Estimating abundance for a savanna elephant population using mark–resight methods: a case study for the Tembe Elephant Park, South Africa

Elephants living in dense woodlands are difficult to count. Many elephant populations in Africa occur in such conditions. Estimates of these populations based on total counts, aerial counts and dung counts often lack information on precision and accuracy. We use standard mark–recapture field methods to obtain estimates of population size with associated confidence limits. We apply this approach to a closed elephant population in the Tembe Elephant Park (300 km²), South Africa. A registration count completed in 4 months gives a known population size. We evaluate mark–recapture models against the known population size. Individual identification profiles obtained for elephants during the registration count and mark–recapture events indicate that at least 167 elephants live in the park. We consider this value as an estimate of the minimum number alive. We include 189 sightings of bulls and 37 sightings of breeding herds in the mark–recapture modelling. Of the models we test (Petersen, Schnabel, Schumacher, Jolly–Seber, Bowden's, Poisson and negative binomial), Bowden's gives an estimate closest to the registration count. Assumptions of the model are not violated. For all models except one (negative binomial), our estimates improve with increased sampling intensity. Confidence intervals do not improve with increased effort except for the Schnabel model. Mark–recapture methods should be considered as reliable estimators of population size for elephants occurring in dense woodlands and forests when other methods cannot be relied on.     

A Bayesian estimate of harbour seal survival using sparse photo-identification data

Survival rates have rarely been estimated for pinniped populations due to the constraints of obtaining unbiased sample data. In this paper, we present an approach for estimating survival probabilities from individual recognition data in the form of photographic documentation of pelage patterns. This method was applied to estimate adult (age 2+) survival for harbour seals in the Moray Firth, NE Scotland. An astronomical telescope was used to obtain digital images of individual seals, and high-quality images were used to document the annual presence or absence of individuals at a single haul-out site over a 4-year period. A total of 95 females, 10 males and 57 individuals of unknown sex were photographically documented during the study period. Survival and recapture probabilities were estimated using Jolly–Seber mark–recapture models in a Bayesian statistical framework. Computer-intensive Markov Chain Monte Carlo methods were used to estimate the probability distributions for the survival and recapture probabilities, conveying the full extent of the uncertainty resulting from unavoidably sparse observational data. The deviance information criterion was used to identify a best-fitting model that accounted for variation in the probability of capture between sexes, with constant survival. The model estimated adult survival as 0.98 (95% probability interval of 0.94–1.00) using our photo-identification data alone, and 0.97 (0.92–0.99) with the use of an informative prior distribution based on previously published estimates of harbour seal survival. This paper represents the first survival estimate for harbour seals in the UK, and the first survival estimate using photo-identification data in any species of pinniped.     

Testing assumptions of mark–recapture protocols for estimating population size using Australian mound-building, subterranean termites

1. Forager population size of two species of mound-building, subterranean termite ( Coptotermes lacteus , Rhinotermitidae and Nasutitermes exitiosus , Termitidae) was estimated using three mark–recapture protocols. These estimates varied widely within and between colonies (≈ 0.3–200 million for C. lacteus and 0.2–3 million for N. exitiosus ). The variation in the estimates is explained in part by violation of the assumptions of the protocols.
2. The fat-stain markers, although persistent in the laboratory, faded rapidly in the field, and were transferable from marked individuals to unmarked individuals by cannibalism.
3. Marked individuals did not mix randomly or evenly with unmarked foraging individuals in space or time, as marked individuals were recaptured in widely varying numbers at different feeding sites sampled simultaneously. Importantly, foragers displayed feeding site fidelity and avoided disturbed feeding sites.
4. The likelihood of recapture differed between castes and instars; there was a higher recapture rate of large workers and soldiers relative to smaller workers.
5. The mark–recapture protocols provided inaccurate and unreliable forager population estimates, up to two orders of magnitude larger than direct counts of entire mound colonies. Thus the weighted mean estimates from more complex triple-mark–recapture protocols were not necessarily better than Lincoln index estimates from simpler single-mark–recapture protocols.
6. Mark–recapture studies may provide useful information about forager behaviour and foraging territories.     

Testing assumptions of mark–recapture theory in the coral reef fish Lutjanus apodus

This study tested assumptions of the Cormack–Jolly–Seber capture–mark–recapture (CMR) model in a population of the tropical snapper Lutjanus apodus in the central Bahamas using a combination of laboratory and field studies. The suitability of three different tag types [passive integrated transponder (PIT) tag, T-anchor tag and fluorescent dye jet-injected into the fins] was assessed. PIT tags were retained well, whereas T-anchor tags and jet-injected dye were not. PIT tags had no detectable effect on the rates of growth or survival of individuals. The capture method (fish trapping) was found to provide a representative sample of the population; however, a positive trap response was identified and therefore the assumption of equal capture probability was violated. This study illustrates an approach that can be used to test some of the critical assumptions of the CMR theory and it demonstrates that CMR methods can provide unbiased estimates of growth and mortality of L. apodus provided that trap response is explicitly modelled when estimating survival probability.     

Estimating the population size of specialised solitary bees

Abstract.  1. Reliable methods for quantifying population size are crucial for strategies to conserve endangered wild-bee species. Estimates of population size obtained through survey walks were compared with estimates obtained through mark–recapture studies in 10 populations of the red-listed solitary bee Andrena hattorfiana in southern Sweden.
2. The mean number of bees observed during survey walks was strongly correlated with estimates of population size obtained with mark–recapture. It was found that 5.5–23.4% (mean 13.4%) of the total population was observed during an average survey walk.
3. One component in mark–recapture analysis is the measure of survival of individuals. In the largest bee population, females of A. hattorfiana that emerged in early season were found to forage for pollen on average 18.4 days.
4. The findings suggest that during large-scale surveys, for example re-inventories for red-listed species, the population size of solitary bees can be quantified reliably and effectively by performing survey walks in a two-step process. The first step consists of survey walks to establish the relationship between number of bee observations per survey walk and mark–recapture population size for a small set of populations. In the second, simple observation survey walks can be performed for a large set of populations. In each population of A. hattorfiana , it is recommended that at least six survey walks are performed.     

Mark–recapture estimates of recruitment, survivorship and population growth rate for the screwworm fly, Cochliomyia hominivorax

Abstract.  Pradel model mark–release–recapture estimates of survivorship, φ , recruitment, f , and the rate of density-independent population growth, λ , are presented for eight mark–recapture studies of the screwworm Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae) from Costa Rica, totalling 19 573 released and 4476 recaptured flies. Corroborative estimates of survivorship and the rate of population growth based on an extensive review of the literature are also reported. Weighted-mean ± standard error of the mean (SEM) mark–release–recapture estimates of survivorship, recruitment and the rate of population growth were φ   =  0.798 ± 0.008, f   = 0.193 ± 0.008 and λ  = 1.005 ± 0.002, respectively. Population doubling time was estimated from λ at 139 days. Estimates of φ and λ from the literature both exceeded those calculated by mark–recapture methods and estimates of population doubling times were consequently shorter.     

The world's smallest whale population?

The North Pacific right whale (Eubalaena japonica) was heavily exploited by both nineteenth century whaling and recent (1960s) illegal Soviet catches. Today, the species remains extremely rare especially in the eastern North Pacific. Here, we use photographic and genotype data to calculate the first mark–recapture estimates of abundance for right whales in the Bering Sea and Aleutian Islands. The estimates were very similar: photographic = 31 (95% CL 23–54), genotyping = 28 (95% CL 24–42). We also estimated the population contains eight females (95% CL 7–18) and 20 males (95% CL 17–37). Although these estimates may relate to a Bering Sea subpopulation, other data suggest that the total eastern North Pacific population is unlikely to be much larger. Its precarious status today—the world''s smallest whale population for which an abundance estimate exists—is a direct consequence of uncontrolled and illegal whaling, and highlights the past failure of international management to prevent such abuses.     

Population regulation and demography in a harvested freshwater crayfish from Madagascar

Despite advances in statistical techniques for investigating population dynamics based on mark–recapture data, the majority of our understanding about demography and regulation comes from relatively few taxa. Most proposed generalisations about the association between demography and variation in population size are based on data from vertebrates, there are few sufficiently detailed invertebrate studies to examine whether these generalisations are widely supported. The population biology of freshwater invertebrates is especially poorly known. We present a large-scale mark–recapture study of an endemic freshwater crayfish from Madagascar ( Astacoides granulimanus ). Variation in density, caused by difference in fishing pressure due to local taboos, allowed us to investigate density-dependent regulation. We found evidence of density dependence in fecundity operating through the proportion of reproductive females by size but no significant evidence of density dependence in growth. Using a prospective analysis based on the elasticities from a size-structured matrix model, we found that both recruitment rates and survival rates of large individuals were strongly associated with deterministic population growth – a result that differs from generalisations drawn from vertebrate studies. A central assumption in mark–recapture studies is that handling does not affect mortality. By treating the number of times an individual was captured as an individual covariate, easily done using the freeware program MARK, we were able to test for, and take account of, handling-induced mortality. Our results show interesting similarities, and important differences, to generalisations based on vertebrate studies and emphasise the importance of population studies on poorly known taxa.     

Three ways of assessing metapopulation structure in the butterfly Plebejus argus

1. Three independent methods were used to investigate population structure in the butterfly Plebejus argus . First, migration and dispersal ability were measured by mark–release–recapture in seven adjacent habitat patches, and by release of butterflies in unoccupied habitat. Secondly, colonization of newly created habitat was observed over 7 years. Finally, genetic differentiation of local populations within a metapopulation was investigated. Sampled local populations included parts of the mark–release–recapture study area.
2. Plebejus argus is relatively sedentary: the maximum movement detected was 395 m, and only 2% of individuals moved further than 100 m between recaptures on different days. None the less, adjacent local populations in the mark–release–recapture study area were linked by occasional migration, with ≈ 1.4% of individuals moving between patches separated by 13–200 m.
3. Despite low mobility, observed colonizations occurred rapidly over distances of 1 km. Because P. argus occurs at high population densities, 1.4% migration can generate enough migrants to colonize newly suitable habitat quickly at this spatial scale.
4. Mark–release–recapture data were used to predict that there would be limited genetic differentiation through drift between local populations at this spatial scale. The prediction was supported by allele frequency data for the same local populations.
5. Genetic differentiation often indicates higher levels of migration than are revealed by the movements of marked individuals. This study shows that when experimental releases and extensive marking are undertaken in areas that are large relative to most movements, indirect measures of gene flow and direct measures of dispersal can concur.
6. Evidence from the three different approaches was complementary, indicating that P. argus occurs as metapopulations within the study area.     

Survival, movement, and resource use of the butterfly Parnassius clodius

Abstract.  1. A mark–recapture study was conducted on the American Apollo butterfly Parnassius clodius Menetries during three field seasons (1998–2000) to examine its movement patterns over the course of a season within a sagebrush meadow in Grand Teton National Park, Wyoming, U.S.A. The study examined how resources affected butterfly distribution patterns and used mark–recapture data to gain insight into movement differences between sexes and over time.
2. The average straight-line movement of P. clodius was 202 m day⁻¹, adjusted for sampling effort at different distances. Movement estimates in all 3 years were highly correlated with the average distance between plots sampled.
3. Butterfly abundance was correlated positively with per cent cover of its host plant Dicentra uniflora , but this relationship decreased in importance during the peak of the flight period when individuals may be more interested in finding mates. There was a weak, positive correlation between butterfly abundance and the abundance of its primary nectar source, Eriogonum umbellatum in 1999, but no relationship in 2000.
4. Survival, recapture, and transition probabilities were estimated using open population, capture–recapture models. Survival and recapture probability decreased over the course of each season, while the probability of moving between plots increased. Recapture probability was significantly lower for females than for males among all 3 years, but there was no difference between the sexes in survival rate.     

How accurate are single site transect data for monitoring butterfly trends? Spatial and temporal issues identified in monitoring Lasiommata megera

Multiple transect counts following Butterfly Monitoring Scheme (UKBMS) guidelines and Jolly–Seber estimates of population size were used to monitor the abundance of second generation Lasiommata megera on a single site in southern England. The two methods resulted in different patterns of emergence being detected. The proportion of the population (estimated by Jolly–Seber) recorded with transect counts depended on the time of day and weather with afternoon transect counts best recording the trend in abundance over the flight period, but even then counts recorded a variable fraction of the population (6.2–51.3%). Increasing the frequency with which transect counts are carried out per week reduced variation and increased the fit of transect counts to Jolly–Seber generated population estimates. However, indices of abundance generated from randomly selected transect counts for L. megera within sampling weeks varied 4-fold and indices for other butterfly species were also highly variable. For L. megera, transect count variability is attributed to non-representative placement of the transect route and changes in the behaviour and spatial distribution in relation to population size and season. We suggest that transect counts need to be fully validated before the data are used to monitor changes of butterfly populations at individual sites.     

Robustness and uncertainty in estimates of butterfly abundance from transect counts

Many butterfly populations are monitored by counting the number of butterflies observed while walking transects during the butterfly’s flight season. Methods for estimating population abundance from these transect counts are appealing because they allow rare populations to be monitored without capture–recapture studies that could harm fragile individuals. An increasingly popular method for estimating abundance from transect counts relies on strong assumptions about the counting process and the processes that govern butterfly population dynamics. Here, we study the statistical performance of this method when underlying model assumptions are violated. We find that estimates of population size are robust to departures from underlying model assumptions, but that the uncertainty in these estimates (i.e., confidence intervals) is substantially underestimated. Alternative bootstrap and Bayesian methods provide better measures of the uncertainty in estimated population size, but are conditional upon knowledge of butterfly detectability. Because of these requirements, a mixed approach that combines data from small capture–recapture studies with transect counts strikes the best balance between accurate monitoring and minimal injury to individuals. Our study is motivated by monitoring studies for St. Francis satyr (Neonympha mitchelli francisci), a rare and relatively immobile butterfly occurring only in the sandhills region of south-central North Carolina, USA.     

A method for rapidly mass laser-marking individually coded ground beetles (Coleoptera: Carabidae) in the field

Abstract.  1. A laser-marking technique is described that may be used to rapidly mass-mark and individually code insects in the field. In this study, ground beetles were marked but the method is applicable to a wide range of organisms with a hard exoskeleton or shell.
2. In a field-scale capture–recapture study conducted in winter wheat, 8266 beetles were coded. Individuals marked in the first week of the trial and recaptured 2 months later retained their codes, which were therefore considered permanent.
3. Assemblages were dominated numerically by Pterostichus cupreus , which formed more than 98% of the total captures. Of the 8046 released P. cupreus , 2269 were recaptured. As an illustration of the use of these data, the POPAN parameterisation of the Jolly–Seber model was used to estimate a whole-field population of 17 237 individuals, equating to a density of 0.46 beetles m⁻².     

Monthly variability of hydroacoustic fish stock estimates in a deep lake and its correlation to gillnet catches

Monthly (April to November) hydroacoustic surveys and parallel gillnet catches were used to determine vendace Coregonus albula abundance, biomass and population dynamics in a deep oligotrophic lake. By hydroacoustic surveys, recruitment of 0+ year vendace could clearly be detected. In contrast, gillnet catches resulted in low numbers of 0+ year fish, and similarly under-represented proportions of the oldest vendace. Consequently, the correlation between hydroacoustics and gillnets with respect to fish numbers and geometric mean fish total length was high only for the age groups 1 + to 4+ years. Annual variability in hydroacoustic estimates offish abundance and biomass was high (CV=26–29%) which reflects the seasonal population dynamics of vendace.     

Declining winter survival and fitness implications associated with latitudinal distribution in Norwegian Greylag Geese Anser anser

The Norwegian Greylag Goose Anser anser population has been increasing steadily over the past few decades, causing increasing nuisance in terms of agricultural crop damage. This, in combination with the importance of Greylags as a hunting target, has called for demographic estimates for the population to assist in management decisions. To this end, we analysed long-term mark–recapture data using Cormack–Jolly-Seber models embedded in program MARK to obtain survival estimates for the population. No sex-specific difference, or age effect on survival after juveniles had completed their first migration (3 months of age), was evident. Mean first-year survival was reported as 0.485 and annual survival of older birds as 0.700. On a monthly basis, survival in Greylags during summer and winter was very similar over the study period. A significant linear decline in winter survival from 0.909 to 0.807 was, however, apparent during the study period. Over the second half of the study (1994–2002), summer survival was about 3% lower than in the first half (1986–94) but no linear relationship was evident. We found a significant inverse relationship between Greylag survival during summer and latitudinal distribution in Norway. A similar relationship was evident between survival and annual bag numbers. The changes in adult survival observed in this study are likely to have had a substantial impact on the growth rate of the Norwegian Greylag population.     

Accuracy and precision of skink counts from artificial retreats

Index counts are commonly used to detect spatial and temporal changes in the size of wildlife populations. For indices to be valid there must be a constant (usually linear) relationship between the index and population size. In a study conducted in the Eglinton Valley (Fiordland, South Island, New Zealand), single-day index counts of common skinks (Oligosoma polychroma) from artificial retreats were compared with capture?mark?recapture (CMR) estimates of population size (N?) obtained by pitfall trapping. Generalised linear models revealed that skink counts from artificial retreats provided a reasonably accurate (P??1, which was high compared with other common skink populations. We recommend: (1) long-term monitoring of common skinks in the Eglinton Valley, using the index method described herein; (2) calibration of index counts against population size estimates collected from other habitats and species.     

Neonatal survival of Steller sea lions (Eumetopias jubatus)

Neonatal survival of Steller sea lions ( Eumetopias jubatus ) are often considered inconsequential to their population dynamics. However, observations of dead animals on rookeries and in surrounding waters suggest that early mortality is not uncommon. This study used the natural markings of adult females in a mark and resighting framework to estimate the apparent survival (φ) of pups with the Cormack–Jolly–Seber model at two sites on Lowrie Island, Alaska from birth to 3 wk old. Estimates varied greatly by site and year; 2002 Area 5:     (95% CI: 0.199, 0.684; n = 21), 2002 Area 1:     (0.437, 0.916; n = 21), 2003 Area 5:     (0.414, 0.738; n = 56), and 2003 Area 1:     (0.695, 0.997; n = 32). The mean estimate across the four area × year combinations was     (0.569, 0.772). Survival was lowest on the first day of life and then leveled off at a higher rate. None of the four environmental covariates we considered (swell height, interaction of tide and swell heights, density, or birth date) were significantly related to neonatal survival. Our results suggest that estimates of first-year survival that do not account for mortality prior to dispersal from the natal rookery may significantly overestimate survival rate.     

Mark—Recapture Accurately Estimates Census for Tuatara,a Burrowing Reptile

Abstract: Estimates of population size are necessary for effective management of threatened and endangered species, but accurate estimation is often difficult when species are cryptic. We evaluated effectiveness of mark–recapture techniques using the Lincoln–Peterson estimator for predicting true census size of a population of tuatara (Sphenodon punctatus), a burrowing reptile that is a conservation priority in New Zealand. We found that Lincoln–Peterson estimates (NŇ = 85) were accurate for predicting the census size (N = 87) after only a 3-day mark–recapture survey. We recommend this method as a cost-effective way to accurately estimate population size for isolated, inaccessible tuatara populations, because it requires limited personnel, expertise, and time, and has low environmental impact on fragile sites.     

Considering sampling bias in close‐kin mark–recapture abundance estimates of Atlantic salmon

Genetic methods for the estimation of population size can be powerful alternatives to conventional methods. Close‐kin mark–recapture (CKMR) is based on the principles of conventional mark–recapture, but instead of being physically marked, individuals are marked through their close kin. The aim of this study was to evaluate the potential of CKMR for the estimation of spawner abundance in Atlantic salmon and how age, sex, spatial, and temporal sampling bias may affect CKMR estimates. Spawner abundance in a wild population was estimated from genetic samples of adults returning in 2018 and of their potential offspring collected in 2019. Adult samples were obtained in two ways. First, adults were sampled and released alive in the breeding habitat during spawning surveys. Second, genetic samples were collected from out‐migrating smolts PIT‐tagged in 2017 and registered when returning as adults in 2018. CKMR estimates based on adult samples collected during spawning surveys were somewhat higher than conventional counts. Uncertainty was small (CV < 0.15), due to the detection of a high number of parent–offspring pairs. Sampling of adults was age‐ and size‐biased and correction for those biases resulted in moderate changes in the CKMR estimate. Juvenile dispersal was limited, but spatially balanced sampling of adults rendered CKMR estimates robust to spatially biased sampling of juveniles. CKMR estimates based on returning PIT‐tagged adults were approximately twice as high as estimates based on samples collected during spawning surveys. We suggest that estimates based on PIT‐tagged fish reflect the total abundance of adults entering the river, while estimates based on samples collected during spawning surveys reflect the abundance of adults present in the breeding habitat at the time of spawning. Our study showed that CKMR can be used to estimate spawner abundance in Atlantic salmon, with a moderate sampling effort, but a carefully designed sampling regime is required.     

CORRECTING AERIAL SURVEY COUNTS OF HARBOR SEALS (PHOCA VITULINA RICHARDSI) IN WASHINGTON AND OREGON

Aerial surveys of harbor seals on land produce only a minimum assessment of the population; a correction factor to account for the missing animals is necessary to estimate total abundance. In 1991 and 1992, VHF radio tags were deployed on harbor seals ( n = 124) at six sites in Washington and Oregon. During aerial surveys a correction factor to account for seals in the water was determined from the proportion of radio-tagged seals on shore during the pupping season. This proportion ranged from 0.54 to 0.74. Among the six sites there was no significant difference in the proportion of animals on shore nor was there a difference in age/sex categories of seals on shore between sites. The pooled correction factor for determining total population abundance was 1.53. An additional 32 seals were radio tagged in 1993 at one of the sites used in 1991. Comparing data from the two years, we found no interannual variation. Aerial surveys of all known harbor seal haul-out sites in Washington ( n = 319) and Oregon ( n = 68) were flown during the peak of the pupping season, 1991–1993. The Washington and Oregon harbor seal population was divided into two stocks based on pupping phenology, morphometics, and genetics. Mean counts for the Washington inland stock were 8,710 in 1991, 9,018 in 1992, and 10,092 in 1993. Oregon and Washington coastal stock mean counts were 18,363 in 1991, 18,556 in 1992, and 17,762 in 1993. Multiplying the annual count by the correction factor yielded estimates of harbor seal abundance in the Washington inland stock of 13,326 (95% CI = 11,637–15,259) for 1991, 13,798 (95% CI = 11,980–15,890) for 1992, and 15,440 (95% CI = 13,382–17,814) for 1993. In the Oregon and Washington coastal stock the corrected estimate of harbor seal abundance was 28,094 (95% CI = 24,697–31,960) in 1991, 28,391 (95% CI = 24,847–32,440) for 1992, and 27,175 (95% CI = 23,879–30,926) for 1993.