Estimating abundance of a recovering transboundary brown bear population with capture-recapture models

Abundance of small populations of large mammals may be assessed using complete counts of the different individuals detected over a time period, so-called minimum detected size (MDS). However, as population is growing larger and its distribution is expanding wider, the risk of under-estimating population size using MDS is increasing sharply due to the rarely fulfilled assumption of perfect detection of all individuals of the population, and as a result, the need to report uncertainty in population size estimates becomes crucial. We addressed these issues within the framework of the monitoring of the critically endangered Pyrenean brown bear population that was on the edge of extinction in the mid-1990s with only five individuals remaining, but was reinforced by 11 bears originated from Slovenia since then. We used Pollock's closed robust design (PCRD) capture-recapture models applied to the cross-border non-invasive sampling data from France, Spain and Andorra to provide the first published annual abundance estimates of the Pyrenean brown bear population and its trends over time. Annual population size increased and displayed a fivefold rise between 2008 and 2020, reaching > 60 individuals in 2020. Detection heterogeneity among individuals may stem from intraspecific home range size disparities making it more likely to find signs of individuals who move more. We found a lower survival rate in cubs than in adults and subadults, since the formers suffer from more mortality risks (such as infanticides, predations, mother death or abandonments) than the latters. Our study provides evidence that the PCRD capture-recapture modelling approach can provide reliable estimates of the size of and trend in large mammal populations, while minimizing bias due to inter-individual heterogeneity in detection probabilities and allowing the quantification of sampling uncertainty surrounding these estimates. Such information is vital for informing management decision-making and assessing population conservation status.

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Estimating the population size of people who inject drugs in Ho Chi Minh City, Vietnam: A two-survey capture-recapture exercise (Preprint)

10.2196/preprints.16459 ◽

2019 ◽

Author(s):

Abu Abdul-Quader

Keyword(s):

Population Size ◽

Illicit Drugs ◽

People Who Inject Drugs ◽

Care Service ◽

Ho Chi Minh City ◽

Size Estimation ◽

Population Size Estimates ◽

Capture Recapture ◽

The City ◽

Size Estimates

BACKGROUND Population size estimation of people who inject drugs (PWID) in Ho Chi Minh City (HCMC), Vietnam relied on the UNAIDS Estimation and Projection Package and reports from the city police department. The two estimates vary widely. OBJECTIVE To estimate the population size of people who inject drugs in Ho Chi Minh City, Vietnam METHODS Using Respondent-driven sampling (RDS), we implemented two-source capture-recapture method to estimate the population size of PWID in HCMC in 2017 in 7 out of 24 districts. The study included men or women aged at least 18 years who reported injecting illicit drugs in the last 90 days and who had lived in the city the past six months. We calculated two sets of size estimates, the first assumed that all participants in each survey round resided in the district where the survey was conducted, the second, used the district of residence as reported by the participant. District estimates were summed to obtain an aggregate estimate for the seven districts. To calculate the city total, we weighted the population size estimates for each district by the inverse of the stratum specific sampling probabilities. RESULTS The first estimate resulted in a population size of 19,155 (95% CI: 17,006–25,039). The second one generated a smaller population size estimate of 12,867 (95% CI: 11,312–17,393). CONCLUSIONS The two-survey capture-recapture exercise provided two disparate estimates of PWID in HCMC. For planning HIV prevention and care service needs among PWID in HCMC, both estimates may need to be taken into consideration together with size estimates from other sources.

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Comparison of capture–recapture estimators of snowshoe hare populations

Canadian Journal of Zoology ◽

10.1139/z94-244 ◽

1994 ◽

Vol 72 (10) ◽

pp. 1800-1807 ◽

Cited By ~ 20

Author(s):

John Boulanger ◽

Charles J. Krebs

Keyword(s):

Population Size ◽

Yukon Territory ◽

Robust Estimator ◽

Snowshoe Hare ◽

Lake Area ◽

Island Populations ◽

Snowshoe Hares ◽

Population Size Estimates ◽

Size Population ◽

Capture Recapture

We used two island populations of snowshoe hares (Lepus americanus) in the Kluane Lake area of the Yukon Territory of Canada to evaluate capture – recapture estimators. These islands were intensively sampled, allowing us to enumerate the actual population size. Population size estimates were calculated using the programs CAPTURE and JOLLY, and estimators were compared for bias characteristics. Results from both islands suggest that the CAPTURE heterogeneity models Mh (jackknife), Mh (Chao), and Mth (time – heterogeneity) and the Jolly – Seber model were approximately unbiased. All other CAPTURE models displayed a negative bias. The CAPTURE model selection routine picked estimation models of different biases for each trapping period, an undesirable result. We conclude that it is best to use one robust estimator such as the Mh (jackknife) with snowshoe hare data.

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Diversion of Fishing Pressure on the Economically Important Species Barbus barbus (Linnaeus, 1758) to Protect the Community Interest Congeneric Barbus meridionalis Risso 1826, Based on a Decision-Support Management System

Transylvanian Review of Systematical and Ecological Research ◽

10.2478/trser-2018-0013 ◽

2018 ◽

Vol 20 (2) ◽

pp. 63-74

Author(s):

Cristina Cismaş ◽

Doru Bănăduc ◽

Angela Curtean-Bănăduc

Keyword(s):

Management System ◽

Conservation Status ◽

System Model ◽

Management Decision ◽

Fishing Pressure ◽

Important Species ◽

Barbus Barbus ◽

Management Actions ◽

Community Interest ◽

Management Decision Making

Abstract The ADONIS:CE instrument has been used in the field of congeners species, Barbus barbus – of economic interest and Barbus meridionalis – of conservation interest, to build a support-system model for management decision-making. Analysis of the habitat needs and the indicators for favorable conservation status have identified pressures and threats to these fish species for which management actions have been proposed. This management system favors the decrease of fishing pressure on Barbus meridionalis species by its transfer to Barbus barbus species.

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shinyrecap: A Shiny Application for Population Size Estimation from Capture-Recapture Data (Preprint)

10.2196/preprints.32645 ◽

2021 ◽

Author(s):

Anne F. McIntyre ◽

Ian E. Fellows ◽

Steve Gutreuter ◽

Wolfgang Hladik

Keyword(s):

Population Size ◽

Sex Workers ◽

Female Sex Workers ◽

Population Size Estimation ◽

Sub Saharan Africa ◽

Size Estimation ◽

Female Sex ◽

Populations At Risk ◽

Population Size Estimates ◽

Capture Recapture

BACKGROUND Capture-recapture is often used to estimate the size of populations at risk for HIV, including female sex workers, men who have sex with men, and people who inject drugs. These population size estimates are critical in determining resource allocation for HIV services geared toward these communities. OBJECTIVE Compared to the commonly used two-source capture-recapture, capture-recapture relying on three (or more) samples can provide more robust PSE but involve far more complex statistical analysis. shinyrecap is designed to provide a user-friendly interface for the field epidemiologist. METHODS shinyrecap is built on the Shiny web application framework for R. This allows it to seamlessly integrate with the sophisticated CRC statistical packages. Additionally, the application may be accessed online or run locally on the user’s machine. RESULTS The application enables users to engage in sample size calculation based on a simulation framework. It assists in the proper formatting of collected data by providing a tool to convert commonly used formats to that used by analysis software. A wide variety of methodologies are supported by the analysis tool, including log-linear, Bayesian model averaging, and Bayesian latent class models. For each methodology, diagnostics and model checking interfaces are provided. CONCLUSIONS Through a use case, we demonstrate the broad utility of this powerful tool with three-source capture-recapture data to produce population size estimation for female sex workers in a subnational unit of a country in sub-Saharan Africa.

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Waterbird population estimates for a key staging site in Kazakhstan: a contribution to wetland conservation on the Central Asian flyway

Bird Conservation International ◽

10.1017/s0959270908000087 ◽

2008 ◽

Vol 18 (1) ◽

pp. 71-86 ◽

Cited By ~ 8

Author(s):

Holger Schielzeth ◽

Götz Eichhorn ◽

Thomas Heinicke ◽

Johannes Kamp ◽

Maxim A. Koshkin ◽

...

Keyword(s):

Population Size ◽

Conservation Status ◽

Steppe Zone ◽

Wetland Conservation ◽

Conservation Strategies ◽

Population Estimates ◽

The South ◽

Migration Routes ◽

South West ◽

Population Size Estimates

AbstractRealistic population size estimates for waterbirds are crucial for the application of wetland conservation strategies, since the identification of internationally important wetlands is based on local numbers relative to the population size of the respective species. Central Asia is a poorly surveyed region that is situated at the intersection of migration routes that lead waterbirds from Western Siberia to the south-west (South-West Asia, East Africa) and to the south-east (South Asia, India). We calculated waterbird population estimates for the Tengiz–Korgalzhyn region, a large wetland complex in the steppe zone of Central Kazakhstan, based on waterbird surveys conducted between 1999 and 2004. For 20 of 43 species analysed the region supported more than 5% of the relevant flyway populations. Five species occurred with more than 40% of the flyway totals, including the Endangered White-headed Duck Oxyura leucocephala and the Vulnerable Dalmatian Pelican Pelecanus crispus. Peak numbers were recorded in summer and autumn and for most species numbers were more than an order of magnitude lower on spring migration compared with autumn migration. We identified 72 individual sites that held more than 20,000 waterbirds or more than 1% of a particular flyway population at least once. These sites are likely to constitute priorities for conservation. The general conservation status of the region is favourable, since many of the important sites are located within a strict nature reserve. However, outside the reserve hunting, fishing and powerline casualties represent conservation issues that should be monitored more carefully in the future.

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Estimates of abundance and apparent survival of coastal dolphins in Port Essington harbour, Northern Territory, Australia

Wildlife Research ◽

10.1071/wr14031 ◽

2014 ◽

Vol 41 (1) ◽

pp. 35 ◽

Cited By ~ 17

Author(s):

Carol Palmer ◽

Lyndon Brooks ◽

Guido J. Parra ◽

Tracey Rogers ◽

Debra Glasgow ◽

...

Keyword(s):

Population Size ◽

Conservation Status ◽

Local Population ◽

Northern Territory ◽

Systematic Sampling ◽

Northern Australia ◽

Apparent Survival ◽

Photo Identification ◽

Population Size Estimates ◽

Sampling Protocols

Context Three dolphin species occur in coastal waters of monsoonal northern Australia: the Australian snubfin (Orcaella heinsohni), humpback (Sousa sp.) and the bottlenose (Tursiops sp.). Their overall population size and trends are poorly known, and their conservation status has been difficult to resolve, but can be expected to deteriorate with likely increased development pressures. Aims We sought to provide an estimate of abundance, and apparent survival, of the three dolphin species at the largely undeveloped harbour of Port Essington (325 km2), Northern Territory, with repeated sampling over a 2.9-year period. Given increasing obligations to undertake population assessments for impact studies at proposed development sites, we assess the strengths and limitations of a systematic sampling program. Methods We used photo-identification data collected during systematic boat-based transect surveys undertaken from 2008 to 2010 and Pollock’s robust capture–recapture design model. Key results Total abundance estimates for the three species were variable across different sampling periods. The estimated number of individuals in the sampled area varied per sampling episode from 136 (s.e. 62) to 222 (s.e. 48) for snubfin, from 48 (s.e. 7) to 207 (s.e. 14) for humpbacks and from 34 (s.e. 6) to 75 (s.e. 9) for bottlenose dolphins. Apparent survival was estimated for snubfin at 0.81 (s.e. 0.11), humpbacks at 0.59 (s.e. 0.12) and bottlenose at 0.51 (s.e. 0.17) per annum. Key conclusions (1) The values derived here provide some of the only estimates of local population size for these species across monsoonal northern Australia; (2) population-size estimates varied considerably among seasons or sampling episodes; (3) the low apparent survival probabilities indicated that many individuals may move at scales larger than the study area; (4) density of snubfin and humpback dolphins in the present study area exceeded the few other estimates available for these species elsewhere in Australia. Implications The present study provided the first baseline estimates of abundance and apparent survival for three coastal dolphin species in monsoonal northern Australia. Such information is becoming increasingly important as development pressures intensify in coastal areas. Sampling protocols for future monitoring and impact assessment need an enhanced consideration of seasonality and scale issues.

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Population size estimates of pink river dolphins (Inia geoffrensis) using mark-recapture methods on photo-identification

Latin American Journal of Aquatic Mammals ◽

10.5597/lajam00177 ◽

2014 ◽

Vol 9 (2) ◽

pp. 132-139 ◽

Cited By ~ 2

Author(s):

Catalina Gómez-Salazar ◽

Hal Whitehead ◽

Fernando Trujillo

Keyword(s):

Population Size ◽

Conservation Status ◽

Freshwater Ecosystems ◽

Mark Recapture ◽

Photo Identification ◽

Population Size Estimate ◽

Population Size Estimates ◽

Inia Geoffrensis ◽

Colombian Amazon ◽

Size Estimates

Population size estimates of pink river dolphins (Inia geoffrensis) are critical to assess the conservation status of this species and the impacts of increasing human stressors in freshwater ecosystems. Photo-identifications of Inia dolphins were collected between February 2007 and August 2009 in two locations of the Colombian Amazon and Orinoco river basins. Population sizes of Inia were obtained by using the closed (Petersen) mark-recapture model on photo-identifications. The total population size estimate for right/left side individuals was 129/71 Inia dolphins (CV=0.36/0.35) in the Amazon location and 125/58 Inia dolphins (CV=0.77/0.69) in the Orinoco location. The survey and analysis protocols were designed to try to meet mark-recapture assumptions. However, photo-identification was incomplete in both study areas, and there could be recruitment and unequal probabilities of capture due to preferences of individuals for certain areas. Further effort should be focused towards expanding the photo-identification catalogues and creating long-term monitoring programs.

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Estimating the Size of Key Populations in Kampala, Uganda: 3-Source Capture-Recapture Study (Preprint)

10.2196/preprints.12118 ◽

2018 ◽

Author(s):

Reena H Doshi ◽

Kevin Apodaca ◽

Moses Ogwal ◽

Rommel Bain ◽

Ermias Amene ◽

...

Keyword(s):

Population Size ◽

Latent Class ◽

Latent Class Model ◽

Key Populations ◽

Size Estimation ◽

Public Health Response ◽

Hiv Epidemic ◽

Population Size Estimates ◽

Capture Recapture ◽

Size Estimates

BACKGROUND Key populations, including people who inject drugs (PWID), men who have sex with men (MSM), and female sex workers (FSW), are disproportionately affected by the HIV epidemic. Understanding the magnitude of, and informing the public health response to, the HIV epidemic among these populations requires accurate size estimates. However, low social visibility poses challenges to these efforts. OBJECTIVE The objective of this study was to derive population size estimates of PWID, MSM, and FSW in Kampala using capture-recapture. METHODS Between June and October 2017, unique objects were distributed to the PWID, MSM, and FSW populations in Kampala. PWID, MSM, and FSW were each sampled during 3 independent captures; unique objects were offered in captures 1 and 2. PWID, MSM, and FSW sampled during captures 2 and 3 were asked if they had received either or both of the distributed objects. All captures were completed 1 week apart. The numbers of PWID, MSM, and FSW receiving one or both objects were determined. Population size estimates were derived using the Lincoln-Petersen method for 2-source capture-recapture (PWID) and Bayesian nonparametric latent-class model for 3-source capture-recapture (MSM and FSW). RESULTS We sampled 467 PWID in capture 1 and 450 in capture 2; a total of 54 PWID were captured in both. We sampled 542, 574, and 598 MSM in captures 1, 2, and 3, respectively. There were 70 recaptures between captures 1 and 2, 103 recaptures between captures 2 and 3, and 155 recaptures between captures 1 and 3. There were 57 MSM captured in all 3 captures. We sampled 962, 965, and 1417 FSW in captures 1, 2, and 3, respectively. There were 316 recaptures between captures 1 and 2, 214 recaptures between captures 2 and 3, and 235 recaptures between captures 1 and 3. There were 109 FSW captured in all 3 rounds. The estimated number of PWID was 3892 (3090-5126), the estimated number of MSM was 14,019 (95% credible interval (CI) 4995-40,949), and the estimated number of FSW was 8848 (95% CI 6337-17,470). CONCLUSIONS Our population size estimates for PWID, MSM, and FSW in Kampala provide critical population denominator data to inform HIV prevention and treatment programs. The 3-source capture-recapture is a feasible method to advance key population size estimation.

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Estimating the Size of Key Populations in Kampala, Uganda: 3-Source Capture-Recapture Study

JMIR Public Health and Surveillance ◽

10.2196/12118 ◽

2019 ◽

Vol 5 (3) ◽

pp. e12118 ◽

Cited By ~ 5

Author(s):

Reena H Doshi ◽

Kevin Apodaca ◽

Moses Ogwal ◽

Rommel Bain ◽

Ermias Amene ◽

...

Keyword(s):

Population Size ◽

Latent Class ◽

Latent Class Model ◽

Key Populations ◽

Size Estimation ◽

Public Health Response ◽

Hiv Epidemic ◽

Population Size Estimates ◽

Capture Recapture ◽

Size Estimates

Background Key populations, including people who inject drugs (PWID), men who have sex with men (MSM), and female sex workers (FSW), are disproportionately affected by the HIV epidemic. Understanding the magnitude of, and informing the public health response to, the HIV epidemic among these populations requires accurate size estimates. However, low social visibility poses challenges to these efforts. Objective The objective of this study was to derive population size estimates of PWID, MSM, and FSW in Kampala using capture-recapture. Methods Between June and October 2017, unique objects were distributed to the PWID, MSM, and FSW populations in Kampala. PWID, MSM, and FSW were each sampled during 3 independent captures; unique objects were offered in captures 1 and 2. PWID, MSM, and FSW sampled during captures 2 and 3 were asked if they had received either or both of the distributed objects. All captures were completed 1 week apart. The numbers of PWID, MSM, and FSW receiving one or both objects were determined. Population size estimates were derived using the Lincoln-Petersen method for 2-source capture-recapture (PWID) and Bayesian nonparametric latent-class model for 3-source capture-recapture (MSM and FSW). Results We sampled 467 PWID in capture 1 and 450 in capture 2; a total of 54 PWID were captured in both. We sampled 542, 574, and 598 MSM in captures 1, 2, and 3, respectively. There were 70 recaptures between captures 1 and 2, 103 recaptures between captures 2 and 3, and 155 recaptures between captures 1 and 3. There were 57 MSM captured in all 3 captures. We sampled 962, 965, and 1417 FSW in captures 1, 2, and 3, respectively. There were 316 recaptures between captures 1 and 2, 214 recaptures between captures 2 and 3, and 235 recaptures between captures 1 and 3. There were 109 FSW captured in all 3 rounds. The estimated number of PWID was 3892 (3090-5126), the estimated number of MSM was 14,019 (95% credible interval (CI) 4995-40,949), and the estimated number of FSW was 8848 (95% CI 6337-17,470). Conclusions Our population size estimates for PWID, MSM, and FSW in Kampala provide critical population denominator data to inform HIV prevention and treatment programs. The 3-source capture-recapture is a feasible method to advance key population size estimation.

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Conservation status of threatened and endemic birds of New Britain, Papua New Guinea

Bird Conservation International ◽

10.1017/s0959270917000156 ◽

2017 ◽

Vol 28 (3) ◽

pp. 439-450

Author(s):

ROBERT A. DAVIS ◽

GUY DUTSON ◽

JUDIT K. SZABO

Keyword(s):

Population Size ◽

Papua New Guinea ◽

Oil Palm ◽

Conservation Status ◽

Bird Species ◽

New Guinea ◽

Old Growth Forest ◽

Population Size Estimates ◽

New Britain ◽

Size Estimates

SummaryNew Britain in the Bismarck Archipelago of Papua New Guinea supports 14 endemic bird species and together with New Ireland, forms an Endemic Bird Area that supports 38 restricted range species. Extensive conversion of lowland forest to oil palm plantations resulted in the loss of over 20% of forest under 100 m altitude between 1989 and 2000. However the rate of loss has subsequently slowed (2.2% loss across all altitudes between 2002 and 2014), and much forest remains at higher altitudes: 72% of New Britain remained forested (including secondary forest) in 2014. Despite the ongoing high threat and rich endemic bird fauna, the state of knowledge of the conservation status of birds in New Britain is very poor. We use an unprecedented dataset based on 415 hours of bird surveys conducted in oil palm plantations, as well as primary and secondary forests at all altitudes, to revise the IUCN status of New Britain’s birds. These data indicate that six species of elevated conservation concern are less dependent on old-growth forest than previously assessed. We recommend reduced population size estimates for one species, New Britain Kingfisher Todiramphus albonotatus. We recommend increased population size estimates for seven species: Pied Cuckoo-dove Reinwardtoena browni, Yellowish Imperial Pigeon Ducula subflavescens, Green-fronted Hanging Parrot Loriculus tener, Blue-eyed Cockatoo Cacatua opthalmica, Violaceous Coucal Centropus violaceous, New Britain Boobook Ninox odiosa and New Britain Thrush Zoothera talaseae. Despite our comprehensive surveys, Slaty-backed Goshawk Accipiter luteoschistaceus, New Britain Sparrowhawk Accipiter brachyurus, New Britain Bronzewing Henicophaps foersteri and Golden Masked-owl Tyto aurantia remain very rarely recorded and require further assessment. With ongoing habitat loss, particularly in lowland areas, New Britain’s birds urgently require more attention.

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