornithological Institute Sempach Switzerland
- Lab of Ornithology Institute of Biology, University of Latvia Riga Latvia
| | - Felix Liechti
- Swiss Ornithological Institute Sempach Switzerland
- Swiss Birdradar Solutions AG Winterthur Switzerland
| | - Daniel Sheldon
- University of Massachusetts Amherst Amherst Massachusetts USA
| |
Collapse
|
17
|
Oliveira T, Carricondo-Sanchez D, Mattisson J, Vogt K, Corradini A, Linnell JDC, Odden J, Heurich M, Rodríguez-Recio M, Krofel M. Predicting kill sites of an apex predator from GPS data in different multiprey systems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2778. [PMID: 36383087 DOI: 10.1002/eap.2778] [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: 05/03/2022] [Revised: 08/11/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Kill rates are a central parameter to assess the impact of predation on prey species. An accurate estimation of kill rates requires a correct identification of kill sites, often achieved by field-checking GPS location clusters (GLCs). However, there are potential sources of error included in kill-site identification, such as failing to detect GLCs that are kill sites, and misclassifying the generated GLCs (e.g., kill for nonkill) that were not field checked. Here, we address these two sources of error using a large GPS dataset of collared Eurasian lynx (Lynx lynx), an apex predator of conservation concern in Europe, in three multiprey systems, with different combinations of wild, semidomestic, and domestic prey. We first used a subsampling approach to investigate how different GPS-fix schedules affected the detection of GLC-indicated kill sites. Then, we evaluated the potential of the random forest algorithm to classify GLCs as nonkills, small prey kills, and ungulate kills. We show that the number of fixes can be reduced from seven to three fixes per night without missing more than 5% of the ungulate kills, in a system composed of wild prey. Reducing the number of fixes per 24 h decreased the probability of detecting GLCs connected with kill sites, particularly those of semidomestic or domestic prey, and small prey. Random forest successfully predicted between 73%-90% of ungulate kills, but failed to classify most small prey in all systems, with sensitivity (true positive rate) lower than 65%. Additionally, removing domestic prey improved the algorithm's overall accuracy. We provide a set of recommendations for studies focusing on kill-site detection that can be considered for other large carnivore species in addition to the Eurasian lynx. We recommend caution when working in systems including domestic prey, as the odds of underestimating kill rates are higher.
Collapse
Affiliation(s)
- Teresa Oliveira
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - David Carricondo-Sanchez
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
| | | | - Kristina Vogt
- Foundation KORA (Carnivore Ecology & Wildlife Management), Ittigen, Switzerland
| | - Andrea Corradini
- Animal Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Italy
| | - John D C Linnell
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - John Odden
- Norwegian Institute for Nature Research, Oslo, Norway
| | - Marco Heurich
- Department of Forestry and Wildlife Management, Inland Norway University of Applied Sciences, Koppang, Norway
- Wildlife Ecology and Wildlife Management, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
- Department of Visitor Management and National Park Monitoring, Forest National Park, Bavarian, Germany
| | | | - Miha Krofel
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
18
|
Pollet IL, McFarlane-Tranquilla L, Burgess NM, Diamond AW, Gjerdrum C, Hedd A, Hoeg R, Jones PL, Mauck RA, Montevecchi WA, Pratte I, Ronconi RA, Shutler D, Wilhelm SI, Mallory ML. Factors influencing mercury levels in Leach's storm-petrels at northwest Atlantic colonies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 860:160464. [PMID: 36427741 DOI: 10.1016/j.scitotenv.2022.160464] [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: 02/15/2022] [Revised: 11/13/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Mercury (Hg) is a globally distributed heavy metal, with negative effects on wildlife. Its most toxic form, methylmercury (MeHg), predominates in aquatic systems. Levels of MeHg in marine predators can vary widely among individuals and populations. Leach's storm-petrels (Hydrobates leucorhous) have elevated levels of Hg but the role of Hg in storm-petrel population declines is unknown. In this study, we used egg and blood samples to study variation in Hg exposure among several northwest Atlantic colonies during breeding seasons, thereby evaluating relative toxicity risk within and among colonies. Total mercury (THg) concentrations were higher with increasing colony latitude, and were more pronounced in blood than in eggs. THg concentrations in blood were mostly associated with low toxicity risk in birds from the southern colonies and moderate risks in birds from the northern colonies; however, those values did not affect hatching or fledging success. THg concentrations in both eggs and blood were positively correlated with δ34S, emphasizing the role of sulfate-reducing bacteria in methylation of THg acquired through marine food webs, which is consistent with enriched δ34S profiles. By associating tracking data from foraging trips with THg from blood, we determined that blood THg levels were higher when storm-petrel's intensive search locations were over deeper waters. We conclude that spatial variation in THg concentrations in Leach's storm-petrels is attributable to differences in ocean depth at foraging locations, both at individual and colony levels. Differences in diet among colonies observed previously are the most likely cause for observed blood THg differences. As one of the few pelagic seabird species breeding in Atlantic Canada, with limited overlap in core foraging areas among colonies, Leach's storm-petrels can be used as biomonitors for less sampled offshore pelagic regions. The global trend in Hg emissions combined with legacy levels warrant continued monitoring for toxicity effects in seabirds.
Collapse
Affiliation(s)
- Ingrid L Pollet
- Acadia University, Department of Biology, Wolfville, Nova Scotia B4P 2R6, Canada; Birds Canada, PO Box 6436, Sackville, New Brunswick E4L 1G6, Canada.
| | | | - Neil M Burgess
- Environment and Climate Change Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Antony W Diamond
- Atlantic Laboratory for Avian Research, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Carina Gjerdrum
- Canadian Wildlife Service, Environment and Climate Change Canada, 45 Alderney Drive, Dartmouth, Nova Scotia B2Y 2N6, Canada
| | - April Hedd
- Environment and Climate Change Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Rielle Hoeg
- Acadia University, Department of Biology, Wolfville, Nova Scotia B4P 2R6, Canada; Birds Canada, PO Box 6436, Sackville, New Brunswick E4L 1G6, Canada
| | | | | | - William A Montevecchi
- Psychology Department, Memorial University, St John's, Newfoundland and Labrador A1C 3C9, Canada
| | - Isabeau Pratte
- Canadian Wildlife Service, Environment and Climate Change Canada, 45 Alderney Drive, Dartmouth, Nova Scotia B2Y 2N6, Canada
| | - Robert A Ronconi
- Canadian Wildlife Service, Environment and Climate Change Canada, 45 Alderney Drive, Dartmouth, Nova Scotia B2Y 2N6, Canada
| | - Dave Shutler
- Acadia University, Department of Biology, Wolfville, Nova Scotia B4P 2R6, Canada
| | - Sabina I Wilhelm
- Environment and Climate Change Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Mark L Mallory
- Acadia University, Department of Biology, Wolfville, Nova Scotia B4P 2R6, Canada
| |
Collapse
|
19
|
Sorel MH, Murdoch AR, Zabel RW, Jorgensen JC, Kamphaus CM, Converse SJ. Juvenile life history diversity is associated with lifetime individual heterogeneity in a migratory fish. Ecosphere 2023. [DOI: 10.1002/ecs2.4366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Mark H. Sorel
- Washington Cooperative Fish and Wildlife Research Unit, School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Andrew R. Murdoch
- Washington Department of Fish and Wildlife North Olympia Washington USA
| | - Richard W. Zabel
- National Marine Fisheries Service Northwest Fisheries Science Center Seattle Washington USA
| | - Jeffrey C. Jorgensen
- National Marine Fisheries Service Northwest Fisheries Science Center Seattle Washington USA
| | - Corey M. Kamphaus
- Yakama Nation Fisheries, Mid‐Columbia Field Station Peshastin Washington USA
| | - Sarah J. Converse
- US Geological Survey, Washington Cooperative Fish and Wildlife Research Unit, School of Environmental and Forest Sciences & School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| |
Collapse
|
20
|
Bassing SB, DeVivo M, Ganz TR, Kertson BN, Prugh LR, Roussin T, Satterfield L, Windell RM, Wirsing AJ, Gardner B. Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2745. [PMID: 36107138 DOI: 10.1002/eap.2745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/05/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Estimating habitat and spatial associations for wildlife is common across ecological studies and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inference to understand how scalable information is from the individual to the population. We used Global Positioning System (GPS) collar (Lagrangian) and camera trap (Eulerian) data for seven species collected simultaneously in eastern Washington (2018-2020) to compare inferences made from different survey perspectives. We fit the respective data streams to resource selection functions (RSFs) and occupancy models and compared estimated habitat- and space-use patterns for each species. Although previous studies have considered whether individual- and population-level data generated comparable information, ours is the first to make this comparison for multiple species simultaneously and to specifically ask whether inferences from the two perspectives differed depending on the focal species. We found general agreement between the predicted spatial distributions for most paired analyses, although specific habitat relationships differed. We hypothesize the discrepancies arose due to differences in statistical power associated with camera and GPS-collar sampling, as well as spatial mismatches in the data. Our research suggests data collected from individual-based sampling methods can capture coarse population-wide patterns for a diversity of species, but results differ when interpreting specific wildlife-habitat relationships.
Collapse
Affiliation(s)
- Sarah B Bassing
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Melia DeVivo
- Washington Department of Fish and Wildlife, Spokane Valley, Washington, USA
| | - Taylor R Ganz
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Brian N Kertson
- Washington Department of Fish and Wildlife, Snoqualmie, Washington, USA
| | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Trent Roussin
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
- Washington Department of Fish and Wildlife, Colville, Washington, USA
| | - Lauren Satterfield
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Rebecca M Windell
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Aaron J Wirsing
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Beth Gardner
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| |
Collapse
|
21
|
McCrea R, King R, Graham L, Börger L. Realising the promise of large data and complex models. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rachel McCrea
- Department of Mathematics and Statistics Lancaster University Lancaster UK
| | - Ruth King
- School of Mathematics and Maxwell Institute for Mathematical Sciences University of Edinburgh Edinburgh UK
| | - Laura Graham
- Geography, Earth & Environmental Sciences University of Birmingham Birmingham UK
- Biodiversity, Ecology & Conservation Group International Institute for Applied Systems Analysis Vienna Austria
| | - Luca Börger
- Department of Biosciences Swansea University Swansea UK
- Centre for Biomathematics Swansea University Swansea UK
| |
Collapse
|
22
|
Lennox RJ, Dahlmo LS, Ford AT, Sortland LK, Vogel EF, Vollset KW. Predation research with electronic tagging. WILDLIFE BIOLOGY 2022. [DOI: 10.1002/wlb3.01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Robert J. Lennox
- Norwegian Inst. for Nature Research Trondheim Norway
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
| | - Lotte S. Dahlmo
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
- Dept of Biological Sciences, Univ. of Bergen Bergen Norway
| | - Adam T. Ford
- Univ. of British Columbia Okanagan Kelowna BC Canada
| | - Lene K. Sortland
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
- Dept of Biological Sciences, Univ. of Bergen Bergen Norway
| | - Emma F. Vogel
- UiT − The Arctic Univ. of Norway, Faculty of Biosciences, Fisheries and Economics Tromsø Norway
| | - Knut Wiik Vollset
- NORCE Norwegian Research Centre, Laboratory for Freshwater Ecology and Inland Fisheries Bergen Norway
| |
Collapse
|
23
|
Wilber MQ, Knapp RA, Smith TC, Briggs CJ. Host density has limited effects on pathogen invasion, disease-induced declines and within-host infection dynamics across a landscape of disease. J Anim Ecol 2022; 91:2451-2464. [PMID: 36285540 DOI: 10.1111/1365-2656.13823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
1. Host density is hypothesized to be a major driver of variability in the responses and outcomes of wildlife populations following pathogen invasion. While the effects of host density on pathogen transmission have been extensively studied, these studies are dominated by theoretical analyses and small-scale experiments. This focus leads to an incomplete picture regarding how host density drives observed variability in disease outcomes in the field. 2. Here, we leveraged a dataset of hundreds of replicate amphibian populations that varied by orders of magnitude in host density. We used these data to test the effects of host density on three outcomes following the arrival of the amphibian-killing fungal pathogen Batrachochytrium dendrobatidis (Bd): the probability that Bd successfully invaded a host population and led to a pathogen outbreak, the magnitude of the host population-level decline following an outbreak and within-host infection dynamics that drive population-level outcomes in amphibian-pathogen systems. 3. Based on previous small-scale transmission experiments, we expected that populations with higher densities would be more likely to experience Bd outbreaks and would suffer larger proportional declines following outbreaks. To test these predictions, we developed and fitted a Hidden Markov Model that accounted for imperfectly observed disease outbreak states in the amphibian populations we surveyed. 4. Contrary to our predictions, we found minimal effects of host density on the probability of successful Bd invasion, the magnitude of population decline following Bd invasion and the dynamics of within-host infection intensity. Environmental conditions, such as summer temperature, winter severity and the presence of pathogen reservoirs, were more predictive of variability in disease outcomes. 5. Our results highlight the limitations of extrapolating findings from small-scale transmission experiments to observed disease trajectories in the field and provide strong evidence that variability in host density does not necessarily drive variability in host population responses following pathogen arrival. In an applied context, we show that feedbacks between host density and disease will not necessarily affect the success of reintroduction efforts in amphibian-Bd systems of conservation concern.
Collapse
Affiliation(s)
- Mark Q Wilber
- Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, Tennessee, USA
| | - Roland A Knapp
- Earth Research Institute, University of California, Santa Barbara, California, USA.,Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, USA
| | - Thomas C Smith
- Earth Research Institute, University of California, Santa Barbara, California, USA.,Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, California, USA
| | - Cheryl J Briggs
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| |
Collapse
|
24
|
Togunov RR, Derocher AE, Lunn NJ, Auger-Méthé M. Drivers of polar bear behavior and the possible effects of prey availability on foraging strategy. MOVEMENT ECOLOGY 2022; 10:50. [PMID: 36384775 PMCID: PMC9670556 DOI: 10.1186/s40462-022-00351-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/09/2022] [Indexed: 06/05/2023]
Abstract
BACKGROUND Change in behavior is one of the earliest responses to variation in habitat suitability. It is therefore important to understand the conditions that promote different behaviors, particularly in areas undergoing environmental change. Animal movement is tightly linked to behavior and remote tracking can be used to study ethology when direct observation is not possible. METHODS We used movement data from 14 polar bears (Ursus maritimus) in Hudson Bay, Canada, during the foraging season (January-June), when bears inhabit the sea ice. We developed an error-tolerant method to correct for sea ice drift in tracking data. Next, we used hidden Markov models with movement and orientation relative to wind to study three behaviors (stationary, area-restricted search, and olfactory search) and examine effects of 11 covariates on behavior. RESULTS Polar bears spent approximately 47% of their time in the stationary drift state, 29% in olfactory search, and 24% in area-restricted search. High energy behaviors occurred later in the day (around 20:00) compared to other populations. Second, olfactory search increased as the season progressed, which may reflect a shift in foraging strategy from still-hunting to active search linked to a shift in seal availability (i.e., increase in haul-outs from winter to the spring pupping and molting seasons). Last, we found spatial patterns of distribution linked to season, ice concentration, and bear age that may be tied to habitat quality and competitive exclusion. CONCLUSIONS Our observations were generally consistent with predictions of the marginal value theorem, and differences between our findings and other populations could be explained by regional or temporal variation in resource availability. Our novel movement analyses and finding can help identify periods, regions, and conditions of critical habitat.
Collapse
Affiliation(s)
- Ron R. Togunov
- Institute for the Oceans and Fisheries, The University of British Columbia, V6T 1Z4 Vancouver, Canada
- Department of Zoology, The University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Andrew E. Derocher
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2E9 Canada
| | - Nicholas J. Lunn
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Edmonton, T6G 2E9 Canada
| | - Marie Auger-Méthé
- Institute for the Oceans and Fisheries, The University of British Columbia, V6T 1Z4 Vancouver, Canada
- Department of Statistics, The University of British Columbia, Vancouver, V6T 1Z4 Canada
| |
Collapse
|
25
|
Patterson A, Gilchrist HG, Robertson GJ, Hedd A, Fifield DA, Elliott KH. Behavioural flexibility in an Arctic seabird using two distinct marine habitats to survive the energetic constraints of winter. MOVEMENT ECOLOGY 2022; 10:45. [PMID: 36329536 PMCID: PMC9635182 DOI: 10.1186/s40462-022-00344-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Homeothermic marine animals in Polar Regions face an energetic bottleneck in winter. The challenges of short days and cold temperatures are exacerbated for flying seabirds with small body size and limited fat stores. We use biologging approaches to examine how habitat, weather, and moon illumination influence behaviour and energetics of a marine bird species, thick-billed murres (Uria lomvia). METHODS We used temperature-depth-light recorders to examine strategies murres use to survive winter in the Northwest Atlantic, where contrasting currents create two distinct marine habitats: cold (-0.1 ± 1.2 °C), shallower water along the Labrador Shelf and warmer (3.1 ± 0.3 °C), deep water in the Labrador Basin. RESULTS In the cold shelf water, murres used a high-energy strategy, with more flying and less diving each day, resulting in high daily energy expenditure and also high apparent energy intake; this strategy was most evident in early winter when day lengths were shortest. By contrast, murres in warmer basin water employed a low-energy strategy, with less time flying and more time diving under low light conditions (nautical twilight and night). In warmer basin water, murres increased diving at night when the moon was more illuminated, likely taking advantage of diel vertically migrating prey. In warmer basin water, murres dove more at night and foraging efficiency increased under negative North Atlantic Oscillation (calmer ocean conditions). CONCLUSIONS The proximity of two distinct marine habitats in this region allows individuals from a single species to use dual (low-energy/high-energy) strategies to overcome winter energy bottlenecks.
Collapse
Affiliation(s)
- Allison Patterson
- Department of Natural Resource Sciences, McGill University, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada.
| | - H Grant Gilchrist
- Environment and Climate Change Canada, National Wildlife Research Centre, 1125 Colonel By Drive, Raven Road, Ottawa, ON, K1A OH3, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL, A1N 4T3, Canada
| | - April Hedd
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL, A1N 4T3, Canada
| | - David A Fifield
- Wildlife Research Division, Environment and Climate Change Canada, 6 Bruce Street, Mount Pearl, NL, A1N 4T3, Canada
| | - Kyle H Elliott
- Department of Natural Resource Sciences, McGill University, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| |
Collapse
|
26
|
|
27
|
Faiman R, Yaro AS, Dao A, Sanogo ZL, Diallo M, Samake D, Yossi O, Veru LM, Graber LC, Conte AR, Kouam C, Krajacich BJ, Lehmann T. Isotopic evidence that aestivation allows malaria mosquitoes to persist through the dry season in the Sahel. Nat Ecol Evol 2022; 6:1687-1699. [PMID: 36216903 DOI: 10.1038/s41559-022-01886-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/11/2022] [Indexed: 11/09/2022]
Abstract
Data suggest that the malaria vector mosquito Anopheles coluzzii persists during the dry season in the Sahel through a dormancy mechanism known as aestivation; however, the contribution of aestivation compared with alternative strategies such as migration is unknown. Here we marked larval Anopheles mosquitoes in two Sahelian villages in Mali using deuterium (2H) to assess the contribution of aestivation to persistence of mosquitoes through the seven-month dry season. After an initial enrichment period, 33% of An. coluzzii mosquitoes were strongly marked. Seven months following enrichment, multiple analysis methods supported the ongoing presence of marked mosquitoes, compatible with the prediction that the fraction of marked mosquitoes should remain stable throughout the dry season if local aestivation is occurring. The results suggest that aestivation is a major persistence mechanism of An. coluzzii in the Sahel, contributing at least 20% of the adults at the onset of rains. This persistence strategy could influence mosquito control and malaria elimination campaigns.
Collapse
Affiliation(s)
- Roy Faiman
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA.
| | - Alpha S Yaro
- Malaria Research and Training Center (MRTC)/Faculty of Medicine, Pharmacy and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Adama Dao
- Malaria Research and Training Center (MRTC)/Faculty of Medicine, Pharmacy and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Zana L Sanogo
- Malaria Research and Training Center (MRTC)/Faculty of Medicine, Pharmacy and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Moussa Diallo
- Malaria Research and Training Center (MRTC)/Faculty of Medicine, Pharmacy and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Djibril Samake
- Malaria Research and Training Center (MRTC)/Faculty of Medicine, Pharmacy and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ousmane Yossi
- Malaria Research and Training Center (MRTC)/Faculty of Medicine, Pharmacy and Odonto-stomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Laura M Veru
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Leland C Graber
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Abigail R Conte
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | - Cedric Kouam
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| | | | - Tovi Lehmann
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA
| |
Collapse
|
28
|
Hollanders M, Royle JA. Know what you don't know: Embracing state uncertainty in disease‐structured multistate models. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthijs Hollanders
- Faculty of Science and Engineering Southern Cross University Lismore New South Wales Australia
| | - J. Andrew Royle
- U.S. Geological Survey, Patuxent Wildlife Research Center Laurel Maryland USA
| |
Collapse
|
29
|
Bacri T, Berentsen GD, Bulla J, Hølleland S. A gentle tutorial on accelerated parameter and confidence interval estimation for hidden Markov models using Template Model Builder. Biom J 2022; 64:1260-1288. [PMID: 35621152 PMCID: PMC9796807 DOI: 10.1002/bimj.202100256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 01/07/2023]
Abstract
A very common way to estimate the parameters of a hidden Markov model (HMM) is the relatively straightforward computation of maximum likelihood (ML) estimates. For this task, most users rely on user-friendly implementation of the estimation routines via an interpreted programming language such as the statistical software environment R. Such an approach can easily require time-consuming computations, in particular for longer sequences of observations. In addition, selecting a suitable approach for deriving confidence intervals for the estimated parameters is not entirely obvious, and often the computationally intensive bootstrap methods have to be applied. In this tutorial, we illustrate how to speed up the computation of ML estimates significantly via the R package TMB. Moreover, this approach permits simple retrieval of standard errors at the same time. We illustrate the performance of our routines using different data sets: first, two smaller samples from a mobile application for tinnitus patients and a well-known data set of fetal lamb movements with 87 and 240 data points, respectively. Second, we rely on larger data sets of simulated data of sizes 2000 and 5000 for further analysis. This tutorial is accompanied by a collection of scripts, which are all available in the Supporting Information. These scripts allow any user with moderate programming experience to benefit quickly from the computational advantages of TMB.
Collapse
Affiliation(s)
- Timothée Bacri
- Department of MathematicsUniversity of BergenBergenNorway
| | - Geir D. Berentsen
- Department of Business and Management ScienceNorwegian School of EconomicsHelleveienBergenNorway
| | - Jan Bulla
- Department of MathematicsUniversity of BergenBergenNorway,Department of Psychiatry and PsychotherapyUniversity of RegensburgUniversitätsstraßeRegensburgGermany
| | - Sondre Hølleland
- Department of Business and Management ScienceNorwegian School of EconomicsHelleveienBergenNorway,Department of Pelagic FishInstitute of Marine ResearchBergenNorway
| |
Collapse
|
30
|
Rautiainen H, Alam M, Blackwell PG, Skarin A. Identification of reindeer fine-scale foraging behaviour using tri-axial accelerometer data. MOVEMENT ECOLOGY 2022; 10:40. [PMID: 36127747 PMCID: PMC9490970 DOI: 10.1186/s40462-022-00339-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Animal behavioural responses to the environment ultimately affect their survival. Monitoring animal fine-scale behaviour may improve understanding of animal functional response to the environment and provide an important indicator of the welfare of both wild and domesticated species. In this study, we illustrate the application of collar-attached acceleration sensors for investigating reindeer fine-scale behaviour. Using data from 19 reindeer, we tested the supervised machine learning algorithms Random forests, Support vector machines, and hidden Markov models to classify reindeer behaviour into seven classes: grazing, browsing low from shrubs or browsing high from trees, inactivity, walking, trotting, and other behaviours. We implemented leave-one-subject-out cross-validation to assess generalizable results on new individuals. Our main results illustrated that hidden Markov models were able to classify collar-attached accelerometer data into all our pre-defined behaviours of reindeer with reasonable accuracy while Random forests and Support vector machines were biased towards dominant classes. Random forests using 5-s windows had the highest overall accuracy (85%), while hidden Markov models were able to best predict individual behaviours and handle rare behaviours such as trotting and browsing high. We conclude that hidden Markov models provide a useful tool to remotely monitor reindeer and potentially other large herbivore species behaviour. These methods will allow us to quantify fine-scale behavioural processes in relation to environmental events.
Collapse
Affiliation(s)
- Heidi Rautiainen
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Moudud Alam
- School of Information and Engineering, Dalarna University, Falun, Sweden
| | - Paul G Blackwell
- School of Mathematics & Statistics, University of Sheffield, Sheffield, UK
| | - Anna Skarin
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| |
Collapse
|
31
|
Pohle J, Adam T, Beumer LT. Flexible estimation of the state dwell-time distribution in hidden semi-Markov models. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
32
|
Carter NH, Pradhan N, Hengaju K, Sonawane C, Sage AH, Grimm V. Forecasting effects of transport infrastructure on endangered tigers: a tool for conservation planning. PeerJ 2022; 10:e13472. [PMID: 35602904 PMCID: PMC9121866 DOI: 10.7717/peerj.13472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/29/2022] [Indexed: 01/14/2023] Open
Abstract
The rapid development of transport infrastructure is a major threat to endangered species worldwide. Roads and railways can increase animal mortality, fragment habitats, and exacerbate other threats to biodiversity. Predictive models that forecast the future impacts to endangered species can guide land-use planning in ways that proactively reduce the negative effects of transport infrastructure. Agent-based models are well suited for predictive scenario testing, yet their application to endangered species conservation is rare. Here, we developed a spatially explicit, agent-based model to forecast the effects of transport infrastructure on an isolated tiger (Panthera tigris) population in Nepal's Chitwan National Park-a global biodiversity hotspot. Specifically, our model evaluated the independent and interactive effects of two mechanisms by which transport infrastructure may affect tigers: (a) increasing tiger mortality, e.g., via collisions with vehicles, and (b) depleting prey near infrastructure. We projected potential impacts on tiger population dynamics based on the: (i) existing transportation network in and near the park, and (ii) the inclusion of a proposed railway intersecting through the park's buffer zone. Our model predicted that existing roads would kill 46 tigers over 20 years via increased mortality, and reduced the adult tiger population by 39% (133 to 81). Adding the proposed railway directly killed 10 more tigers over those 20 years; deaths that reduced the overall tiger population by 30 more individuals (81 to 51). Road-induced mortality also decreased the proportion of time a tiger occupied a given site by 5 years in the 20-year simulation. Interestingly, we found that transportation-induced depletion of prey decreased tiger occupancy by nearly 20% in sites close to roads and the railway, thereby reducing tiger exposure to transportation-induced mortality. The results of our model constitute a strong argument for taking into account prey distributions into the planning of roads and railways. Our model can promote tiger-friendly transportation development, for example, by improving Environmental Impact Assessments, identifying "no go" zones where transport infrastructure should be prohibited, and recommending alternative placement of roads and railways.
Collapse
Affiliation(s)
- Neil H. Carter
- University of Michigan, Ann Arbor, United States of America
| | - Narendra Pradhan
- International Union for Conservation of Nature, Kathmandu, Nepal
| | - Krishna Hengaju
- International Union for Conservation of Nature, Kathmandu, Nepal
| | | | - Abigail H. Sage
- US Fish and Wildlife Service, Wenatchee, United States of America
| | - Volker Grimm
- Helmholtz Centre for Environmental Research –UFZ, Leipzig, Germany
| |
Collapse
|
33
|
Valle D, Jameel Y, Betancourt B, Azeria ET, Attias N, Cullen J. Automatic selection of the number of clusters using Bayesian clustering and sparsity-inducing priors. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2524. [PMID: 34918421 DOI: 10.1002/eap.2524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/14/2021] [Accepted: 07/09/2021] [Indexed: 06/14/2023]
Abstract
Clustering is a ubiquitous task in ecological and environmental sciences and multiple methods have been developed for this purpose. Because these clustering methods typically require users to a priori specify the number of groups, the standard approach is to run the algorithm for different numbers of groups and then choose the optimal number using a criterion (e.g., AIC or BIC). The problem with this approach is that it can be computationally expensive to run these clustering algorithms multiple times (i.e., for different numbers of groups) and some of these information criteria can lead to an overestimation of the number of groups. To address these concerns, we advocate for the use of sparsity-inducing priors within a Bayesian clustering framework. In particular, we highlight how the truncated stick-breaking (TSB) prior, a prior commonly adopted in Bayesian nonparametrics, can be used to simultaneously determine the number of groups and estimate model parameters for a wide range of Bayesian clustering models without requiring the fitting of multiple models. We illustrate the ability of this prior to successfully recover the true number of groups for three clustering models (two types of mixture models, applied to GPS movement data and species occurrence data, as well as the species archetype model) using simulated data in the context of movement ecology and community ecology. We then apply these models to armadillo movement data in Brazil, plant occurrence data from Alberta (Canada), and bird occurrence data from North America. We believe that many ecological and environmental sciences applications will benefit from Bayesian clustering methods with sparsity-inducing priors given the ubiquity of clustering and the associated challenge of determining the number of groups. Two R packages, EcoCluster and bayesmove, are provided that enable the straightforward fitting of these models with the TSB prior.
Collapse
Affiliation(s)
- Denis Valle
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| | - Yusuf Jameel
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| | - Brenda Betancourt
- Department of Statistics, University of Florida, Gainesville, Florida, USA
| | - Ermias T Azeria
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Nina Attias
- Ecology and Conservation Graduate Program, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Joshua Cullen
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
34
|
Ferreira EM, Valerio F, Medinas D, Fernandes N, Craveiro J, Costa P, Silva JP, Carrapato C, Mira A, Santos SM. Assessing behaviour states of a forest carnivore in a road-dominated landscape using Hidden Markov Models. NATURE CONSERVATION 2022. [DOI: 10.3897/natureconservation.47.72781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Anthropogenic infrastructures and land-use changes are major threats to animal movements across heterogeneous landscapes. Yet, the behavioural consequences of such constraints remain poorly understood. We investigated the relationship between the behaviour of the Common genet (Genetta genetta) and road proximity, within a dominant mixed forest-agricultural landscape in southern Portugal, fragmented by roads. Specifically, we aimed to: (i) identify and characterise the behavioural states displayed by genets and related movement patterns; and (ii) understand how behavioural states are influenced by proximity to main paved roads and landscape features. We used a multivariate Hidden Markov Model (HMM) to characterise the fine-scale movements (10-min fixes GPS) of seven genets tracked during 187 nights (mean 27 days per individual) during the period 2016–2019, using distance to major paved roads and landscape features as predictors. Our findings indicated that genet’s movement patterns were composed of three basic behavioural states, classified as “resting” (short step-lengths [mean = 10.6 m] and highly tortuous), “foraging” (intermediate step-lengths [mean = 46.1 m] and with a wide range in turning angle) and “travelling” (longer step-lengths [mean = 113.7 m] and mainly linear movements). Within the genet’s main activity-period (17.00 h-08.00 h), the movement model predicts that genets spend 36.7% of their time travelling, 35.4% foraging and 28.0% resting. The probability of genets displaying the travelling state was highest in areas far away from roads (> 500 m), whereas foraging and resting states were more likely in areas relatively close to roads (up to 500 m). Landscape features also had a pronounced effect on behaviour state occurrence. More specifically, travelling was most likely to occur in areas with lower forest edge density and close to riparian habitats, while foraging was more likely to occur in areas with higher forest edge density and far away from riparian habitats. The results suggest that, although roads represent a behavioural barrier to the movement of genets, they also take advantage of road proximity as foraging areas. Our study demonstrates that the HMM approach is useful for disentangling movement behaviour and understanding how animals respond to roadsides and fragmented habitats. We emphasise that road-engaged stakeholders need to consider movement behaviour of genets when targeting management practices to maximise road permeability for wildlife.
Collapse
|
35
|
Newman K, King R, Elvira V, de Valpine P, McCrea RS, Morgan BJT. State‐space Models for Ecological Time Series Data: Practical Model‐fitting. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ken Newman
- School of Mathematics University of Edinburgh Edinburgh UK
- Biomathematics and Statistics Scotland Edinburgh UK
| | - Ruth King
- School of Mathematics University of Edinburgh Edinburgh UK
| | - Víctor Elvira
- School of Mathematics University of Edinburgh Edinburgh UK
| | - Perry de Valpine
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - Rachel S. McCrea
- School of Mathematics, Statistics and Actuarial Science University of Kent Canterbury UK
| | - Byron J. T. Morgan
- School of Mathematics, Statistics and Actuarial Science University of Kent Canterbury UK
| |
Collapse
|
36
|
Hodel FH, Fieberg JR. Circular‐Linear
Copulae for Animal Movement Data. Methods Ecol Evol 2022; 13:1001-1013. [PMID: 35915739 PMCID: PMC9314651 DOI: 10.1111/2041-210x.13821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
Abstract
Animal movement is often modelled in discrete time, formulated in terms of steps taken between successive locations at regular time intervals. Steps are characterized by the distance between successive locations (step lengths) and changes in direction (turn angles). Animals commonly exhibit a mix of directed movements with large step lengths and turn angles near 0 when travelling between habitat patches and more wandering movements with small step lengths and uniform turn angles when foraging. Thus, step lengths and turn angles will typically be cross‐correlated. Most models of animal movement assume that step lengths and turn angles are independent, likely due to a lack of available alternatives. Here, we show how the method of copulae can be used to fit multivariate distributions that allow for correlated step lengths and turn angles. We describe several newly developed copulae appropriate for modelling animal movement data and fit these distributions to data collected on fishers (Pekania pennanti). The copulae are able to capture the inherent correlation in the data and provide a better fit than a model that assumes independence. Further, we demonstrate via simulation that this correlation can impact movement patterns (e.g. rates of dispersion overtime). We see many opportunities to extend this framework (e.g. to consider autocorrelation in step attributes) and to integrate it into existing frameworks for modelling animal movement and habitat selection. For example, copulae could be used to more accurately sample available locations when conducting habitat‐selection analyses.
Collapse
Affiliation(s)
- Florian H. Hodel
- Department of Fisheries and Wildlife, Michigan State University East Lansing MI USA
| | - John R. Fieberg
- Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul MN USA
| |
Collapse
|
37
|
Whoriskey K, Baktoft H, Field C, Lennox RJ, Babyn J, Lawler E, Mills Flemming J. Predicting aquatic animal movements and behavioural states from acoustic telemetry arrays. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kim Whoriskey
- Department of Statistics Dalhousie University Halifax Nova Scotia Canada
| | - Henrik Baktoft
- National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
| | - Chris Field
- Department of Statistics Dalhousie University Halifax Nova Scotia Canada
| | | | - Jonathan Babyn
- Department of Statistics Dalhousie University Halifax Nova Scotia Canada
| | - Ethan Lawler
- Department of Statistics Dalhousie University Halifax Nova Scotia Canada
| | | |
Collapse
|
38
|
Glennie R, Adam T, Leos‐Barajas V, Michelot T, Photopoulou T, McClintock BT. Hidden Markov Models: Pitfalls and Opportunities in Ecology. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard Glennie
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews KY16 9LZ UK
| | - Timo Adam
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews KY16 9LZ UK
| | | | - Théo Michelot
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews KY16 9LZ UK
| | - Theoni Photopoulou
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews KY16 9LZ UK
| | - Brett T. McClintock
- Marine Mammal Laboratory NOAA‐NMFS Alaska Fisheries Science Center Seattle USA
| |
Collapse
|
39
|
Thindwa D, Wolter N, Pinsent A, Carrim M, Ojal J, Tempia S, Moyes J, McMorrow M, Kleynhans J, von Gottberg A, French N, Cohen C, Flasche S. Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study. PLoS Comput Biol 2021; 17:e1009680. [PMID: 34941865 PMCID: PMC8699682 DOI: 10.1371/journal.pcbi.1009680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant’s age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (≥18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9–80.5%) than older children (5–17 years-old) (31.7–50.0%) or adults (11.5–23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7–15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91–1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2–12.8 vs 6.0 days, 95%CI: 5.6–6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507–714 vs 389, 95%CI: 311.1–435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission. We assessed the contribution of HIV-infected adults to household pneumococcal transmission by applying a hidden Markov model to pneumococcal cohort data comprising 115,595 nasopharyngeal samples from 1,684 individuals in rural and urban settings in South Africa. We estimated 14.4% of sample misclassifications (false negatives), representing 85.6% sensitivity of a test that was used to detect pneumococcus. Pneumococcal carriage prevalence and acquisition rates, and average duration were usually higher in younger or older children than adults. The use of ART and antibiotics reduced the average carriage duration across all age and HIV groups, and carriage acquisition risks increased in larger household sizes. Despite the longer average carriage duration and higher median carriage density in HIV-infected than HIV-uninfected adults, we found similar carriage acquisition and onward transmission risks in the dual groups. These findings suggest that vaccinating HIV-infected adults on ART with PCV would reduce their risk for pneumococcal disease but may add little to the indirect protection against carriage of the rest of the population.
Collapse
Affiliation(s)
- Deus Thindwa
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- * E-mail:
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Amy Pinsent
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Aquarius Population Health, London, United Kingdom
| | - Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - John Ojal
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- KEMRI-Wellcome Trust Research Programme, Geographic Medicine Centre, Kilifi, Kenya
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- MassGenics, Duluth, Georgia, United States of America
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Meredith McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil French
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Science, Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, United Kingdom
| | | | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| |
Collapse
|
40
|
Sidrow E, Heckman N, Fortune SME, Trites AW, Murphy I, Auger‐Méthé M. Modelling multi‐scale, state‐switching functional data with hidden Markov models. CAN J STAT 2021. [DOI: 10.1002/cjs.11673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Evan Sidrow
- Department of Statistics University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
| | - Nancy Heckman
- Department of Statistics University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
| | - Sarah M. E. Fortune
- Marine Mammal Research Unit University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
| | - Andrew W. Trites
- Department of Zoology University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
- Institute for the Oceans and Fisheries University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
| | - Ian Murphy
- Department of Biostatistics University of Florida Gainesville 32611 FL U.S.A
| | - Marie Auger‐Méthé
- Department of Statistics University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
- Institute for the Oceans and Fisheries University of British Columbia Vancouver V6T 1Z4 British Columbia Canada
| |
Collapse
|
41
|
Gangloff EJ, Leos-Barajas V, Demuth G, Zhang H, Kelly CD, Bronikowski AM. Movement modeling and patterns of within- and among-individual behavioral variation across time scales in neonate garter snakes (Thamnophis elegans). Behav Ecol Sociobiol 2021. [DOI: 10.1007/s00265-021-03099-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
42
|
Barraquand F, Nielsen ÓK. Survival rates of adult and juvenile gyrfalcons in Iceland: estimates and drivers. PeerJ 2021; 9:e12404. [PMID: 34900413 PMCID: PMC8621780 DOI: 10.7717/peerj.12404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 10/07/2021] [Indexed: 11/25/2022] Open
Abstract
Knowledge of survival rates and their potential covariation with environmental drivers, for both adults and juveniles, is paramount to forecast the population dynamics of long-lived animals. Long-lived bird and mammal populations are indeed very sensitive to change in survival rates, especially that of adults. Here we report the first survival estimates for the Icelandic gyrfalcon (Falco rusticolus) obtained by capture-mark-recapture methods. We use a mark-recapture-recovery model combining live and dead encounters into a unified analysis, in a Bayesian framework. Annual survival was estimated at 0.83 for adults and 0.40 for juveniles. Positive effects of main prey density on juvenile survival (5% increase in survival from min to max density) were possible though not likely. Weather effects on juvenile survival were even less likely. The variability in observed lifespan suggests that adult birds could suffer from human-induced alteration of survival rates.
Collapse
Affiliation(s)
- Frédéric Barraquand
- Institute of Mathematics of Bordeaux, CNRS, Talence, France
- Integrative and Theoretical Ecology, Labex COTE, University of Bordeaux, Pessac, France
| | | |
Collapse
|
43
|
Elek Z, Růžičková J, Ódor P. Individual decisions drive the changes in movement patterns of ground beetles between forestry management types. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00805-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractMoving from one habitat to another, the dispersal of individuals has consequences for their conditions, population dynamics and gene flow. Our major motivation was to explore the effects of different forestry treatments, such as preparation (partial) cuts and clear cuts, on the selected population of the forest ground beetle, Carabus coriaceus (Coleoptera: Carabidae). We tagged six individuals (three males and three females) with small radio-transmitters and each was released in the treatment habitat core, at the edges and in the core of control forests respectively. The recorded trajectories were divided into two major movement phases: a random walk and a directional movement using hidden Markov models. Our results revealed that in the core zone of preparation cuts, the random walk and the directional movement were equally distributed in the trajectory. A clear directional movement was observed in the clear cuts suggesting the beetles moved directly toward the adjacent (control) forest interior. The trajectories at the edges of both treatments were dominated by the random walk and so for the controls. These results suggest that forest ground beetles can avoid the forestry treatments especially clear cuts, however edge habitats and (the studied) preparation cuts can mitigate the migration constraints due to their more favorable environmental conditions compared to clear cuts.
Collapse
|
44
|
Cullen JA, Poli CL, Fletcher RJ, Valle D. Identifying latent behavioural states in animal movement with M4, a nonparametric Bayesian method. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua A. Cullen
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| | - Caroline L. Poli
- School of Natural Resources and Environment University of Florida Gainesville FL USA
| | - Robert J. Fletcher
- Department of Wildlife Ecology and Conservation University of Florida Gainesville FL USA
| | - Denis Valle
- School of Forest Resources and Conservation University of Florida Gainesville FL USA
| |
Collapse
|
45
|
Auger‐Méthé M, Newman K, Cole D, Empacher F, Gryba R, King AA, Leos‐Barajas V, Mills Flemming J, Nielsen A, Petris G, Thomas L. A guide to state–space modeling of ecological time series. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1470] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marie Auger‐Méthé
- Department of Statistics University of British Columbia Vancouver British Columbia V6T 1Z4 Canada
- Institute for the Oceans and Fisheries University of British Columbia Vancouver British Columbia V6T 1Z4 Canada
| | - Ken Newman
- Biomathematics and Statistics Scotland Edinburgh EH9 3FD UK
- School of Mathematics University of Edinburgh Edinburgh EH9 3FD UK
| | - Diana Cole
- School of Mathematics, Statistics and Actuarial Science University of Kent Canterbury Kent CT2 7FS UK
| | - Fanny Empacher
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews KY16 9LZ UK
| | - Rowenna Gryba
- Department of Statistics University of British Columbia Vancouver British Columbia V6T 1Z4 Canada
- Institute for the Oceans and Fisheries University of British Columbia Vancouver British Columbia V6T 1Z4 Canada
| | - Aaron A. King
- Center for the Study of Complex Systems and Departments of Ecology & Evolutionary Biology and Mathematics University of Michigan Ann Arbor Michigan 48109 USA
| | - Vianey Leos‐Barajas
- Department of Statistics University of Toronto Toronto Ontario M5G 1X6 Canada
- School of the Environment University of Toronto Toronto Ontario M5S 3E8 Canada
| | - Joanna Mills Flemming
- Department of Mathematics and Statistics Dalhousie University Halifax Nova Scotia B3H 4R2 Canada
| | - Anders Nielsen
- National Institute for Aquatic Resources Technical University of Denmark Kgs. Lyngby 2800 Denmark
| | - Giovanni Petris
- Department of Mathematical Sciences University of Arkansas Fayetteville Arkansas 72701 USA
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling University of St Andrews St Andrews KY16 9LZ UK
| |
Collapse
|
46
|
Harrison XA. A brief introduction to the analysis of time-series data from biologging studies. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200227. [PMID: 34176325 PMCID: PMC8237163 DOI: 10.1098/rstb.2020.0227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/24/2022] Open
Abstract
Recent advances in tagging and biologging technology have yielded unprecedented insights into wild animal physiology. However, time-series data from such wild tracking studies present numerous analytical challenges owing to their unique nature, often exhibiting strong autocorrelation within and among samples, low samples sizes and complicated random effect structures. Gleaning robust quantitative estimates from these physiological data, and, therefore, accurate insights into the life histories of the animals they pertain to, requires careful and thoughtful application of existing statistical tools. Using a combination of both simulated and real datasets, I highlight the key pitfalls associated with analysing physiological data from wild monitoring studies, and investigate issues of optimal study design, statistical power, and model precision and accuracy. I also recommend best practice approaches for dealing with their inherent limitations. This work will provide a concise, accessible roadmap for researchers looking to maximize the yield of information from complex and hard-won biologging datasets. This article is part of the theme issue 'Measuring physiology in free-living animals (Part II)'.
Collapse
Affiliation(s)
- Xavier A. Harrison
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| |
Collapse
|
47
|
Togunov RR, Derocher AE, Lunn NJ, Auger‐Méthé M. Characterising menotactic behaviours in movement data using hidden Markov models. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ron R. Togunov
- Institute for the Oceans and Fisheries The University of British Columbia Vancouver BC Canada
- Department of Zoology The University of British Columbia Vancouver BC Canada
| | - Andrew E. Derocher
- Department of Biological Sciences University of Alberta Edmonton AB Canada
| | - Nicholas J. Lunn
- Department of Biological Sciences University of Alberta Edmonton AB Canada
- Wildlife Research Division, Science and Technology Branch Environment and Climate Change Canada Edmonton AB Canada
| | - Marie Auger‐Méthé
- Institute for the Oceans and Fisheries The University of British Columbia Vancouver BC Canada
- Department of Statistics University of British Columbia Vancouver BC Canada
| |
Collapse
|
48
|
Lennox RJ, Westrelin S, Souza AT, Šmejkal M, Říha M, Prchalová M, Nathan R, Koeck B, Killen S, Jarić I, Gjelland K, Hollins J, Hellstrom G, Hansen H, Cooke SJ, Boukal D, Brooks JL, Brodin T, Baktoft H, Adam T, Arlinghaus R. A role for lakes in revealing the nature of animal movement using high dimensional telemetry systems. MOVEMENT ECOLOGY 2021; 9:40. [PMID: 34321114 PMCID: PMC8320048 DOI: 10.1186/s40462-021-00244-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/11/2021] [Indexed: 05/13/2023]
Abstract
Movement ecology is increasingly relying on experimental approaches and hypothesis testing to reveal how, when, where, why, and which animals move. Movement of megafauna is inherently interesting but many of the fundamental questions of movement ecology can be efficiently tested in study systems with high degrees of control. Lakes can be seen as microcosms for studying ecological processes and the use of high-resolution positioning systems to triangulate exact coordinates of fish, along with sensors that relay information about depth, temperature, acceleration, predation, and more, can be used to answer some of movement ecology's most pressing questions. We describe how key questions in animal movement have been approached and how experiments can be designed to gather information about movement processes to answer questions about the physiological, genetic, and environmental drivers of movement using lakes. We submit that whole lake telemetry studies have a key role to play not only in movement ecology but more broadly in biology as key scientific arenas for knowledge advancement. New hardware for tracking aquatic animals and statistical tools for understanding the processes underlying detection data will continue to advance the potential for revealing the paradigms that govern movement and biological phenomena not just within lakes but in other realms spanning lands and oceans.
Collapse
Affiliation(s)
- Robert J Lennox
- Laboratory for Freshwater Ecology and Inland Fisheries (LFI) at NORCE Norwegian Research Centre, Nygårdsporten 112, 5008, Bergen, Norway.
| | - Samuel Westrelin
- INRAE, Aix Marseille Univ, Pôle R&D ECLA, RECOVER, 3275 Route de Cézanne - CS 40061, 13182 Cedex 5, Aix-en-Provence, France
| | - Allan T Souza
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Marek Šmejkal
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Milan Říha
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Marie Prchalová
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Ran Nathan
- Movement Ecology Lab, Department of Ecology, Evolution, and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 102 Berman Bldg, Edmond J. Safra Campus at Givat Ram, 91904, Jerusalem, Israel
| | - Barbara Koeck
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Shaun Killen
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Ivan Jarić
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Karl Gjelland
- Norwegian Institute of Nature Research, Tromsø, Norway
| | - Jack Hollins
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
- University of Windsor, Windsor, ON, Canada
| | - Gustav Hellstrom
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Henry Hansen
- Karlstads University, Universitetsgatan 2, 651 88, Karlstad, Sweden
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Bergen, Germany
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - David Boukal
- Faculty of Science, Department of Ecosystem Biology, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jill L Brooks
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Tomas Brodin
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Henrik Baktoft
- Technical University of Denmark, Vejlsøvej 39, Building Silkeborg-039, 8600, Silkeborg, Denmark
| | - Timo Adam
- Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Robert Arlinghaus
- Department of Biology and Ecology of Fishes, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Bergen, Germany
- Division of Integrative Fisheries Management, Humboldt-Universität zu Berlin, Bergen, Germany
| |
Collapse
|
49
|
Chimienti M, Beest FM, Beumer LT, Desforges J, Hansen LH, Stelvig M, Schmidt NM. Quantifying behavior and life‐history events of an Arctic ungulate from year‐long continuous accelerometer data. Ecosphere 2021. [DOI: 10.1002/ecs2.3565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Marianna Chimienti
- Department of Bioscience Aarhus University Frederiksborgvej 399 Roskilde4000Denmark
| | - Floris M. Beest
- Department of Bioscience Aarhus University Frederiksborgvej 399 Roskilde4000Denmark
- Arctic Research Centre Aarhus University Ny Munkegade 116 Aarhus C8000Denmark
| | - Larissa T. Beumer
- Department of Bioscience Aarhus University Frederiksborgvej 399 Roskilde4000Denmark
- Arctic Research Centre Aarhus University Ny Munkegade 116 Aarhus C8000Denmark
| | - Jean‐Pierre Desforges
- Department of Bioscience Aarhus University Frederiksborgvej 399 Roskilde4000Denmark
- Arctic Research Centre Aarhus University Ny Munkegade 116 Aarhus C8000Denmark
- Natural Resource Sciences McGill University Ste Anne de Bellevue QuebecH9X 3V9Canada
| | - Lars H. Hansen
- Department of Bioscience Aarhus University Frederiksborgvej 399 Roskilde4000Denmark
- Arctic Research Centre Aarhus University Ny Munkegade 116 Aarhus C8000Denmark
| | - Mikkel Stelvig
- Centre for Zoo and Wild Animal Health Copenhagen Zoo Frederiksberg2000Denmark
| | - Niels Martin Schmidt
- Department of Bioscience Aarhus University Frederiksborgvej 399 Roskilde4000Denmark
- Arctic Research Centre Aarhus University Ny Munkegade 116 Aarhus C8000Denmark
| |
Collapse
|
50
|
McClintock BT. Worth the effort? A practical examination of random effects in hidden Markov models for animal telemetry data. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13619] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brett T. McClintock
- Marine Mammal Laboratory Alaska Fisheries Science Center NOAA National Marine Fisheries Service Seattle WA USA
| |
Collapse
|