Estimating species occurrence, abundance, and detection probability using zero-inflated distributions
S.J. Wenger, Mary C. Freeman
2008, Ecology (89) 2953-2959
Researchers have developed methods to account for imperfect detection of species with either occupancy (presence-absence) or count data using replicated sampling. We show how these approaches can be combined to simultaneously estimate occurrence, abundance, and detection probability by specifying a zero-inflated distribution for abundance. This approach may be...
Monitoring in the context of structured decision-making and adaptive management
J. E. Lyons, M.C. Runge, H. P. Laskowski, W. L. Kendall
2008, Journal of Wildlife Management (72) 1683-1692
In a natural resource management setting, monitoring is a crucial component of an informed process for making decisions, and monitoring design should be driven by the decision context and associated uncertainties. Monitoring itself can play >3 roles. First, it is important for state-dependent decision-making, as when managers need...
Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican parrot
S.R. Beissenger, J.M. Wunderle Jr., J.M. Meyers, B.-E. Saether, S. Engen
2008, Ecological Monographs (78) 185-203
The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct...
Effects of human activity of breeding American Oystercatchers, Cumberland Island National Seashore, Georgia, USA
J. B. Sabine, J.M. Meyers, C. T. Moore, Sara H. Schweitzer
2008, Waterbirds (31) 70-82
Abstract.-Increased human use of coastal areas threatens the United States population of American Oystercatchers (Haematopus palliatus), a species of special concern. Biologists often attribute its low numbers and reproductive success to human disturbance, but the mechanism by which human presence reduces reproductive success is not well understood. During...
Comparative analysis of distribution and abundance of West Nile and Eastern Equine Encephalomyelitis virus vectors in Suffolk County, New York, using human population density and land use/cover data
I. Rochlin, K. Harding, H. S. Ginsberg, S.R. Campbell
2008, Journal of Medical Entomology (45) 563-571
Five years of CDC light trap data from Suffolk County, NY, were analyzed to compare the applicability of human population density (HPD) and land use/cover (LUC) classification systems to describe mosquito abundance and to determine whether certain mosquito species of medical importance tend to be more common in urban (defined...
Importance of sampling design and analysis in animal population studies: a comment on Sergio et al
M. Kery, J. Andrew Royle, Hans Schmid
2008, Journal of Applied Ecology (45) 981-986
1. The use of predators as indicators and umbrellas in conservation has been criticized. In the Trentino region, Sergio et al. (2006; hereafter SEA) counted almost twice as many bird species in quadrats located in raptor territories than in controls. However, SEA detected astonishingly few species. We...
Potential environmental contaminant risks to avian species at important bird areas in the northeastern United States
Barnett A. Rattner, B.K. Ackerson
2008, Integrated Environmental Assessment and Management (4) 344-357
Environmental contaminants can have profound effects on birds, acting from the molecular through population levels of biological organization. An analysis of potential contaminant threats was undertaken at 52 Important Bird Areas (IBAs) within the northeastern Atlantic coast drainage. Using geographic information system methodology, data layers describing or integrating...
Multi-scale occupancy estimation and modelling using multiple detection methods
James D. Nichols, Larissa L. Bailey, Allan F. O’Connell, Neil W. Talancy, Evan H. Campbell Grant, Andrew T. Gilbert, Elizabeth M. Annand, Thomas P. Husband, James E. Hines
2008, Journal of Applied Ecology (45) 1321-1329
Occupancy estimation and modelling based on detection–nondetection data provide an effective way of exploring change in a species’ distribution across time and space in cases where the species is not always detected with certainty. Today, many monitoring programmes target multiple species, or life stages within a species, requiring the use...
A hierarchical model for spatial capture-recapture data
J. Andrew Royle, K.V. Young
2008, Ecology (89) 2281-2289
Estimating density is a fundamental objective of many animal population studies. Application of methods for estimating population size from ostensibly closed populations is widespread, but ineffective for estimating absolute density because most populations are subject to short-term movements or so-called temporary emigration. This phenomenon invalidates the resulting estimates...
Juvenile survival in a tropical population of roseate terns: Interannual variation and effect of tick parasitism
David Monticelli, Jaime A. Ramos, James E. Hines, James D. Nichols, Jeffrey A. Spendelow
2008, Marine Ecology Progress Series (365) 277-287
Many demographic studies on long-lived seabirds have focused on the estimation of adult survival, but much less is known about survival during the early years of life, especially in tropical species. We report analyses of a capture–recapture dataset of 685 roseate terns ringed as fledglings and adults between 1998 and...
A double-observer method to estimate detection rate during aerial waterfowl surveys
M.D. Koneff, J. Andrew Royle, M.C. Otto, J.S. Wortham, J.K. Bidwell
2008, Journal of Wildlife Management (72) 1641-649
We evaluated double-observer methods for aerial surveys as a means to adjust counts of waterfowl for incomplete detection. We conducted our study in eastern Canada and the northeast United States utilizing 3 aerial-survey crews flying 3 different types of fixed-wing aircraft. We reconciled counts of front- and rear-seat...
Annual recapture and survival rates of two non-breeding adult populations of Roseate Terns Stema dougallii captured on the Great Barrier Reef, Australia, and estimates of their population sizes
P. O’Neill, C.D.T. Minton, I.C.T. Nisbet, J.E. Hines
2008, Waterbirds (31) 338-345
Capture-recapture data from two disparate breeding populations of Roseate Terns (Sterna dougallii) captured together as non-breeding individuals from 2002 to 2007 in the southern Great Barrier Reef. Australia were analyzed for both survival rate and recapture rate. The average annual survival rate for the birds from the Asian...
A new species of Percina (Perciformes: Percidae) from the Apalachicola River drainage, southeastern United States
Mary C. Freeman, B. J. Freeman, N.M. Burkhead, C.A. Straight
2008, Zootaxa (1963) 25-42
Percina crypta, the Halloween Darter, is described as a new species endemic to the Chattahoochee and Flint River systems in Georgia and Alabama. Percina crypta differs from sympatric Percina nigrofasciata in having narrowly separated dorsal saddles (inter-saddle spaces typically less than or equal to saddle width, compared to frequently wider...
Tidal marshes as disequilibrium landscapes? Lags between morphology and Holocene sea level change
M. L. Kirwan, A.B. Murray
2008, Geophysical Research Letters (35) 1-5
Historical acceleration in the rate of global sea level rise and recent observations of marsh degradation highlight the importance of understanding how marshes respond to sea level change. Here, we use an existing numerical model to demonstrate that marsh morphology, and its effect on biological productivity and vertical accretion,...
Presence-nonpresence surveys of golden-cheeked warblers: detection, occupancy and survey effort
C.A. Watson, F.W. Weckerly, Jeff S. Hatfield, C.C. Farquhar, P.S. Williamson
2008, Animal Conservation (11) 484-492
Surveys to detect the presence or absence of endangered species may not consistently cover an area, account for imperfect detection or consider that detection and species presence at sample units may change within a survey season. We evaluated a detection?nondetection survey method for the federally endangered golden-cheeked warbler (GCWA)...
Stream fish occurrence in response to impervious cover, historic land use, and hydrogeomorphic factors
Seth J. Wenger, James T. Peterson, Mary C. Freeman, Byron J. Freeman, D. David Homans
2008, Canadian Journal of Fisheries and Aquatic Sciences (65) 1250-1264
We evaluated competing models explaining the occurrence of five stream fishes in an urbanizing watershed to determine the relative importance of (a) impervious surface and other indicators of current land use, (b) historic land use (e.g., agriculture, impoundments), and (c) hydrogeomorphic characteristics (e.g., stream size, elevation, geology). For four of...
Sediment ingestion rates in waterfowl (Anatidae) and their use in environmental risk assessment
W. Nelson Beyer, Matthew C. Perry, Peter C. Osenton
2008, Integrated Environmental Assessment and Management (4) 246-251
When waterfowl (Anatidae) ingest sediment as they feed, they are exposed to the environmental contaminants in those sediments. The rate of ingestion may be key to assessing environmental risk. Rates of sediment ingestion were estimated as from <2% to 22% in 16 species of waterfowl collected in the northeastern United...
Combining Breeding Bird Survey and Christmas Bird Count data to evaluate seasonal components of population change in Northern Bobwhite
W.A. Link, J.R. Sauer, D.K. Niven
2008, Journal of Wildlife Management (72) 44-51
Annual surveys of wildlife populations provide information about annual rates of change in populations but provide no information about when such changes occur. However, by combining data from 2 annual surveys, conducted in different parts of the year, seasonal components of population change can be estimated. We describe a hierarchical...
A hierarchical model for estimating change in American Woodcock populations
J.R. Sauer, W.A. Link, W. L. Kendall, J.R. Kelley, D.K. Niven
2008, Journal of Wildlife Management (72) 204-214
The Singing-Ground Survey (SGS) is a primary source of information on population change for American woodcock (Scolopax minor). We analyzed the SGS using a hierarchical log-linear model and compared the estimates of change and annual indices of abundance to a route regression analysis of SGS data. We also grouped SGS...
Efficient implementation of the Metropolis-Hastings algorithm, with application to the Cormack?Jolly?Seber model
W.A. Link, R. J. Barker
2008, Environmental and Ecological Statistics (15) 79-87
Judicious choice of candidate generating distributions improves efficiency of the Metropolis-Hastings algorithm. In Bayesian applications, it is sometimes possible to identify an approximation to the target posterior distribution; this approximate posterior distribution is a good choice for candidate generation. These observations are applied to analysis of the Cormack?Jolly?Seber...
Modeling individual effects in the Cormack-Jolly-Seber Model: A state-space formulation
J. Andrew Royle
2008, Biometrics (64) 364-370
In population and evolutionary biology, there exists considerable interest in individual heterogeneity in parameters of demographic models for open populations. However, flexible and practical solutions to the development of such models have proven to be elusive. In this article, I provide a state-space formulation of open population capture-recapture...
Effect of climate fluctuations on long-term vegetation dynamics in Carolina bay wetlands
C.L. Stroh, D. De Steven, G.R. Guntenspergen
2008, Wetlands (28) 17-27
Carolina bays and similar depression wetlands of the U.S. Southeastern Coastal Plain have hydrologic regimes that are driven primarily by rainfall. Therefore, climate fluctuations such as drought cycles have the potential to shape long-term vegetation dynamics. Models suggest two potential long-term responses to hydrologic fluctuations, either cyclic change...
Estimation and correction of visibility bias in aerial surveys of wintering ducks
A.T. Pearse, P.D. Gerard, S.J. Dinsmore, R.M. Kaminski, K. J. Reinecke
2008, Journal of Wildlife Management (72) 808-813
Incomplete detection of all individuals leading to negative bias in abundance estimates is a pervasive source of error in aerial surveys of wildlife, and correcting that bias is a critical step in improving surveys. We conducted experiments using duck decoys as surrogates for live ducks to estimate bias associated...
Hierarchical Bayes estimation of species richness and occupancy in spatially replicated surveys
M. Kery, J. Andrew Royle
2008, Journal of Applied Ecology (45) 589-598
1. Species richness is the most widely used biodiversity metric, but cannot be observed directly as, typically, some species are overlooked. Imperfect detectability must therefore be accounted for to obtain unbiased species-richness estimates. When richness is assessed at multiple sites, two approaches can be used to estimate species...
Hierarchical modeling of cluster size in wildlife surveys
J. Andrew Royle
2008, Journal of Agricultural, Biological, and Environmental Statistics (13) 23-36
Clusters or groups of individuals are the fundamental unit of observation in many wildlife sampling problems, including aerial surveys of waterfowl, marine mammals, and ungulates. Explicit accounting of cluster size in models for estimating abundance is necessary because detection of individuals within clusters is not independent and detectability of...
