Abundance and conservation status of the Yangtze finless porpoise in the Yangtze River, China

The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) is endemic to the middle and lower reaches of the Yangtze River, China. It is the only freshwater population of porpoises in the world and is currently listed as Endangered by IUCN. In November and December 2006 we used two boats and line transect methods to survey the entire current range of the population, except for two lakes (Poyang and Dongting). Sighting results were similar for both boats, so we pooled all data and analyzed them using two line transect models and a strip transect model. All models produced similar estimates of abundance (1111, 1225 and 1000). We then added independent estimates of the number of porpoises from the two lakes for a total estimate of approximately 1800 porpoises. Our findings indicate that the population continues to decline and that its distribution is becoming more fragmented. Our current estimate in the main river is slightly less than half the estimate from surveys between 1984 and 1991 (which was probably an underestimate). We also found an apparent gap in the distribution of porpoises between Yueyang and Shishou (∼150 km), where sightings had previously been common. Continued threats to Yangtze finless porpoises include bycatch in unregulated and unselective fishing, habitat degradation through dredging, pollution and noise, vessel strikes and water development. Immediate protective measures are urgently needed to ensure the persistence of finless porpoises in the Yangtze River. The survey design and analytical methods developed in this study might be appropriate for surveys of cetaceans in other river systems.     

Point-Based Mark-Recapture Distance Sampling

Avian surveys using point sampling for abundance estimation have either focused on distance sampling or more commonly mark-recapture to correct for detection bias. Combining mark-recapture and distance sampling (MRDS) has become an effective tool for line transects, but it has been largely ignored in point sampling literature. We describe MRDS and show that the previously published methods for point sampling are special cases. Using simulated data and golden-cheeked warbler (Dendroica chrysoparia) survey data from Texas, we demonstrate large differences in abundance estimates resulting from different independence assumptions. Data and code are provided in supplementary materials.     

Spatial models for line transect sampling

This article develops methods for fitting spatial models to line transect data. These allow animal density to be related to topographical, environmental, habitat, and other spatial variables, helping wildlife managers to identify the factors that affect abundance. They also enable estimation of abundance for any subarea of interest within the surveyed region, and potentially yield estimates of abundance from sightings surveys for which the survey design could not be randomized, such as surveys conducted from platforms of opportunity. The methods are illustrated through analyses of data from a shipboard sightings survey of minke whales in the Antarctic.     

Environmental monitoring using populations of birds and small mammals: Analyses of sampling effort

Characteristics of bird and small mammal communities can be valuable in monitoring for impacts on specific plots of land. In Utah (USA), significant differences were found among years, habitats and seasons in bird and small mammal abundance, species diversity, and species richness; thus, estimates of these characteristics are consistent and repeatable and can be used for detecting change. Also, bird and small mammal communities are dependent on a wide variety of food resources and habitat characteristics; thus they should reflect a variety of impacts.A comparison is made between two methods of handling bird data from transects: enumeration (individual birds per km) and density (birds per unit area). Correlation between the two was high (r = 0·93). However, density estimates may be necessary to trace an impact to a particular group, guild or species and possibly to its cause.An analysis is made of how much sampling is necessary to make an adequate estimate of the characteristics of bird and small mammal communities. Estimates of bird abundance, species richness and species diversity (from enumeration) may be obtained with three repetitions of 2 km of transect. Three repetitions are also sufficient to estimate abundance of small mammals on 12 by 12 trapping grids. To estimate species richness and species diversity, however, four or more repetitions are needed. Small mammal community characteristics are not well predicted by trapping on transects or small grids except in grids 9 by 9 or larger. These results of sampling effort may only apply to certain habitats but data from bird and small mammal communities should be useful in environmental monitoring at any site.     

Models for Jointly Estimating Abundances of Two Unmarked Site-Associated Species Subject to Imperfect Detection

In ecological field surveys, it is often of interest to estimate the abundance of species. It is frequently the case that unmarked animals are counted on different sites over several time occasions. A natural starting point to model these data, while accounting for imperfect detection, is by using Royle’s N-mixture model (Biometrics 60:108–115, 2004). Subsequently, many multivariate extensions have been proposed to model communities as a whole. However, these approaches are used to study species richness and other community-level variables and do not focus on the relationship between two site-associated species. Here, we extend the N-mixture modelling framework to model two site-associated species abundances jointly and propose to measure the influence of one species’ abundance on the populations of the other and study how this changes over time and space. By including a new parameter in the abundance distribution of one of the species, linking it to abundance of the other, our proposed model treats extra variability as an effect induced by an associated species’ abundance and allows one to study how environmental covariates may affect this. Using results from simulation studies, we show that the model is able to recover true parameter estimates. We illustrate our approach using data from bald eagles and mallards obtained in the 2015 survey of the North American Breeding Bird Survey. By using the joint model, we were able to separate overdispersion from mallard-induced variability and hence what would be accounted for with a dispersion parameter in the univariate framework for the eagles was explained by covariates related to mallard abundance in the joint model. Our approach represents an attractive, yet simple, way of modelling site-associated species populations jointly. Conservation ecologists can use the approach to devise management strategies based on the strength of association between species, which may be due to direct interactions and/or environmental effects affecting both species’ populations. Also, mathematical ecologists can use this framework to develop tools for studying population dynamics under different scenarios. Supplementary materials accompanying this paper appear on-line.     

Distribution, status, and conservation of radiated tortoises (Geochelone radiata) in Madagascar

The radiated tortoise, Geochelone radiata, one of Madagascar’s four endemic tortoises, occupies a narrow band of xeric spiny forest along the island’s southwest coast. Traditionally avoided by indigenous tribes, these tortoises are now routinely harvested for food. An accurate assessment of human exploitation remains problematic, however, hindered by limited, dated statistics available on tortoise populations. To update the radiated tortoise’s status and distribution, we established a series of line transects at seven localities across its range and implemented a mark-recapture study at one of these localities (Cap Sainte Marie). Tortoises currently range from south of Tulear to east of Cap Sainte Marie, at density estimates spanning 27-5744 tortoises/km². The mark-recapture estimate for Cap Sainte Marie (1905-2105 tortoises/km²) was substantially higher than its transect estimate (654 tortoises/km²) though comparable to actual tortoise captures (1438) there. Thus, our transect density values probably err as underestimates, and from these data, we calculate a conservative total population size of 12 million radiated tortoises. We also examined mitochondrial DNA sequences (ND4 gene) for two individuals/locality in a preliminary assessment of genetic variation across the species’ range. Only two ND4 haplotypes were recovered, the more common haplotype representing 13 of the 14 individuals. We offer several conservation recommendations in light of our survey results.     

Monitoring distributions using call surveys: estimating site occupancy, detection probabilities and inferring absence

Monitoring programs serve to track changes in the distribution and abundance of species. A major problem with most monitoring programs is that species detection is imperfect and some populations are inevitably missed. Therefore, in most monitoring programs the true distribution of a species will be underestimated. Here, we report a field test of the reliability and performance of a commonly used method to monitor the distribution of amphibians (anuran call surveys). We surveyed the distribution of four anuran species in western Switzerland, and estimated detection probabilities to account for imperfect species detection and used these estimates to adjust our estimate of site occupancy (i.e., distribution). Next, we assessed how detection probabilities were affected by weather and how site occupancy was affected by site specific covariates. For one species (Hyla arborea), call surveys proved efficient in determining the regional distribution with only few site visits because detection probabilities were relatively high. The call surveys apparently missed many populations of another common species (Bufo calamita) because detection probabilities were lower. Two other species (Bombina variegata and Alytes obstetricans) were uncommon and strong inference from the analysis is not possible. Thus, multispecies surveys may be inefficient for rare species. Estimates of detection probabilities were used to calculate how many site visits are necessary to infer the absence of a species with some predetermined statistical certainty. The implications of “false absences” are important in ecology as they are known to bias usual habitat suitability models and overestimate extinction/colonization events in metapopulations. Large-scale monitoring programs would benefit from the application of an estimation-based approach to monitoring the distribution of species.     

Motorways and bird traffic casualties: Carcasses surveys and scavenging bias

Most survey methods developed to estimate abundance of killed animals on motorways may be biased due to the unequal detectability of carcasses, their persistence time on the lanes, and scavengers activities. Unbiased surveys are needed to evaluate the relationships between bird casualties (mortality), motorways characteristics, and the neighbouring avifauna. The present study conducted on four motorways in France, aimed to evaluate factors affecting persistence and encounter probabilities and variations in scavenging activity to obtain unbiased estimates of bird traffic casualties. Each motorway was surveyed once per season during multiple years and we used capture–recapture methods to estimate detection and carcass persistence rates. Results showed that surveys by car were as efficient as surveys by foot in detecting carcasses on the pavement, but less efficient for carcasses on verges. Passeriformes represented the most numerous casualties, and the Barn Owl (Tyto alba) was the most frequently killed species. Encounter probabilities were constant and high (0.957 ± 0.007). Average daily persistence probability was 0.976 ± 0.003. Persistence probabilities were higher for large and old carcasses, during summer, and differed between seasons, but were relatively similar between years. Scavenging activities, estimated using experimental carcasses disposed on the safe lanes of motorways, varied between years, seasons, and differed between diurnal and nocturnal periods. A peak in scavenging activity occurred during diurnal periods in spring. Results suggest that surveys must take into account carcass characteristics and seasonal variability to obtain unbiased estimates of road killed birds on motorways, as well as variation in scavenging rates.     

Camera-trapping forest-woodland wildlife of western Uganda reveals how gregariousness biases estimates of relative abundance and distribution

Camera traps are increasingly used to estimate relative abundance and distribution of wildlife. These methods are powerful and efficient ways to inventory multiple species simultaneously and count rare, secretive individuals across landscapes. However the estimation methods demand assumptions about relative capture probability that may not hold well for gregarious animals. We present results from the first systematic, camera-trap study in forest-woodland, western Uganda. Within a landscape of seven protected areas with globally important biodiversity, we detected >36 species of large mammals and birds in 8841 camera-trap days. Species photographed in groups of two or more individuals produced higher estimates of relative abundance and wider distribution than species photographed as single individuals. We propose these findings reflect higher detectability for animals that forage or travel in groups. We discuss how capture-recapture theory should be adapted to account for both non-independence among individuals in groups and for the interaction between individual and temporal variation in capture probability. We also identify several species that deserve greater conservation attention in Uganda and beyond. Among them, leopards were unexpectedly rare, especially when compared to the sympatric African golden cat. We recommend against a recent policy on leopard trophy hunting, at least in western Uganda.     

Comparing population growth rates using weighted bootstrapping: Guiding the conservation management of Petrogale xanthopus xanthopus (yellow-footed rock-wallaby)

In this study we compare estimates of the long-term mean stochastic population growth rates, E[r] for Petrogale xanthopus xanthopus (yellow-footed rock-wallaby), a threatened Australian species. In fluctuating environments such as semi-arid areas, herbivore populations respond directly to changes in the biomass of food resources. Biomass is generally correlated with rainfall, so it is often useful to model annual population growth rates of herbivores directly with rainfall. Models of this nature are referred to as numerical response models. The factors that are thought to threaten this species include competition from introduced herbivores and predation from foxes. Annual aerial survey data collected from 1997 to 2004 over approximately 600 km of transect line were analyzed in seven zones within South Australia. Using the Ivlev numerical response model, the annual population growth rates were found to correlate best with the rain that fell in the seven-month period immediately prior to the surveys. Not surprisingly, positive growth rates were found to be associated with higher rainfalls in this period, while negative growth rates were associated with lower rainfalls. We also used weighted bootstrapping to calculate confidence intervals around our estimates of long-term mean stochastic population growth rates, E[r]. The findings suggest that the estimates of E[r] are positive in areas where there is fox and herbivore management. However, we found no evidence that this species will decline in the absence of these treatments.     

A quick method for estimating butterfly numbers during surveys

This paper describes how the size of butterfly populations may be quickly assessed during surveys. The method is a development of Pollard's transect technique, which measures changes in adult numbers in time on fixed sites. In this development, comparability between counts made in the same season on different sites is achieved by ensuring that the transect representatively samples each population, and that the results take account of the length of transect, size of site, and the recording date. The accuracy and usefulness of the method are assessed, using examples taken from six recent surveys. It is concluded that the method gives an accurate measurement of numbers for species that fly freely in open habitats, and an adequate, but less accurate, estimate for species that aggregate or fly in heterogeneous habitats.     

Likelihood-based inference for clustered line transect data

The uncertainty in estimation of spatial animal density from line transect surveys depends on the degree of spatial clustering in the animal population. To quantify the clustering we model line transect data as independent thinnings of spatial shot-noise Cox processes. Likelihood-based inference is implemented using Markov chain Monte Carlo (MCMC) methods to obtain efficient estimates of spatial clustering parameters. Uncertainty is addressed using parametric bootstrap or by consideration of posterior distributions in a Bayesian setting. Maximum likelihood estimation and Bayesian inference are compared in an example concerning minke whales in the northeast Atlantic.     

Zigzag survey designs in line transect sampling

Zigzag survey lines are frequently used in shipboard and aerial line transect surveys of animal populations. Analysis proceeds assuming that coverage probability through the survey region is uniform. We show that the two types of zigzag design that are in wide use do not generally have this property, and explore the degree of bias in abundance estimates that can be anticipated. We construct a zigzag design for convex survey regions that has even coverage probability with respect to distance along a design axis. We also provide Horvitz-Thompson estimators that allow coverage probability to vary by location through the survey region.     

Estimation of detection probability in aerial surveys of antarctic pack-ice seals

We use line transect detection functions together with generalized linear and additive models to estimate detection probability when detection on the line (“g(0)”) may not be certain. The methods provide a flexible way of modeling detection probability for independent observer surveys, and for investigating the effects of explanatory variables. Analysis of data from an aerial survey of pack-ice seals produced g(0) estimates substantially below 1 for some observers (it varied from 0.80 to 0.98), demonstrated a fairly complex dependence of detection probability on covariates, and showed negative correlation between observers’ search width and their g(0). In addition to illustrating the utility of generalized additive models for capturing the effect of covariates on detection probability, the analysis suggests that detection functions may be sufficiently variable that use of g(0) correction factors obtained from other surveys would be inadvisable. We recommend that estimation of g(0) be considered for all aerial surveys; if g(0) is found to be very close to 1, estimation from subsequent surveys under the assumption that it is 1 may be reasonable, but without any estimation of g(0), the assumption that it is 1 is a matter of faith.     

Resolving conflicts between butterfly host resource abundance and genet population size estimates for a vegetatively spreading, threatened grassland legume

Population size estimates are an integral part of rare plant conservation, but common abundance measurements such as cover and ramet number may not accurately index genet population size for vegetatively spreading species. Population monitoring of Kincaid’s lupine (threatened species) populations occurs through genet-anonymous leaf cover and raceme counts despite extensive, non-adventitious rhizome growth. While the current monitoring scheme provides important resource abundance measurements for the endangered Fender’s blue butterfly, whose larvae feed on Kincaid’s lupine leaves, the methods are not appropriate for estimating lupine genet number. Major axis regression revealed well supported statistical relationships between cover, raceme, and plantlet (a measurement of modular plant growth) density within six study patches (n = 3 populations) of Kincaid’s lupine (R² > 0.90) and when all patch data were combined (R² > 0.91). Genet population size estimates from genotype only data with ACE (an estimator used to infer species richness) were similar to estimates derived from a combination of plantlet density and genet to plantlet ratios (genotype derived) in small, more thoroughly genotyped lupine patches. However, genet number estimates from ACE were 3–5-fold greater in less intensely genotyped patches. Genet-anonymous plant abundance measurements, such as cover, can be used to estimate genet number in populations of vegetatively spreading plants provided they are calibrated with a unit of modular plant growth. Calibration of vegetative measurements, consistency of between population relationships, and closer scrutiny of highly supported statistical models may be necessary to develop more pertinent monitoring methods for rare, vegetatively spreading plants.     

Accounting for Lack of Independence and Partial Overlap of Observation Zones in Line-Transect Mark-Recapture Distance Sampling

Line-transect mark-recapture distance sampling methods can be used to estimate abundance when at least two observers sight and record distances to detected groups of individuals within the survey area. However, a lack of independence between the observer’s detections will cause biased abundance estimates. Studies are also typically designed such that there is complete overlap of the regions searched by the two observers, but that may not always be possible. Here we detail an intuitive approach for line-transect distance sampling applications based upon logistic regression to account for a potential lack of independence by using the detections of one observer as a covariate in the detection function of the second observer. Partial overlap of the observer survey regions can be addressed by constraining detection probability to equal 0 for the respective observer outside of the overlap zone. We show via simulation that the method provides reliable estimates of abundance and is not affected by random unmodeled heterogeneity in detection probability. The method is illustrated by estimating abundance within the covered region of an aerial line-transect survey for New Zealand’s endemic Hector’s dolphin (Cephalorhynchus hectori hectori) conducted in the austral summer of 2013, the motivating application for this work. Supplementary materials accompanying this paper appear on-line.     

Post-fire succession affects abundance and survival but not detectability in a knob-tailed gecko

Altered fire regimes threaten the persistence of many animal species globally, thus understanding how fire affects demographic processes is critical for conservation. Using 2 years of mark-recapture data from the Australian gecko Nephrurus stellatus, we investigated the effect of fire on (i) detectability to reliably measure post-fire changes in abundance, and (ii) survival and reproductive rates to investigate the mechanisms of successional change. Data were collected from two conservation reserves each with three different fire categories based on time since the last fire. “Early”, “medium” and “late” sites had 2–3, 7–9 and 42–48 years since fire, respectively. A robust design modelling framework was used to estimate the effect of fire category on abundance, survival and capture probability while also examining the influence of temperature and behaviour on detectability. Geckos showed trap-shy behaviour and detectability increased significantly with increasing temperature but was not affected by time since fire. Accounting for detectability, geckos were more abundant in the medium than the early sites, and were rare in the late sites. Although trends in survival are more difficult to address with short-term data, our results showed lower monthly survival rates, but higher fecundity in the early than the medium sites. These results were possibly related to successional changes in predation, the thermal environment, and food availability. We demonstrated how mark-recapture analysis can show the causes of animal fire responses while realistically accounting for detectability. Such information is necessary to provide a predictive framework to guide fire management for biodiversity.     

A gamma-shaped detection function for line-transect surveys with mark-recapture and covariate data

We have developed a procedure for estimating animal population size from aerial survey data collected simultaneously by two observers on the same sighting platform. We used a line transect sample design where transects follow elevation contours in mountainous terrain. Because our 10 data sets from aerial line transect surveys, conducted over a terrestrial environment, consistently show unimodal detection shapes, we chose a gamma-shaped detection function that is unimodal and admits covariates. We fit models separately to data from each observer, and then used all of the data to estimate the probabilities at the apex of the detection curves. We used a Horvitz-Thompson estimator to estimate the population size. We illustrate our procedure on a recently collected brown bear data set.     

Estimating impacts of poison operations on non-target species using mark-recapture analysis and simulation modelling: an example with saddlebacks

Poison operations to control or eradicate exotic mammals are a key component of conservation management in the South Pacific. They also result in by-kill of native species. It is therefore important to develop reliable methods for estimating by-kill and assessing its impact. The North Island saddleback (Philesturnus carunculatus rufusater), a rare New Zealand forest bird, was reintroduced to Mokoia Island in 1992, and 4 years later there was an aerial drop of cereal pellets containing Brodifacoum aimed at eradicating mice. We used mark-recapture analysis on resighting data collected from 1992 to 1997 to estimate the by-kill of saddlebacks attributable to this poison drop. We nominated a set of candidate models to explain the data, and compared these using Akaike's Information Criterion. The analysis showed that saddleback survival was substantially lower than expected in the 6-week interval after the poison drop, taking age, density dependence, season and random variation into account. Taking expected survival rates into account, the probability of an adult being killed was estimated to be 0.45 (95% CI=0.34-0.56), and the probability of a juvenile being killed was estimated to be 0.35 (95% CI=−0.05-0.75). We then used a simulation model developed for the population to assess the longer-term impact of this mortality. While the mortality set back the expansion of the population by 1-2 years, we predicted that the population would have recovered fairly quickly and ultimately reach the same carrying capacity. Mark-recapture analysis permits precise estimates of background survival rates unconfounded by seasonal or random variation.     

Counting elusive animals: Comparing field and genetic census of the entire mountain gorilla population of Bwindi Impenetrable National Park, Uganda

Accurate population size estimates are an essential part of every effective management plan for conserving endangered species. However, censusing rare and elusive wild animals is challenging and often relies on counting indirect signs, such as nests or feces. Despite widespread use, the accuracy of such estimates has rarely been evaluated. Here we compare an estimate of population size derived solely from field data with that obtained from a combination of field and genetic data for the critically endangered population of mountain gorillas (Gorilla beringei beringei) in Bwindi Impenetrable National Park, Uganda. After genotyping DNA from 384 fecal samples at 16 microsatellite loci, the population size estimate was reduced by 10.1% to 302 individuals, compared with 336 gorillas estimated using the traditional nest-count based method alone. We found that both groups and lone silverbacks were double-counted in the field and that individuals constructed multiple nests with an overall rate of 7.8%, resulting in the overestimation of the population size in the absence of genetic data. Since the error associated with the traditional field method exceeded the estimated population growth of 5% in the last 4 years, future genetic censusing will be needed to determine how the population size is changing. This study illustrates that newly improved molecular methods allow fast, efficient and relatively affordable genotyping of several hundred samples, suggesting that genetic censusing can be widely applied to provide accurate and reliable population size estimates for a wide variety of species.