Variation In Detection Probability Research Articles

Predicting above-ground density and distribution of small mammal prey species at large spatial scales.

Grassland and shrub-steppe ecosystems are increasingly threatened by anthropogenic activities. Loss of native habitats may negatively impact important small mammal prey species. Little information, however, is available on the impact of habitat variability on density of small mammal prey species at broad spatial scales. We examined the relationship between small mammal density and remotely-sensed environmental covariates in shrub-steppe and grassland ecosystems in Wyoming, USA. We sampled four sciurid and leporid species groups using line transect methods, and used hierarchical distance-sampling to model density in response to variation in vegetation, climate, topographic, and anthropogenic variables, while accounting for variation in detection probability. We created spatial predictions of each species’ density and distribution. Sciurid and leporid species exhibited mixed responses to vegetation, such that changes to native habitat will likely affect prey species differently. Density of white-tailed prairie dogs (Cynomys leucurus), Wyoming ground squirrels (Urocitellus elegans), and leporids correlated negatively with proportion of shrub or sagebrush cover and positively with herbaceous cover or bare ground, whereas least chipmunks showed a positive correlation with shrub cover and a negative correlation with herbaceous cover. Spatial predictions from our models provide a landscape-scale metric of above-ground prey density, which will facilitate the development of conservation plans for these taxa and their predators at spatial scales relevant to management.

Diel Variation in Detection and Vocalization Rates of King (Rallus elegans) and Clapper (Rallus crepitans) Rails in Intracoastal Waterways

Abstract. Surveys for secretive marsh birds could be improved with refinements to address regional and species-specific variation in detection probabilities and optimal times of day to survey. Diel variation in relation to naive occupancy, detection rates, and vocalization rates of King (Rallus elegans) and Clapper (R. crepitans) rails were studied in intracoastal waterways in Virginia, USA. Autonomous acoustic devices recorded vocalizations of King and Clapper rails at 75 locations for 48-hr periods within a marsh complex. Naive King and Clapper rail occupancy did not vary hourly at either the marsh or the study area level. Combined King and Clapper rail detections and vocalizations varied across marshes, decreased as the sampling season progressed, and, for detections, was greatest during low rising tides (P < 0.01). Hourly variation in vocalization and detection rates did not show a pattern but occurred between 7.8% of pairwise comparisons for detections and 10.5% of pairwise comparisons for vocalizati...

Using areas of known occupancy to identify sources of variation in detection probability of raptors: taking time lowers replication effort for surveys.

Species occurring at low density can be difficult to detect and if not properly accounted for, imperfect detection will lead to inaccurate estimates of occupancy. Understanding sources of variation in detection probability and how they can be managed is a key part of monitoring. We used sightings data of a low-density and elusive raptor (white-headed vulture Trigonoceps occipitalis) in areas of known occupancy (breeding territories) in a likelihood-based modelling approach to calculate detection probability and the factors affecting it. Because occupancy was known a priori to be 100%, we fixed the model occupancy parameter to 1.0 and focused on identifying sources of variation in detection probability. Using detection histories from 359 territory visits, we assessed nine covariates in 29 candidate models. The model with the highest support indicated that observer speed during a survey, combined with temporal covariates such as time of year and length of time within a territory, had the highest influence on the detection probability. Averaged detection probability was 0.207 (s.e. 0.033) and based on this the mean number of visits required to determine within 95% confidence that white-headed vultures are absent from a breeding area is 13 (95% CI: 9–20). Topographical and habitat covariates contributed little to the best models and had little effect on detection probability. We highlight that low detection probabilities of some species means that emphasizing habitat covariates could lead to spurious results in occupancy models that do not also incorporate temporal components. While variation in detection probability is complex and influenced by effects at both temporal and spatial scales, temporal covariates can and should be controlled as part of robust survey methods. Our results emphasize the importance of accounting for detection probability in occupancy studies, particularly during presence/absence studies for species such as raptors that are widespread and occur at low densities.

Use ofAtlanticForest protected areas by free‐ranging dogs: estimating abundance and persistence of use

AbstractWorldwide, domestic dogs (Canis familiaris) are one of the most common carnivoran species in natural areas and their populations are still increasing. Dogs have been shown to impact wildlife populations negatively, and their occurrence can alter the abundance, behavior, and activity patterns of native species. However, little is known about abundance and density of the free‐ranging dogs that use protected areas. Here, we used camera trap data with an open‐robust design mark–recapture model to estimate the number of dogs that used protected areas in Brazilian Atlantic Forest. We estimated the time period these dogs used the protected areas, and explored factors that influenced the probability of continued use (e.g., season, mammal richness, proportion of forest), while accounting for variation in detection probability. Dogs in the studied system were categorized as rural free‐ranging, and their abundance varied widely across protected areas (0–73 individuals). Dogs used protected areas near human houses for longer periods (e.g., &gt;50% of sampling occasions) compared to more distant areas. We found no evidence that their probability of continued use varied with season or mammal richness. Dog detection probability decreased linearly among occasions, possibly due to the owners confining their dogs after becoming aware of our presence. Comparing our estimates to those for native carnivoran, we found that dogs were three to 85 times more abundant than ocelots (Leopardus pardalis), two to 25 times more abundant than puma (Puma concolor), and approximately five times more abundant than the crab‐eating fox (Cerdocyon thous). Combining camera trapping data with modern mark–recapture methods provides important demographic information on free‐ranging dogs that can guide management strategies to directly control dogs' abundance and ranging behavior.

Improved analysis of lek count data using N‐mixture models

ABSTRACTThe greater sage‐grouse (Centrocercus urophasianus) is a species of conservation concern in western North America that is experiencing ongoing population declines due to habitat loss, energy development, disease, and other factors. It is therefore imperative to have robust estimates of population size and trends in this species across its range as part of monitoring, management, and conservation efforts. Greater sage‐grouse are typically monitored by conducting counts of males at breeding leks, but the relationship between this index and true population size is unknown. In an attempt to improve the analyses of this population index, we examined the potential of N‐mixture models to evaluate population size, detection probability, and trend in greater sage‐grouse using lek count data collected over space and time. We used simulations to test how well the models recovered abundance and growth rate parameters with increasingly sparse count data. We found that the models correctly recovered parameters for scenarios with both constant and variable detection probability, even with up to 90% of the data missing, where 95% of simulations contained the true population growth rate parameter value within the 95% credible interval. We then applied the model to 13 years of lek count data from Montana, USA, collected at 2 spatial scales. Statewide, we determined that the population was decreasing by 7% per year on average over this time period, and that mean annual detection probability ranged from 0.20 to 0.76. In contrast, regressions of naïve counts over time showed a 9% annual decrease in population size with a confidence interval spanning 0. High interannual variability in detection probability demonstrates that naïve counts do not accurately measure interannual variability in population size, and may lead to misleading trends in population size over time. Although N‐mixture models still have limitations, they are a promising approach for conducting robust analyses of population trends for species that aggregate at discrete breeding sites, even when datasets are sparse or uneven. © 2016 The Wildlife Society.

Estimating Riverwide Abundance of Juvenile Fish Populations: How Much Sampling is Enough?

AbstractEstimating riverwide abundance of juvenile fish populations is challenging because detection probability is typically low and juveniles can be patchily distributed over large areas. We used a hierarchical Bayesian model to estimate the abundance of juvenile steelhead Oncorhynchus mykiss in two rivers in British Columbia over 3 years based on a multigear, two‐phase sampling design. These estimates were used to drive a simulation model to evaluate how the precision of abundance estimates varied with the number of single‐pass index and mark–recapture sites that were sampled, the proportion of shoreline sampled, and the mean and variation of detection probability and fish density across sites. The extent of variation in fish densities across index sites was the most important factor influencing the precision of river‐wide abundance estimates, and increasing the number of index sites was the best approach to reduce variability in abundance estimates. River size, which controls the proportion of habitat sampled for a given level of sampling effort, had a moderate effect on precision, but only when the extent of site‐to‐site variation in fish density was high. Factors affecting detection probability, such as the number of mark–recapture sites, the mean detection probability, or the extent of variation in detection probability across sites, had much less influence on precision of abundance estimates unless the proportion of river sampled was high. Hierarchical Bayesian models are no substitute for collecting informative data, but they improve our understanding of variance structure, which is critical for providing realistic estimates of uncertainty and designing informative and efficient sampling programs.Received July 16, 2015; accepted October 7, 2015 Published online March 8, 2016

Effect of Test Coverage and Change Point on Software Reliability Growth Based on Time Variable Fault Detection Probability

In past four decades, many software reliability growth models (SRGMs) have been proposed to enhance the reliability of the software system. During the testing process potential fault sites are sensitized to detect the faults. Fault detection probability increases as learning and maturity of the testing personnel increases. Therefore, in this paper a time variant fault detection probability has been introduced and integrated into s-shaped coverage SRGM. Experimental results shows that the proposed model is better and will be helpful to improve the accuracy of the software reliability estimation.

Detection of a global aquatic invasive amphibian, Xenopus laevis, using environmental DNA

Detection is crucial in the study and control of invasive species but it may be limited by methodological issues. In amphibians, classical survey techniques exhibit variable detection probability depending on species and are often constrained by climatic conditions often requiring several site visits. Furthermore, detection may be reduced at low density because probability capture (passive traps), or activity (acoustic surveys) drop. Such limits may impair the study of invasive species because low density is typical of the onset of colonisation on a site. In the last few years, environmental DNA (eDNA) methods have proved their ability to detect the presence of aquatic species. We developed here an eDNA method to detectXenopus laevisin ponds. This austral African species is now present worldwide because of its use in biology and as a pet. Populations have settled and expanded on several continents so that it is now considered as one of the major invasive amphibians in the World. We detected the presence ofX. laevisat density as low as 1 ind/100 m2and found a positive relationship between density in ponds and rate of DNA amplification. Results show that eDNA can be successfully applied to survey invasive populations ofX. laeviseven at low density in order to confirm suspected cases of introduction, delimit the expansion of a colonized range, or monitor the efficiency of a control program.

Vertical and temporal variability in the probability of detection of fruit-feeding butterflies and moths (Lepidoptera) in tropical forest

One important source of variation present in all biodiversity sampling protocols is species detection probability (i.e. the probability of observing a species, given that it is present at a site). In tropical forests, many species have very low probability of detection, and thus they can be easily overlooked. Measuring the detection probability (detectability) of these species is important to determine the sampling effort required to accurately record them. In the present study, the variation of detectability of fruit-feeding butterflies and moths between strata (understory vs. canopy), temporally across sampling months, and in relation to observed abundance were examined in the Amazon and Atlantic forests using models of logistic regression. These results enabled the estimation of the sampling effort required to detect a given fraction of the total assemblage. Species detectability was positively correlated with observed abundance for both butterflies and moths. In the Amazon, most species were more detectable in a specific stratum (canopy or understory). Biblidinae, Charaxinae and Satyrini showed temporal variation in detection probability in Atlantic Forest, with distinct peaks during July–August, November, and March. In contrast, Brassolini and Coeini showed peak detectability in January and March, respectively. The vertical and temporal variation in detection probability means that sampling effort must be applied strategically to the correct seasons and strata to improve the accuracy of results. The estimated minimum sampling effort to detect 70% of the species present in these tropical forests is 428 trap-days in Atlantic Forest and 1435 trap-days in the Central Amazon forest.

Movement of invasive adult lionfish Pterois volitans using telemetry: importance of controls to estimate and explain variable detection probabilities

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 527:205-220 (2015) - DOI: https://doi.org/10.3354/meps11241 Movement of invasive adult lionfish Pterois volitans using telemetry: importance of controls to estimate and explain variable detection probabilities Nathan M. Bacheler1,*, Paula E. Whitfield2, Roldan C. Muñoz1, Brett B. Harrison2, Craig A. Harms3, Christine A. Buckel2 1Southeast Fisheries Science Center, National Marine Fisheries Service, NOAA, 101 Pivers Island Road, Beaufort, North Carolina 28516, USA 2Center for Coastal Fisheries and Habitat Research, NOAA, 101 Pivers Island Road, Beaufort, North Carolina 28516, USA 3Department of Clinical Sciences and Center for Marine Sciences and Technology, North Carolina State University, 303 College Circle, Morehead City, North Carolina 28557, USA *Corresponding author: nate.bacheler@noaa.gov ABSTRACT: The Indo-Pacific lionfish Pterois volitans has invaded western Atlantic Ocean coastal habitats over the past 2 decades and has the potential to cause major ecological changes in reef fish communities. While many aspects of lionfish ecology in their invaded range have been examined, there is a paucity of information on movements of lionfish, particularly adults. We surgically implanted ultrasonic transmitters into 25 lionfish at a natural hard bottom area off North Carolina (USA) in December 2008 and February 2009, and used an array of remote underwater receivers to monitor movements in the study area for up to 6 mo. We also affixed a control transmitter in the study area to assess changes in transmitter detection rate as a function of multiple variables, and used a generalized additive model to show that the control transmitter detection rate declined with time, increasing water temperature, and increasing wave period. Despite variable detection probabilities, we found that telemetered lionfish remaining in the study area displayed high site fidelity to areas no broader than 400 m in diameter; daily movements were nearly always <150 m. By estimating variable detection rates of transmitters and lionfish movements, we provided information that can be useful in understanding the spatial scale of lionfish impact and developing management or mitigation strategies for this invasive species. KEY WORDS: Indo-Pacific lionfish · Invasive species · Acoustic tagging · Range test · Ultrasonic transmitter · Telemetry · Movements · Receiver array Full text in pdf format PreviousNextCite this article as: Bacheler NM, Whitfield PE, Muñoz RC, Harrison BB, Harms CA, Buckel CA (2015) Movement of invasive adult lionfish Pterois volitans using telemetry: importance of controls to estimate and explain variable detection probabilities. Mar Ecol Prog Ser 527:205-220. https://doi.org/10.3354/meps11241 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 527. Online publication date: May 07, 2015 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2015 Inter-Research.

Recreation changes the use of a wild landscape by corvids

ABSTRACT As urban areas have grown in population, use of nearby natural areas for outdoor recreation has also increased, potentially influencing bird distribution in landscapes managed for conservation. Members of the family Corvidae (crows, ravens, jays, and magpies) have strong interactions with humans and may be directly affected by recreation in wild landscapes. In Mount Rainier National Park, we evaluated the effects of vegetation, visitor use, and the availability of human-subsidized food on the use of landscape features by 4 corvid species: Steller's Jay (Cyanocitta stelleri), Gray Jay (Perisoreus canadensis), Common Raven (Corvus corax), and Clark's Nutcracker (Nucifraga columbiana). We conducted >1,400 point counts across areas that varied in habitat and in the degree of human recreational impact. We calculated predicted occupancy values while allowing for variation in detection probability. In addition to species-specific suites of vegetation and landscape variables, we found that patterns of hu...

Temporally adaptive sampling: a case study in rare species survey design with marbled salamanders (Ambystoma opacum).

Improving detection rates for elusive species with clumped distributions is often accomplished through adaptive sampling designs. This approach can be extended to include species with temporally variable detection probabilities. By concentrating survey effort in years when the focal species are most abundant or visible, overall detection rates can be improved. This requires either long-term monitoring at a few locations where the species are known to occur or models capable of predicting population trends using climatic and demographic data. For marbled salamanders (Ambystoma opacum) in Massachusetts, we demonstrate that annual variation in detection probability of larvae is regionally correlated. In our data, the difference in survey success between years was far more important than the difference among the three survey methods we employed: diurnal surveys, nocturnal surveys, and dipnet surveys. Based on these data, we simulate future surveys to locate unknown populations under a temporally adaptive sampling framework. In the simulations, when pond dynamics are correlated over the focal region, the temporally adaptive design improved mean survey success by as much as 26% over a non-adaptive sampling design. Employing a temporally adaptive strategy costs very little, is simple, and has the potential to substantially improve the efficient use of scarce conservation funds.

The influence of road characteristics and species on detection probabilities of carnivore faeces

Context Determining reliable estimates of carnivore population size and distributions are paramount for developing informed conservation and management plans. Traditionally, invasive sampling has been employed to monitor carnivores, but non-invasive sampling has the advantage of not needing to capture the animal and is generally less expensive. Faeces sampling is a common non-invasive sampling technique and future use is forecasted to increase due to the low costs and logistical ease of sampling, and more advanced techniques in landscape and conservation genetics. For many species, faeces sampling often occurs on or alongside roads. Despite the commonality of road-based faeces sampling, detectability issues are often not addressed. Aim We sought to test whether faeces detection probabilities varied by species – coyote (Canis latrans) versus kit fox (Vulpes macrotis) – and to test whether road characteristics influenced faeces detection probabilities. Methods We placed coyote and kit fox faeces along roads, quantified road characteristics, and then subsequently conducted ‘blind’ road-based faeces detection surveys in Utah during 2012 and 2013. Technicians that surveyed the faeces deposition transects had no knowledge of the locations of the placed faeces. Key results Faeces detection probabilities for kit foxes and coyotes were 45% and 74%, respectively; larger faeces originated from coyotes and were more readily detected. Misidentification of placed faeces was rare and did not differ by species. The width of survey roads and the composition of a road’s surface influenced detection probabilities. Conclusion We identified factors that can influence faeces detection probabilities. Not accounting for variable detection probabilities of different species or not accounting for or reducing road-based variables influencing faeces detection probabilities could hamper reliable counts of mammalian faeces, and could potentially reduce precision of population estimates derived from road-based faeces deposition surveys. Implications We recommend that wildlife researchers acknowledge and account for imperfect faeces detection probabilities during faecal sampling. Steps can be taken during study design to improve detection probabilities, and during the analysis phase to account for variable detection probabilities.

Probit models for capture–recapture data subject to imperfect detection, individual heterogeneity and misidentification

As noninvasive sampling techniques for animal populations have become more popular, there has been increasing interest in the development of capture-recapture models that can accommodate both imperfect detection and misidentification of individuals (e.g., due to genotyping error). However, current methods do not allow for individual variation in parameters, such as detection or survival probability. Here we develop misidentification models for capture-recapture data that can simultaneously account for temporal variation, behavioral effects and individual heterogeneity in parameters. To facilitate Bayesian inference using our approach, we extend standard probit regression techniques to latent multinomial models where the dimension and zeros of the response cannot be observed. We also present a novel Metropolis-Hastings within Gibbs algorithm for fitting these models using Markov chain Monte Carlo. Using closed population abundance models for illustration, we re-visit a DNA capture-recapture population study of black bears in Michigan, USA and find evidence of misidentification due to genotyping error, as well as temporal, behavioral and individual variation in detection probability. We also estimate a salamander population of known size from laboratory experiments evaluating the effectiveness of a marking technique commonly used for amphibians and fish. Our model was able to reliably estimate the size of this population and provided evidence of individual heterogeneity in misidentification probability that is attributable to variable mark quality. Our approach is more computationally demanding than previously proposed methods, but it provides the flexibility necessary for a much broader suite of models to be explored while properly accounting for uncertainty introduced by misidentification and imperfect detection. In the absence of misidentification, our probit formulation also provides a convenient and efficient Gibbs sampler for Bayesian analysis of traditional closed population capture-recapture data.

The road less travelled: assessing variation in mammal detection probabilities with camera traps in a semi-arid biodiversity hotspot

Camera traps are an increasingly popular tool for monitoring medium to large mammals, but the influence of camera trap placement on the detection probabilities of different species has seldom been investigated. In this study we explore the influence of roads on the detection probability of medium to large mammals in three vegetation types in the Little Karoo, an arid biodiversity hotspot. We placed cameras in nine 100 m-long transects, running perpendicular from roads within a conservation area. The camera traps were spaced at ~25 m intervals, and were active for an average of 88 days each. Detection probabilities relative to distance from roads showed extensive variation between species and habitat types. There was no clear relationship between distance from the road and the detection probability of most species and guilds, although carnivore detection probability declined significantly as distance from roads increased in all vegetation types. Our results suggest that there is considerable inter-specific variation in detection probability that is significantly influenced by camera trap location relative to roads. Therefore studies that seek to maximise the detection rates of particular species or guilds (e.g. carnivores) by placing cameras on prominent roads and trails are unlikely to provide reliable estimates of the relative abundance of the broader range of sympatric species; a trend observed elsewhere but hitherto untested in arid environments. We recommend that future studies employ a mixed design of cameras located on- and off-roads to provide better estimates of biodiversity in general and predators specifically.

Estimating Effects of Habitat Characteristics on Abundances of Three Species of Secretive Marsh Birds in Central Florida

Abstract. Wetland loss has led to population declines of many species of North American marsh birds. However, due to the secretive nature of many of these species, there is uncertainty about their population status and habitat requirements. Recently developed techniques, such as the Standardized North American Marsh Bird Monitoring Protocol and analytical methods that account for variable detection probabilities, can be used to improve both the quality and quantity of information about secretive marsh birds. In 2009 and 2010, point counts were conducted using the marsh bird monitoring protocol to count Least Bittern (Ixobrychus exilis), Purple Gallinule (Porphyrio martinica) and Limpkin (Aramus guarauna) in the Kissimmee Chain of Lakes, Florida. Habitat factors thought to influence abundance were compared using competing hierarchical mixture models. Abundance of Least Bittern had a positive relationship with amounts of emergent vegetative cover and interspersion (i.e., vegetation to water edge). Purple Ga...

Lek fidelity and movement among leks by male Greater Sage‐grouse Centrocercus urophasianus: a capture‐mark‐recapture approach

Males in lek mating systems tend to exhibit high fidelity to breeding leks despite substantial evidence of skewed mating success among males. Although movements between leks are often reported to be rare, such movements provide a mechanism for an individual to improve lifetime fitness in response to heterogeneity in reproductive conditions. Additionally, estimates of apparent movements among leks are potentially biased due to unaccounted variation in detection probability across time and space. We monitored breeding male Greater Sage‐grouse Centrocercus urophasianus on 13 leks in eastern Nevada over a 10‐year period, and estimated movement rates among leks using capture‐mark‐recapture methods. We expected that male movement rates among leks would be low, despite predictions of low breeding success for most males, and that detection rates would be highly variable among leks and years. We used a robust design multistate analysis in Program mark to estimate probability of movements among leks, while accounting for imperfect detection of males. Male Sage‐grouse were extremely faithful to their leks; the annual probability of a male moving away from its original lek of capture was approximately 3% (se = 0.01). Detection probabilities varied substantially among leks (range = 0.21–0.95), and among years (range = 0.30–0.76), but remained relatively constant within years at each lek. These results suggest that male Sage‐grouse dispersal is either rare, or consists primarily of dispersal of sub‐adults from their natal areas prior to the breeding season. The study highlights the benefits of robust design multistate models over standard ‘live‐encounter’ analyses, as they not only permit estimation of additional parameters, such as movement rates, but also allow for more precise parameter estimates that are less sensitive to heterogeneity in detection rates. Additionally, as these data were collected using capture‐mark‐recapture methods, our approach to estimating movement rates would be beneficial in systems where radiotagging is detrimental to the study organism.

Partitioning of $$\alpha $$ α and $$\beta $$ β diversity using hierarchical Bayesian modeling of species distribution and abundance

Diversity partitioning is becoming widely used to decompose the total number of species recorded in an area or region \((\gamma )\) into the average number of species within samples \((\alpha )\) and the average difference in species composition \((\beta )\) among samples. Single-value metrics of \(\alpha \) and \(\beta \) diversity are popular because they may be applied at multiple scales and because of their ease in computation and interpretation. Studies thus far, however, have emphasized observed diversity components or comparisons to randomized, null distributions. In addition, prediction of \(\alpha \) and \(\beta \) components using environmental or spatial variables has been limited to more extensive data sets because multiple samples are required to estimate single \(\alpha \) and \(\beta \) components. Lastly, observed diversity components do not incorporate variation in detection probabilities among species or samples. In this study, we used hierarchical Bayesian models of species abundances to provide predictions of \(\alpha \) and \(\beta \) components in species richness and composition using environmental and spatial variables. We illustrate our approach using butterfly data collected from 26 grassland remnants to predict spatially nested patterns of \(\alpha \) and \(\beta \) based on the predicted counts of butterflies. Diversity partitioning using a Bayesian hierarchical model incorporated variation in detection probabilities by butterfly species and habitat patches, and provided prediction intervals for \(\alpha \) and \(\beta \) components using environmental and spatial variables.

Quantifying the Effect of Competition for Detection between Coeluting Peptides on Detection Probabilities in Mass-Spectrometry-Based Proteomics

There are many factors that contribute to the variation in detection probabilities of proteins in LC-MS/MS experiments, and currently little is known about their relative importance. In this study, we analyze the effect of competition for detection between coeluting peptides on peptide detection probability. Using a novel method for estimating peptide detection probabilities, we show that these probabilities can vary by an order of magnitude between peptides that elute from the liquid chromatograph at the same time as many other peptides and those that elute with fewer other peptides. To explore these results, we use a mathematical model to show that competition for detection between peptides is expected to be a major source of missed detections in complex mixtures because there will be many MS/MS scanning intervals that contain more coeluting peptides than can be subjected to MS/MS analysis. Our data and simulation results show that the number of coeluting peptides is a primary determinant of whether a peptide will be detected. In our data, this had a several-fold larger effect on peptide detection probability than did peptide abundance. Furthermore, the distribution of elution times for the most frequently detected peptides was strongly shifted toward values where there were few coeluting peptides, indicating that the number of coeluting peptides is a major determinant of whether a peptide is proteotypic.

Snake co‐occurrence patterns are best explained by habitat and hypothesized effects of interspecific interactions

Snakes often occur in species-rich assemblages, and sympatry is thought to be facilitated primarily by low diet overlap, not interspecific interactions. We selected, a priori, three species pairs consisting of species that are morphologically and taxonomically similar and may therefore be likely to engage in interspecific, consumptive competition. We then examined a large-scale database of snake detection/nondetection data and used occupancy modelling to determine whether these species occur together more or less frequently than expected by chance while accounting for variation in detection probability among species and incorporating important habitat categories in the models. For some snakes, we obtained evidence that the probabilities that habitat patches are used are influenced by the presence of potentially competing congeneric species. Specifically, timber rattlesnakes (Crotalus horridus) were less likely than expected by chance to use areas that also contained eastern diamond-backed rattlesnakes (Crotalus adamanteus) when the proportion of evergreen forest was relatively high. Otherwise, they occurred together more often than expected by chance. Complex relationships were revealed between habitat use, detection probabilities and occupancy probabilities of North American racers (Coluber constrictor) and coachwhips (Coluber flagellum) that indicated the probability of competitive exclusion increased with increasing area of grassland habitat, although there was some model uncertainty. Cornsnakes (Pantherophis guttatus or Pantherophis slowinskii) and ratsnakes (Pantherophis alleghaniensis, Pantherophis spiloides, or Pantherophis obsoletus) exhibited differences in habitat selection, but we obtained no evidence that patterns of use for this species pair were influenced by current interspecific interactions. Overall, our results are consistent with the hypothesis that competitive interactions influence snake assemblage composition; the strength of these effects was affected by landscape-scale habitat features. Furthermore, we suggest that current interspecific interactions may influence snake occupancy, challenging the paradigm that contemporary patterns of snake co-occurrence are largely a function of diet partitioning that arose over evolutionary time.