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Kays R, Wikelski M. The Internet of Animals: what it is, what it could be. Trends Ecol Evol 2023; 38:859-869. [PMID: 37263824 DOI: 10.1016/j.tree.2023.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 06/03/2023]
Abstract
One of the biggest trends in ecology over the past decade has been the creation of standardized databases. Recently, this has included live data, formal linkages between disparate databases, and automated analytics, a synergy that we recognize as the Internet of Animals (IoA). Early IoA systems relate animal locations to remote-sensing data to predict species distributions and detect disease outbreaks, and use live data to inform management of endangered species. However, meeting the future potential of the IoA concept will require solving challenges of taxonomy, data security, and data sharing. By linking data sets, integrating live data, and automating workflows, the IoA has the potential to enable discoveries and predictions relevant to human societies and the conservation of animals.
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Affiliation(s)
- Roland Kays
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA; North Carolina Museum of Natural Sciences, Raleigh, NC, USA; Smithsonian Tropical Research Institute, Balboa, Republic of Panama.
| | - Martin Wikelski
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama; Department of Animal Migration, Max Planck Institute of Animal Behaviour, Radolfzell, Germany; Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
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2
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Smith JW, Johnson LR, Thomas RQ. Assessing Ecosystem State Space Models: Identifiability and Estimation. JOURNAL OF AGRICULTURAL, BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2023. [DOI: 10.1007/s13253-023-00531-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
AbstractHierarchical probability models are being used more often than non-hierarchical deterministic process models in environmental prediction and forecasting, and Bayesian approaches to fitting such models are becoming increasingly popular. In particular, models describing ecosystem dynamics with multiple states that are autoregressive at each step in time can be treated as statistical state space models (SSMs). In this paper, we examine this subset of ecosystem models, embed a process-based ecosystem model into an SSM, and give closed form Gibbs sampling updates for latent states and process precision parameters when process and observation errors are normally distributed. Here, we use simulated data from an example model (DALECev) and study the effects changing the temporal resolution of observations on the states (observation data gaps), the temporal resolution of the state process (model time step), and the level of aggregation of observations on fluxes (measurements of transfer rates on the state process). We show that parameter estimates become unreliable as temporal gaps between observed state data increase. To improve parameter estimates, we introduce a method of tuning the time resolution of the latent states while still using higher-frequency driver information and show that this helps to improve estimates. Further, we show that data cloning is a suitable method for assessing parameter identifiability in this class of models. Overall, our study helps inform the application of state space models to ecological forecasting applications where (1) data are not available for all states and transfers at the operational time step for the ecosystem model and (2) process uncertainty estimation is desired.
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3
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Tucker AM, McGowan CP, Nuse BL, Lyons JE, Moore CT, Smith DR, Sweka JA, Anstead KA, DeRose‐Wilson A, Clark NA. Estimating recruitment rate and population dynamics at a migratory stopover site using an integrated population model. Ecosphere 2023. [DOI: 10.1002/ecs2.4439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
- Anna M. Tucker
- U.S. Geological Survey, Iowa Cooperative Fish and Wildlife Research Unit Iowa State University Ames Iowa USA
| | - Conor P. McGowan
- U.S. Geological Survey, Florida Cooperative Fish and Wildlife Research Unit University of Florida Gainesville Florida USA
| | - Bryan L. Nuse
- Bird Conservancy of the Rockies Ft. Collins Colorado USA
| | - James E. Lyons
- U.S. Geological Survey, Eastern Ecological Science Center at the Patuxent Research Refuge Laurel Maryland USA
| | - Clinton T. Moore
- U.S. Geological Survey, Georgia Cooperative Fish and Wildlife Research Unit University of Georgia Athens Georgia USA
| | - David R. Smith
- U.S. Geological Survey, Eastern Ecological Science Center at Leetown Kearneysville West Virginia USA
| | - John A. Sweka
- U.S. Fish and Wildlife Service, Northeast Fishery Center Lamar Pennsylvania USA
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4
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Millsap BA, Gedir JV, Abadi F, Gould MJ, Madden K. A two‐sex integrated population model reveals intersexual differences in life history strategies in Cooper's hawks. Ecosphere 2023. [DOI: 10.1002/ecs2.4368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Brian A. Millsap
- Division of Migratory Bird Management U.S. Fish and Wildlife Service Albuquerque New Mexico USA
| | - Jay V. Gedir
- Department of Fish, Wildlife and Conservation Ecology New Mexico State University Las Cruces New Mexico USA
| | - Fitsum Abadi
- Department of Fish, Wildlife and Conservation Ecology New Mexico State University Las Cruces New Mexico USA
| | - Matthew J. Gould
- Department of Fish, Wildlife and Conservation Ecology New Mexico State University Las Cruces New Mexico USA
| | - Kristin Madden
- Division of Migratory Bird Management U.S. Fish and Wildlife Service Albuquerque New Mexico USA
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5
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Sinnott EA, Thompson FR, Weegman MD, Thompson TR, Mosloff AR, Hedges RK, Loncarich FL. Evaluation of seasonal site-level demography and management for northern bobwhite using integrated population models. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2022.110211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Duriez O, Pilard P, Saulnier N, Boudarel P, Besnard A. Windfarm collisions in medium‐sized raptors: even increasing populations can suffer strong demographic impacts. Anim Conserv 2022. [DOI: 10.1111/acv.12818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- O. Duriez
- CEFE, Univ Montpellier, CNRS EPHE‐PSL University, IRD Montpellier France
| | - P. Pilard
- Ligue pour la Protection des Oiseaux – Mission Rapaces Mas Thibert France
| | - N. Saulnier
- Ligue pour la Protection des Oiseaux – Association Locale Hérault Villeveyrac France
| | | | - A. Besnard
- CEFE, Univ Montpellier, CNRS EPHE‐PSL University, IRD Montpellier France
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7
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Udell B, Martin J, Romagosa C, Waddle H, Johnson F, Falk B, Yackel Adams A, Funck S, Ketterlin J, Suarez E, Mazzotti F. Open removal models with temporary emigration and population dynamics to inform invasive animal management. Ecol Evol 2022; 12:e9173. [PMID: 35991280 PMCID: PMC9382647 DOI: 10.1002/ece3.9173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 11/07/2022] Open
Abstract
Removal sampling data are the primary source of monitoring information for many populations (e.g., invasive species, fisheries). Population dynamics, temporary emigration, and imperfect detection are common sources of variation in monitoring data and are key parameters for informing management. We developed two open robust-design removal models for simultaneously modeling population dynamics, temporary emigration, and imperfect detection: a random walk linear trend model (estimable without ancillary information), and a 2-age class informed population model (InfoPM, closely related to integrated population models) that incorporated prior information for age-structured vital rates and relative juvenile availability. We applied both models to multiyear, removal trapping time-series of a large invasive lizard (Argentine black and white tegu, Salvator merianae) in three management areas of South Florida to evaluate the effectiveness of management programs. Although estimates of the two models were similar, the InfoPMs generally returned more precise estimates, partitioned dynamics into births, deaths, net migration, and provided a decision support tool to predict population dynamics under different effort scenarios while accounting for uncertainty. Trends in tegu superpopulation abundance estimates were increasing in two management areas despite generally high removal rates. However, tegu abundance appeared to decline in the Core management area, where trapping density was the highest and immigration the lowest. Finally, comparing abundance predictions of no-removal scenarios to those estimated in each management area suggested significant population reductions due to management. These results suggest that local tegu population control via systematic trapping may be feasible with high enough trap density and limited immigration; and highlights the value of these trapping programs. We provided the first estimates of tegu abundance, capture probabilities, and population dynamics, which is critical for effective management. Furthermore, our models are applicable to a wide range of monitoring programs (e.g., carcass recovery or removal point-counts).
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Affiliation(s)
- Bradley Udell
- Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFloridaUSA
| | - Julien Martin
- Wetland and Aquatic Research CenterU.S. Geological SurveyGainesvilleFloridaUSA
- Eastern Ecological Science CenterU.S. Geological SurveyLaurelMarylandUSA
| | - Christina Romagosa
- Wildlife Ecology and ConservationUniversity of FloridaGainesvilleFloridaUSA
| | - Hardin Waddle
- Wetland and Aquatic Research CenterU.S. Geological SurveyGainesvilleFloridaUSA
| | - Fred Johnson
- Department of BioscienceAarhus UniversityRøndeDenmark
| | - Bryan Falk
- Fort Collins Science CenterU.S. Geological SurveyFort CollinsColoradoUSA
- South Florida Natural Resources CenterNational Park ServiceHomesteadFloridaUSA
| | - Amy Yackel Adams
- Fort Collins Science CenterU.S. Geological SurveyFort CollinsColoradoUSA
| | - Sarah Funck
- Florida Fish and Wildlife Conservation CommissionWest Palm BeachFloridaUSA
| | - Jennifer Ketterlin
- South Florida Natural Resources CenterNational Park ServiceHomesteadFloridaUSA
| | - Eric Suarez
- Florida Fish and Wildlife Conservation CommissionWest Palm BeachFloridaUSA
| | - Frank Mazzotti
- Fort Lauderdale Research and Education CenterUniversity of FloridaDavieFloridaUSA
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8
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Zimmerman GS, Millsap BA, Abadi F, Gedir JV, Kendall WL, Sauer JR. Estimating allowable take for an increasing bald eagle population in the United States. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Guthrie S. Zimmerman
- U.S. Fish and Wildlife Service, Division of Migratory Bird Management 3020 State University Drive East Modoc Hall, Suite 2007 Sacramento CA 95819 USA
| | - Brian A. Millsap
- U.S. Fish and Wildlife Service, Division of Migratory Bird Management 2105 Osuna NE Albuquerque NM 87113 USA
| | - Fitsum Abadi
- Department of Fish Wildlife, and Conservation Ecology, New Mexico State University P. O. Box 30003, MSC 4901 Las Cruces NM 88003 USA
| | - Jay V. Gedir
- Department of Fish Wildlife, and Conservation Ecology, New Mexico State University P. O. Box 30003, MSC 4901 Las Cruces NM 88003 USA
| | - William L. Kendall
- U.S. Geological Survey, Colorado Cooperative Fish and Wildlife Research Unit Colorado State University 1484 Campus Delivery Fort Collins CO 80523 USA
| | - John R. Sauer
- U.S. Geological Survey, Eastern Ecological Science Center 12100 Beech Forest Road Laurel MD 20708 USA
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9
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Koons DN, Riecke TV, Boomer GS, Sedinger BS, Sedinger JS, Williams PJ, Arnold TW. A niche for null models in adaptive resource management. Ecol Evol 2022; 12:e8541. [PMID: 35127044 PMCID: PMC8794763 DOI: 10.1002/ece3.8541] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022] Open
Abstract
As global systems rapidly change, our collective ability to predict future ecological dynamics will become increasingly important for successful natural resource management. By merging stakeholder objectives with system uncertainty, and by adapting actions to changing systems and knowledge, adaptive resource management (ARM) provides a rigorous platform for making sound decisions in a changing world. Critically, however, applications of ARM could be improved by employing benchmarks (i.e., points of reference) for determining when learning is occurring through the cycle of monitoring, modeling, and decision-making steps in ARM. Many applications of ARM use multiple model-based hypotheses to identify and reduce systematic uncertainty over time, but generally lack benchmarks for gauging discovery of scientific evidence and learning. This creates the danger of thinking that directional changes in model weights or rankings are indicative of evidence for hypotheses, when possibly all competing models are inadequate. There is thus a somewhat obvious, but yet to be filled niche for including benchmarks for learning in ARM. We contend that carefully designed "ecological null models," which are structured to produce an expected ecological pattern in the absence of a hypothesized mechanism, can serve as suitable benchmarks. Using a classic case study of mallard harvest management that is often used to demonstrate the successes of ARM for learning about ecological mechanisms, we show that simple ecological null models, such as population persistence (Nt +1 = Nt ), provide more robust near-term forecasts of population abundance than the currently used mechanistic models. More broadly, ecological null models can be used as benchmarks for learning in ARM that trigger the need for discarding model parameterizations and developing new ones when prevailing models underperform the ecological null model. Identifying mechanistic models that surpass these benchmarks will improve learning through ARM and help decision-makers keep pace with a rapidly changing world.
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Affiliation(s)
- David N. Koons
- Department of Fish, Wildlife, and Conservation BiologyGraduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
| | - Thomas V. Riecke
- Department of Natural Resources and Environmental ScienceUniversity of NevadaRenoNevadaUSA
- Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevadaUSA
| | - G. Scott Boomer
- Division of Migratory Bird ManagementU.S. Fish and Wildlife ServiceLaurelMarylandUSA
| | - Benjamin S. Sedinger
- College of Natural ResourcesUniversity of Wisconsin – Stevens PointStevens PointWisconsinUSA
| | - James S. Sedinger
- Department of Natural Resources and Environmental ScienceUniversity of NevadaRenoNevadaUSA
| | - Perry J. Williams
- Department of Natural Resources and Environmental ScienceUniversity of NevadaRenoNevadaUSA
| | - Todd W. Arnold
- Department of Fisheries, Wildlife and Conservation BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
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10
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Barras AG, Blache S, Schaub M, Arlettaz R. Variation in Demography and Life-History Strategies Across the Range of a Declining Mountain Bird Species. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.780706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Species- and population-specific responses to their environment may depend to a large extent on the spatial variation in life-history traits and in demographic processes of local population dynamics. Yet, those parameters and their variability remain largely unknown for many cold-adapted species, which are exposed to particularly rapid rates of environmental change. Here, we compared the demographic traits and dynamics for an emblematic bird species of European mountain ecosystems, the ring ouzel (Turdus torquatus). Using integrated population models fitted in a Bayesian framework, we estimated the survival probability, productivity and immigration of two populations from the Western European Alps, in France (over 11 years) and Switzerland (over 6 years). Juvenile apparent survival was lower and immigration rate higher in the Swiss compared to the French population, with the temporal variation in population growth rate driven by different demographic processes. Yet, when compared to populations in the northwestern part of the range, in Scotland, these two Alpine populations both showed a much lower productivity and higher adult survival, indicating a slower life-history strategy. Our results suggest that demographic characteristics can substantially vary across the discontinuous range of this passerine species, essentially due to contrasted, possibly locally evolved life-history strategies. This study therefore raises the question of whether flexibility in life-history traits is widespread among boreo-alpine species and if it might provide adaptive potential for coping with current environmental change.
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11
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Paquet M, Knape J, Arlt D, Forslund P, Pärt T, Flagstad Ø, Jones CG, Nicoll MAC, Norris K, Pemberton JM, Sand H, Svensson L, Tatayah V, Wabakken P, Wikenros C, Åkesson M, Low M. Integrated population models poorly estimate the demographic contribution of immigration. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthieu Paquet
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Jonas Knape
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Debora Arlt
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
- SLU Swedish Species Information Centre Swedish University of Agricultural Sciences Uppsala Sweden
| | - Pär Forslund
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tomas Pärt
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Carl G. Jones
- Mauritian Wildlife Foundation Vacoas Mauritius
- Durrell Wildlife Conservation Trust Trinity UK
| | | | | | - Josephine M. Pemberton
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Håkan Sand
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Linn Svensson
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences Inland Norway University of Applied Sciences Hamar Norway
| | - Camilla Wikenros
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Mikael Åkesson
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Matthew Low
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
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12
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Nater CR, Eide NE, Pedersen ÅØ, Yoccoz NG, Fuglei E. Contributions from terrestrial and marine resources stabilize predator populations in a rapidly changing climate. Ecosphere 2021. [DOI: 10.1002/ecs2.3546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Chloé R. Nater
- Norwegian Polar Institute Tromsø Norway
- Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
- Department of Arctic and Marine Biology UIT – The Arctic University of Norway Tromsø Norway
| | - Nina E. Eide
- Norwegian Institute for Nature Research Trondheim Norway
| | | | - Nigel G. Yoccoz
- Department of Arctic and Marine Biology UIT – The Arctic University of Norway Tromsø Norway
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13
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Moeller AK, Nowak JJ, Neufeld L, Bradley M, Manseau M, Wilson P, McFarlane S, Lukacs PM, Hebblewhite M. Integrating counts, telemetry, and non‐invasive DNA data to improve demographic monitoring of an endangered species. Ecosphere 2021. [DOI: 10.1002/ecs2.3443] [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)
- Anna K. Moeller
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana USA
| | | | | | - Mark Bradley
- Parks Canada, Jasper National Park Jasper Alberta Canada
| | - Micheline Manseau
- Landscape Science and Technology Division Environment and Climate Change Canada Ottawa Ontario Canada
- Biology Department Trent University Peterborough Ontario Canada
| | - Paul Wilson
- Biology Department Trent University Peterborough Ontario Canada
| | - Samantha McFarlane
- Landscape Science and Technology Division Environment and Climate Change Canada Ottawa Ontario Canada
- Biology Department Trent University Peterborough Ontario Canada
| | - Paul M. Lukacs
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana USA
| | - Mark Hebblewhite
- Wildlife Biology Program Department of Ecosystem and Conservation Sciences W.A. Franke College of Forestry and Conservation University of Montana Missoula Montana USA
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14
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Weegman MD, Arnold TW, Clark RG, Schaub M. Partial and complete dependency among data sets has minimal consequence on estimates from integrated population models. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e2258. [PMID: 33176007 DOI: 10.1002/eap.2258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Integrated population models (IPMs) are widely used to combine disparate data sets in joint analysis to better understand population dynamics and provide guidance for conservation activities. An often-cited assumption of IPMs is independence among component data sets within the combined likelihood. Dependency among data sets should lead to underestimation of variance and bias because individuals contribute data to more than one data set. In practice, studied individuals often occur in multiple data sets in IPMs (i.e., overlap), which is one way for the independence assumption to be violated. Such cases have the potential to dissuade practitioners and limit application of IPMs to solve emerging ecological problems. We assessed precision and bias of demographic rates estimated from IPMs using a complete gradient (0-100%) of overlap among data sets, wide ranges in demographic rates (e.g., survival 0.1-0.8) and sample sizes (100-1,200 individuals) and variable data sources. We compared results from our simulations with those from IPMs constructed using empirical data on tree swallows (Tachycineta bicolor) where data sets either had complete overlap or included different individuals. Contrary to previous investigators, we found no substantive bias or uncertainty in any demographic rate from IPMs derived from data sets with complete overlap. While variability in demographic rates was greater at low sample sizes (i.e., low capture, recapture, and survey probabilities), there were negligible differences in the posterior mean or root mean square error of demographic rates among IPMs with strong dependence vs. complete independence among data sets. Our simulations suggest IPMs can be designed using only capture-recapture data or harvest and capture-recovery data where population estimates are obtained from the same data as survival and productivity data. While we encourage researchers to carefully consider the modeling approach best suited for their data sets, our results suggest that dependence among data sets does not generally compromise IPM estimates. Thus, violation of the independence assumption should not dissuade researchers from the application of IPMs in ecological research.
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Affiliation(s)
- Mitch D Weegman
- School of Natural Resources, University of Missouri, Columbia, Missouri, 65211, USA
| | - Todd W Arnold
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, Minnesota, 55108, USA
| | - Robert G Clark
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E2, Canada
- Prairie and Northern Wildlife Research Centre, Environment and Climate Change Canada, Saskatoon, Saskatchewan, S7N 0X4, Canada
| | - Michael Schaub
- Swiss Ornithological Institute, Sempach, 6204, Switzerland
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15
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A modelling framework for integrating reproduction, survival and count data when projecting the fates of threatened populations. Oecologia 2021; 195:627-640. [PMID: 33646386 DOI: 10.1007/s00442-021-04871-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 02/03/2021] [Indexed: 01/09/2023]
Abstract
A key goal of ecological research is to obtain reliable estimates of population demographic rates, abundance and trends. However, a common challenge when studying wildlife populations is imperfect detection or breeding observation, which results in unknown survival status and reproductive output for some individuals. It is important to account for undetected individuals in population models because they contribute to population abundance and dynamics, and can have implications for population management. Promisingly, recent methodological advances provide us with the tools to integrate data from multiple independent sources to gain insights into the unobserved component of populations. We use data from five reintroduced populations of a threatened New Zealand bird, the hihi (Notiomystis cincta), to develop an integrated population modelling framework that allows missing values for survival status, sex and reproductive output to be modelled. Our approach combines parallel matrices of encounter and reproduction histories from marked individuals, as well as counts of unmarked recruits detected at the start of each breeding season. Integrating these multiple data types enabled us to simultaneously model survival and reproduction of detected individuals, undetected individuals and unknown (never detected) individuals to derive parameter estimates and projections based on all available data, thereby improving our understanding of population dynamics and enabling full propagation of uncertainty. The methods presented will be especially useful for management programmes for populations that are intensively monitored but where individuals are still imperfectly detected, as will be the case for most threatened wild populations.
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16
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Rose JP, Kupferberg SJ, Wheeler CA, Kleeman PM, Halstead BJ. Estimating the survival of unobservable life stages for a declining frog with a complex life history. Ecosphere 2021. [DOI: 10.1002/ecs2.3381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jonathan P. Rose
- Santa Cruz Field Station Western Ecological Research Center U.S. Geological Survey 2885 Mission Street Santa Cruz California95060USA
| | - Sarah J. Kupferberg
- Department of Integrative Biology University of California, Berkeley 3040 Valley Life Sciences Building #3140 Berkeley California94720USA
| | - Clara A. Wheeler
- Pacific Southwest Research Station Redwood Science Lab USDA Forest Service Arcata California95521USA
| | - Patrick M. Kleeman
- Point Reyes Field Station Western Ecological Research Center U.S. Geological Survey 1 Bear Valley Road Point Reyes Station California94956USA
| | - Brian J. Halstead
- Dixon Field Station Western Ecological Research Center U.S. Geological Survey 800 Business Park Drive, Suite D Dixon California95620USA
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17
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Hostetler JA, Martin J, Kosempa M, Edwards HH, Rood KA, Barton SL, Runge MC. Reconstructing population dynamics of a threatened marine mammal using multiple data sets. Sci Rep 2021; 11:2702. [PMID: 33514785 PMCID: PMC7846604 DOI: 10.1038/s41598-021-81478-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
Models of marine mammal population dynamics have been used extensively to predict abundance. A less common application of these models is to reconstruct historical population dynamics, filling in gaps in observation data by integrating information from multiple sources. We developed an integrated population model for the Florida manatee (Trichechus manatus latirostris) to reconstruct its population dynamics in the southwest region of the state over the past 20 years. Our model improved precision of key parameter estimates and permitted inference on poorly known parameters. Population growth was slow (averaging 1.02; 95% credible interval 1.01-1.03) but not steady, and an unusual mortality event in 2013 led to an estimated net loss of 332 (217-466) manatees. Our analyses showed that precise estimates of abundance could be derived from estimates of vital rates and a few input estimates of abundance, which may mean costly surveys to estimate abundance don't need to be conducted as frequently. Our study also shows that retrospective analyses can be useful to: (1) model the transient dynamics of age distribution; (2) assess and communicate the conservation status of wild populations; and (3) improve our understanding of environmental effects on population dynamics and thus enhance our ability to forecast.
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Affiliation(s)
- Jeffrey A. Hostetler
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA ,grid.462979.70000 0001 2287 7477Present Address: Patuxent Wildlife Research Center, U.S. Fish and Wildlife Service, Laurel, MD 20708 USA
| | - Julien Martin
- grid.2865.90000000121546924Wetland and Aquatic Research Center, U.S. Geological Survey, Gainesville, FL 32653 USA ,grid.2865.90000000121546924U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, St. Petersburg, FL 33701 USA
| | - Michael Kosempa
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA
| | - Holly H. Edwards
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA
| | - Kari A. Rood
- grid.427218.a0000 0001 0556 4516Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL 33701 USA
| | - Sheri L. Barton
- grid.285683.20000 0000 8907 1788Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL 34236 USA
| | - Michael C. Runge
- grid.2865.90000000121546924Patuxent Wildlife Research Center, U.S. Geological Survey, 12100 Beech Forest Road, Laurel, MD 20708 USA
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18
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Elbroch LM, Ferguson JM, Quigley H, Craighead D, Thompson DJ, Wittmer HU. Reintroduced wolves and hunting limit the abundance of a subordinate apex predator in a multi-use landscape. Proc Biol Sci 2020; 287:20202202. [PMID: 33171087 PMCID: PMC7735271 DOI: 10.1098/rspb.2020.2202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 10/16/2020] [Indexed: 11/12/2022] Open
Abstract
Top-down effects of apex predators are modulated by human impacts on community composition and species abundances. Consequently, research supporting top-down effects of apex predators occurs almost entirely within protected areas rather than the multi-use landscapes dominating modern ecosystems. Here, we developed an integrated population model to disentangle the concurrent contributions of a reintroduced apex predator, the grey wolf, human hunting and prey abundances on vital rates and abundance of a subordinate apex predator, the puma. Increasing wolf numbers had strong negative effects on puma fecundity, and subadult and adult survival. Puma survival was also influenced by density dependence. Overall, puma dynamics in our multi-use landscape were more strongly influenced by top-down forces exhibited by a reintroduced apex predator, than by human hunting or bottom-up forces (prey abundance) subsidized by humans. Quantitatively, the average annual impact of human hunting on equilibrium puma abundance was equivalent to the effects of 20 wolves. Historically, wolves may have limited pumas across North America and dictated puma scarcity in systems lacking sufficient refugia to mitigate the effects of competition.
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Affiliation(s)
| | - Jake M. Ferguson
- School of Life Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | | | | | - Daniel J. Thompson
- Large Carnivore Section, Wyoming Game and Fish Department, 260 Buena Vista Dr., Lander, WY 82520, USA
| | - Heiko U. Wittmer
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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19
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Paquet M, Arlt D, Knape J, Low M, Forslund P, Pärt T. Why we should care about movements: Using spatially explicit integrated population models to assess habitat source-sink dynamics. J Anim Ecol 2020; 89:2922-2933. [PMID: 32981078 PMCID: PMC7756878 DOI: 10.1111/1365-2656.13357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022]
Abstract
Assessing the source–sink status of populations and habitats is of major importance for understanding population dynamics and for the management of natural populations. Sources produce a net surplus of individuals (per capita contribution to the metapopulation > 1) and will be the main contributors for self‐sustaining populations, whereas sinks produce a deficit (contribution < 1). However, making these types of assessments is generally hindered by the problem of separating mortality from permanent emigration, especially when survival probabilities as well as moved distances are habitat‐specific. To address this long‐standing issue, we propose a spatial multi‐event integrated population model (IPM) that incorporates habitat‐specific dispersal distances of individuals. Using information about local movements, this IPM adjusts survival estimates for emigration outside the study area. Analysing 24 years of data on a farmland passerine (the northern wheatear Oenanthe oenanthe), we assessed habitat‐specific contributions, and hence the source–sink status and temporal variation of two key breeding habitats, while accounting for habitat‐ and sex‐specific local dispersal distances of juveniles and adults. We then examined the sensitivity of the source–sink analysis by comparing results with and without accounting for these local movements. Estimates of first‐year survival, and consequently habitat‐specific contributions, were higher when local movement data were included. The consequences from including movement data were sex specific, with contribution shifting from sink to likely source in one habitat for males, and previously noted habitat differences for females disappearing. Assessing the source–sink status of habitats is extremely challenging. We show that our spatial IPM accounting for local movements can reduce biases in estimates of the contribution by different habitats, and thus reduce the overestimation of the occurrence of sink habitats. This approach allows combining all available data on demographic rates and movements, which will allow better assessment of source–sink dynamics and better informed conservation interventions.
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Affiliation(s)
- Matthieu Paquet
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Debora Arlt
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.,SLU Swedish Species Information Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jonas Knape
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Matthew Low
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pär Forslund
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tomas Pärt
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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20
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Affiliation(s)
- Qing Zhao
- School of Natural Resources University of Missouri Columbia MO USA
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21
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Baker CM, Bode M. Recent advances of quantitative modeling to support invasive species eradication on islands. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christopher M. Baker
- School of Mathematics and Statistics, The University of Melbourne Melbourne Victoria Australia
- Melbourne Centre for Data Science, The University of Melbourne Melbourne Victoria Australia
- Centre of Excellence for Biosecurity Risk Analysis The University of Melbourne Melbourne Victoria Australia
| | - Michael Bode
- School of Mathematical Sciences, Queensland University of Technology Brisbane Queensland Australia
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22
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Schaub M, Ullrich B. A drop in immigration results in the extinction of a local woodchat shrike population. Anim Conserv 2020. [DOI: 10.1111/acv.12639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Schaub
- Swiss Ornithological Institute Sempach Switzerland
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23
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Hinrichs MP, Price NB, Gruntorad MP, Pope KL, Fontaine JJ, Chizinski CJ. Understanding Sportsperson Retention and Reactivation Through License Purchasing Behavior. WILDLIFE SOC B 2020. [DOI: 10.1002/wsb.1088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Matthew P. Hinrichs
- U.S. Department of AgricultureNRCS, Salem, SD 57058, USA, and School of Natural Resources, University of Nebraska Lincoln NE 68583 USA
| | - Nathaniel B. Price
- School of Natural Resources, University of Nebraska Lincoln NE 68583 USA
| | | | - Kevin L. Pope
- U.S. Geological Survey—Nebraska Cooperative Fish and Wildlife Research Unit, and School of Natural ResourcesUniversity of Nebraska Lincoln NE 68583 USA
| | - Joseph J. Fontaine
- Nebraska Cooperative Fish and Wildlife Research Unit, and School of Natural ResourcesUniversity of Nebraska Lincoln NE 68583 USA
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24
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Schmidt JH, Robison HL. Using Distance Sampling‐Based Integrated Population Models to Identify Key Demographic Parameters. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joshua H. Schmidt
- Central Alaska NetworkNational Park Service 4175 Geist Road Fairbanks AK 99709 USA
| | - Hillary L. Robison
- Western Arctic National ParklandsU.S. National Park Service P.O. Box 1029 Kotzebue AK 99752 USA
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25
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Gamble A, Garnier R, Chambert T, Gimenez O, Boulinier T. Next-generation serology: integrating cross-sectional and capture-recapture approaches to infer disease dynamics. Ecology 2020; 101:e02923. [PMID: 31655002 DOI: 10.1002/ecy.2923] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 01/27/2023]
Abstract
Two approaches have been classically used in disease ecology to estimate epidemiological parameters from field studies: cross-sectional sampling from unmarked individuals and longitudinal capture-recapture setups, which generally involve more limited numbers of marked individuals due to cost and logistical constraints. Although the benefits of longitudinal setups are increasingly acknowledged in the disease ecology community, cross-sectional data remain largely overrepresented in the literature, probably because of the inherent costs of longitudinal surveys. In this context, we used simulated data to compare the performances of cross-sectional and longitudinal designs to estimate the force of infection (i.e., the rate at which susceptible individuals become infected). Then, inspired from recent method developments in quantitative ecology, we explore the benefits of integrating both cross-sectional (seroprevalences) and longitudinal (individuals histories) data sets. In doing so, we investigate the effects of host species life history, antibody persistence, and degree of a priori knowledge and uncertainty on demographic and epidemiological parameters, as those are expected to affect in different ways the level of inference possible from the data. Our results highlight how those elements are important to consider in determining optimal sampling designs. In the case of long-lived species exposed to infectious agents resulting in persistent antibody responses, integrated designs are especially valuable as they benefit from the performances of longitudinal designs even with relatively small longitudinal sample sizes. As an illustration, we apply this approach to a combination of empirical and simulated data inspired from a case of bats exposed to a rabies virus. Overall, this work highlights that serology field studies could greatly benefit from the opportunity of integrating cross-sectional and longitudinal designs.
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Affiliation(s)
- Amandine Gamble
- CEFE, CNRS, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France.,Department of Ecology and Evolutionary Biology, University of California, 610 Charles E. Young Dr. South, Los Angeles, 90095-7239, USA
| | - Romain Garnier
- Department of Biology, Georgetown University, 37th and O Streets, Washington, 20057, USA
| | - Thierry Chambert
- CEFE, CNRS, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Olivier Gimenez
- CEFE, CNRS, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France
| | - Thierry Boulinier
- CEFE, CNRS, University of Montpellier, EPHE, University Paul Valéry Montpellier 3, IRD, Montpellier, France
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26
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Johnson FA, Zimmerman GS, Jensen GH, Clausen KK, Frederiksen M, Madsen J. Using integrated population models for insights into monitoring programs: An application using pink-footed geese. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2019.108869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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27
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Millon A, Lambin X, Devillard S, Schaub M. Quantifying the contribution of immigration to population dynamics: a review of methods, evidence and perspectives in birds and mammals. Biol Rev Camb Philos Soc 2019; 94:2049-2067. [DOI: 10.1111/brv.12549] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Alexandre Millon
- Aix Marseille Université, CNRS, IRD, Avignon Université, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Technopôle Arbois‐Méditerranée, Bât. Villemin – BP 80 F‐13545 Aix‐en‐Provence cedex 04 France
| | - Xavier Lambin
- School of Biological SciencesUniversity of Aberdeen Tillydrone Avenue, Zoology Building, University of Aberdeen, AB24 2TZ Aberdeen U.K
| | - Sébastien Devillard
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive F‐69100 Villeurbanne France
| | - Michael Schaub
- Swiss Ornithological Institute Seerose 1, 6204 Sempach Switzerland
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