How to estimate population size in crocodylians? Population ecology of American crocodiles in Coiba Island as study case

Studies on food habits are fundamental to understanding the ecology of a species and its interactions with the community to which it belongs. Among crocodylians, diet affects a variety of biological, physiological, and behavioral characteristics. However, despite having one of the largest distributions across the Americas, some aspects of Crocodylus acutus’ natural history remain poorly studied, particularly in insular areas. We characterized American crocodiles’ food habits in Coiba Island, Panama, assessing ontogenetic dietary variation and dietary overlap by age group and size. We captured and collected stomach content samples from 49 individuals from four transects from March to December 2013. From these samples, we could taxonomically identify three phyla, four subphyla, eight classes, 11 orders, 17 families, 14 genera, and 12 species as prey items. However, not all samples could be identified to the lowest taxon (species), having most of them identified only to family level. Large juveniles had the largest proportion of prey items and subadults the largest proportion of gastroliths and vegetal content. Percent occurrence per major categories (insects, arachnids, crustaceans, fish, reptiles, birds, and mammals) showed crustaceans and insects as the most prominent groups of prey items on this island. Overlapping group analysis showed a reduction in the consumption of invertebrates (crustaceans and insects) as individuals aged. However, these items were the most common throughout all American crocodiles sampled. Dietary overlap analyses showed a likely ontogenetic dietary partitioning with high overlap (>60%) between small and large juveniles and low overlap (<30%) among small juveniles, subadults, and adults. To date, 71 species have been reported as prey items for American crocodiles. However, relying on prey items identified only to genus, we had at least 97 prey items. Thus, C. acutus can be defined as generalist with a broad spectrum of prey inhabiting all types of habitats and having all types of consumption classifications. Overall, American crocodiles inhabiting coastal areas present some differences in both dietary composition and structure with those dwelling inland and freshwater habitats as well as an interindividual diet variation, which reflects the plasticity and adaptability of C. acutus to a variety of conditions.

Global biodiversity hotspots are rich in endemic insect species, many of which are threatened by the ongoing anthropogenic pressures on their habitats. The Cape region (South Africa) is one of these biodiversity hotspots, maintaining a high number of endemics. However, the ecology of most insect species in this region remains poorly understood. The two Orthoptera species Betiscoides meridionalis and Betiscoides parva are endemic to the Cape region and specialized on restio vegetation. They are threatened by increasing wildfire frequencies and invasions of non-native plant species. However, this information has been inferred from habitat changes, whereas no ecological study on these species has been conducted since they have been described. In order to facilitate conservation management, information on the ecology of these species is urgently required. The aim of our study was (1) to obtain data on the population ecology (particularly population sizes and mobility), and (2) to study the behavior of both species in response to environmental factors. For this purpose a mark-recapture-study and an observational behavior study were conducted. Both species had small population sizes and a low mobility with males moving greater distances than females. Wind had a strong influence on the behavior of Betiscoides, particularly on the small males of B. parva. Future studies might thus focus on the question whether wind-exposure is a critical factor for habitat choice of this species. We strongly recommend enhancing the connectivity of restio habitats and restoring these habitats to prevent extinction of specialized insect species.

Conservation of large predators has long been a challenge for biologists due to the limited information we have about their ecology, generally low numbers in the wild, large home ranges and the continuous expansion of human settlements. The American crocodile (Crocodylus acutus) is a typical apex predator, that has suffered from all of these characteristic problems, especially the latter one. Humans have had a major impact on the recovery of this species throughout its range, even though most of the countries it inhabits have banned hunting. The last decade has made it clear that in order to implement sound conservation and management programs, we must increase our understanding of crocodile spatial ecology. However, in only two countries where American crocodiles have telemetry studies even been published. Herein we have characterized the spatial ecology of C. acutus on Coiba Island, Panama, by radio-tracking (VHF transmitters) 24 individuals between 2010 and 2013, to determine movement patterns, home range, and habitat use. We have then compared our findings with those of previous studies to develop the most comprehensive assessment of American crocodile spatial ecology to date. Females showed a higher average movement distance (AMD) than males; similarly, adults showed a higher AMD than sub-adults and juveniles. However, males exhibited larger home ranges than females, and concomitantly sub-adults had larger home ranges than juveniles, hatchlings, and adults. There was an obvious relationship between seasonal precipitation and AMD, with increased AMD in the dry and “low-wet” seasons, and reduced AMD during the “true” wet season. We found disaggregate distributions according to age groups throughout the 9 habitat types in the study area; adults and hatchlings inhabited fewer habitat types than juveniles and sub-adults. These sex- and age-group discrepancies in movement and habitat choice are likely due to the influences of reproductive biology and Coiba’s precipitation cycle. Juveniles also showed distinct movement patterns and home ranges; however, with sexual maturation and development, these behaviors became more characteristic of adults and sub-adults. Ours is one of a very small number of studies that will allow future management and conservation planning to be based on the comprehensive integration of the spatial ecology of a Neotropical crocodylian apex predator.

Obtaining an accurate quantification of population size is often of prime importance in ecology and conservation biology (e.g. population viability analysis, a basic step for assessing species and population status in a given area and guiding effective conservation). When obtaining a reliable quantification of absolute (vs. relative) population size is required, Mark–Release–Recapture (MRR) is a method of choice for many organisms. This is a highly reliable but costly procedure in terms of time and potential impact on species and sites. Consequently, less costly alternatives are highly desirable for conservation and population ecologists.We present here a simplifiedMRRprotocol to mitigate this cost of repeatedMRRsampling with little compromise on the quality of the population size estimation. Using one of the largest existing butterflyMRRdatabases, collected on two fritillary species over a period of 20 years and >20 populations in Belgium, we assessed the possibility to reduce the effort of collectingMRRdata while keeping accurate quantification of total population size. By downsampling from the full datasets and calculating a range of demographic census metrics, we specifically investigated whether marking individuals is necessary, and whether the number of sampling sessions can be reduced.We found that (1) counting individuals is not enough: some individual marking, even in a simplistic way to differentiate newly recorded from previously seen individuals, is essential for estimating population size. (2) A simple linear conversion function (number of “missed” individuals for each marked one) can be used to compute population size from the number of individuals marked over a small number ofMRRsampling sessions. (3) Parameterizing this function is system specific, because it depends on detectability of individuals, but only requires an initial effort of traditional high‐effortMRRin a few populations encompassing the expected range of population size, combined with previous knowledge on the species about potential factors affecting detectability.Our simplifiedMRRprotocol should allow scientists to obtain absolute population size estimates almost as good as with traditional high‐effortMRR, but at a cost lowered in both the marking procedure and the intensity of field visits.

Identification of individuals based on morphological patterns is a strategy used primarily in human forensics that has also been applied successfully in several wildlife scenarios. To date, no study has evaluated the potential of these techniques on American Crocodiles (Crocodylus acutus). We assessed whether the dorsal scute number and pattern of 110 American Crocodiles captured from the wild on Coiba Island, Panama could be used for individual recognition. We estimated scute variation using the number and position of scutes, testing both a binary and a coded assessment for scute presence and pattern, respectively. We analyzed scute patterns using 21 transverse scute lines (TSL) including the three most prominent scutes present on each side of the vertebral column axis. We found significant differences in the number of scutes per TSL and longitudinal scute lines (LSL) by individual. Based on both the binary and coded analyses, we identified all American Crocodiles assessed at the individual leve...

The number of animals in a population is conventionally estimated by capture–recapture without modelling the spatial relationships between animals and detectors. Problems arise with non‐spatial estimators when individuals differ in their exposure to traps or the target population is poorly defined. Spatially explicit capture–recapture (SECR) methods devised recently to estimate population density largely avoid these problems. Some applications require estimates of population size rather than density, and population size in a defined area may be obtained as a derived parameter from SECR models. While this use of SECR has potential benefits over conventional capture–recapture, including reduced bias, it is unfamiliar to field biologists and no study has examined the precision and robustness of the estimates. We used simulation to compare the performance of SECR and conventional estimators of population size with respect to bias and confidence interval coverage for several spatial scenarios. Three possible estimators for the sampling variance of realised population size all performed well. The precision of SECR estimates was nearly the same as that of the null‐model conventional population estimator. SECR estimates of population size were nearly unbiased (relative bias 0–10%) in all scenarios, including surveys in randomly generated patchy landscapes. Confidence interval coverage was near the nominal level. We used SECR to estimate the population of a species of skink Oligosoma infrapunctatum from pitfall trapping. The estimated number in the area bounded by the outermost traps differed little between a homogeneous density model and models with a quadratic trend in density or a habitat effect on density, despite evidence that the latter models fitted better. Extrapolation of trend models to a larger plot may be misleading. To avoid extrapolation, a large region of interest should be sampled throughout, either with one continuous trapping grid or with clusters of traps dispersed widely according to a probability‐based and spatially representative sampling design.

Simple SummaryThe objective of our study was to evaluate the mention of uncertainty (i.e., variance) associated with population size estimates within U.S. recovery plans for endangered animals. To do this we reviewed all finalized recovery plans for listed terrestrial vertebrate species. We found that more recent recovery plans reported more estimates of population size and uncertainty. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty. We recommend that updated recovery plans combine uncertainty of population size estimates with a minimum detectable difference to aid in successful recovery. United States recovery plans contain biological information for a species listed under the Endangered Species Act and specify recovery criteria to provide basis for species recovery. The objective of our study was to evaluate whether recovery plans provide uncertainty (e.g., variance) with estimates of population size. We reviewed all finalized recovery plans for listed terrestrial vertebrate species to record the following data: (1) if a current population size was given, (2) if a measure of uncertainty or variance was associated with current estimates of population size and (3) if population size was stipulated for recovery. We found that 59% of completed recovery plans specified a current population size, 14.5% specified a variance for the current population size estimate and 43% specified population size as a recovery criterion. More recent recovery plans reported more estimates of current population size, uncertainty and population size as a recovery criterion. Also, bird and mammal recovery plans reported more estimates of population size and uncertainty compared to reptiles and amphibians. We suggest the use of calculating minimum detectable differences to improve confidence when delisting endangered animals and we identified incentives for individuals to get involved in recovery planning to improve access to quantitative data.

Abstract. We assessed the reproductive ecology of the American crocodile (Crocodylus acutus) on Coiba Island, Panama from January–December 2013. We examined nest site characteristics from January–April and hatchling survivorship from April–December. Ten nests were examined at three nesting localities where 30% of the nests were found under forest canopies and 70% were exposed to sunlight (distance to nearest tree = 280 ± 110 cm). Half of the nests were built closer to the sea and the other half closer to bodies of freshwater (700 ± 360 cm). The nest dimensions were 17.5 ± 7.8 cm from the top of the clutch to the surface, 42.9 ± 9.9 cm from the bottom of the clutch to the surface, and 35.9 ± 3.6 cm wide at the top of the nest cavity. The average soil conditions in the nests consistently had high concentrations of potassium (69.3 mL/L) and manganese (9.2 mg/L), moderate concentrations of phosphorus (6.6 mg/L) and iron (3.7 mg/L), and low concentrations of zinc (0.5 mg/L) and copper (0.0 mL/L). Cation exchan...

HIV prevalence is disproportionately high among female sex workers compared to the general population. Many African countries lack useful data on the size of female sex worker populations to inform national HIV programmes. A female sex worker size estimation exercise using three different venue-based methodologies was conducted among female sex workers in all provinces of Rwanda in August 2010. The female sex worker national population size was estimated using capture–recapture and enumeration methods, and the multiplier method was used to estimate the size of the female sex worker population in Kigali. A structured questionnaire was also used to supplement the data. The estimated number of female sex workers by the capture–recapture method was 3205 (95% confidence interval: 2998–3412). The female sex worker size was estimated at 3348 using the enumeration method. In Kigali, the female sex worker size was estimated at 2253 (95% confidence interval: 1916–2524) using the multiplier method. Nearly 80% of all female sex workers in Rwanda were found to be based in the capital, Kigali. This study provided a first-time estimate of the female sex worker population size in Rwanda using capture–recapture, enumeration, and multiplier methods. The capture–recapture and enumeration methods provided similar estimates of female sex worker in Rwanda. Combination of such size estimation methods is feasible and productive in low-resource settings and should be considered vital to inform national HIV programmes.

Estimating population size is essential for many applications in population ecology, so capture–recapture techniques to do this are often taught in secondary school classrooms and introductory university units. However, few classroom simulations of capture–recapture consider the sensitivity of results to sampling intensity, the important concept that the population size calculated is an estimate with error attached, or the consequences of violating assumptions underpinning particular capture–recapture models. We describe a simple approach to teaching the Lincoln index method of capture–recapture using packs of playing cards. Students can trial different sampling intensities, calculate 95% confidence intervals for population estimates, and explore the consequences of violating specific assumptions.

Accurate estimation of wildlife population size is central to effective management and conservation but is notoriously difficult for rare and cryptic carnivores. Mark–recapture methods can reliably estimate the abundance of large carnivores but are sensitive to departures from the assumption of equal catchability, which is probable for territorial and social carnivores. We empirically analysed how pride area, age and sex, group size and pride size of lionsPanthera leoand possession of a kill affect the performance of the sight–resight method relative to concurrent total counts. We stratified the population by pride area to obtain a better sample size for reliable population size estimation, and determined the composition and size of each pride. Marking and recapture involved merely identifying and re‐identifying individual lions. The per cent of the population marked in each pride area varied from 33.3 to 100. Twenty‐six estimates of pride size for 22 different pride areas and repeat surveys in five pride areas were made between September 1990 and April 1992. The second samples involved sampling with replacement, soBailey's (1952)bias‐corrected estimator for closed populations was applied. Increasing the per cent of the population marked improved accuracy only when the number of lions marked in a pride area was at least seven. Estimates were somewhat poorer when the number marked was less than seven but improved with more markings, but no estimate of population size was biased high. Age, sex, group size, pride size and feeding events all influenced the sightability of lions. Notably, females (>1 year) were sighted or resighted in proportion to their presence in the population, whereas similarly aged males, adults or subadults fluctuated erratically about their population proportions. Sight–resight surveys of territorial and social carnivores are reliable but can be costly and time consuming.

Estimates of population size are needed in populations targeted by recreational fisheries, to determine their conservational status and to formulate fishing regulations. Mark–recapture monitoring is a promising tool for this because of the increased popularity of catch‐and‐release angling. Northern pike, Esox lucius L., population sizes were estimated in four lakes based on experimental mark–recapture fishing using a hierarchical Bayesian model that also estimated natural mortality. The approach was compared with output from traditional Petersen’s population size estimates. Despite intensive fishing with multiple gears, the population size estimates suggested that a substantial proportion of individuals remained unobserved by fishing. Petersen’s estimates depended on the assumed rate of natural mortality, and no mortality rate scenario matched with the Bayesian estimates. Consequently, the number of individuals caught by recreational anglers is a poor proxy of population size for which estimations should be carried out using a modelling approach that also estimates natural mortality.

Demographic data provide a basis for understanding the life history and ecology of species, factors which are vital for informing conservation efforts; however, little is known regarding the population ecology of most snake species, including the threatened Eastern Indigo Snake ( Drymarchon couperi ). We used 11 years (1999–2009) of capture‐mark‐recapture (CMR) and 2.5 years (2003–2005) of radiotelemetry data from southeastern Georgia, USA, in a CMR modeling framework to estimate apparent survival, capture and transition probabilities, and evaluate factors influencing these parameters. The model‐averaged estimate of overall apparent annual survival probability was 0.700 (±0.030 SE) and is comparable to that obtained from known fate analysis (radiotelemetry) at the same site. Body size positively influenced survival, regardless of sex. Capture probability differed seasonally by sex, suggesting lower capture probability for females in fall and males in winter. There was no evidence for effect of precipitation or site‐specific differences in survival. Model averaged estimate of annual adult survival estimated using multistate CMR models was 0.738 ± 0.030 and 0.515 ± 0.189 for subadults. We estimated population growth rate ( λ ) and elasticity (proportional sensitivity) of λ to vital rates using a stage‐structured matrix population model. Population growth rate ranged from 0.96 to 1.03 depending on the value of the probability of transitioning from subadult to adult stage. The λ was proportionally most sensitive to changes in adult survival rate, followed by subadult survival. Our results suggest that protecting adult snakes and their habitats would result in the highest likelihood of long‐term population stability and growth.

An approach to multi-class imbalanced problem in ecology using machine learning

Coenagrion mercuriale is rare in the UK and is threatened across Europe. Ischnura pumilio is also threatened in the UK. Both species have suffered population declines in recent years and are vulnerable to habitat fragmentation and loss. Yet, reliable population size and survival estimates are scarce in odonate species. This study provides mark–release–recapture estimates of these parameters for UK stronghold populations of both species. Surveys were performed at four locations in southern England between 2001 and 2006. A total of 12 071 adult individuals were marked across nine populations. Mark–release–recapture modelling techniques were used to provide survival and recapture probabilities and population size estimates. This study presents the first Horvitz–Thompson estimates of population size in odonates, which are among the highest reported for damselflies. Maximum estimates for a single site were 63 662 ± 4997 for C. mercuriale and 7453 ± 382 for I. pumilio . More males than females were captured at all sites, but calculated estimates indicated a female‐biased sex ratio in adult I. pumilio at one location. Daily survival probability is among the highest published for damselflies. Male and female survival was equal or very similar in all populations. Further effects of maturity, age, site, and time on survival were identified. Estimated population sizes are much greater than previously thought, suggesting that where habitat is maintained, populations of threatened odonates can be very large. Furthermore, greater proportions of females have been estimated where wider searching techniques were employed. This has implications for future study design if estimates are to be reliably used for conservation management.