1
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Martínez AE, Ponciano JM, Gomez JP, Valqui T, Novoa J, Antezana M, Biscarra G, Camerlenghi E, Carnes BH, Huayanca Munarriz R, Parra E, Plummer IM, Fitzpatrick JW, Robinson SK, Socolar JB, Terborgh J. The structure and organisation of an Amazonian bird community remains little changed after nearly four decades in Manu National Park. Ecol Lett 2023; 26:335-346. [PMID: 36604979 DOI: 10.1111/ele.14159] [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: 07/16/2021] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023]
Abstract
Documenting patterns of spatiotemporal change in hyper-diverse communities remains a challenge for tropical ecology yet is increasingly urgent as some long-term studies have shown major declines in bird communities in undisturbed sites. In 1982, Terborgh et al. quantified the structure and organisation of the bird community in a 97-ha. plot in southeastern Peru. We revisited the same plot in 2018 using the same methodologies as the original study to evaluate community-wide changes. Contrary to longitudinal studies of other neotropical bird communities (Tiputini, Manaus, and Panama), we found little change in community structure and organisation, with increases in 5, decreases in 2 and no change in 7 foraging guilds. This apparent stability suggests that large forest reserves such as the Manu National Park, possibly due to regional topographical influences on precipitation, still provide the conditions for establishing refugia from at least some of the effects of global change on bird communities.
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Affiliation(s)
- Ari E Martínez
- Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, California, Berkeley, USA.,Department of Biological Sciences, California State University, Long Beach, California, USA
| | - José M Ponciano
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Juan P Gomez
- Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Thomas Valqui
- Facultad de Ciencias Forestales, Universidad Nacional Agraria, La Molina, Perú.,CORBIDI, Lima, Perú
| | | | | | - Gabriela Biscarra
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Ettore Camerlenghi
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | | | | | - Eliseo Parra
- San Francisco State University, San Francisco, California, USA
| | - Isabella M Plummer
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | | | - Scott K Robinson
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Jacob B Socolar
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - John Terborgh
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
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2
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Contreras F, Goijman AP, Coda JA, Serafini VN, Priotto JW. Bird occupancy in intensively managed agroecosystems under large-scale organic and conventional farming in Argentina: A multi-species approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150301. [PMID: 34536860 DOI: 10.1016/j.scitotenv.2021.150301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Several studies in European and North American agroecosystems conclude that organic farming benefits birds compared to conventional farming. Nevertheless, there are some biases toward these geographic regions and farm size. Argentinian agroecosystems are particularly homogeneous with large arable fields and sparse uncultivated field margins (i.e. large-scale homogenous cropping systems). In Argentina only 0.55% of the total farmland is under organic farming. Thus, our aims were to assess differences in bird occupancy between organic versus conventional farming regimes, and whether bird occupancy varied in relation to annual crop proportion in both farming regimes in central Argentina agroecosystems. We surveyed 156 points in farms under conventional and 154 in organic farming regimes during two bird-breeding seasons. We used multi-species occupancy models with a Bayesian approach to estimate bird occupancy. We observed that the type of farming regime (organic in relation to conventional) had a weak effect on avian occupancy, varying by species and groups. Probability of occupancy was higher for a few insectivorous and omnivorous species but lower for carnivores in organic farms in relation to conventional ones. The proportion of annual crops was positively correlated with occupancy of an insectivore aerial forager, some insectivore foliage gleaners, a granivore, and some omnivorous species in organic farms, but not conventional farms. This work contributes to reducing geographic and small-scale heterogeneous cropping system biases in the avian agroecological literature. Our results, together with future studies needed to assess landscape configuration and composition, and resource availability for birds in each farming regime, will allow the evaluation of organic farming as a tool for the conservation of bird species in large-scale homogeneous cropping systems in temperate regions.
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Affiliation(s)
- Facundo Contreras
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina.
| | - Andrea P Goijman
- Instituto de Recursos Biológicos, CIRN, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
| | - José A Coda
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - Vanesa N Serafini
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
| | - José W Priotto
- Grupo de Investigaciones en Ecología Poblacional y Comportamental (GIEPCO), Instituto de Ciencias de la Tierra, Biodiversidad y Ambiente (ICBIA), Universidad Nacional de Río Cuarto - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Córdoba, Argentina
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3
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Hamer AJ, Schmera D, Mahony MJ. Multi-species occupancy modeling provides novel insights into amphibian metacommunity structure and wetland restoration. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e2293. [PMID: 33432692 DOI: 10.1002/eap.2293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/22/2020] [Accepted: 10/06/2020] [Indexed: 06/12/2023]
Abstract
A fundamental goal of community ecology is to understand species-habitat relationships and how they shape metacommunity structure. Recent advances in occupancy modeling enable habitat relationships to be assessed for both common and rare species within metacommunities using multi-species occupancy models (MSOM). These models account for imperfect species detection and offer considerable advantages over other analytical tools commonly used for community analyses under the elements of metacommunity structure (EMS) framework. Here, we demonstrate that MSOM can be used to infer habitat relationships and test metacommunity theory, using amphibians. Repeated frog surveys were undertaken at 55 wetland sites in southeastern Australia. We detected 11 frog species from three families (Limnodynastidae, Myobatrachidae, and Pelodryadidae). The rarest species was detected at only one site whereas the most common species was detected at 42 sites (naive occupancy rate 0.02-0.76). Two models were assessed representing two competing hypotheses; the best-supported model included the covariates distance to the nearest site (connectivity), wetland area, presence of the non-native eastern mosquitofish (Gambusia holbrooki), proportion cover of emergent vegetation, an interaction term between Gambusia and emergent vegetation cover, and the proportion canopy cover over a site. Hydroperiod played no detectable role in metacommunity structure. We found species-habitat relationships that fit with current metacommunity theory: occupancy increased with wetland area and connectivity. There was a strong negative relationship between occupancy and the presence of predatory Gambusia, and a positive interaction between Gambusia and emergent vegetation. The presence of canopy cover strongly increased occupancy for several tree frog species, highlighting the importance of terrestrial habitat for amphibian community structure. We demonstrated how responses by amphibians to environmental covariates at the species level can be linked to occupancy patterns at the metacommunity scale. Our results have clear management implications: wetland restoration projects for amphibians and likely other taxa should maximize wetland area and connectivity, establish partial canopy cover, and eradicate Gambusia or provide aquatic vegetation to mitigate the impact of this non-native fish. We strongly advocate the use of MSOM to elucidate the habitat drivers behind animal occupancy patterns and to derive unbiased occupancy estimates for monitoring programs.
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Affiliation(s)
- Andrew J Hamer
- Centre for Ecological Research, GINOP Sustainable Ecosystems Group, Klebelsberg K. u. 3, Tihany, H-8237, Hungary
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg K. u. 3, Tihany, H-8237, Hungary
| | - Dénes Schmera
- Centre for Ecological Research, Balaton Limnological Institute, Klebelsberg K. u. 3, Tihany, H-8237, Hungary
| | - Michael J Mahony
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, 2308, Australia
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4
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Sollmann R, Eaton MJ, Link WA, Mulondo P, Ayebare S, Prinsloo S, Plumptre AJ, Johnson DS. A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02249. [PMID: 33140872 DOI: 10.1002/eap.2249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Community occupancy models estimate species-specific parameters while sharing information across species by treating parameters as sampled from a common distribution. When communities consist of discrete groups, shrinkage of estimates toward the community mean can mask differences among groups. Infinite-mixture models using a Dirichlet process (DP) distribution, in which the number of latent groups is estimated from the data, have been proposed as a solution. In addition to community structure, these models estimate species similarity, which allows testing hypotheses about whether traits drive species response to environmental conditions. We develop a community occupancy model (COM) using a DP distribution to model species-level parameters. Because clustering algorithms are sensitive to dimensionality and distinctiveness of clusters, we conducted a simulation study to explore performance of the DP-COM with different dimensions (i.e., different numbers of model parameters with species-level DP random effects) and under varying cluster differences. Because the DP-COM is computationally expensive, we compared its estimates to a COM with a normal random species effect. We further applied the DP-COM model to a bird data set from Uganda. Estimates of the number of clusters and species cluster identity improved with increasing difference among clusters and increasing dimensions of the DP; but the number of clusters was always overestimated. Estimates of number of sites occupied and species and community-level covariate coefficients on occupancy probability were generally unbiased with (near-) nominal 95% Bayesian Credible Interval coverage. Accuracy of estimates from the normal and the DP-COM was similar. The DP-COM clustered 166 bird species into 27 clusters regarding their affiliation with open or woodland habitat and distance to oil wells. Estimates of covariate coefficients were similar between a normal and the DP-COM. Except sunbirds, species within a family were not more similar in their response to these covariates than the overall community. Given that estimates were consistent between the normal and the DP-COM, and considering the computational burden for the DP models, we recommend using the DP-COM only when the analysis focuses on community structure and species similarity, as these quantities can only be obtained under the DP-COM.
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Affiliation(s)
- Rahel Sollmann
- Department of Wildlife, Fish, and Conservation Biology, University of California Davis, 1088 Academic Surge, One Shields Ave, Davis, California, 95616, USA
| | - Mitchell Joseph Eaton
- Southeast Climate Adaptation Science Center, U.S. Geological Survey, North Carolina State University, 127 David Clark Labs, Campus Box 7617, Raleigh, North Carolina, 27695, USA
| | - William A Link
- Patuxent Wildlife Research Center, U.S. Geological Survey, Laurel, Maryland, 20708, USA
| | - Paul Mulondo
- Wildlife Conservation Society, PO Box 7487, Kampala, Uganda
| | - Samuel Ayebare
- Wildlife Conservation Society, PO Box 7487, Kampala, Uganda
| | - Sarah Prinsloo
- Wildlife Conservation Society, PO Box 7487, Kampala, Uganda
| | - Andrew J Plumptre
- KBA Secretariat, c/o BirdLife International, David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ, United Kingdom
| | - Devin S Johnson
- Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, 98115, USA
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5
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Ogle K, Barber JJ. Ensuring identifiability in hierarchical mixed effects Bayesian models. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2020; 30:e02159. [PMID: 32365250 DOI: 10.1002/eap.2159] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/29/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
Ecologists are increasingly familiar with Bayesian statistical modeling and its associated Markov chain Monte Carlo (MCMC) methodology to infer about or to discover interesting effects in data. The complexity of ecological data often suggests implementation of (statistical) models with a commensurately rich structure of effects, including crossed or nested (i.e., hierarchical or multi-level) structures of fixed and/or random effects. Yet, our experience suggests that most ecologists are not familiar with subtle but important problems that often arise with such models and with their implementation in popular software. Of foremost consideration for us is the notion of effect identifiability, which generally concerns how well data, models, or implementation approaches inform about, i.e., identify, quantities of interest. In this paper, we focus on implementation pitfalls that potentially misinform subsequent inference, despite otherwise informative data and models. We illustrate the aforementioned issues using random effects regressions on synthetic data. We show how to diagnose identifiability issues and how to remediate these issues with model reparameterization and computational and/or coding practices in popular software, with a focus on JAGS, OpenBUGS, and Stan. We also show how these solutions can be extended to more complex models involving multiple groups of nested, crossed, additive, or multiplicative effects, for models involving random and/or fixed effects. Finally, we provide example code (JAGS/OpenBUGS and Stan) that practitioners can modify and use for their own applications.
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Affiliation(s)
- Kiona Ogle
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, 86011, USA
| | - Jarrett J Barber
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, 86011, USA
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6
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Dornak LL, Aycrigg JL, Sauer J, Conway CJ. Assessing the efficacy of protected and multiple-use lands for bird conservation in the U.S. PLoS One 2020; 15:e0239184. [PMID: 32997702 PMCID: PMC7526929 DOI: 10.1371/journal.pone.0239184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 09/01/2020] [Indexed: 11/18/2022] Open
Abstract
Setting land aside has long been a primary approach for protecting biodiversity; however, the efficacy of this approach has been questioned. We examined whether protecting lands positively influences bird species in the U.S., and thus overall biodiversity. We used the North American Breeding Bird Survey and Protected Areas Database of the U.S. to assess effects of protected and multiple-use lands on the prevalence and long-term population trends of imperiled and non-imperiled bird species. We evaluated whether both presence and proportional area of protected and multiple-use lands surrounding survey routes affected prevalence and population trends for imperiled and non-imperiled species. Regarding presence of these lands surrounding these survey routes, our results suggest that imperiled and non-imperiled species are using the combination of protected and multiple-use lands more than undesignated lands. We found no difference between protected and multiple-use lands. Mean population trends were negative for imperiled species in all land categories and did not differ between the land categories. Regarding proportion of protected lands surrounding the survey routes, we found that neither the prevalence nor population trends of imperiled or non-imperiled species was positively associated with any land category. We conclude that, although many species (in both groups) tend to be using these protected and multiple-use lands more frequently than undesignated lands, this protection does not appear to improve population trends. Our results may be influenced by external pressures (e.g., habitat fragmentation), the size of protected lands, the high mobility of birds that allows them to use a combination of all land categories, and management strategies that result in similar habitat between protected and multiple-use lands, or our approach to detect limited relationships. Overall, our results suggest that the combination of protected and multiple-use lands is insufficient, alone, to prevent declines in avian biodiversity at a national scale.
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Affiliation(s)
- L. Lynnette Dornak
- Department of Geography, University of Wisconsin-Platteville, Platteville, Wisconsin, United States of America
| | - Jocelyn L. Aycrigg
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, United States of America
| | - John Sauer
- U.S. Geological Survey Patuxent Wildlife Research Center, Laurel, Maryland, United States of America
| | - Courtney J. Conway
- U.S. Geological Survey, Idaho Cooperative Fish and Wildlife Research Unit, Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, United States of America
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7
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Beesley LS, Pusey BJ, Douglas MM, Gwinn DC, Canham CA, Keogh CS, Pratt OP, Kennard MJ, Setterfield SA. New insights into the food web of an Australian tropical river to inform water resource management. Sci Rep 2020; 10:14294. [PMID: 32868852 PMCID: PMC7459293 DOI: 10.1038/s41598-020-71331-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 08/10/2020] [Indexed: 11/21/2022] Open
Abstract
Rivers around the world are threatened by altered flow due to water resource development. Altered flow can change food webs and impact riverine energetics. The Fitzroy River, in northern Australia, is targeted for development but uncertainty remains about the sources of carbon supporting the food web, particularly in the lowlands—the region most likely to be impacted by water extraction. This study used stable isotopes to investigate if algal biofilm is the main carbon source sustaining fish in lowland habitats. We also sought evidence that large-bodied migratory fish were transporting remote carbon around the system. Our results revealed that local algal biofilm carbon was the dominant source of energy sustaining fish in wet season floodplain habitats, but that fish in main-channel pools during the dry season were increasingly dependent on other carbon sources, such as leaf litter or phytoplankton. We found no evidence that large-bodied fish were transporting remote carbon from the floodplain or estuary into the lower main-channel of the river. We recommend that water planners take a precautionary approach to policy until sufficient food web evidence is amassed.
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Affiliation(s)
- Leah S Beesley
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia. .,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia.
| | - Bradley J Pusey
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Research Institute for Environment and Livelihoods, Charles Darwin University, Darwin, 0909, Australia
| | - Michael M Douglas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Research Institute for Environment and Livelihoods, Charles Darwin University, Darwin, 0909, Australia.,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia
| | - Daniel C Gwinn
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Biometric Research, South Fremantle, 6162, Australia
| | - Caroline A Canham
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia
| | - Chris S Keogh
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia
| | - Oliver P Pratt
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia
| | - Mark J Kennard
- Australian Rivers Institute, Griffith University, Brisbane, Australia.,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia
| | - Samantha A Setterfield
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia.,Northern Australia Environmental Resources Hub, National Environmental Science Program, Casuarina, Australia
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8
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Soto-Shoender JR, Gwinn DC, Sovie A, McCleery RA. Life-history traits moderate the susceptibility of native mammals to an invasive predator. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02278-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Smith MJ, Ruykys L, Palmer B, Palmer N, Volck G, Thomasz A, Riessen N. The impact of a fox‐ and cat‐free safe haven on the bird fauna of remnant vegetation in southwestern Australia. Restor Ecol 2020. [DOI: 10.1111/rec.13105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael J. Smith
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
- Ecosystem Restoration and Intervention Ecology Research Group, School of Biological SciencesThe University of Western Australia 35 Stirling Highway Crawley WA 6009 Australia
| | - Laura Ruykys
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
| | - Bryony Palmer
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
- Ecosystem Restoration and Intervention Ecology Research Group, School of Biological SciencesThe University of Western Australia 35 Stirling Highway Crawley WA 6009 Australia
| | - Nicola Palmer
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
| | - Georgia Volck
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
| | - Adele Thomasz
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
| | - Noel Riessen
- Australian Wildlife Conservancy PO Box 8070 Subiaco East WA 6008 Australia
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10
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Abstract
Abstract
Island biogeography theory (IBT) explains and estimates large-scale ecological patterns among islands and isolated habitat patches. Specifically, IBT predicts that the number of species per habitat patch differs as a function of area and isolation as a result of local colonization and extinction. Accurate estimates of species richness are essential for testing predictions of IBT, but differences in detectability of species can lead to bias in empirical data. Hierarchical community models correct for imperfect detection by leveraging information from across the community to estimate species-specific occupancy and detection probabilities. Using the fragmented Ozark glades as our model system, we constructed a hierarchical community model to 1) estimate site-level and regional species richness of small mammals while correcting for detection error, and 2) determine environmental covariates driving occupancy. We sampled 16 glades in southwestern Missouri in summer 2016–2017 and quantified mammal community structure within the glade network. The detected species pool included eight species, and the model yielded a regional species estimate of 8.6 species, with a mean of 3.47 species per glade. Species richness increased with patch area but not isolation, and effects of patch shape varied between species in the community.
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Affiliation(s)
- Emily M Beasley
- Department of Biology, Missouri State University, Springfield, MO, USA
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Sean P Maher
- Department of Biology, Missouri State University, Springfield, MO, USA
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11
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Guzy JC, Halloran KM, Homyack JA, Thornton-Frost JE, Willson JD. Differential responses of amphibian and reptile assemblages to size of riparian buffers within managed forests. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01995. [PMID: 31483894 DOI: 10.1002/eap.1995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 07/12/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
Streamside management zones (i.e., riparian buffers; SMZs) are commonly implemented within managed forests to protect water quality but may also provide habitat for riparian-associated wildlife. Yet, little research has rigorously addressed the value of SMZs for wildlife, particularly for cryptic species such as amphibians and reptiles. Previous studies of herpetofauna within SMZs have focused on one or a few stream-associated species, and questions remain regarding variation among species or guilds and what role SMZs serve toward conservation of herpetofaunal diversity in managed forests. However, recent statistical advances have improved our ability to analyze large multi-species presence-absence data sets, accounting for low detection rates typical for some herpetofaunal species. Our study represents an extensive landscape-scale examination of herpetofaunal communities within SMZs using a multi-species occupancy approach. We conducted four replicate surveys at 102 headwater streams, spanning a gradient of SMZ widths and adjacent forest stand ages, within the Ouachita Mountains, Arkansas, USA. We used a hierarchical Bayesian community occupancy model to estimate species richness and species-specific occupancy responses to SMZ and overstory characteristics, accounting for variation in occupancy and detection attributable to site and sampling covariates. We documented high richness (37 species) within SMZs. Across the herpetofaunal community, occupancy and species richness were consistently positively associated with SMZ width, with maximum predicted richness of 30 species occurring at sites with buffers extending 51 m on either side of the stream. However, we documented considerable variation among groups and species within groups, underscoring the potential for different responses to forest management among taxa. Reptile predicted richness increased more rapidly up to SMZs of ~35 m, whereas maximum salamander predicted richness was not seen until an SMZ width of 55 m. Estimated salamander richness was highest within SMZs embedded in mature managed pine stands and was higher in SMZs comprised of a deciduous or mixed overstory vs. a pine overstory. Compared to salamanders, more anuran species showed high mean estimated occupancy (>75%) at narrower SMZs (<30 m). Collectively, our results indicate that SMZs surrounding small first-order streams in intensively managed forests not only protect water quality, but also can support diverse amphibian and reptile communities.
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Affiliation(s)
- Jacquelyn C Guzy
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kelly M Halloran
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Jessica A Homyack
- Weyerhaeuser Company, 505 North Pearl Street, Centralia, Washington, 98531, USA
| | | | - John D Willson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
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12
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Gwinn DC, Middleton JA, Beesley L, Close P, Quinton B, Storer T, Davies PM. Hierarchical multi-taxa models inform riparian vs. hydrologic restoration of urban streams in a permeable landscape. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2018; 28:385-397. [PMID: 29178482 DOI: 10.1002/eap.1654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 10/04/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
The degradation of streams caused by urbanization tends to follow predictable patterns; however, there is a growing appreciation for heterogeneity in stream response to urbanization due to the local geoclimatic context. Furthermore, there is building evidence that streams in mildly sloped, permeable landscapes respond uncharacteristically to urban stress calling for a more nuanced approach to restoration. We evaluated the relative influence of local-scale riparian characteristics and catchment-scale imperviousness on the macroinvertebrate assemblages of streams in the flat, permeable urban landscape of Perth, Western Australia. Using a hierarchical multi-taxa model, we predicted the outcomes of stylized stream restoration strategies to increase the riparian integrity at the local scale or decrease the influences of imperviousness at the catchment scale. In the urban streams of Perth, we show that local-scale riparian restoration can influence the structure of macroinvertebrate assemblages to a greater degree than managing the influences of catchment-scale imperviousness. We also observed an interaction between the effect of riparian integrity and imperviousness such that the effect of increased riparian integrity was enhanced at lower levels of catchment imperviousness. This study represents one of few conducted in flat, permeable landscapes and the first aimed at informing urban stream restoration in Perth, adding to the growing appreciation for heterogeneity of the Urban Stream Syndrome and its importance for urban stream restoration.
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Affiliation(s)
- Daniel C Gwinn
- Biometric Research, Fremantle, Western Australia, Australia
| | - Jen A Middleton
- Centre of Excellence in Natural Resource Management, University of Western Australia, PO Box 5771, Albany, Western Australia, Australia
- Cooperative Research Centre for Water Sensitive Cities, Clayton, Victoria, Australia
| | - Leah Beesley
- Centre of Excellence in Natural Resource Management, University of Western Australia, PO Box 5771, Albany, Western Australia, Australia
- Cooperative Research Centre for Water Sensitive Cities, Clayton, Victoria, Australia
| | - Paul Close
- Centre of Excellence in Natural Resource Management, University of Western Australia, PO Box 5771, Albany, Western Australia, Australia
- Cooperative Research Centre for Water Sensitive Cities, Clayton, Victoria, Australia
| | - Belinda Quinton
- Cooperative Research Centre for Water Sensitive Cities, Clayton, Victoria, Australia
- Department of Water, Government of Western Australian, Perth, Western Australia, Australia
| | - Tim Storer
- Cooperative Research Centre for Water Sensitive Cities, Clayton, Victoria, Australia
- Department of Water, Government of Western Australian, Perth, Western Australia, Australia
| | - Peter M Davies
- Centre of Excellence in Natural Resource Management, University of Western Australia, PO Box 5771, Albany, Western Australia, Australia
- Cooperative Research Centre for Water Sensitive Cities, Clayton, Victoria, Australia
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13
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Gomez JP, Robinson SK, Blackburn JK, Ponciano JM. An efficient extension of N-mixture models for multi-species abundance estimation. Methods Ecol Evol 2018; 9:340-353. [PMID: 29892335 PMCID: PMC5992910 DOI: 10.1111/2041-210x.12856] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study we propose an extension of the N-mixture family of models that targets an improvement of the statistical properties of rare species abundance estimators when sample sizes are low, yet typical for tropical studies. The proposed method harnesses information from other species in an ecological community to correct each species' estimator. We provide guidance to determine the sample size required to estimate accurately the abundance of rare tropical species when attempting to estimate the abundance of single species.We evaluate the proposed methods using an assumption of 50 m radius plots and perform simulations comprising a broad range of sample sizes, true abundances and detectability values and a complex data generating process. The extension of the N-mixture model is achieved by assuming that the detection probabilities are drawn at random from a beta distribution in a multi-species fashion. This hierarchical model avoids having to specify a single detection probability parameter per species in the targeted community. Parameter estimation is done via Maximum Likelihood.We compared our multi-species approach with previously proposed multi-species N-mixture models, which we show are biased when the true densities of species in the community are less than seven individuals per 100 hectares. The beta N-mixture model proposed here outperforms the traditional Multi-species N-mixture model by allowing the estimation of organisms at lower densities and controlling the bias in the estimation.We illustrate how our methodology can be used to suggest sample sizes required to estimate the abundance of organisms, when these are either rare, common or abundant. When the interest is full communities, we show how the multi-species approaches, and in particular our beta model and estimation methodology, can be used as a practical solution to estimate organism densities from rapid inventory datasets. The statistical inferences done with our model via Maximum Likelihood can also be used to group species in a community according to their detectabilities.
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Affiliation(s)
- Juan Pablo Gomez
- Department of Biology, University of Florida, Gainesville, Florida
- Florida Museum of Natural History, Gainesville, Florida
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
| | | | - Jason K Blackburn
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville Florida
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida
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14
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Bush CL, Guzy JC, Halloran KM, Swartwout MC, Kross CS, Willson JD. Distribution and Abundance of Introduced Seal Salamanders (Desmognathus monticola) in Northwest Arkansas, USA. COPEIA 2017. [DOI: 10.1643/ch-17-579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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15
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Huang Q, Sauer JR, Dubayah RO. Multidirectional abundance shifts among North American birds and the relative influence of multifaceted climate factors. GLOBAL CHANGE BIOLOGY 2017; 23:3610-3622. [PMID: 28295885 DOI: 10.1111/gcb.13683] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 02/01/2017] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
Shifts in species distributions are major fingerprint of climate change. Examining changes in species abundance structures at a continental scale enables robust evaluation of climate change influences, but few studies have conducted these evaluations due to limited data and methodological constraints. In this study, we estimate temporal changes in abundance from North American Breeding Bird Survey data at the scale of physiographic strata to examine the relative influence of different components of climatic factors and evaluate the hypothesis that shifting species distributions are multidirectional in resident bird species in North America. We quantify the direction and velocity of the abundance shifts of 57 permanent resident birds over 44 years using a centroid analysis. For species with significant abundance shifts in the centroid analysis, we conduct a more intensive correlative analysis to identify climate components most strongly associated with composite change of abundance within strata. Our analysis focus on two contrasts: the relative importance of climate extremes vs. averages, and of temperature vs. precipitation in strength of association with abundance change. Our study shows that 36 species had significant abundance shifts over the study period. The average velocity of the centroid is 5.89 km·yr-1 . The shifted distance on average covers 259 km, 9% of range extent. Our results strongly suggest that the climate change fingerprint in studied avian distributions is multidirectional. Among 6 directions with significant abundance shifts, the northwestward shift was observed in the largest number of species (n = 13). The temperature/average climate model consistently has greater predictive ability than the precipitation/extreme climate model in explaining strata-level abundance change. Our study shows heterogeneous avian responses to recent environmental changes. It highlights needs for more species-specific approaches to examine contributing factors to recent distributional changes and for comprehensive conservation planning for climate change adaptation.
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Affiliation(s)
- Qiongyu Huang
- Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA
| | - John R Sauer
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, MD, USA
| | - Ralph O Dubayah
- Department of Geographical Sciences, University of Maryland, College Park, MD, USA
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16
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Ray C, Saracco JF, Holmgren ML, Wilkerson RL, Siegel RB, Jenkins KJ, Ransom JI, Happe PJ, Boetsch JR, Huff MH. Recent stability of resident and migratory landbird populations in National Parks of the Pacific Northwest. Ecosphere 2017. [DOI: 10.1002/ecs2.1902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Chris Ray
- The Institute for Bird Populations; Point Reyes Station California 94956 USA
| | - James F. Saracco
- The Institute for Bird Populations; Point Reyes Station California 94956 USA
| | - Mandy L. Holmgren
- The Institute for Bird Populations; Point Reyes Station California 94956 USA
| | - Robert L. Wilkerson
- The Institute for Bird Populations; Point Reyes Station California 94956 USA
| | - Rodney B. Siegel
- The Institute for Bird Populations; Point Reyes Station California 94956 USA
| | - Kurt J. Jenkins
- U.S. Geological Survey; Forest and Rangeland Ecosystem Science Center; Olympic Field Station Port Angeles Washington 98362 USA
| | - Jason I. Ransom
- North Cascades National Park Service Complex; Sedro-Woolley Washington 98284 USA
| | | | | | - Mark H. Huff
- Mount Rainier National Park; Ashford Washington 98304 USA
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17
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Ahrestani FS, Saracco JF, Sauer JR, Pardieck KL, Royle JA. An integrated population model for bird monitoring in North America. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2017; 27:916-924. [PMID: 28036137 DOI: 10.1002/eap.1493] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/28/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
Integrated population models (IPMs) provide a unified framework for simultaneously analyzing data sets of different types to estimate vital rates, population size, and dynamics; assess contributions of demographic parameters to population changes; and assess population viability. Strengths of an IPM include the ability to estimate latent parameters and improve the precision of parameter estimates. We present a hierarchical IPM that combines two broad-scale avian monitoring data sets: count data from the North American Breeding Bird Survey (BBS) and capture-recapture data from the Monitoring Avian Productivity and Survivorship (MAPS) program. These data sets are characterized by large numbers of sample sites and observers, factors capable of inducing error in the sampling and observation processes. The IPM integrates the data sets by modeling the population abundance as a first-order autoregressive function of the previous year's population abundance and vital rates. BBS counts were modeled as a log-linear function of the annual index of population abundance, observation effects (observer identity and first survey year), and overdispersion. Vital rates modeled included adult apparent survival, estimated from a transient Cormack-Jolly-Seber model using MAPS data, and recruitment (surviving hatched birds from the previous season + dispersing adults) estimated as a latent parameter. An assessment of the IPM demonstrated it could recover true parameter values from 200 simulated data sets. The IPM was applied to data sets (1992-2008) of two bird species, Gray Catbird (Dumetella carolinensis) and Wood Thrush (Hylocichla mustelina) in the New England/Mid-Atlantic coastal Bird Conservation Region of the United States. The Gray Catbird population was relatively stable (trend +0.4% per yr), while the Wood Thrush population nearly halved (trend -4.5% per yr) over the 17-yr study period. IPM estimates of population growth rates, adult survival, and detection and residency probabilities were similar and as precise as estimates from the stand-alone BBS and CJS models. A benefit of using the IPM was its ability to estimate the latent recruitment parameter. Annual growth rates for both species correlated more with recruitment than survival, and the relationship for Wood Thrush was stronger than for Gray Catbird. The IPM's unified modeling framework facilitates integration of these important data sets.
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Affiliation(s)
- Farshid S Ahrestani
- The Institute of Bird Populations, P.O. Box 1346, Point Reyes, California, 94956, USA
- Foundation for Ecological Research, Advocacy and Learning, Pondicherry, 605012, India
| | - James F Saracco
- The Institute of Bird Populations, P.O. Box 1346, Point Reyes, California, 94956, USA
| | - John R Sauer
- USGS Patuxent Wildlife Research Center, 11510 American Holly Drive, Laurel, Maryland, 20708, USA
| | - Keith L Pardieck
- USGS Patuxent Wildlife Research Center, 11510 American Holly Drive, Laurel, Maryland, 20708, USA
| | - J Andrew Royle
- USGS Patuxent Wildlife Research Center, 11510 American Holly Drive, Laurel, Maryland, 20708, USA
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18
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Soykan CU, Sauer J, Schuetz JG, LeBaron GS, Dale K, Langham GM. Population trends for North American winter birds based on hierarchical models. Ecosphere 2016. [DOI: 10.1002/ecs2.1351] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Candan U. Soykan
- Conservation Science National Audubon Society 220 Montgomery St. Suite 1000 San Francisco California 94104 USA
| | - John Sauer
- Patuxent Wildlife Research Center U.S. Geological Survey 12100 Beech Forest Road Laurel Maryland 20708 USA
| | - Justin G. Schuetz
- Conservation Science National Audubon Society 220 Montgomery St. Suite 1000 San Francisco California 94104 USA
| | - Geoffrey S. LeBaron
- Citizen Science National Audubon Society 2300 Computer Avenue, I‐49 Willow Grove Pennsylvania 19090 USA
| | - Kathy Dale
- Citizen Science National Audubon Society 2300 Computer Avenue, I‐49 Willow Grove Pennsylvania 19090 USA
| | - Gary M. Langham
- National Audubon Society 1200 18th Street, NW, Suite 500 Washington D.C. 20036 USA
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19
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Study of biological communities subject to imperfect detection: bias and precision of community N-mixture abundance models in small-sample situations. Ecol Res 2016. [DOI: 10.1007/s11284-016-1340-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Goijman AP, Conroy MJ, Bernardos JN, Zaccagnini ME. Multi-Season Regional Analysis of Multi-Species Occupancy: Implications for Bird Conservation in Agricultural Lands in East-Central Argentina. PLoS One 2015; 10:e0130874. [PMID: 26086250 PMCID: PMC4472512 DOI: 10.1371/journal.pone.0130874] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 05/26/2015] [Indexed: 11/18/2022] Open
Abstract
Rapid expansion and intensification of agriculture create challenges for the conservation of biodiversity and associated ecosystem services. In Argentina, the total row crop planted area has increased in recent decades with the expansion of soybean cultivation, homogenizing the landscape. In 2003 we started the first long-term, large-scale bird monitoring program in agroecosystems of central Argentina, in portions of the Pampas and Espinal ecoregions. Using data from this program, we evaluated the effect of land use and cover extent on birds between 2003-2012, accounting for imperfect detection probabilities using a Bayesian hierarchical, multi-species and multi-season occupancy model. We tested predictions that species diversity is positively related to habitat heterogeneity, which in intensified agroecosystems is thought to be mediated by food availability; thus the extent of land use and cover is predicted to affect foraging guilds differently. We also infer about ecosystem services provisioning and inform management recommendations for conservation of birds. Overall our results support the predictions. Although many species within each guild responded differently to land use and native forest cover, we identified generalities for most trophic guilds. For example, granivorous gleaners, ground insectivores and omnivores responded negatively to high proportions of soybean, while insectivore gleaners and aerial foragers seemed more tolerant. Habitat heterogeneity would likely benefit most species in an intensified agroecosystem, and can be achieved with a diversity of crops, pastures, and natural areas within the landscape. Although most studied species are insectivores, potentially beneficial for pest control, some guilds such as ground insectivores are poorly represented, suggesting that agricultural intensification reduces ecological functions, which may be recovered through management. Continuation of the bird monitoring program will allow us to continue to inform for conservation of birds in agroecosystems, identify research needed to reduce key uncertainties, and anticipate the effects of changes in agriculture in central Argentina.
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Affiliation(s)
- Andrea Paula Goijman
- Instituto de Recursos Biológicos, CIRN, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
- D.B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA United States of America
| | - Michael. J. Conroy
- D.B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA United States of America
| | - Jaime Nicolás Bernardos
- EEA Ing. Agr. Guillermo Covas, Instituto Nacional de Tecnología Agropecuaria (INTA), Anguil, La Pampa, Argentina
| | - María Elena Zaccagnini
- Instituto de Recursos Biológicos, CIRN, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Buenos Aires, Argentina
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21
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Davis AJ, Hooten MB, Phillips ML, Doherty PF. An integrated modeling approach to estimating Gunnison sage-grouse population dynamics: combining index and demographic data. Ecol Evol 2014; 4:4247-57. [PMID: 25540687 PMCID: PMC4267864 DOI: 10.1002/ece3.1290] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/14/2014] [Accepted: 09/25/2014] [Indexed: 11/12/2022] Open
Abstract
Evaluation of population dynamics for rare and declining species is often limited to data that are sparse and/or of poor quality. Frequently, the best data available for rare bird species are based on large-scale, population count data. These data are commonly based on sampling methods that lack consistent sampling effort, do not account for detectability, and are complicated by observer bias. For some species, short-term studies of demographic rates have been conducted as well, but the data from such studies are typically analyzed separately. To utilize the strengths and minimize the weaknesses of these two data types, we developed a novel Bayesian integrated model that links population count data and population demographic data through population growth rate (λ) for Gunnison sage-grouse (Centrocercus minimus). The long-term population index data available for Gunnison sage-grouse are annual (years 1953–2012) male lek counts. An intensive demographic study was also conducted from years 2005 to 2010. We were able to reduce the variability in expected population growth rates across time, while correcting for potential small sample size bias in the demographic data. We found the population of Gunnison sage-grouse to be variable and slightly declining over the past 16 years.
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Affiliation(s)
- Amy J Davis
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University Fort Collins, Colorado, 80523
| | - Mevin B Hooten
- U.S. Geological Survey, Colorado Cooperative Fish and Wildlife Research Unit, Colorado State University Fort Collins, Colorado, 80523 ; Department of Fish, Wildlife, and Conservation Biology, Colorado State University Fort Collins, Colorado, 80523
| | - Michael L Phillips
- Colorado Parks and Wildlife 317 W. Prospect Rd, Fort Collins, Colorado, 80526
| | - Paul F Doherty
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University Fort Collins, Colorado, 80523
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22
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Johnson D, Fritz L. agTrend: A Bayesian approach for estimating trends of aggregated abundance. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12231] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Devin S. Johnson
- National Marine Mammal Laboratory; Alaska Fisheries Science Center NOAA National Marine Fisheries Service; Seattle WA USA
| | - Lowell Fritz
- National Marine Mammal Laboratory; Alaska Fisheries Science Center NOAA National Marine Fisheries Service; Seattle WA USA
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23
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Barnagaud JY, Barbaro L, Papaïx J, Deconchat M, Brockerhoff EG. Habitat filtering by landscape and local forest composition in native and exotic New Zealand birds. Ecology 2014; 95:78-87. [PMID: 24649648 DOI: 10.1890/13-0791.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Untangling the relative influences of environmental filtering and biotic interactions on species coexistence at various spatial scales is a long-held issue in community ecology. Separating these processes is especially important to understand the influences of introduced exotic species on the composition of native communities. For this aim, we investigated coexistence patterns in New Zealand exotic and native birds along multiple-scale habitat gradients. We built a Bayesian hierarchical model, contrasting the abundance variations of 10 native and 11 exotic species in 501 point counts spread along landscape and local-scale gradients of forest structure and composition. Although native and exotic species both occurred in a wide range of habitats, they were separated by landscape-level variables. Exotic species were most abundant in exotic conifer plantations embedded in farmland matrices, while native birds predominated in areas dominated by continuous native forest. In exotic plantation forests, and to a lesser extent in native forests, locally co-occurring exotic and native species were segregated along a gradient of vegetation height. These results support the prediction that exotic and native bird species are segregated along gradients related to anthropogenic disturbance and habitat availability. In addition, native and exotic species overlapped little in a multivariate functional space based on 10 life history traits associated with habitat selection. Hence, habitat segregation patterns were probably mediated more by environmental filtering processes than by competition at landscape and local scales.
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24
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Pacifici K, Zipkin EF, Collazo JA, Irizarry JI, DeWan A. Guidelines for a priori grouping of species in hierarchical community models. Ecol Evol 2014; 4:877-88. [PMID: 24772267 PMCID: PMC3997306 DOI: 10.1002/ece3.976] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/07/2014] [Indexed: 12/04/2022] Open
Abstract
Recent methodological advances permit the estimation of species richness and occurrences for rare species by linking species-level occurrence models at the community level. The value of such methods is underscored by the ability to examine the influence of landscape heterogeneity on species assemblages at large spatial scales. A salient advantage of community-level approaches is that parameter estimates for data-poor species are more precise as the estimation process "borrows" from data-rich species. However, this analytical benefit raises a question about the degree to which inferences are dependent on the implicit assumption of relatedness among species. Here, we assess the sensitivity of community/group-level metrics, and individual-level species inferences given various classification schemes for grouping species assemblages using multispecies occurrence models. We explore the implications of these groupings on parameter estimates for avian communities in two ecosystems: tropical forests in Puerto Rico and temperate forests in northeastern United States. We report on the classification performance and extent of variability in occurrence probabilities and species richness estimates that can be observed depending on the classification scheme used. We found estimates of species richness to be most precise and to have the best predictive performance when all of the data were grouped at a single community level. Community/group-level parameters appear to be heavily influenced by the grouping criteria, but were not driven strictly by total number of detections for species. We found different grouping schemes can provide an opportunity to identify unique assemblage responses that would not have been found if all of the species were analyzed together. We suggest three guidelines: (1) classification schemes should be determined based on study objectives; (2) model selection should be used to quantitatively compare different classification approaches; and (3) sensitivity of results to different classification approaches should be assessed. These guidelines should help researchers apply hierarchical community models in the most effective manner.
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Affiliation(s)
- Krishna Pacifici
- North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State UniversityRaleigh, North Carolina, 27695
| | - Elise F Zipkin
- Department of Zoology, Michigan State UniversityEast Lansing, Michigan, 48824
| | - Jaime A Collazo
- U.S. Geological Survey, North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State UniversityRaleigh, North Carolina, 27695
| | - Julissa I Irizarry
- North Carolina Cooperative Fish and Wildlife Research Unit, Department of Applied Ecology, North Carolina State UniversityRaleigh, North Carolina, 27695
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25
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The North American Breeding Bird Survey 1966–2011: Summary Analysis and Species Accounts. ACTA ACUST UNITED AC 2013. [DOI: 10.3996/nafa.79.0001] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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26
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Evaluating δ15N–body size relationships across taxonomic levels using hierarchical models. Oecologia 2013; 173:1159-68. [DOI: 10.1007/s00442-013-2715-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 06/10/2013] [Indexed: 10/26/2022]
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27
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Dudaniec RY, Rhodes JR, Worthington Wilmer J, Lyons M, Lee KE, McAlpine CA, Carrick FN. Using multilevel models to identify drivers of landscape-genetic structure among management areas. Mol Ecol 2013; 22:3752-65. [PMID: 23730800 DOI: 10.1111/mec.12359] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 04/02/2013] [Accepted: 04/05/2013] [Indexed: 11/26/2022]
Abstract
Landscape genetics offers a powerful approach to understanding species' dispersal patterns. However, a central obstacle is to account for ecological processes operating at multiple spatial scales, while keeping research outcomes applicable to conservation management. We address this challenge by applying a novel multilevel regression approach to model landscape drivers of genetic structure at both the resolution of individuals and at a spatial resolution relevant to management (i.e. local government management areas: LGAs) for the koala (Phascolartos cinereus) in Australia. Our approach allows for the simultaneous incorporation of drivers of landscape-genetic relationships operating at multiple spatial resolutions. Using microsatellite data for 1106 koalas, we show that, at the individual resolution, foliage projective cover (FPC) facilitates high gene flow (i.e. low resistance) until it falls below approximately 30%. Out of six additional land-cover variables, only highways and freeways further explained genetic distance after accounting for the effect of FPC. At the LGA resolution, there was significant variation in isolation-by-resistance (IBR) relationships in terms of their slopes and intercepts. This was predominantly explained by the average resistance distance among LGAs, with a weaker effect of historical forest cover. Rates of recent landscape change did not further explain variation in IBR relationships among LGAs. By using a novel multilevel model, we disentangle the effect of landscape resistance on gene flow at the fine resolution (i.e. among individuals) from effects occurring at coarser resolutions (i.e. among LGAs). This has important implications for our ability to identify appropriate scale-dependent management actions.
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Affiliation(s)
- Rachael Y Dudaniec
- School of Geography, Planning and Environmental Management, The University of Queensland, Brisbane, QLD, 4072, Australia.
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28
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Sauer JR, Blank PJ, Zipkin EF, Fallon JE, Fallon FW. Using multi-species occupancy models in structured decision making on managed lands. J Wildl Manage 2012. [DOI: 10.1002/jwmg.442] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Cam E. ‘Each site has its own survival probability, but information is borrowed across sites to tell us about survival in each site’: random effects models as means of borrowing strength in survival studies of wild vertebrates. Anim Conserv 2012. [DOI: 10.1111/j.1469-1795.2012.00533.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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Halstead BJ, Wylie GD, Coates PS, Valcarcel P, Casazza ML. Bayesian shared frailty models for regional inference about wildlife survival. Anim Conserv 2011. [DOI: 10.1111/j.1469-1795.2011.00495.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- B. J. Halstead
- U.S. Geological Survey; Western Ecological Research Center; Dixon Field Station; Dixon; CA; USA
| | - G. D. Wylie
- U.S. Geological Survey; Western Ecological Research Center; Dixon Field Station; Dixon; CA; USA
| | - P. S. Coates
- U.S. Geological Survey; Western Ecological Research Center; Dixon Field Station; Dixon; CA; USA
| | - P. Valcarcel
- U.S. Geological Survey; Western Ecological Research Center; Dixon Field Station; Dixon; CA; USA
| | - M. L. Casazza
- U.S. Geological Survey; Western Ecological Research Center; Dixon Field Station; Dixon; CA; USA
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31
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32
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Ruiz-Gutiérrez V, Zipkin EF. Detection biases yield misleading patterns of species persistence and colonization in fragmented landscapes. Ecosphere 2011. [DOI: 10.1890/es10-00207.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Yamaura Y, Andrew Royle J, Kuboi K, Tada T, Ikeno S, Makino S. Modelling community dynamics based on species-level abundance models from detection/nondetection data. J Appl Ecol 2010. [DOI: 10.1111/j.1365-2664.2010.01922.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Essington TE, Paulsen CE. Quantifying Hypoxia Impacts on an Estuarine Demersal Community Using a Hierarchical Ensemble Approach. Ecosystems 2010. [DOI: 10.1007/s10021-010-9372-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lahoz-Monfort JJ, Morgan BJT, Harris MP, Wanless S, Freeman SN. A capture-recapture model for exploring multi-species synchrony in survival. Methods Ecol Evol 2010. [DOI: 10.1111/j.2041-210x.2010.00050.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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DeWan AA, Zipkin EF. An integrated sampling and analysis approach for improved biodiversity monitoring. ENVIRONMENTAL MANAGEMENT 2010; 45:1223-1230. [PMID: 20237922 DOI: 10.1007/s00267-010-9457-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 02/11/2010] [Indexed: 05/28/2023]
Abstract
Successful biodiversity conservation requires high quality monitoring data and analyses to ensure scientifically defensible policy, legislation, and management. Although monitoring is a critical component in assessing population status and trends, many governmental and non-governmental organizations struggle to develop and implement effective sampling protocols and statistical analyses because of the magnitude and diversity of species in conservation concern. In this article we describe a practical and sophisticated data collection and analysis framework for developing a comprehensive wildlife monitoring program that includes multi-species inventory techniques and community-level hierarchical modeling. Compared to monitoring many species individually, the multi-species approach allows for improved estimates of individual species occurrences, including rare species, and an increased understanding of the aggregated response of a community to landscape and habitat heterogeneity. We demonstrate the benefits and practicality of this approach to address challenges associated with monitoring in the context of US state agencies that are legislatively required to monitor and protect species in greatest conservation need. We believe this approach will be useful to regional, national, and international organizations interested in assessing the status of both common and rare species.
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Affiliation(s)
- Amielle A DeWan
- Conservation Planning, Defenders of Wildlife, Washington, DC 20036-4604, USA.
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Zipkin EF, DeWan A, Andrew Royle J. Impacts of forest fragmentation on species richness: a hierarchical approach to community modelling. J Appl Ecol 2009. [DOI: 10.1111/j.1365-2664.2009.01664.x] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Russell RE, Royle JA, Saab VA, Lehmkuhl JF, Block WM, Sauer JR. Modeling the effects of environmental disturbance on wildlife communities: avian responses to prescribed fire. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2009; 19:1253-1263. [PMID: 19688932 DOI: 10.1890/08-0910.1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Prescribed fire is a management tool used to reduce fuel loads on public lands in forested areas in the western United States. Identifying the impacts of prescribed fire on bird communities in ponderosa pine (Pinus ponderosa) forests is necessary for providing land management agencies with information regarding the effects of fuel reduction on sensitive, threatened, and migratory bird species. Recent developments in occupancy modeling have established a framework for quantifying the impacts of management practices on wildlife community dynamics. We describe a Bayesian hierarchical model of multi-species occupancy accounting for detection probability, and we demonstrate the model's usefulness for identifying effects of habitat disturbances on wildlife communities. Advantages to using the model include the ability to estimate the effects of environmental impacts on rare or elusive species, the intuitive nature of the modeling, the incorporation of detection probability, the estimation of parameter uncertainty, the flexibility of the model to suit a variety of experimental designs, and the composite estimate of the response that applies to the collection of observed species as opposed to merely a small subset of common species. Our modeling of the impacts of prescribed fire on avian communities in a ponderosa pine forest in Washington indicate that prescribed fire treatments result in increased occupancy rates for several bark-insectivore, cavity-nesting species including a management species of interest, Black-backed Woodpeckers (Picoides arcticus). Three aerial insectivore species, and the ground insectivore, American Robin (Turdus migratorius), also responded positively to prescribed fire, whereas three foliage insectivores and two seed specialists, Clark's Nutcracker (Nucifraga columbiana) and the Pine Siskin (Carduelis pinus), declined following treatments. Land management agencies interested in determining the effects of habitat manipulations on wildlife communities can use these methods to provide guidance for future management activities.
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Affiliation(s)
- Robin E Russell
- U.S. Forest Service, Rocky Mountain Research Station, 1648 S. 7th Avenue, Montana State University Campus, Bozeman, Montana 59717, USA.
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Hobbs NT, Hilborn R. Alternatives to statistical hypothesis testing in ecology: a guide to self teaching. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2006; 16:5-19. [PMID: 16705957 DOI: 10.1890/04-0645] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Statistical methods emphasizing formal hypothesis testing have dominated the analyses used by ecologists to gain insight from data. Here, we review alternatives to hypothesis testing including techniques for parameter estimation and model selection using likelihood and Bayesian techniques. These methods emphasize evaluation of weight of evidence for multiple hypotheses, multimodel inference, and use of prior information in analysis. We provide a tutorial for maximum likelihood estimation of model parameters and model selection using information theoretics, including a brief treatment of procedures for model comparison, model averaging, and use of data from multiple sources. We discuss the advantages of likelihood estimation, Bayesian analysis, and meta-analysis as ways to accumulate understanding across multiple studies. These statistical methods hold promise for new insight in ecology by encouraging thoughtful model building as part of inquiry, providing a unified framework for the empirical analysis of theoretical models, and by facilitating the formal accumulation of evidence bearing on fundamental questions.
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Affiliation(s)
- N Thompson Hobbs
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA.
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Clark JS, Ferraz G, Oguge N, Hays H, DiCostanzo J. HIERARCHICAL BAYES FOR STRUCTURED, VARIABLE POPULATIONS: FROM RECAPTURE DATA TO LIFE-HISTORY PREDICTION. Ecology 2005. [DOI: 10.1890/04-1348] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Helms SE, Hunter MD. Variation in plant quality and the population dynamics of herbivores: there is nothing average about aphids. Oecologia 2005; 145:197-204. [PMID: 15891845 DOI: 10.1007/s00442-005-0060-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2004] [Accepted: 02/03/2005] [Indexed: 10/25/2022]
Abstract
In the attempt to use results from small-scale studies to make large-scale predictions, it is critical that we take into account the greater spatial heterogeneity encountered at larger spatial scales. An important component of this heterogeneity is variation in plant quality, which can have a profound influence on herbivore population dynamics. This influence is particularly relevant when we consider that the strength of density dependence can vary among host plants and that the strength of density dependence determines the difference between exponential and density- dependent growth. Here, we present some simple models and analyses designed to examine the impact of variable plant quality on the dynamics of insect herbivore populations, and specifically the consequences of variation in the strength of density dependence among host plants. We show that average values of herbivore population growth parameters, calculated from plants that vary in quality, do not predict overall population growth. Furthermore, we illustrate that the quality of a few individual plants within a larger plant population can dominate herbivore population growth. Our results demonstrate that ignoring spatial heterogeneity that exists in herbivore population growth on plants that differ in quality can lead to a misunderstanding of the mechanisms that underlie population dynamics.
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Affiliation(s)
- Sandra E Helms
- Institute of Ecology, University of Georgia, Athens, GA 30602-2202, USA.
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Maunder MN. Population viability analysis based on combining Bayesian, integrated, and hierarchical analyses. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2004. [DOI: 10.1016/j.actao.2003.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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