Estimates Of Capture Probability Research Articles

A Modeling Framework for Quantifying Spatial Recruitment Dynamics Using Abundance Estimation and Sibship Analysis

Quantifying recruitment at the sibling group offers a powerful methodology for understanding density-dependent and environmental drivers of recruitment. We propose a modeling framework that combines sibship and abundance estimation datasets to estimate mean sibling group size, sibling group size process error, environmental and density-dependent effects on sibling group size, dispersal, and mortality rate. Geographic states in the model consist of discrete habitat patches connected via dispersal. Simulations were used to investigate the influence of sampling processes and sibling group size on parameter estimation within our modeling framework. Mean sibling-group size, environmental effects on recruitment, and dispersal rate among habitat patches were estimated with high accuracy under a wide range of sampling conditions, including imprecise out-of-model estimates of capture probability and subsampling both within and among habitat patches. Density-dependent effects on recruitment and process error tended to be estimated with lower accuracy, though accuracy improved as sibling group size or sampling intensity increased. The main contribution of this research is a flexible quantitative modeling framework for parameterizing mechanistic models of recruitment dynamics with empirical sibship data.

Densidad poblacional del tigrillo (Leopardus pardalis) en el valle del Cerrejón, La Guajira, Colombia

A pesar de su amplia distribución geográfica, los patrones de abundancia del tigrillo (Leopardus pardalis) son poco conocidos en paisajes transformados. En este trabajo se evaluó la densidad poblacional de esta especie en la Mina del Cerrejón (Guajira, Colombia) por medio de 68 días de fotocapturas con 27 estaciones de fototrampeo. Dos estimadores poblacionales fueron utilizados:1) Estimadores de probabilidad de captura y tamaño poblacional para poblaciones cerradas con datos de recaptura en el programa Capture® y 2) el índice de Lincoln-Petersen. Basados en los patrones de manchas de la piel, se identificaron ocho tigrillos: cuatro machos, dos hembras y dos individuos no sexados. La densidad de tigrillos en la zona varía entre 22 y 24 individuos /100km², dependiendo del estimador utilizado. Las estimaciones de densidad se encuentran dentro de lo reportado en la literatura ecológica de la especie en diferentes tipos de hábitats. Por lo tanto, los resultados de este estudio sugieren que esta especie puede ajustarse a áreas intervenidas siempre y cuando haya la presencia de hábitat idóneo en áreas aledañas.

Incorporating estimates of capture probability and river network covariance in novel habitat – abundance models: Assessing the effects of conservation stocking on catchment-scale production of juvenile Atlantic salmon (Salmo salar) from a long-term electrofishing dataset

There are increasing calls for “conservation stocking” to counter declines in Atlantic salmon (Salmo salar) populations, the assumption being that stocking can bypass population bottlenecks and increase recruitment over natural processes. However, there are too few quantitative studies with sufficient data to assess the efficacy of conservation stocking. The Girnock Burn is a unique long-term monitoring site where adult and juvenile salmon numbers have been monitored for over 50 years, including 11 years with conservation stocking. Adults were monitored at a fixed trap and juveniles were monitored by electrofishing. In stocked years, ova were incubated in surface water to reduce density-independent over-winter mortality. In eight years, eyed ova were stocked at uniform densities to reduce local density-dependence. In three years, stocking replicated natural spatial variability in ova deposition removing any potential benefits of reduced local density-dependence. Juvenile production was estimated by summing the product of reach-scale density estimates and river area obtained from a novel spatial statistical river network model that incorporated the effects of capture probability, habitat and stock level. Capture probability varied with life-stage (age 0+ fry or ≥1+ parr), electrofishing pass and day of the year, but importantly also exhibited a positive temporal trend across years. Survival from ova to fry was density-independent and higher under uniform stocking than natural spawning or simulated natural spawning. Under uniform stocking, fry densities varied smoothly with altitude, while under natural spawning and simulated natural spawning, fry exhibited a more patchy distribution. Increased fry production did not translate to increased parr production, which was strongly density-dependent. This likely reflected the inability of fry to move between stocked locations and suitable overwintering habitat, decreasing survival between fry and parr life-stages. Consequently, there was no overall benefit of stocking. The modelling framework used in this study provides a valuable approach for interpreting long-term datasets where site locations, equipment and staffing vary over time. The long-term Girnock dataset was valuable in separating management action from natural population regulation and permitting understanding of ecological processes. The study indicates that conservation stocking can be ineffective, even where implemented to best scientific standards. It is therefore recommended that a detailed understanding of local population dynamics is obtained, and a realistic appraisal of the expected benefits of stocking is undertaken, before management actions are considered.

Effects of environmental covariates and density on the catchability of fish populations and interpretation of catch per unit effort trends

Quantifying temporal and spatial trends in abundance or relative abundance is required to evaluate effects of harvest and changes in habitat for exploited and endangered fish populations. In many cases, the proportion of the population or stock that is captured (catchability or capture probability) is unknown but is often assumed to be constant over space and time. We used data from a large-scale mark-recapture study to evaluate the extent of spatial and temporal variation, and the effects of fish density, fish size, and environmental covariates, on the capture probability of rainbow trout (Oncorhynchus mykiss) in the Colorado River, AZ. Estimates of capture probability for boat electrofishing varied 5-fold across five reaches, 2.8-fold across the range of fish densities that were encountered, 2.1-fold over 19 trips, and 1.6-fold over five fish size classes. Shoreline angle and turbidity were the best covariates explaining variation in capture probability across reaches and trips. Patterns in capture probability were driven by changes in gear efficiency and spatial aggregation, but the latter was more important. Failure to account for effects of fish density on capture probability when translating a historical catch per unit effort time series into a time series of abundance, led to 2.5-fold underestimation of the maximum extent of variation in abundance over the period of record, and resulted in unreliable estimates of relative change in critical years. Catch per unit effort surveys have utility for monitoring long-term trends in relative abundance, but are too imprecise and potentially biased to evaluate population response to habitat changes or to modest changes in fishing effort.

Modelling capture probability of Atlantic salmon (Salmo salar) from a diverse national electrofishing dataset: Implications for the estimation of abundance

Estimates of juvenile fish abundance are commonly used to assess fish population health and to underpin assessment tools used in environmental and fisheries management such as the EU Water Framework Directive and EU Habitats Directive. Accurate and precise estimates of capture probability are important for estimating fish abundance from electrofishing data. This paper presents the findings of a maximum likelihood approach for modelling spatio-temporal variability in capture probability of Atlantic salmon in a large (2,837 samples) and diverse national electrofishing dataset. Capture probability was related to explanatory variables indicative of (1) equipment, personnel and protocols, (2) fish size, (3) fish behaviour, (4) habitat, and (5) time. A linear modelling approach allowed for flexible model specification, including smoothers and spatial effects, and rapid model specification, fitting and selection. The use of GIS variables as proxies for directly observed habitat characteristics allowed capture probability to be modelled using aggregated data where there were no common meta-data or habitat recording protocols. Modelled capture probabilities provided more precise estimates of abundance than sample-wise estimates and more accurate estimates than those obtained when assuming constant capture probability. Fisheries and environmental managers should routinely model capture probability when estimating fish abundance from electrofishing data, especially where datasets are geographically widespread, cover a large environmental range or have been collated across multiple organisations. Capture probability models can also facilitate the legitimate use of single pass electrofishing data in assessments of fish abundance providing that there is sufficient spatio-temporal coverage of multi-pass data.

Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture–recapture data

Summary Temporary migration – where individuals can leave and re‐enter a sampled population – is a feature of many capture–mark–recapture (CMR) studies of mobile populations which, if unaccounted for, can lead to biased estimates of population capture probabilities and consequently biased estimates of population abundance. We present a method for incorporating radiotelemetry data within a CMR study to eliminate bias due to temporary migration using a Bayesian state‐space model. Our results indicate that using a relatively small number of telemetry tags, it is possible to greatly reduce bias in estimates of capture probabilities using telemetry data to model transition probabilities in and out of the sampling area. In a capture–recapture data set for trout Cod in the Murray river, Australia, accounting for temporary migration led to overall higher estimates of capture probabilities than models assuming permanent or zero migration. Also, individual heterogeneity in detectability can be managed through explicit modelling. We show how accounting for temporary migration when estimating capture probabilities can be used to estimate the abundance and size distribution of a population as though it were closed. Our model provides a basis for more complex models that might integrate telemetry data into other CMR scenarios, thus allowing for greater precision in estimates of vital rates that might otherwise be biased by temporary migration. Our results highlight the importance of accounting for migration in survey design and parameter estimation, and the potential scope for supplementing large‐scale CMR data sets with a subset of auxiliary data that provide information on processes that are hidden to primary sampling processes.

Comparison of Electrofishing Techniques to Detect Larval Lampreys in Wadeable Streams in the Pacific Northwest

AbstractWe evaluated the probability of detecting larval lampreys using different methods of backpack electrofishing in wadeable streams in the U.S. Pacific Northwest. Our primary objective was to compare capture of lampreys using electrofishing with standard settings for salmon and trout to settings specifically adapted for capture of lampreys. Field work consisted of removal sampling by means of backpack electrofishing in 19 sites in streams representing a broad range of conditions in the region. Captures of lampreys at these sites were analyzed with a modified removal‐sampling model and Bayesian estimation to measure the relative odds of capture using the lamprey‐specific settings compared with the standard salmonid settings. We found that the odds of capture were 2.66 (95% credible interval, 0.87–78.18) times greater for the lamprey‐specific settings relative to standard salmonid settings. When estimates of capture probability were applied to estimating the probabilities of detection, we found high (>0.80) detectability when the actual number of lampreys in a site was greater than 10 individuals and effort was at least two passes of electrofishing, regardless of the settings used. Further work is needed to evaluate key assumptions in our approach, including the evaluation of individual‐specific capture probabilities and population closure. For now our results suggest comparable results are possible for detection of lampreys by using backpack electrofishing with salmonid‐ or lamprey‐specific settings.Received December 28, 2012; accepted July 10, 2013

Detection experiments with humans implicate visual predation as a driver of colour polymorphism dynamics in pygmy grasshoppers

BackgroundAnimal colour patterns offer good model systems for studies of biodiversity and evolution of local adaptations. An increasingly popular approach to study the role of selection for camouflage for evolutionary trajectories of animal colour patterns is to present images of prey on paper or computer screens to human ‘predators’. Yet, few attempts have been made to confirm that rates of detection by humans can predict patterns of selection and evolutionary modifications of prey colour patterns in nature. In this study, we first analyzed encounters between human ‘predators’ and images of natural black, grey and striped colour morphs of the polymorphic Tetrix subulata pygmy grasshoppers presented on background images of unburnt, intermediate or completely burnt natural habitats. Next, we compared detection rates with estimates of capture probabilities and survival of free-ranging grasshoppers, and with estimates of relative morph frequencies in natural populations.ResultsThe proportion of grasshoppers that were detected and time to detection depended on both the colour pattern of the prey and on the type of visual background. Grasshoppers were detected more often and faster on unburnt backgrounds than on 50% and 100% burnt backgrounds. Striped prey were detected less often than grey or black prey on unburnt backgrounds; grey prey were detected more often than black or striped prey on 50% burnt backgrounds; and black prey were detected less often than grey prey on 100% burnt backgrounds. Rates of detection mirrored previously reported rates of capture by humans of free-ranging grasshoppers, as well as morph specific survival in the wild. Rates of detection were also correlated with frequencies of striped, black and grey morphs in samples of T. subulata from natural populations that occupied the three habitat types used for the detection experiment.ConclusionsOur findings demonstrate that crypsis is background-dependent, and implicate visual predation as an important driver of evolutionary modifications of colour polymorphism in pygmy grasshoppers. Our study provides the clearest evidence to date that using humans as ‘predators’ in detection experiments may provide reliable information on the protective values of prey colour patterns and of natural selection and microevolution of camouflage in the wild.

Population Abundance and Sex Ratio of the Viviparous Freshwater FishPoeciliopsis baenschi(Poeciliidae) Throughout its Range in Western Mexico

We estimated population abundance and sex ratio for a freshwater live-bearing fish species (Poeciliopsis baenschi) that inhabits fluvial systems in western Mexico. We conducted mark-recapture experiments in 6 distinct populations. We used both our catch data as well as estimates of capture probability to calculate the number of individuals per unit water volume for adult males, adult females, and juveniles. Overall, abundance varied among sites from 23.8 individuals · m-3 to 363.2 individuals · m-3. In most of our study sites, the estimated sex ratio was markedly biased toward females (up to 11 females per male). We discuss the potential causes and implications of the observed demographic features.

Improving abundance estimates from electrofishing removal sampling

Estimates of fish abundance from electrofishing surveys depend on accurate estimation of capture probability. We examine in this paper how estimates of capture probability and abundance of Atlantic salmon from multi-pass removal sampling can be improved by comparing the results of an experimental programme of closed electrofishing sites within selected rivers in west-central Norway, and those obtained from open electrofishing sites established for monitoring long-term juvenile Atlantic salmon population abundance within the Burrishoole catchment, western Ireland. We first establish that the Carle & Strub method provides a more robust estimate of population abundance than the Zippin and Seber methods. We then show how prior information on capture probability may be used to improve the accuracy of the abundance estimate in open sites. We also show that the use of prior information with single-pass electrofishing may improve the accuracy of the abundance estimate so that it is comparable with that of multi-pass electrofishing in terms of stock prediction while requiring less sampling effort.

Application of a Multistate Model to Estimate Culvert Effects on Movement of Small Fishes

AbstractWhile it is widely acknowledged that culverted road‐stream crossings may impede fish passage, effects of culverts on movement of nongame and small‐bodied fishes have not been extensively studied and studies generally have not accounted for spatial variation in capture probabilities. We estimated probabilities for upstream and downstream movement of small (30‐120 mm standard length) benthic and water column fishes across stream reaches with and without culverts at four road‐stream crossings over a 4‐6‐week period. Movement and reach‐specific capture probabilities were estimated using multistate capture‐recapture models. Although none of the culverts were complete barriers to passage, only a bottomless‐box culvert appeared to permit unrestricted upstream and downstream movements by benthic fishes based on model estimates of movement probabilities. At two box culverts that were perched above the water surface at base flow, observed movements were limited to water column fishes and to intervals when runoff from storm events raised water levels above the perched level. Only a single fish was observed to move through a partially embedded pipe culvert. Estimates for probabilities of movement over distances equal to at least the length of one culvert were low (e.g., generally ≤0.03, estimated for 1‐2‐week intervals) and had wide 95% confidence intervals as a consequence of few observed movements to nonadjacent reaches. Estimates of capture probabilities varied among reaches by a factor of 2 to over 10, illustrating the importance of accounting for spatially variable capture rates when estimating movement probabilities with capture‐recapture data. Longer‐term studies are needed to evaluate temporal variability in stream fish passage at culverts (e.g., in relation to streamflow variability) and to thereby better quantify the degree of population fragmentation caused by road‐stream crossings with culverts.

Evaluation of non-invasive genetic sampling methods for estimating tiger population size

There is often a conservation need to estimate population abundances of elusive, low-density, wide-ranging carnivore species. Because of logistical constraints, investigators often employ non-invasive ‘captures’ that may involve ‘genetic’ or ‘photographic’ sampling in such cases. Established capture–recapture (CR) methods offer a powerful analytical tool for such data. In this paper, we developed a rigorous combination of captive, laboratory and field-based protocols for identifying individual tigers ( Panthera tigris) from fecal DNA. We explored trade-offs between numbers of microsatellite loci used for reliable individual identifications and the need for higher capture rates for robust analyses. Our field surveys of scats were also specifically designed for CR analyses, enabling us to test for population closure, estimate capture probabilities and tiger abundance. Consequently, we could compare genetic capture estimates to results of a ‘photographic capture’ study of tigers at the same site. The estimates using the heterogeneity model ( M h-Jackknife) for fecal DNA survey were [ M t+1 = 26; p ¯ ˆ = 0.09 and N ˆ ( S E ˆ [ N ˆ ] )=66 (12.98)] in close agreement with those from the photographic survey [( M t+1 = 29; p ¯ ˆ = 0.04 and N ˆ ( S E ˆ [ N ˆ ] ) = 66 (13.8)]. Our results revealed that designing field surveys of scats explicitly for CR data analyses generate reliable estimates of capture probability and abundance for elusive, low density species such as tigers. The study also highlights the importance of rigorous field survey and laboratory protocols for reliable abundance estimation in contexts where other approaches such as camera-trapping or physical tagging of animals may not be practical options.

Subsampling photographic capture‐recapture data of tigers (Panthera tigris) to minimize closure violation and improve estimate precision: a case study

AbstractMost studies using photographic capture‐recapture methodology estimate parameters of interest with ecological and sampling uncertainties. However, the effect of sampling effort on assumption violation and estimate precision has seldom been described using empirical data in studies estimating population size of tigers (Panthera tigris tigris). In this study, we evaluate the influence of trap effort (trap area, mean cell area and trap density) on the assumption of geographic closure and their relationship with estimated capture probability. We do this by subsampling capture histories obtained for tigers from 30 trapping stations within the Chilla range of Rajaji National Park, India. We assessed the importance of trapping effort on geographic closure by estimating fidelity () and immigration () under the Pradel model. Estimate precision (CV% []) was evaluated based on estimates of capture probability (). Results of the Pradel analysis suggested that larger trap area (TA) ensured geographic closure, while high trap densities (TD) exhibited sex‐specific heterogeneity in recapture probabilities p. Simulation results suggested a significant positive correlation between estimates of () and TD. With increase in estimated capture probability, estimate precision (CV% []) also improved sharply. Comparison of prior studies towards optimizing sampling strategies is often compromised due to the difference in scale and methods of sampling. Therefore, we urge that subsampling within a dataset as illustrated in our study may prove to be an advantageous step towards standardizing photographic capture‐recapture sampling methodology for management objectives.

Efficacy of PIT tags and an autonomous antenna system to study the juvenile life stage of an estuarine-dependent fish

Many marine fishes use spatially distinct habitats as juveniles and adults. Determining which juvenile habitats are most important to sustaining adult populations (i.e., which habitats are nurseries) has proven difficult, in part due to challenges in estimating survival of juveniles in putative nursery habitats. Recent technological advances have made large- scale tagging efforts a viable approach to estimating survival of juvenile fishes by increasing recapture rates and enabling the use of individual-identification tags. These techniques, using Passive Integrated Transponder (PIT) tags and autonomous antenna detection systems (antenna), have been successfully applied in freshwater environments. This paper reports the adaptation of these techniques to estuarine mangrove creeks (salinity: 2-28%) for research of the juvenile life stage on an estuarine-dependent marine fish, Centropomus undecimalis. Retention rate of PIT tags in juveniles .120 mm standard length was 100%, with no mortality. The antenna detection field covered 48% of the creek water column, and the antenna was experimentally determined to detect approximately 67% of tagged fish that swam through. Overall recapture rate of tagged fish by the antenna was .40%. This recapture rate is higher than the sparse data typical of traditional tag-recapture studies. A time-dependent Jolly-Seber model was fit to the data, providing estimates of capture probability (0.8) and weekly apparent survival (0.41) that will be invaluable in comparing juvenile habitats of different quality (e.g., natural versus anthropogenically degraded). This research demonstrates the viability of this approach to fish research in estuarine habitats.

CAPTURE-RECAPTURE ESTIMATES OF HECTOR'S DOLPHIN ABUNDANCE AT BANKS PENINSULA, NEW ZEALAND

Capture-recapture techniques have been extensively used to estimate survival rates of Hector's dolphins at Banks Peninsula, but not abundance. We analyzed nine seasons of photo-identification data using a model-fitting approach in the computer program MARK, and then used MARK's estimates of capture probabilities to calculate the abundance of distinctive individuals. We extrapolated these estimates to include unmarked individuals using five seasons of data on the proportion of identifiable individuals in this population, obtained from “random photography.” This capture-recapture approach suggests a 1996 population of about 1,100 (CV = 0.21). This is very similar to the 1997 line-transect estimate of about 900 (CV = 0.28), especially considering that the two techniques do not necessarily measure the same thing. An important advantage of the capture-recapture approach stems from the inherent versatility of photo-ID data. If the sampling design is appropriate, an unbiased abundance estimate can be achieved as a spin-off from work directed at other questions. However, in our view, line-transect estimates are easier to interpret because the sampling design is explicit.

UNDERSTANDING SURVIVAL AND ABUNDANCE OF OVERWINTERING WARBLERS: DOES RAINFALL MATTER?

We investigated relationships between warbler abundance and survival rates measured on a Puerto Rican wintering site and rainfall patterns measured on the wintering site and in regions where these warblers breed, as estimated using stable-isotope analysis (δD) of feathers collected from wintering birds. We banded birds using constant-effort mist netting from January 1989–2003 in the Gu´nica Forest of southwestern Puerto Rico. Black-and-white Warblers (Mniotilta varia), American Redstarts (Setophaga ruticilla), and Ovenbirds (Seiurus aurocapilla) dominated the Neotropical migrant capture totals each winter, with resulting sample sizes large enough to estimate survival rates. Estimates of capture probability from survival modeling allowed us to estimate abundance from mist-netting capture totals for Black-and-white Warblers and Ovenbirds. Stable-hydrogen isotopes showed that the three focal species came mostly from the eastern United States. Black-and-white Warbler abundance was related to rainfall total deviations from normal in Guánica Forest, and Ovenbird abundance was related to total annual rainfall in the United States. Survival models with rainfall covariates were weakly supported overall, but apparent survival of Black-and-white Warblers and American Redstarts was negatively related to rain during the first 6 months of the year at Guánica, and Ovenbird survival was related to rainfall during the spring in the southeastern U.S. Abundance and apparent survival exhibited similar, species-specific patterns of association with rainfall for Black-and-white Warblers and Ovenbirds. Winter rainfall was important to demographic parameters of Black-and-white Warblers, and breeding-season rain was important to Ovenbirds. Entendiendo los Patrones de Supervivencia y Abundancia de Parúlidos Residentes de Invierno: ¿Es Importante la Precipitación? Resumen. Investigamos las relaciones entre la abundancia y las tasas de supervivencia de parúlidos residentes de invierno en Puerto Rico y los patrones de precipitación de los sitios invernales y de las áreas de anidación, éstas últimas deducidas a partir del análisis de isótopos estables (δD) en plumas colectadas de las aves migratorias. Las aves fueron capturadas y anilladas utilizando redes de niebla en el Bosque de Guánica en el suroeste de Puerto Rico durante el mes de enero, desde 1989 hasta el 2003. Las especies de aves neotropicales con mayor número de capturas totales durante cada invierno fueron Mniotilta varia, Setophaga ruticilla y Seiurus aurocapilla, con un tamaño de muestra lo suficientemente grande como para estimar sus tasas de supervivencia. La estimación de las probabilidades de captura a partir de los modelos de supervivencia nos permitieron evaluar la abundancia utilizando datos de capturas totales para Mniotilta varia y Seiurus aurocapilla. Los isótopos de hidrógeno estable mostraron que las tres especies de aves focales provinieron principalmente de la región Este de Estados Unidos. La abundancia de Mniotilta varia estuvo relacionada a las variaciones totales de precipitación en el Bosque de Guánica y la abundancia de Seiurus aurocapilla estuvo relacionada a la precipitación anual total en los Estados Unidos. Los modelos de supervivencia con covariables de precipitación tuvieron muy poco respaldo. Sin embargo, la supervivencia aparente de Mniotilta varia y Setophaga ruticilla estuvo relacionada negativamente a la precipitación durante los primeros seis meses del año en Guánica y la supervivencia de Seiurus aurocapilla estuvo relacionada a la precipitación durante la estación de primavera en el sureste de Estados Unidos. La abundancia y la supervivencia aparente mostraron patrones de asociación similares y específicos para cada especie con la precipitación para Mniotilta varia y Seiurus aurocapilla. La precipitación de invierno fue un factor importante para determinar los patrones demográficos de Mniotilta varia y la precipitación durante la temporada de anidación también fue un factor significativo para Seiurus aurocapilla.

On the use of secondary capture-recapture samples to estimate temporary emigration and breeding proportions

The use of the Cormack-Jolly-Seber model under a standard sampling scheme of one sample per time period, when the Jolly-Seber assumption that all emigration is permanent does not hold, leads to the confounding of temporary emigration probabilities with capture probabilities. This biases the estimates of capture probability when temporary emigration is a completely random process, and both capture and survival probabilities when there is a temporary trap response in temporary emigration, or it is Markovian. The use of secondary capture samples over a shorter interval within each period, during which the population is assumed to be closed (Pollock's robust design), provides a second source of information on capture probabilities. This solves the confounding problem, and thus temporary emigration probabilities can be estimated. This process can be accomplished in an ad hoc fashion for completely random temporary emigration and to some extent in the temporary trap response case, but modelling the complete sam...