Species Detection Probability Research Articles

Method learning caused a first‐time observer effect in a newly started breeding bird survey

Capsule A first‐time observer effect in the new French breeding bird survey (BBS) was found to result from new observers learning how to use the point count method on randomly selected sites. Aims To estimate the first‐year effect in a newly started BBS, to look for correlates and test for a temporal trend in learning. Methods Trends of 105 species were estimated using data from 2001–2007 obtained by 1100 observers conducting point counts over 1535 randomly selected squares. I estimated the average increase in detected numbers between the first and all subsequent years of survey at a site. Results Observers counted 4.3% more birds in subsequent years than during the initial year of survey. This first‐year effect decreased from 2001 to 2007 (by an average of 2% per year). It was not related to most variables known to influence species detection probability. Only species with songs of lower sound frequencies (ranging from 0.5 to 8 kHz here) displayed a greater increase in locally detected numbers. Conclusion The detected first‐year effect was the result of method learning by new observers who had not previously conducted point counts or visited randomly selected sites. The learning effect was larger for species with songs of lower sound frequency which are harder to hear during the dawn chorus.

Topological phase in two flavor neutrino oscillations

We show that the phase appearing in neutrino flavor oscillation formulae has a geometric and topological contribution. We identify a topological phase appearing in the two flavor neutrino oscillation formula using Pancharatnam's prescription of quantum collapses between non-orthogonal states. Such quantum collapses appear naturally in the expression for appearance and survival probabilities of neutrinos. Our analysis applies to neutrinos propagating in vacuum or through matter. For the minimal case of two flavors with CP conservation, our study shows for the first time that there is a geometric interpretation of the neutrino oscillation formulae for the detection probability of neutrino species.

Using soundscape recordings to estimate bird species abundance, richness, and composition

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An inventory of mammalian pests in a New Zealand city

Urban ecosystems include many habitat types supporting native flora and fauna. These habitats may also sustain populations of introduced mammalian pests, although relatively little is known about the composition or distributions of these species in urban environments. We made a preliminary survey of the distribution and relative abundance of pest mammals across three urban habitat types (gully, amenity park, residential) in Hamilton, New Zealand. Tracking tunnel and WaxTag® surveys showed that: (1) rats (Rattus rattus or R. norvegicus), mice (Mus musculus) and brushtail possums (Tricho‐surus vulpecula) were detected most often and in highest abundances in gullies, were relatively rare in amenity parks, and were not detected in residential areas; (2) hedgehogs (Erinaceus europaeus) were regularly detected in all habitats; and (3) mustelids were not detected in any habitat. Live trapping in areas where rats were detected captured 21 rats, of which 19 were R. rattus. Scat and animal sign surveys found evidence of lagomorphs in amenity parks and gullies but not in residential areas. Cats (Felis catus) were detected in all habitats. These data suggest that important mammalian pests other than cats are either absent (mustelids) or comparatively rare (rats) in urban Hamilton and largely confined to gully habitats. Further research is needed to determine whether detection probabilities of target species vary significantly between the species and habitats we sampled, and to quantify the impact that mammalian pests might have in limiting populations of other animals, especially avifauna.

Teasing out biological effects and sampling artifacts when using occupancy rate in monitoring programs

ABSTRACT Recent declines in biodiversity stress the need for rigorous and reliable multispecies monitoring programs. A potential weakness of monitoring programs is a reliance on raw counts and the assumption either of complete detection or of constant detection probability for each species, regardless of the sampling situation. Until recently, these assumptions have largely remained untested and, therefore, to help insure accuracy, bird-monitoring programs have depended on standardization of counts and counts of longer duration. We tested the effectiveness of these strategies for providing unbiased occupancy rates using a method designed to accommodate situations where species detection probabilities are less than one and heterogeneous. We tested the effect of potential sources of heterogeneity in detection probability (vegetation structure, wind velocity, cloud cover, date, and time) on occupancy rate estimates of 13 bird species in southern France. We compared adjusted and raw occupancy rates for two sampling durations (10 and 20 min). Differences between raw and adjusted occupancy rates were low even for the shorter count duration, suggesting that standardized long counts should produce reliable estimates of occupancy rates even in the absence of correction by an appropriate method. This enhances the value of past monitoring programs where long standardized counts were used, but with designs that do not allow corrected estimates. However, we found that detection probability was heterogeneous for most species and that vegetation structure was an important source of heterogeneity. The possible effects of habitat on detection probability should be of special concern for long-term monitoring programs conducted in landscapes where habitats vary across time or space. Las recientes tasas de reducción en biodiversidad realzan la necesidad de programas de monitoreo rigurosos y confiables diseñados para múltiples especies. Una debilidad potencial de estos programas de monitoreo es depender en conteos crudos y tener que asumir detecciones completas o probabilidades de detección constante para cada especie, para casi todo tipo de situación. Hasta hace muy poco, los supuestos mencionados, no habían sido puesto a pruebas, y por ende, para ayudar a determinar su exactitud, los programas de monitoreos de aves dependieron de la estandarización de conteos y conteos de larga duración. Pusimos a pruebas la efectividad de dichas estrategias para proveer tasas de ocupación sin sesgo, utilizando un método designado para acomodar la situación en donde la probabilidad de detectar una especie era menos de uno (1) y heterogénea. Probamos la efectividad de fuentes potenciales de heterogeneidad en la probabilidad de detección (estructura de la vegetación, velocidad del viento, cubierta de nubes, fecha y hora del dia) en estimados de tasas de ocupación de 13 especies de aves en el sur de Francia. Comparamos las tasas de ocupación cruda con una ocupación ajustada para dos periodos de monitoreo (10 y 20 minutos). Las diferencias entre las tasas de ocupación cruda y ajustada fueron bajas aún para los periodos cortos de conteo, lo que sugiere que conteos largos estandarizados deben producir unos estimados confiables inclusive bajo la ausencia de corrección para un método apropiado. Esto incrementa el valor de programas pasados de monitoreo, en donde se utilizaron conteos largos estandarizados, pero con diseños que no permitieron la corrección de dichos estimados. Sin embargo, encontramos que la probabilidad de detección fue heterogenea para la mayoría de las especies y que la estructura de la vegetación es una fuente importante de heterogeneidad. El posible efecto del habitat, en la probabilidad de detección, debe ser de especial preocupación para proyectos de monitoreo a largo alcance, en escenarios en donde el hábitat varíe a través del espacio y tiempo.

FACTORS INFLUENCING SPECIES RICHNESS AND COMMUNITY COMPOSITION OF BREEDING BIRDS IN A DESERT RIPARIAN CORRIDOR

The San Pedro River in southeastern Arizona is one of the last free-flowing rivers in the southwestern United States that maintains significant stretches of perennial water. While critical for birds, this river is vulnerable to salt cedar (tamarisk, Tamarix spp.) invasion, woody encroachment into grassland, and alteration of hydrologic regime resulting from groundwater pumping. Bird species richness and community composition metrics provide a means to assess effects of management or conservation efforts. To estimate these metrics, we used methods that incorporated species detection probabilities from data collected at 160 points at 23 sites on the San Pedro River during 1998–2001. Species richness, co-occurrence, and uniqueness were estimated as a function of four riparian vegetation types (cottonwood-willow [Populus-Salix], salt cedar, mesquite [Prosopis spp.], and grassland), three hydrologic regimes (perennial, intermittent, and ephemeral), and riparian location (floodplain and terrace). We found significantly higher species richness in cottonwood and mesquite compared with salt cedar and grassland. Intermittent and perennial flow sites had higher species richness compared with ephemeral. Cottonwood and mesquite supported more unique species compared with grassland and salt cedar, and cottonwood or perennial sites supported canopy or water-dependent species, for which habitat is rare on the landscape. Within the intermittent class, salt cedar maintained an estimated 0–2 unique species compared with native woody vegetation types, while cottonwood and mesquite contributed an estimated 20–21 unique species compared with salt cedar. Thus, while maintaining relatively high species richness, salt cedar contributed little to regional avian diversity compared with native woody riparian vegetation. This research has important implications for regional conservation planning and riparian restoration efforts.

Role of Current Versus Historical Hydrology in Amphibian Species Turnover within Local Pond Communities

This study explored how historical and current hydrological conditions covaried with colonization and occupancy probabilities for 14 pond-breeding amphibians at 32 natural sinkhole ponds over a five-year period. Occupancy and colonization were estimated independently for breeding adults and juvenile recruits (metamorphs) of each species using proportion of area occupied (PAO) models that incorporated species detection probabilities. Model selection revealed whether historical or current hydrological conditions are more important in determining occupancy and colonization probabilities for each species. Adults and metamorphs of ranids and most salamanders had occupancy and colonization rates that were best estimated by models that incorporated each pond's historical hydrology. A comparison of colonization and occupancy dynamics for history dependent species indicates that these species contribute little to species turnover within local pond communities. Adult occupancy and colonization of hylid, bufonid, and a pelobatid species were more dependent on the immediate hydrology of a pond within a year. Recruitment dynamics of these same anuran species were best fit by models that incorporated both current and historical pond hydrology. In some years, these species had high probabilities of producing metamorphs in ponds where they had not produced metamorphs in the previous year. Increases or stability in colonization probabilities between years sometimes coincided with stable occupancy probabilities, indicating that these opportunistic species are responsible for species turnover in local communities. Short-term species turnover within local amphibian communities appears to be driven by these opportunistic species and linked to major changes in weather between consecutive years.

Detection probability of Golden-winged Warblers during point counts with and without playback recordings

ABSTRACT Use of point-count data to estimate population sizes of North American landbirds may be challenged by limitations on detection probability of particular species, thereby requiring correction factors to ensure accurate estimates. We estimated detection probability of Golden-winged Warblers (Vermivora chrysoptera) during 3-min point-count surveys conducted both with and without use of playback recordings in a mixed shrubland-forest habitat (clearcut area) and a 60-m wide electric transmission line right-of-way (ROW) in central Pennsylvania from 20 May to 17 June 2002–2003. In addition, we assessed the value of playback with respect to response rates of warblers and distance within which warblers approached the observer. Without playback, detection probability was approximately 23% in the clearcut area and 61% in the ROW. Use of playback resulted in 7% and 19% net increases in probability at the clearcut area and the ROW, respectively; proportional increase was approximately 30% for both habitats. Warblers responded to playback 68% of the time, but response rate was greater within 100 m (72%) than beyond (53%). Most responses (85%) included approach of the warbler toward the observer, and most individuals approached within 10 m. We conclude that 3-min point counts with playback do not yield detection probabilities sufficient to estimate population size of Golden-winged Warblers without use of correction factors. Furthermore, detection probability in mixed shrubland-forest habitats can be much lower than in linear habitats such as utility ROWs. Efforts to estimate population size of Golden-winged Warblers from data of the North American Breeding Bird Survey should recognize that habitat structure has much influence on detection probability as it relates to distance at which an observer can hear (or see) warblers. Accordingly, we recommend that such efforts incorporate a maximum detection distance of 100–150 m in mixed shrubland-forest habitats.

DETERMINANTS OF LOCAL EXTINCTION AND TURNOVER RATES IN URBAN BIRD COMMUNITIES

Studying the effects of urbanization on the dynamics of communities has become a priority for biodiversity conservation. The consequences of urbanization are mainly an increased fragmentation of the original landscapes associated with a decrease in the amount of favorable habitats and an increased pressure of human activities on the remaining patches suitable for wildlife. Patterns of bird species richness have been studied at different levels of urbanization, but little is known about the temporal dynamics of animal communities in urban landscapes. In particular, urbanization is expected to have stronger negative effects on migratory breeding bird communities than on sedentary ones, which should lead to different patterns of change in composition. Using an estimation method accounting for heterogeneity in species detection probability and data collected between 2001 and 2003 within a suburban area near the city of Paris, France, we tested whether these communities differ in their local extinction and turnover rates. We considered the potential effects of patch size and distance to Paris' center as a measure of the degree of urbanization around the patches. As expected, local rates of extinction and turnover were higher for migratory than for sedentary species, and they were negatively related to patch size for migratory species. Mean species richness of the sedentary species increased during the study period and their local turnover rate was negatively related to the distance to the urban core, showing a trend to colonize the most urban patches. These results highlight the very dynamic nature of the composition of some local bird communities in fragmented habitats and help to identify factors affecting colonization and extinction.

Associations between anuran tadpoles and salinity in a landscape mosaic of wetlands impacted by secondary salinisation

Summary1. The secondary salinisation of wetlands is a global problem that poses a great threat to most freshwater biodiversity, including amphibians. We examined tadpole diversity in relation to wetland conductivity (our proxy for salinity) in wetlands in south‐eastern Australia to better understand (i) how salinity and amphibian diversity interact and (ii) the threat posed by secondary salinisation.2. Six tadpole species were trapped in 56 wetlands that reflected a typical salinity gradient for the study region. We developed Bayesian models to examine the relationships between conductivity and both the probability of species occupancy and expected number of species with the imperfect detection probability of species accounted for in the models.3. The probability of occupancy for all species and expected species number was negatively associated with wetland conductivity. Our results predict that conductivity should not limit tadpole presence below about 3000 μS cm−1 at 25 °C (approximately 6% seawater) in the region, but will largely exclude amphibian larvae beyond about 6000 μS cm−1 at 25 °C (approximately 12% seawater).4. We also detected subtle among‐species differences in salinity tolerance. The results reported here show that tadpoles in the study region are likely to be negatively affected by projected future increases in salinisation.

APPLICATION OF LAPLACE'S BOUNDARY‐MODE APPROXIMATIONS TO ESTIMATE SPECIES AND SHARED SPECIES RICHNESS

SummaryThe Laplace method for approximating integrals is a useful technique in a number of research fields. This paper shows that it also has interesting applications in biological and ecological statistical inferences. When sample abundance or replicated incidence (i.e., presence or absence) records of each species are available, the expected low‐order frequency counts in heterogeneous communities can be approximated by the Laplace method when the species discovery or detection probabilities are bounded from below by a constant. The approximation formulae as applied to one community can then be used to derive estimators of species richness and to examine their performance. The approach is also extended to obtain simple and new estimators for the number of shared species in two communities. The replicated species incidence data recorded by competing teams of the Hong Kong Big Bird Race for the years 1999 and 2000 are used to estimate the number of resident birds in Hong Kong and to illustrate the method of estimation.

Comparative dynamics of avian communities across edges and interiors of North American ecoregions

AbstractAim Based on a priori hypotheses, we developed predictions about how avian communities might differ at the edges vs. interiors of ecoregions. Specifically, we predicted lower species richness and greater local turnover and extinction probabilities for regional edges. We tested these predictions using North American Breeding Bird Survey (BBS) data across nine ecoregions over a 20‐year time period.Location Data from 2238 BBS routes within nine ecoregions of the United States were used.Methods The estimation methods used accounted for species detection probabilities < 1. Parameter estimates for species richness, local turnover and extinction probabilities were obtained using the program COMDYN. We examined the difference in community‐level parameters estimated from within exterior edges (the habitat interface between ecoregions), interior edges (the habitat interface between two bird conservation regions within the same ecoregion) and interior (habitat excluding interfaces). General linear models were constructed to examine sources of variation in community parameters for five ecoregions (containing all three habitat types) and all nine ecoregions (containing two habitat types).Results Analyses provided evidence that interior habitats and interior edges had on average higher bird species richness than exterior edges, providing some evidence of reduced species richness near habitat edges. Lower average extinction probabilities and turnover rates in interior habitats (five‐region analysis) provided some support for our predictions about these quantities. However, analyses directed at all three response variables, i.e. species richness, local turnover, and local extinction probability, provided evidence of an interaction between habitat and region, indicating that the relationships did not hold in all regions.Main conclusions The overall predictions of lower species richness, higher local turnover and extinction probabilities in regional edge habitats, as opposed to interior habitats, were generally supported. However, these predicted tendencies did not hold in all regions.

Estimation of local extinction rates when species detectability covaries with extinction probability: is it a problem?

Estimating the rate of change of the composition of communities is of direct interest to address many fundamental and applied questions in ecology. One methodological problem is that it is hard to detect all the species present in a community. Nichols et al. presented an estimator of the local extinction rate that takes into account species probability of detection, but little information is available on its performance. However, they predicted that if a covariance between species detection probability and local extinction rate exists in a community, the estimator of local extinction rate complement would be positively biased.Here, we show, using simulations over a wide range of parameters that the estimator performs reasonably well. The bias induced by biological factors appears relatively weak. The most important factor enhancing the performance (bias and precision) of the local extinction rate complement estimator is sampling effort. Interestingly, a potentially important biological bias, such as the covariance effect, improves the estimation for small sampling efforts, without inducing a supplementary overestimation when these sampling efforts are high. In the field, all species are rarely detectable so we recommend the use of such estimators that take into account heterogeneity in species detection probability when estimating vital rates responsible for community changes.

Post-precipitation bias in band-tailed pigeon surveys conducted at mineral sites

Many animal surveys to estimate populations or index trends include protocol prohibiting counts during rain but fail to address effects of rainfall preceding the count. Prior research on Pacific Coast band-tailed pigeons (Patagioenas fasciata monilis) documented declines in use of mineral sites during rainfall. We hypothesized that prior precipitation was associated with a short-term increase in use of mineral sites following rain. We conducted weekly counts of band-tailed pigeons at 19 Pacific Northwest mineral sites in 2001 and 20 sites in 2002. Results from regression analysis indicated higher counts ≤2 days after rain (11.31±5.00% [x̄±SE]) compared to ≥3 days. Individual index counts conducted ≤2 days after rain were biased high, resulting in reduced ability to accurately estimate population trends. Models of band-tailed pigeon visitation rates throughout the summer showed increased mineral-site counts during both June and August migration periods, relative to the July breeding period. Our research supported previous studies recommending that mineral-site counts used to index the band-tailed pigeon population be conducted during July. We further recommend conducting counts ≥3 days after rain to avoid weather-related bias in index estimation. The design of other population sampling strategies that rely on annual counts should consider the influence of aberrant weather not only coincident with but also preceding surveys if weather patterns are thought to influence behavior or detection probability of target species.

FACTORS AFFECTING SPECIES DISTRIBUTION PREDICTIONS: A SIMULATION MODELING EXPERIMENT

Geospatial species sample data (e.g., records with location information from natural history museums or annual surveys) are rarely collected optimally, yet are increasingly used for decisions concerning our biological heritage. Using computer simulations, we examined factors that could affect the performance of autologistic regression (ALR) models that predict species occurrence based on environmental variables and spatially correlated presence/absence data. We used a factorial experiment design to examine the effects of survey design, spatial contiguity, and species detection probability and applied the results of ten replications of each factorial combination to an ALR model. We used additional simulations to assess the effects of sample size and environmental data error on model performance. Predicted distribution maps were compared to simulated distribution maps, considered “truth,” and evaluated using several metrics: omission and commission error counts, residual sums of squares (RSS), and areas under receiver operating characteristic curves (AUC). Generally, model performance was better using random and stratified survey designs than when using other designs. Adaptive survey designs were an exception to this generalization under the omission error performance criterion. Surveys using rectangular quadrats, designed to emulate roadside surveys, resulted in models with better performance than those using square quadrats (using AUC, RSS, and omission error metrics) and were most similar in performance to a systematic quadrat design. Larger detection probabilities, larger sample sizes, contiguous distributions, and fewer environmental data errors generally improved model performance. Results suggest that spatially biased sample data, e.g., data collected along roads, could result in model performance near that of systematic quadrat designs even in the presence of potentially confounding factors such as contiguity of distributions, detection probability, sample size, and environmental data error.

Effect of sampling effort and species detectability on volunteer based anuran monitoring programs

A central question to the usefulness of surveys for estimating population trends is whether the surveys adequately represent the biological communities that are being monitored. There are two approaches to address this issue; the first is to statistically adjust site occupancy using species detection probabilities, and the second is to determine the minimum sampling effort required to adequately represent the communities. We focused on the latter approach, using data from two anuran monitoring programs, the Ontario Backyard Frog survey (1992–2001) and the Ontario Bait Frog survey (2001–2003). We determined the minimum sampling effort required to adequately represent the anuran community, and demonstrated the pitfalls of examining population trends when detection probabilities are less than one and vary either temporally or spatially. We found that approximately 12 and 24 randomly sampled nights were required to detect 80% and 90% of species richness, respectively. Detection probabilities varied among species, and were highest for spring peepers (Pseudacris crucifer) and green frogs (Rana clamitans), and lowest for wood frogs (Rana sylvatica) and northern leopard frogs (Rana pipiens). Variation in detection probabilities is likely associated with species specific differences in calling strategies and breeding periods. Anuran monitoring programs that use three stratified sampling periods require site occupancies to be adjusted using detection probabilities in order to adequately represent anuran communities. Failing to account for differences in detection probabilities may result in false significant differences in site occupancy rates. The issues raised here are not limited to monitoring anurans, but are suitable for surveys of many taxa.

Stream salamanders as indicators of stream quality in Maryland, USA

Biological indicators are critical to the protection of small, headwater streams and the ecological values they provide. Maryland and other state monitoring programs have determined that fish indicators are ineffective in small streams, where stream salamanders may replace fish as top predators. Because of their life history, physiology, abundance, and ubiquity, stream salamanders are likely representative of biological integrity in these streams. The goal of this study was to determine whether stream salamanders are effective indicators of ecological conditions across biogeographic regions and gradients of human disturbance. During the summers of 2001 and 2002, we intensively surveyed for stream salamanders at 76 stream sites located west of the Maryland Coastal Plain, sites also monitored by the Maryland Biological Stream Survey (MBSS) and City of Gaithersburg. We found 1,584 stream salamanders, including all eight species known in Maryland, using two 15 × 2 m transects and two 4 m2 quadrats that spanned both stream bank and channel. We performed removal sampling on transects to estimate salamander species detection probabilities, which ranged from 0.67-0.85. Stepwise regressions identified 15 of 52 non-salamander variables, representing water quality, physical habitat, land use, and biological conditions, which best predicted salamander metrics. Indicator development involved (1) identifying reference (non-degraded) and degraded sites (using percent forest, shading, riparian buffer width, aesthetic rating, and benthic macroinvertebrate and fish indices of biotic integrity); (2) testing 12 candidate salamander metrics (representing species richness and composition, abundance, species tolerance, and reproductive function) for their ability to distinguish reference from degraded sites; and (3) combining metrics into an index that effectively discriminated sites according to known stream conditions. Final indices for Highlands, Piedmont, and Non-Coastal Plain regions comprised four metrics: number of species, number of salamanders, number of intolerant salamanders, and number of adult salamanders, producing classification efficiencies between 87% and 90%. Partial validation of these indices was obtained when a test of the number of salamanders metric produced an 82% correct classification of 618 MBSS sites surveyed in 1995-97. This study supports the use of stream salamander monitoring and a composite stream salamander index of biotic integrity (SS-IBI) to determine stream quality in Maryland.

DISENTANGLING SAMPLING AND ECOLOGICAL EXPLANATIONS UNDERLYING SPECIES–AREA RELATIONSHIPS

We used a probabilistic approach to address the influence of sampling ar- tifacts on the form of species-area relationships (SARs). We developed a model in which the increase in observed species richness is a function of sampling effort exclusively. We assumed that effort depends on area sampled, and we generated species-area curves under that model. These curves can be realistic looking. We then generated SARs from avian data, comparing SARs based on counts with those based on richness estimates. We used an approach to estimation of species richness that accounts for species detection probability and, hence, for variation in sampling effort. The slopes of SARs based on counts are steeper than those of curves based on estimates of richness, indicating that the former partly reflect failure to account for species detection probability. SARs based on estimates reflect eco- logical processes exclusively, not sampling processes. This approach permits investigation of ecologically relevant hypotheses. The slope of SARs is not influenced by the slope of the relationship between habitat diversity and area. In situations in which not all of the species are detected during sampling sessions, approaches to estimation of species richness integrating species detection probability should be used to investigate the rate of increase in species richness with area.

Closed mark-recapture models to estimate species richness: An example using data on epigeal spiders

Species richness is a fundamental ecological property. The problem of estimating the number of species is quite similar to that of estimating the population size of a single species. Some authors of mark-recapture statistics have proposed using some of these methods to estimate species richness. This necessitates understanding how the recording probabilities of individuals differ from those of species. In particular, the species of a species pool are likely to exhibit a wide range of recording probabilities. Depending on sampling conditions, temporal or spatial variation in species detection probability may also occur, making model M th estimators particularly useful. Empirical detection probabilities and estimates of species numbers using three coverage, one point, and two jackknife estimators are presented for series of spatial and temporal trapping occasions of epigeal spiders.

Inferences about nested subsets structure when not all species are detected

Comparisons of species composition among isolated ecological communities of different size have often provided evidence that the species in communities with lower species richness form nested subsets of the species in larger communities. In the vast majority of studies, the question of nested subsets has been addressed using information on presence‐absence, where a “0” is interpreted as the absence of a given species from a given location. Most of the methodological discussion in earlier studies investigating nestedness concerns the approach to generation of model‐based matrices corresponding to the null hypothesis of a nonnested pattern. However, it is most likely that in many situations investigators cannot detect all the species present in the location sampled. The possibility that zeros in incidence matrices reflect nondetection rather than absence of species has not been considered in studies addressing nested subsets, even though the position of zeros in these matrices forms the basis of earlier inference methods. These sampling artifacts are likely to lead to erroneous conclusions about both variation over space in species richness, and the degree of similarity of the various locations. Here we propose an approach to investigation of nestedness, based on statistical inference methods explicitly incorporating species detection probability, that take into account the probabilistic nature of the sampling process. We use presence‐absence data collected under Pollock's robust capture‐recapture design, and resort to an estimator of species richness originally developed for closed populations to assess the proportion of species shared by different locations. We develop testable predictions corresponding to the null hypothesis of a nonnested pattern, and an alternative hypothesis of perfect nestedness. We also present an index for assessing the degree of nestedness of a system of ecological communities. We illustrate our approach using avian data from the North American Breeding Bird Survey collected in Florida Keys.