Publications by authors named "Larissa L Bailey"

40 Publications

Individual heterogeneity influences the effects of translocation on urban dispersal of an invasive reptile.

Mov Ecol 2022 Jan 15;10(1). Epub 2022 Jan 15.

The University of Texas at Austin, Department of Statistics and Data Sciences, Welch 5.216, 105 E 24th St D9800, Austin, TX, 78705-1576, USA.

Background: Invasive reptiles pose a serious threat to global biodiversity, but early detection of individuals in an incipient population is often hindered by their cryptic nature, sporadic movements, and variation among individuals. Little is known about the mechanisms that affect the movement of these species, which limits our understanding of their dispersal. Our aim was to determine whether translocation or small-scale landscape features affect movement patterns of brown treesnakes (Boiga irregularis), a destructive invasive predator on the island of Guam.

Methods: We conducted a field experiment to compare the movements of resident (control) snakes to those of snakes translocated from forests and urban areas into new urban habitats. We developed a Bayesian hierarchical model to analyze snake movement mechanisms and account for attributes unique to invasive reptiles by incorporating multiple behavioral states and individual heterogeneity in movement parameters.

Results: We did not observe strong differences in mechanistic movement parameters (turning angle or step length) among experimental treatment groups. We found some evidence that translocated snakes from both forests and urban areas made longer movements than resident snakes, but variation among individuals within treatment groups weakened this effect. Snakes translocated from forests moved more frequently from pavement than those translocated from urban areas. Snakes translocated from urban areas moved less frequently from buildings than resident snakes. Resident snakes had high individual heterogeneity in movement probability.

Conclusions: Our approach to modeling movement improved our understanding of invasive reptile dispersal by allowing us to examine the mechanisms that influence their movement. We also demonstrated the importance of accounting for individual heterogeneity in population-level analyses, especially when management goals involve eradication of an invasive species.
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http://dx.doi.org/10.1186/s40462-022-00300-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8761355PMC
January 2022

Patch utilization and flower visitations by wild bees in a honey bee-dominated, grassland landscape.

Ecol Evol 2021 Nov 10;11(21):14888-14904. Epub 2021 Oct 10.

U.S. Geological Survey Northern Prairie Wildlife Research Center Jamestown North Dakota USA.

Understanding habitat needs and patch utilization of wild and managed bees has been identified as a national research priority in the United States. We used occupancy models to investigate patterns of bee use across 1030 transects spanning a gradient of floral resource abundance and richness and distance from apiaries in the Prairie Pothole Region (PPR) of the United States. Estimates of transect use by honey bees were nearly 1.0 during our 3.5-month sampling period, suggesting honey bees were nearly ubiquitous across transects. Wild bees more frequently used transects with higher flower richness and more abundant flowers; however, the effect size of the native flower abundance covariate (  = 3.90 ± 0.65 [1SE]) was four times greater than the non-native flower covariate (  = 0.99 ± 0.17). We found some evidence that wild bee use was lower at transects near commercial apiaries, but the effect size was imprecise (  = 1.4 ± 0.81). Honey bees were more frequently detected during sampling events with more non-native flowers and higher species richness but showed an uncertain relationship with native flower abundance. Of the 4039 honey bee and flower interactions, 85% occurred on non-native flowers, while only 43% of the 738 wild bee observations occurred on non-native flowers. Our study suggests wild bees and honey bees routinely use the same resource patches in the PPR but often visit different flowering plants. The greatest potential for resource overlap between honey bees and wild bees appears to be for non-native flowers in the PPR. Our results are valuable to natural resource managers tasked with supporting habitat for managed and wild pollinators in agroecosystems.
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http://dx.doi.org/10.1002/ece3.8174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8571640PMC
November 2021

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics.

Ecology 2020 11;101(11):e03128

Independent researcher, Rua Afonso Pena, 226, Lavras, MG, 37200-000, Brazil.

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data.
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http://dx.doi.org/10.1002/ecy.3128DOI Listing
November 2020

Using a multistate occupancy approach to determine molecular diagnostic accuracy and factors affecting avian haemosporidian infections.

Sci Rep 2020 05 21;10(1):8480. Epub 2020 May 21.

Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.

The use of a sensitive and accurate parasite detection methodology is crucial in studies exploring prevalence of parasites in host populations or communities, and uncertainty in identifying parasite genera and/or lineages may limit the understanding of host-parasite interactions. Here, we used a multistate occupancy approach that accounts for imperfect detection to assess whether sex and breeding season influenced the prevalence of a specific Haemoproteus lineage (TARUF02) in a white-lined tanager population. Likewise, we explored whether the probability of detecting the target parasite in an infected bird using PCR and sequencing analyses may be influenced by season and host sex. We found little evidence that sex influenced the probability of an individual host being infected by a haemosporidian parasite. Conversely, we found that the probability of infection by Haemoproteus TARUF02 was ~30% higher during the breeding season, reflecting a higher prevalence of this parasite in this season. The probability that PCR detects DNA of haemosporidian parasite was higher for female birds, suggesting that they are more prone to be parasitized with parasitemia levels that are more successfully detected by molecular analysis. Sequencing successfully determined the Haemoproteus TARUF02 lineage in 60% of samples collected during the breeding season and 84% of samples collected during the non-breeding season. Understanding the ecology of hosts and aspects of their physiology that may influence the parasite infection is essential to better understanding of hemoparasite infections and how parasites influence their native hosts, through decreasing reproductive success, lifespan, and/or survival.
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http://dx.doi.org/10.1038/s41598-020-65523-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242334PMC
May 2020

NEOTROPICAL XENARTHRANS: a data set of occurrence of xenarthran species in the Neotropics.

Ecology 2019 07 23;100(7):e02663. Epub 2019 Apr 23.

Xenarthrans-anteaters, sloths, and armadillos-have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data.
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http://dx.doi.org/10.1002/ecy.2663DOI Listing
July 2019

The past and future roles of competition and habitat in the range-wide occupancy dynamics of Northern Spotted Owls.

Ecol Appl 2019 04 5;29(3):e01861. Epub 2019 Mar 5.

Oregon Cooperative Fish and Wildlife Research Unit, Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, 97331, USA.

Slow ecological processes challenge conservation. Short-term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus on identifying drivers of Northern Spotted Owl (Strix occidentalis caurina) territorial occupancy dynamics across 11 study areas spanning their geographic range and forecasting response to potential management actions. Competition with Barred Owls (Strix varia) has increased Spotted Owl territory extinction probabilities across all study areas and driven recent declines in Spotted Owl populations. Without management intervention, the Northern Spotted Owl subspecies will be extirpated from parts of its current range within decades. In the short term, Barred Owl removal can be effective. Over longer time spans, however, maintaining or improving habitat conditions can help promote the persistence of northern spotted owl populations. In most study areas, habitat effects on expected Northern Spotted Owl territorial occupancy are actually greater than the effects of competition from Barred Owls. This study suggests how intensive management actions (removal of a competitor) with rapid results can complement a slower management action (i.e., promoting forest succession).
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http://dx.doi.org/10.1002/eap.1861DOI Listing
April 2019

Multistate occupancy modeling improves understanding of amphibian breeding dynamics in the Greater Yellowstone Area.

Ecol Appl 2019 01;29(1):e01825

National Park Service, Greater Yellowstone Network, 2327 University Way, Suite 2, Bozeman, Montana, 59715, USA.

Discerning the determinants of species occurrence across landscapes is fundamental to their conservation and management. In spatially and climatologically complex landscapes, explaining the dynamics of occurrence can lead to improved understanding of short- vs. long-term trends and offer novel insight on local vs. regional change. We examined the changes in occupancy for two species of anurans with different life histories over a decade using hundreds of wetland sites in Yellowstone and Grand Teton National Parks. To account for the joint dynamics of wetland drying and amphibian breeding, we adopted a multistate occupancy model as a means to investigate mechanistic relationships of observed occurrence patterns with climatological drivers of wetland hydrologic variability. This approach allowed us to decompose occupancy dynamics into habitat changes caused by wetland drying and amphibian breeding activity, conditional on available water and previous breeding state. Over our 10-yr time series, we observed considerable variability in climate drivers and the proportion of dry wetlands. Boreal chorus frogs (Pseudacris maculata) were more responsive to changes in wetland inundation status than Columbia spotted frogs (Rana luteiventris), as indicated by higher breeding colonization probabilities under favorable (wet) conditions. Both species had high probabilities of breeding persistence in permanently inundated wetlands with prior breeding. Despite the absence of multi-year drought in our time series, mechanistic relationships described here offer insights on how future climate variation may result in reduced and/or shifted occurrence patterns for pond-breeding anurans in the Greater Yellowstone Area. Further, our modeling approach may prove valuable in evaluating determinants of occurrence for other species that are dependent on wetlands or other dynamic habitats.
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http://dx.doi.org/10.1002/eap.1825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017861PMC
January 2019

Quantifying climate sensitivity and climate-driven change in North American amphibian communities.

Nat Commun 2018 09 25;9(1):3926. Epub 2018 Sep 25.

U.S. Geological Survey, Patuxent Wildlife Research Center, SO Conte Anadromous Fish Lab, 1 Migratory Way, Turners Falls, MA, 01376, USA.

Changing climate will impact species' ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using >500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in winter conditions. Based on the relationships we measure, recent changes in climate cannot explain why local species richness of North American amphibians has rapidly declined. However, changing climate does explain why some populations are declining faster than others. Our results provide important insights into how amphibians respond to climate and a general framework for measuring climate impacts on species richness.
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http://dx.doi.org/10.1038/s41467-018-06157-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156563PMC
September 2018

Beyond the swab: ecosystem sampling to understand the persistence of an amphibian pathogen.

Oecologia 2018 Sep 2;188(1):319-330. Epub 2018 Jun 2.

Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, USA.

Understanding the ecosystem-level persistence of pathogens is essential for predicting and measuring host-pathogen dynamics. However, this process is often masked, in part due to a reliance on host-based pathogen detection methods. The amphibian pathogens Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal) are pathogens of global conservation concern. Despite having free-living life stages, little is known about the distribution and persistence of these pathogens outside of their amphibian hosts. We combine historic amphibian monitoring data with contemporary host- and environment-based pathogen detection data to obtain estimates of Bd occurrence independent of amphibian host distributions. We also evaluate differences in filter- and swab-based detection probability and assess inferential differences arising from using different decision criteria used to classify samples as positive or negative. Water filtration-based detection probabilities were lower than those from swabs but were > 10%, and swab-based detection probabilities varied seasonally, declining in the early fall. The decision criterion used to classify samples as positive or negative was important; using a more liberal criterion yielded higher estimates of Bd occurrence than when a conservative criterion was used. Different covariates were important when using the liberal or conservative criterion in modeling Bd detection. We found evidence of long-term Bd persistence for several years after an amphibian host species of conservation concern, the boreal toad (Anaxyrus boreas boreas), was last detected. Our work provides evidence of long-term Bd persistence in the ecosystem, and underscores the importance of environmental samples for understanding and mitigating disease-related threats to amphibian biodiversity.
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http://dx.doi.org/10.1007/s00442-018-4167-6DOI Listing
September 2018

Host-pathogen metapopulation dynamics suggest high elevation refugia for boreal toads.

Ecol Appl 2018 06 7;28(4):926-937. Epub 2018 May 7.

Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.

Emerging infectious diseases are an increasingly common threat to wildlife. Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an emerging infectious disease that has been linked to amphibian declines around the world. Few studies exist that explore amphibian-Bd dynamics at the landscape scale, limiting our ability to identify which factors are associated with variation in population susceptibility and to develop effective in situ disease management. Declines of boreal toads (Anaxyrus boreas boreas) in the southern Rocky Mountains are largely attributed to chytridiomycosis but variation exists in local extinction of boreal toads across this metapopulation. Using a large-scale historic data set, we explored several potential factors influencing disease dynamics in the boreal toad-Bd system: geographic isolation of populations, amphibian community richness, elevational differences, and habitat permanence. We found evidence that boreal toad extinction risk was lowest at high elevations where temperatures may be suboptimal for Bd growth and where small boreal toad populations may be below the threshold needed for efficient pathogen transmission. In addition, boreal toads were more likely to recolonize high elevation sites after local extinction, again suggesting that high elevations may provide refuge from disease for boreal toads. We illustrate a modeling framework that will be useful to natural resource managers striving to make decisions in amphibian-Bd systems. Our data suggest that in the southern Rocky Mountains high elevation sites should be prioritized for conservation initiatives like reintroductions.
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http://dx.doi.org/10.1002/eap.1699DOI Listing
June 2018

Design- and model-based recommendations for detecting and quantifying an amphibian pathogen in environmental samples.

Ecol Evol 2017 12 12;7(24):10952-10962. Epub 2017 Nov 12.

Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins CO USA.

Accurate pathogen detection is essential for developing management strategies to address emerging infectious diseases, an increasingly prominent threat to wildlife. Sampling for free-living pathogens outside of their hosts has benefits for inference and study efficiency, but is still uncommon. We used a laboratory experiment to evaluate the influences of pathogen concentration, water type, and qPCR inhibitors on the detection and quantification of () using water filtration. We compared results pre- and post-inhibitor removal, and assessed inferential differences when single versus multiple samples were collected across space or time. We found that qPCR inhibition influenced both detection and quantification in natural water samples, resulting in biased inferences about occurrence and abundance. Biases in occurrence could be mitigated by collecting multiple samples in space or time, but biases in quantification were persistent. Differences in concentration resulted in variation in detection probability, indicating that occupancy modeling could be used to explore factors influencing heterogeneity in abundance among samples, sites, or over time. Our work will influence the design of studies involving amphibian disease dynamics and studies utilizing environmental DNA (eDNA) to understand species distributions.
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http://dx.doi.org/10.1002/ece3.3616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5743658PMC
December 2017

ATLANTIC-CAMTRAPS: a dataset of medium and large terrestrial mammal communities in the Atlantic Forest of South America.

Ecology 2017 Nov;98(11):2979

Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, SCEN Trecho 02, Edifício Sede, Brasília, DF, 70818-900, Brasil.

Our understanding of mammal ecology has always been hindered by the difficulties of observing species in closed tropical forests. Camera trapping has become a major advance for monitoring terrestrial mammals in biodiversity rich ecosystems. Here we compiled one of the largest datasets of inventories of terrestrial mammal communities for the Neotropical region based on camera trapping studies. The dataset comprises 170 surveys of medium to large terrestrial mammals using camera traps conducted in 144 areas by 74 studies, covering six vegetation types of tropical and subtropical Atlantic Forest of South America (Brazil and Argentina), and present data on species composition and richness. The complete dataset comprises 53,438 independent records of 83 species of mammals, includes 10 species of marsupials, 15 rodents, 20 carnivores, eight ungulates and six armadillos. Species richness averaged 13 species (±6.07 SD) per site. Only six species occurred in more than 50% of the sites: the domestic dog Canis familiaris, crab-eating fox Cerdocyon thous, tayra Eira barbara, south American coati Nasua nasua, crab-eating raccoon Procyon cancrivorus and the nine-banded armadillo Dasypus novemcinctus. The information contained in this dataset can be used to understand macroecological patterns of biodiversity, community, and population structure, but also to evaluate the ecological consequences of fragmentation, defaunation, and trophic interactions.
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http://dx.doi.org/10.1002/ecy.1998DOI Listing
November 2017

Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies.

Evol Appl 2016 08 4;9(7):879-91. Epub 2016 Feb 4.

Department of Biology Colorado State University Fort Collins CO USA; Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA.

Genetic rescue, an increase in population growth owing to the infusion of new alleles, can aid the persistence of small populations. Its use as a management tool is limited by a lack of empirical data geared toward predicting effects of gene flow on local adaptation and demography. Experimental translocations provide an ideal opportunity to monitor the demographic consequences of gene flow. In this study we take advantage of two experimental introductions of Trinidadian guppies to test the effects of gene flow on downstream native populations. We individually marked guppies from the native populations to monitor population dynamics for 3 months before and 26 months after gene flow. We genotyped all individuals caught during the first 17 months at microsatellite loci to classify individuals by their genetic ancestry: native, immigrant, F1 hybrid, F2 hybrid, or backcross. Our study documents a combination of demographic and genetic rescue over multiple generations under fully natural conditions. Within both recipient populations, we found substantial and long-term increases in population size that could be attributed to high survival and recruitment caused by immigration and gene flow from the introduction sites. Our results suggest that low levels of gene flow, even from a divergent ecotype, can provide a substantial demographic boost to small populations, which may allow them to withstand environmental stochasticity.
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http://dx.doi.org/10.1111/eva.12356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947150PMC
August 2016

Quantitative evidence for the effects of multiple drivers on continental-scale amphibian declines.

Sci Rep 2016 05 23;6:25625. Epub 2016 May 23.

U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, 80526, United States of America.

Since amphibian declines were first proposed as a global phenomenon over a quarter century ago, the conservation community has made little progress in halting or reversing these trends. The early search for a "smoking gun" was replaced with the expectation that declines are caused by multiple drivers. While field observations and experiments have identified factors leading to increased local extinction risk, evidence for effects of these drivers is lacking at large spatial scales. Here, we use observations of 389 time-series of 83 species and complexes from 61 study areas across North America to test the effects of 4 of the major hypothesized drivers of declines. While we find that local amphibian populations are being lost from metapopulations at an average rate of 3.79% per year, these declines are not related to any particular threat at the continental scale; likewise the effect of each stressor is variable at regional scales. This result - that exposure to threats varies spatially, and populations vary in their response - provides little generality in the development of conservation strategies. Greater emphasis on local solutions to this globally shared phenomenon is needed.
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http://dx.doi.org/10.1038/srep25625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4876446PMC
May 2016

Multi-scale occupancy approach to estimate Toxoplasma gondii prevalence and detection probability in tissues: an application and guide for field sampling.

Int J Parasitol 2016 08 4;46(9):563-70. Epub 2016 May 4.

Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada.

Increasingly, birds are recognised as important hosts for the ubiquitous parasite Toxoplasma gondii, although little experimental evidence exists to determine which tissues should be tested to maximise the detection probability of T. gondii. Also, Arctic-nesting geese are suspected to be important sources of T. gondii in terrestrial Arctic ecosystems, but the parasite has not previously been reported in the tissues of these geese. Using a domestic goose model, we applied a multi-scale occupancy framework to demonstrate that the probability of detection of T. gondii was highest in the brain (0.689, 95% confidence interval=0.486, 0.839) and the heart (0.809, 95% confidence interval=0.693, 0.888). Inoculated geese had an estimated T. gondii infection probability of 0.849, (95% confidence interval=0.643, 0.946), highlighting uncertainty in the system, even under experimental conditions. Guided by these results, we tested the brains and hearts of wild Ross's Geese (Chen rossii, n=50) and Lesser Snow Geese (Chen caerulescens, n=50) from Karrak Lake, Nunavut, Canada. We detected 51 suspected positive tissue samples from 33 wild geese using real-time PCR with melt-curve analysis. The wild goose prevalence estimates generated by our multi-scale occupancy analysis were higher than the naïve estimates of prevalence, indicating that multiple PCR repetitions on the same organs and testing more than one organ could improve T. gondii detection. Genetic characterisation revealed Type III T. gondii alleles in six wild geese and Sarcocystis spp. in 25 samples. Our study demonstrates that Arctic nesting geese are capable of harbouring T. gondii in their tissues and could transport the parasite from their southern overwintering grounds into the Arctic region. We demonstrate how a multi-scale occupancy framework can be used in a domestic animal model to guide resource-limited sample collection and tissue analysis in wildlife. Secondly, we confirm the value of traditional occupancy in optimising T. gondii detection probability in tissue samples.
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http://dx.doi.org/10.1016/j.ijpara.2016.04.003DOI Listing
August 2016

A Model to Inform Management Actions as a Response to Chytridiomycosis-Associated Decline.

Ecohealth 2017 03 7;14(Suppl 1):144-155. Epub 2016 Apr 7.

U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA.

Decision-analytic models provide forecasts of how systems of interest will respond to management. These models can be parameterized using empirical data, but sometimes require information elicited from experts. When evaluating the effects of disease in species translocation programs, expert judgment is likely to play a role because complete empirical information will rarely be available. We illustrate development of a decision-analytic model built to inform decision-making regarding translocations and other management actions for the boreal toad (Anaxyrus boreas boreas), a species with declines linked to chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd). Using the model, we explored the management implications of major uncertainties in this system, including whether there is a genetic basis for resistance to pathogenic infection by Bd, how translocation can best be implemented, and the effectiveness of efforts to reduce the spread of Bd. Our modeling exercise suggested that while selection for resistance to pathogenic infection by Bd could increase numbers of sites occupied by toads, and translocations could increase the rate of toad recovery, efforts to reduce the spread of Bd may have little effect. We emphasize the need to continue developing and parameterizing models necessary to assess management actions for combating chytridiomycosis-associated declines.
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http://dx.doi.org/10.1007/s10393-016-1117-9DOI Listing
March 2017

Interspecific interactions between wild felids vary across scales and levels of urbanization.

Ecol Evol 2015 Dec 9;5(24):5946-61. Epub 2015 Dec 9.

Department of Fish, Wildlife, and Conservation Biology Graduate Degree Program in Ecology Colorado State University Fort Collins Colorado 80523.

Ongoing global landscape change resulting from urbanization is increasingly linked to changes in species distributions and community interactions. However, relatively little is known about how urbanization influences competitive interactions among mammalian carnivores, particularly related to wild felids. We evaluated interspecific interactions between medium- and large-sized carnivores across a gradient of urbanization and multiple scales. Specifically, we investigated spatial and temporal interactions of bobcats and pumas by evaluating circadian activity patterns, broad-scale seasonal interactions, and fine-scale daily interactions in wildland-urban interface (WUI), exurban residential development, and wildland habitats. Across levels of urbanization, interspecific interactions were evaluated using two-species and single-species occupancy models with data from motion-activated cameras. As predicted, urbanization increased the opportunity for interspecific interactions between wild felids. Although pumas did not exclude bobcats from areas at broad spatial or temporal scales, bobcats responded behaviorally to the presence of pumas at finer scales, but patterns varied across levels of urbanization. In wildland habitat, bobcats avoided using areas for short temporal periods after a puma visited an area. In contrast, bobcats did not appear to avoid areas that pumas recently visited in landscapes influenced by urbanization (exurban development and WUI habitat). In addition, overlap in circadian activity patterns between bobcats and pumas increased in exurban development compared to wildland habitat. Across study areas, bobcats used sites less frequently as the number of puma photographs increased at a site. Overall, bobcats appear to shape their behavior at fine spatial and temporal scales to reduce encounters with pumas, but residential development can potentially alter these strategies and increase interaction opportunities. We explore three hypotheses to explain our results of how urbanization affected interspecific interactions that consider activity patterns, landscape configuration, and animal scent marking. Altered competitive interactions between animals in urbanized landscapes could potentially increase aggressive encounters and the frequency of disease transmission.
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http://dx.doi.org/10.1002/ece3.1812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717346PMC
December 2015

ESTIMATING TOXOPLASMA GONDII EXPOSURE IN ARCTIC FOXES (VULPES LAGOPUS) WHILE NAVIGATING THE IMPERFECT WORLD OF WILDLIFE SEROLOGY.

J Wildl Dis 2016 Jan;52(1):47-56

1  University of Saskatchewan, Department of Veterinary Microbiology, 52 Campus Drive, Saskatoon, Saskatchewan S7N 5B4, Canada.

Although the protozoan parasite Toxoplasma gondii is ubiquitous in birds and mammals worldwide, the full suite of hosts and transmission routes is not completely understood, especially in the Arctic. Toxoplasma gondii occurrence in humans and wildlife can be high in Arctic regions, despite apparently limited opportunities for transmission of oocysts shed by felid definitive hosts. Arctic foxes (Vulpes lagopus) are under increasing anthropogenic and ecologic pressure, leading to population declines in parts of their range. Our understanding of T. gondii occurrence in arctic foxes is limited to only a few regions, but mortality events caused by this parasite have been reported. We investigated the exposure of arctic foxes to T. gondii in the Karrak Lake goose colony, Queen Maud Gulf Migratory Bird Sanctuary, Nunavut, Canada. Following an occupancy-modeling framework, we performed replicated antibody testing on serum samples by direct agglutination test (DAT), indirect fluorescent antibody test (IFAT), and an indirect enzyme-linked immunosorbent assay (ELISA) that can be used in multiple mammalian host species. As a metric of test performance, we then estimated the probability of detecting T. gondii antibodies for each of the tests. Occupancy estimates for T. gondii antibodies in arctic foxes under this framework were between 0.430 and 0.758. Detection probability was highest for IFAT (0.716) and lower for DAT (0.611) and ELISA (0.464), indicating that the test of choice for antibody detection in arctic foxes might be the IFAT. We document a new geographic record of T. gondii exposure in arctic foxes and demonstrate an emerging application of ecologic modeling techniques to account for imperfect performance of diagnostic tests in wildlife species.
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http://dx.doi.org/10.7589/2015-03-075DOI Listing
January 2016

Using Bayesian Population Viability Analysis to Define Relevant Conservation Objectives.

PLoS One 2015 10;10(12):e0144786. Epub 2015 Dec 10.

Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, Colorado, United States of America.

Adaptive management provides a useful framework for managing natural resources in the face of uncertainty. An important component of adaptive management is identifying clear, measurable conservation objectives that reflect the desired outcomes of stakeholders. A common objective is to have a sustainable population, or metapopulation, but it can be difficult to quantify a threshold above which such a population is likely to persist. We performed a Bayesian metapopulation viability analysis (BMPVA) using a dynamic occupancy model to quantify the characteristics of two wood frog (Lithobates sylvatica) metapopulations resulting in sustainable populations, and we demonstrate how the results could be used to define meaningful objectives that serve as the basis of adaptive management. We explored scenarios involving metapopulations with different numbers of patches (pools) using estimates of breeding occurrence and successful metamorphosis from two study areas to estimate the probability of quasi-extinction and calculate the proportion of vernal pools producing metamorphs. Our results suggest that ≥50 pools are required to ensure long-term persistence with approximately 16% of pools producing metamorphs in stable metapopulations. We demonstrate one way to incorporate the BMPVA results into a utility function that balances the trade-offs between ecological and financial objectives, which can be used in an adaptive management framework to make optimal, transparent decisions. Our approach provides a framework for using a standard method (i.e., PVA) and available information to inform a formal decision process to determine optimal and timely management policies.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144786PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684342PMC
June 2016

The effects of urbanization on population density, occupancy, and detection probability of wild felids.

Ecol Appl 2015 Oct;25(7):1880-95

Urbanization is a primary driver of landscape conversion, with far-reaching effects on landscape pattern and process, particularly related to the population characteristics of animals. Urbanization can alter animal movement and habitat quality, both of which can influence population abundance and persistence. We evaluated three important population characteristics (population density, site occupancy, and species detection probability) of a medium-sized and a large carnivore across varying levels of urbanization. Specifically, we studied bobcat and puma populations across wildland, exurban development, and wildland-urban interface (WUI) sampling grids to test hypotheses evaluating how urbanization affects wild felid populations and their prey. Exurban development appeared to have a greater impact on felid populations than did habitat adjacent to a major urban area (i.e., WUI); estimates of population density for both bobcats and pumas were lower in areas of exurban development compared to wildland areas, whereas population density was similar between WUI and wildland habitat. Bobcats and pumas were less likely to be detected in habitat as the amount of human disturbance associated with residential development increased at a site, which was potentially related to reduced habitat quality resulting from urbanization. However, occupancy of both felids was similar between grids in both study areas, indicating that this population metric was less sensitive than density. At the scale of the sampling grid, detection probability for bobcats in urbanized habitat was greater than in wildland areas, potentially due to restrictive movement corridors and funneling of animal movements in landscapes influenced by urbanization. Occupancy of important felid prey (cottontail rabbits and mule deer) was similar across levels of urbanization, although elk occupancy was lower in urbanized areas. Our study indicates that the conservation of medium- and large-sized felids associated with urbanization likely will be most successful if large areas of wildland habitat are maintained, even in close proximity to urban areas, and wildland habitat is not converted to low-density residential development.
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http://dx.doi.org/10.1890/14-1664.1DOI Listing
October 2015

Conserving tigers in working landscapes.

Conserv Biol 2016 06 4;30(3):649-60. Epub 2016 Feb 4.

Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, 80523, Colorado, U.S.A.

Tiger (Panthera tigris) conservation efforts in Asia are focused on protected areas embedded in human-dominated landscapes. A system of protected areas is an effective conservation strategy for many endangered species if the network is large enough to support stable metapopulations. The long-term conservation of tigers requires that the species be able to meet some of its life-history needs beyond the boundaries of small protected areas and within the working landscape, including multiple-use forests with logging and high human use. However, understanding of factors that promote or limit the occurrence of tigers in working landscapes is incomplete. We assessed the relative influence of protection status, prey occurrence, extent of grasslands, intensity of human use, and patch connectivity on tiger occurrence in the 5400 km(2) Central Terai Landscape of India, adjacent to Nepal. Two observer teams independently surveyed 1009 km of forest trails and water courses distributed across 60 166-km(2) cells. In each cell, the teams recorded detection of tiger signs along evenly spaced trail segments. We used occupancy models that permitted multiscale analysis of spatially correlated data to estimate cell-scale occupancy and segment-scale habitat use by tigers as a function of management and environmental covariates. Prey availability and habitat quality, rather than protected-area designation, influenced tiger occupancy. Tiger occupancy was low in some protected areas in India that were connected to extensive areas of tiger habitat in Nepal, which brings into question the efficacy of current protection and management strategies in both India and Nepal. At a finer spatial scale, tiger habitat use was high in trail segments associated with abundant prey and large grasslands, but it declined as human and livestock use increased. We speculate that riparian grasslands may provide tigers with critical refugia from human activity in the daytime and thereby promote tiger occurrence in some multiple-use forests. Restrictions on human-use in high-quality tiger habitat in multiple-use forests may complement existing protected areas and collectively promote the persistence of tiger populations in working landscapes.
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http://dx.doi.org/10.1111/cobi.12633DOI Listing
June 2016

Toxoplasma gondii exposure in arctic-nesting geese: A multi-state occupancy framework and comparison of serological assays.

Int J Parasitol Parasites Wildl 2014 Aug 30;3(2):147-53. Epub 2014 Jun 30.

Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, Saskatchewan S7N5B4, Canada.

The zoonotic parasite, Toxoplasma gondii, has a worldwide distribution and a cosmopolitan suite of hosts. In arctic tundra regions, the definitive felid hosts are rare to absent and, while the complete transmission routes in such regions have yet to be fully elucidated, trophic and vertical routes are likely to be important. Wild birds are common intermediate hosts of T. gondii, and in the central Canadian arctic, geese are probable vectors of the parasite from temperate latitudes to the arctic regions. Our objective was to estimate seroprevalence of T. gondii in Ross's and Lesser Snow Geese from the Karrak Lake ecosystem in Nunavut, Canada. After harvesting geese by shotgun, we collected blood on filter paper strips and tested the eluate for T. gondii antibodies by indirect fluorescent antibody test (IFAT) and direct agglutination test (DAT). We estimated seroprevalence using a multi-state occupancy model, which reduced bias by accounting for imperfect detection, and compared these estimates to a naïve estimator. Ross's Geese had a 0.39 probability of seropositivity, while for Lesser Snow Geese the probability of positive for T. gondii antibodies was 0.36. IFAT had a higher antibody detection probability than DAT, but IFAT also had a higher probability of yielding ambiguous or unclassifiable results. The results of this study indicate that Ross's Geese and Lesser Snow Geese migrating to the Karrak Lake region of Nunavut are routinely exposed to T. gondii at some point in their lives and that they are likely intermediate hosts of the parasite. Also, we were able to enhance our estimation of T. gondii seroprevalence by using an occupancy approach that accounted for both false-negative and false-positive detections and by using multiple diagnostic tests in the absence of a gold standard serological assay for wild geese.
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http://dx.doi.org/10.1016/j.ijppaw.2014.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142267PMC
August 2014

Demography of a reintroduced population: moving toward management models for an endangered species, the Whooping Crane.

Ecol Appl 2014 Jul;24(5):927-37

The reintroduction of threatened and endangered species is now a common method for reestablishing populations. Typically, a fundamental objective of reintroduction is to establish a self-sustaining population. Estimation of demographic parameters in reintroduced populations is critical, as these estimates serve multiple purposes. First, they support evaluation of progress toward the fundamental objective via construction of population viability analyses (PVAs) to predict metrics such as probability of persistence. Second, PVAs can be expanded to support evaluation of management actions, via management modeling. Third, the estimates themselves can support evaluation of the demographic performance of the reintroduced population (e.g., via comparison with wild populations). For each of these purposes, thorough treatment of uncertainties in the estimates is critical. Recently developed statistical methods (namely, hierarchical Bayesian implementations of state-space models) allow for effective integration of different types of uncertainty in estimation. We undertook a demographic estimation effort for a reintroduced population of endangered Whooping Cranes with the purpose of ultimately developing a Bayesian PVA for determining progress toward establishing a self-sustaining population, and for evaluating potential management actions via a Bayesian PVA-based management model. We evaluated individual and temporal variation in demographic parameters based upon a multi-state, mark-recapture model. We found that survival was relatively high across time and varied little by sex. There was some indication that survival varied by release method. Survival was similar to that observed in the wild population. Although overall reproduction in this reintroduced population is poor, birds formed social pairs when relatively young, and once a bird was in a social pair, it had a nearly 50% chance of nesting the following breeding season. Also, once a bird had nested, it had a high probability of nesting again. These results are encouraging, considering that survival and reproduction have been major challenges in past reintroductions of this species. The demographic estimates developed will support construction of a management model designed to facilitate exploration of management actions of interest, and will provide critical guidance in future planning for this reintroduction. An approach similar to what we describe could be usefully applied to many reintroduced populations.
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http://dx.doi.org/10.1890/13-0559.1DOI Listing
July 2014

Trends in amphibian occupancy in the United States.

PLoS One 2013 22;8(5):e64347. Epub 2013 May 22.

United States Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, Oregon, United States of America.

Though a third of amphibian species worldwide are thought to be imperiled, existing assessments simply categorize extinction risk, providing little information on the rate of population losses. We conducted the first analysis of the rate of change in the probability that amphibians occupy ponds and other comparable habitat features across the United States. We found that overall occupancy by amphibians declined 3.7% annually from 2002 to 2011. Species that are Red-listed by the International Union for Conservation of Nature (IUCN) declined an average of 11.6% annually. All subsets of data examined had a declining trend including species in the IUCN Least Concern category. This analysis suggests that amphibian declines may be more widespread and severe than previously realized.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064347PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3661441PMC
January 2014

Experimental investigation of false positive errors in auditory species occurrence surveys.

Ecol Appl 2012 Jul;22(5):1665-74

United States Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Road, Laurel, Maryland 20708, USA.

False positive errors are a significant component of many ecological data sets, which in combination with false negative errors, can lead to severe biases in conclusions about ecological systems. We present results of a field experiment where observers recorded observations for known combinations of electronically broadcast calling anurans under conditions mimicking field surveys to determine species occurrence. Our objectives were to characterize false positive error probabilities for auditory methods based on a large number of observers, to determine if targeted instruction could be used to reduce false positive error rates, and to establish useful predictors of among-observer and among-species differences in error rates. We recruited 31 observers, ranging in abilities from novice to expert, who recorded detections for 12 species during 180 calling trials (66,960 total observations). All observers made multiple false positive errors, and on average 8.1% of recorded detections in the experiment were false positive errors. Additional instruction had only minor effects on error rates. After instruction, false positive error probabilities decreased by 16% for treatment individuals compared to controls with broad confidence interval overlap of 0 (95% CI:--46 to 30%). This coincided with an increase in false negative errors due to the treatment (26%;--3 to 61%). Differences among observers in false positive and in false negative error rates were best predicted by scores from an online test and a self-assessment of observer ability completed prior to the field experiment. In contrast, years of experience conducting call surveys was a weak predictor of error rates. False positive errors were also more common for species that were played more frequently but were not related to the dominant spectral frequency of the call. Our results corroborate other work that demonstrates false positives are a significant component of species occurrence data collected by auditory methods. Instructing observers to only report detections they are completely certain are correct is not sufficient to eliminate errors. As a result, analytical methods that account for false positive errors will be needed, and independent testing of observer ability is a useful predictor for among-observer variation in observation error rates.
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http://dx.doi.org/10.1890/11-2129.1DOI Listing
July 2012

Colonization and extinction in dynamic habitats: an occupancy approach for a Great Plains stream fish assemblage.

Ecology 2012 Apr;93(4):858-67

Colorado State University, Department of fish, Wildlife, and Conservation Biology, Fort Collins, Colorado 80523-1474, USA.

Despite the importance of habitat in determining species distribution and persistence, habitat dynamics are rarely modeled in studies of metapopulations. We used an integrated habitat-occupancy model to simultaneously quantify habitat change, site fidelity, and local colonization and extinction rates for larvae of a suite of Great Plains stream fishes in the Arikaree River, eastern Colorado, USA, across three years. Sites were located along a gradient of flow intermittency and groundwater connectivity. Hydrology varied across years: the first and third being relatively wet and the second dry. Despite hydrologic variation, our results indicated that site suitability was random from one year to the next. Occupancy probabilities were also independent of previous habitat and occupancy state for most species, indicating little site fidelity. Climate and groundwater connectivity were important drivers of local extinction and colonization, but the importance of groundwater differed between periods. Across species, site extinction probabilities were highest during the transition from wet to dry conditions (range: 0.52-0.98), and the effect of groundwater was apparent with higher extinction probabilities for sites not fed by groundwater. Colonization probabilities during this period were relatively low for both previously dry sites (range: 0.02-0.38) and previously wet sites (range: 0.02-0.43). In contrast, no sites dried or remained dry during the transition from dry to wet conditions, yielding lower but still substantial extinction probabilities (range: 0.16-0.63) and higher colonization probabilities (range: 0.06-0.86), with little difference among sites with and without groundwater. This approach of jointly modeling both habitat change and species occupancy will likely be useful to incorporate effects of dynamic habitat on metapopulation processes and to better inform appropriate conservation actions.
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http://dx.doi.org/10.1890/11-1515.1DOI Listing
April 2012

Efficient species-level monitoring at the landscape scale.

Conserv Biol 2012 Jun;26(3):432-41

Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA.

Monitoring the population trends of multiple animal species at a landscape scale is prohibitively expensive. However, advances in survey design, statistical methods, and the ability to estimate species presence on the basis of detection-nondetection data have greatly increased the feasibility of species-level monitoring. For example, recent advances in monitoring make use of detection-nondetection data that are relatively inexpensive to acquire, historical survey data, and new techniques in genetic evaluation. The ability to use indirect measures of presence for some species greatly increases monitoring efficiency and reduces survey costs. After adjusting for false absences, the proportion of sample units in a landscape where a species is detected (occupancy) is a logical state variable to monitor. Occupancy monitoring can be based on real-time observation of a species at a survey site or on evidence that the species was at the survey location sometime in the recent past. Temporal and spatial patterns in occupancy data are related to changes in animal abundance and provide insights into the probability of a species' persistence. However, even with the efficiencies gained when occupancy is the monitored state variable, the task of species-level monitoring remains daunting due to the large number of species. We propose that a small number of species be monitored on the basis of specific management objectives, their functional role in an ecosystem, their sensitivity to environmental changes likely to occur in the area, or their conservation importance.
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http://dx.doi.org/10.1111/j.1523-1739.2012.01855.xDOI Listing
June 2012

Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification.

Ecology 2011 Jul;92(7):1422-8

United States Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Road, Laurel, Maryland 20708, USA.

Efforts to draw inferences about species occurrence frequently account for false negatives, the common situation when individuals of a species are not detected even when a site is occupied. However, recent studies suggest the need to also deal with false positives, which occur when species are misidentified so that a species is recorded as detected when a site is unoccupied. Bias in estimators of occupancy, colonization, and extinction can be severe when false positives occur. Accordingly, we propose models that simultaneously account for both types of error. Our approach can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur. We illustrate properties of the estimators with simulations and data for three species of frogs. We show that models that account for possible misidentification have greater support (lower AIC for two species) and can yield substantially different occupancy estimates than those that do not. When the potential for misidentification exists, researchers should consider analytical techniques that can account for this source of error, such as those presented here.
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http://dx.doi.org/10.1890/10-1396.1DOI Listing
July 2011

Life history benefits of residency in a partially migrating pond-breeding amphibian.

Ecology 2011 Jun;92(6):1236-46

Department of Biology, 238 Gilmer Hall, University of Virginia, Charlottesville, Virginia 22904, USA.

Species with partial migration, where a portion of a population migrates and the other remains residential, provide the opportunity to evaluate conditions for migration and test mechanisms influencing migratory decisions. We conducted a five-year study of two populations of red-spotted newts (Notophthalmus viridescens), composed of individuals that either remain as residents in the breeding pond over the winter or migrate to the terrestrial habitat. We used multistate mark-recapture methods to (1) test for differences in survival probability between migrants and residents, (2) determine if migrants breed every year or skip opportunities for reproduction, and (3) estimate the frequency of individuals switching migratory tactic. We used estimates of life history parameters from the natural populations in combination with previous experimental work to evaluate processes maintaining partial migration at the population level and to assess mechanisms influencing the decision to migrate. Based on capture-recapture information on over 3000 individuals, we found that newts can switch migratory tactics over their lifetime. We conclude that migrants and residents coexist through conditional asymmetries, with residents having higher fitness and inferior individuals adopting the migrant tactic. We found that newts are more likely to switch from residency to migrating than the reverse and males were more likely to remain as residents. Migration differences between the sexes are likely driven by reproduction benefits of residency for males and high energetic costs of breeding resulting in lower breeding frequencies for females. Environmental conditions also influence partial migration within a population; we found support for density-dependent processes in the pond strongly influencing the probability of migrating. Our work illustrates how migration can be influenced by a complex range of individual and environmental factors and enhances our understanding of the conditions necessary for the evolution and maintenance of partial migration within populations.
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http://dx.doi.org/10.1890/11-0133.1DOI Listing
June 2011
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