Integrating high-speed videos in capture-mark-recapture studies of insects.
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ABSTRACT:
SUBMITTER: Khelifa R
PROVIDER: S-EPMC8207387 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Recently developed capture-mark-recapture methods allow us to account for capture heterogeneity among individuals in the form of discrete mixtures and continuous individual random effects. In this article, we used simulations and two case studies to evaluate the effectiveness of continuously distributed individual random effects at removing potential bias due to capture heterogeneity, and to evaluate in what situation the added complexity of these models is justified. Simulations and case studies showed that ignoring individual capture heterogeneity generally led to a small negative bias in survival estimates and that individual random effects effectively removed this bias. As expected, accounting for capture heterogeneity also led to slightly less precise survival estimates. Our case studies also showed that accounting for capture heterogeneity increased in importance towards the end of study. Though ignoring capture heterogeneity led to a small bias in survival estimates, such bias may greatly impact management decisions. We advocate reducing potential heterogeneity at the sampling design stage. Where this is insufficient, we recommend modelling individual capture heterogeneity in situations such as when a large proportion of the individuals has a low detection probability (e.g. in the presence of floaters) and situations where the most recent survival estimates are of great interest (e.g. in applied conservation).
| S-EPMC3639964 | biostudies-literature
Project description:Population parameters of poorly marked gregarious species are difficult to estimate. This is the case for common dolphins (Delphinus sp.), a genus known for its lack of distinctive marks resulting in a low mark ratio. Furthermore, the widespread nature of common dolphins results in low recaptures. We developed reliable photo-identification protocols to ensure accurate identification of individuals in the Hauraki Gulf, New Zealand. These protocols combined the use of nicks and notches and pigmentation patterns for identification and included the development of a distinctiveness threshold. The data were further stratified by the level of distinctiveness of each individual (as distinctive or highly-distinctive). Photo-identification surveys were conducted from January 2010 to December 2013. Mark-recapture techniques were implemented through a POPAN super-population approach to estimate seasonal apparent survival, capture probability and abundance of dolphins. A total of 2,083 unique adult common dolphins were identified, 51.3% were classified as D1 (highly distinctive; n = 1,069) and 48.7% as D2 (distinctive; n = 1,014). Of all individuals identified, 34.3% (n = 704) were re-sighted over subsequent years. The proportion of marked dolphins (when compared to unmarked dolphins) was 26.3% for D1 and 46.4% for D1 & D2, respectively. Apparent survival was estimated at 0.767 (CI = 0.694-0.827) for D1 animals, and 0.796 (CI = 0.729-0.850) for D1 & D2 combined. For D1 only, seasonal abundance varied from 732 (CI = 460-1,177) in autumn 2010 to 5,304 (CI = 4,745-5,930) in spring 2013. While the inclusion of D2 individuals may offer a more precise estimate of total abundance, the inability to determine additional sources of bias (for example, arising from under or overestimated mark ratios) meant that estimates for D1 individuals were deemed the least biased for this population. The photo-identification protocol, stratification of the data and steps taken to eliminate potential model violations provided a useful and novel approach to estimate population parameters for common dolphins. These approaches could be implemented for other large gregarious populations (≥500 individuals) of animals with poor natural markings.
| S-EPMC6040702 | biostudies-literature
Project description:It is necessary to estimate the population abundance of deer for managing their populations. However, most estimates are from high-density populations inhabiting the forests of North America or Europe; there is currently a lack of necessary knowledge regarding low-density deer populations in different forest habitats. In this article, we used fecal DNA based on the capture-mark-recapture method to estimate the population abundance of Siberian roe deer (Capreolus pygargus) in Liangshui National Nature Reserve in the Lesser Xing'an Mountains, northeast China, where the deer population was found to be of a low density by limited studies. We used a robust survey design to collect 422 fecal pellet groups in 2016 and extracted DNA from those samples, generating 265 different genotypes; we thus identified 77 deer individuals based on six microsatellite markers (Roe1, Roe8, Roe9, BM757, MB25 and OarFCB304). With capture and recapture records of these 77 individuals, the abundance of roe deer was estimated to be 87 deer (80-112, 95% CI) using the Program CAPTURE. Using an effective sampling area which resulted from the mean maximum recapture distance (MMRD), we converted the population abundance to a density of 2.9 deer/km2 (2.7-3.7, 95% CI). Our study estimated the roe deer population abundance by a feces-based capture-mark-recapture approach in northeast China, successfully demonstrating the applicability of non-invasive genetic sampling in monitoring populations of deer in this area, which contributes to the development of low-density deer population ecology and management.
| S-EPMC7401656 | biostudies-literature
Project description:Error-tolerant likelihood-based match calling presents a promising technique to accurately identify recapture events in genetic mark-recapture studies by combining probabilities of latent genotypes and probabilities of observed genotypes, which may contain genotyping errors. Combined with clustering algorithms to group samples into sets of recaptures based upon pairwise match calls, these tools can be used to reconstruct accurate capture histories for mark-recapture modelling. Here, we assess the performance of a recently introduced error-tolerant likelihood-based match-calling model and sample clustering algorithm for genetic mark-recapture studies. We assessed both biallelic (i.e. single nucleotide polymorphisms; SNP) and multiallelic (i.e. microsatellite; MSAT) markers using a combination of simulation analyses and case study data on Pacific walrus (Odobenus rosmarus divergens) and fishers (Pekania pennanti). A novel two-stage clustering approach is demonstrated for genetic mark-recapture applications. First, repeat captures within a sampling occasion are identified. Subsequently, recaptures across sampling occasions are identified. The likelihood-based matching protocol performed well in simulation trials, demonstrating utility for use in a wide range of genetic mark-recapture studies. Moderately sized SNP (64+) and MSAT (10-15) panels produced accurate match calls for recaptures and accurate non-match calls for samples from closely related individuals in the face of low to moderate genotyping error. Furthermore, matching performance remained stable or increased as the number of genetic markers increased, genotyping error notwithstanding.
| S-EPMC5210676 | biostudies-literature
Project description:Spatial capture-recapture (SCR) models have become the preferred tool for estimating densities of carnivores. Within this family of models are variants requiring identification of all individuals in each encounter (SCR), a subset of individuals only (generalized spatial mark-resight, gSMR), or no individual identification (spatial count or spatial presence-absence). Although each technique has been shown through simulation to yield unbiased results, the consistency and relative precision of estimates across methods in real-world settings are seldom considered. We tested a suite of models ranging from those only requiring detections of unmarked individuals to others that integrate remote camera, physical capture, genetic, and global positioning system (GPS) data into a hybrid model, to estimate population densities of black bears, bobcats, cougars, and coyotes. For each species, we genotyped fecal DNA collected with detection dogs during a 20-d period. A subset of individuals from each species was affixed with GPS collars bearing unique markings and resighted by remote cameras over 140 d contemporaneous with scat collection. Camera-based gSMR models produced density estimates that differed by <10% from genetic SCR for bears, cougars, and coyotes once important sources of variation (sex or behavioral status) were controlled for. For bobcats, SCR estimates were 33% higher than gSMR. The cause of the discrepancies in estimates was likely attributable to challenges designing a study compatible for species with disparate home range sizes and the difficulty of collecting sufficient data in a timeframe in which demographic closure could be assumed. Unmarked models estimated densities that varied greatly from SCR, but estimates became more consistent in models wherein more individuals were identifiable. Hybrid models containing all data sources exhibited the most precise estimates for all species. For studies in which only sparse data can be obtained and the strictest model assumptions are unlikely to be met, we suggest researchers use caution making inference from models lacking individual identity. For best results, we further recommend the use of methods requiring at least a subset of the population is marked and that multiple data sets are incorporated when possible.
| S-EPMC9286611 | biostudies-literature
Project description:Trap-awareness and related phenomena whereby successive capture events are not independent is a feature of the majority of capture-recapture studies. This phenomenon was up to now difficult to incorporate in open population models and most authors have chosen to neglect it although this may have damaging consequences. Focusing on the situation where animals exhibit a trap response at the occasion immediately following one where they have been trapped but revert to their original naïve state if they are missed once, we show that trap-dependence is more naturally viewed as a state transition and is amenable to the current models of capture-recapture. This approach has the potential to accommodate lasting or progressively waning trap effects.
| S-EPMC3292565 | biostudies-literature
Project description:Photographic capture-recapture is a valuable tool for obtaining demographic information on wildlife populations due to its noninvasive nature and cost-effectiveness. Recently, several computer-aided photo-matching algorithms have been developed to more efficiently match images of unique individuals in databases with thousands of images. However, the identification accuracy of these algorithms can severely bias estimates of vital rates and population size. Therefore, it is important to understand the performance and limitations of state-of-the-art photo-matching algorithms prior to implementation in capture-recapture studies involving possibly thousands of images. Here, we compared the performance of four photo-matching algorithms; Wild-ID, I3S Pattern+, APHIS, and AmphIdent using multiple amphibian databases of varying image quality. We measured the performance of each algorithm and evaluated the performance in relation to database size and the number of matching images in the database. We found that algorithm performance differed greatly by algorithm and image database, with recognition rates ranging from 100% to 22.6% when limiting the review to the 10 highest ranking images. We found that recognition rate degraded marginally with increased database size and could be improved considerably with a higher number of matching images in the database. In our study, the pixel-based algorithm of AmphIdent exhibited superior recognition rates compared to the other approaches. We recommend carefully evaluating algorithm performance prior to using it to match a complete database. By choosing a suitable matching algorithm, databases of sizes that are unfeasible to match "by eye" can be easily translated to accurate individual capture histories necessary for robust demographic estimates.
| S-EPMC5552938 | biostudies-other
Project description:Capture-recapture (CR) models are an essential tool for estimating demographic parameters in most animal and some plant populations. To avoid drawing incorrect conclusions in any statistical inference, a crucial prerequisite is to assess the goodness of fit of a general model to the data. In CR models, a frequent cause of lack of fit, is the so-called transience effect, which is due to a lower expectation of re-observation of individuals marked for the first time as compared to other individuals. The transience effect may result either from different biological causes or from the sampling procedure. A transience effect is usually treated by distinguishing at least two age-classes in the survival probability, but other approaches may be more suitable. Here we develop a conceptual and analytical framework for including a transience effect in capture-recapture models. We show the implementation of two additional parametrizations that incorporate a transience effect. With these parametrizations, we can directly estimate the "transience probability" defined as the probability that a newly caught individual disappear from the population beyond what is expected based on the behavior of the previously caught individuals in the same sample. Additionally, these parametrizations allow testing biological hypotheses concerning drivers affecting this probability. Results from our case study show differences between parametrizations, with the parametrization most currently used giving different estimates, especially when including covariates. We advocate for a unifying framework for treating a transience effect, that helps clarifying the ideas and terminology, and where the biological reasons should be the rule for choosing the appropriate analytical procedure. This framework will also open new and powerful ways for the detection and exploration of ecological processes such as the costs of the first reproduction or the deleterious effects of some types of marking.
| S-EPMC6752852 | biostudies-literature
Project description:BackgroundParasite evolution is hypothesized to select for levels of parasite virulence that maximise transmission success. When host population densities fluctuate, low levels of virulence with limited impact on the host are expected, as this should increase the likelihood of surviving periods of low host density. We examined the effects of Morogoro arenavirus on the survival and recapture probability of multimammate mice (Mastomys natalensis) using a seven-year capture-mark-recapture time series. Mastomys natalensis is the natural host of Morogoro virus and is known for its strong seasonal density fluctuations.ResultsAntibody presence was negatively correlated with survival probability (effect size: 5-8% per month depending on season) but positively with recapture probability (effect size: 8%).ConclusionsThe small negative correlation between host survival probability and antibody presence suggests that either the virus has a negative effect on host condition, or that hosts with lower survival probability are more likely to obtain Morogoro virus infection, for example due to particular behavioural or immunological traits. The latter hypothesis is supported by the positive correlation between antibody status and recapture probability which suggests that risky behaviour might increase the probability of becoming infected.
| S-EPMC5806307 | biostudies-literature
Project description:Mark-recapture techniques have been widely used and specialized to study organisms throughout the field of biology. To mark-recapture ticks (Ixodida), we have created a simple method to mark ticks using nail polish applied with an insect pin secured in a pencil that allows for a variety of questions to be answered. For measuring tick control efficacy, estimating population estimates, or measuring movement of ticks, this inexpensive mark-recapture method has been easily applied in the field and in the lab to provide useful data to answer a variety of questions about ticks.
| S-EPMC7604875 | biostudies-literature