Section: Ecology
Topic: Ecology, Population biology
Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets
10.24072/pcjournal.348 - Peer Community Journal, Volume 3 (2023), article no. e122.
Get full text PDF Peer reviewed and recommended by PCI
1. The development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models over the past few decades have greatly improved the assessment of population demographic rates to address ecological and conservation questions. In particular, multi-state models, which offer flexibility in analysing complex study systems, have gained popularity within the ecological community. In this study, we focus on the issue of mark loss and the associated recycling of remarked individuals, which requires further exploration given the increasing use of these models. 2. To fill this knowledge gap, we employed a wide range of simulation scenarios that reflect commonly encountered real case studies, drawing inspiration from the survival rates of 700 vertebrate species. Using a multi-state, Arnason-Schwartz (AS) modelling framework, we estimated the effects of mark loss and recycled individuals on parameter estimates. We assessed parameter bias by simulating a metapopulation system with varying capture and survival rates. Additionally, we demonstrated how mark loss can be easily estimated and accounted for using a 10-year empirical CMR dataset of bats. The bats were individually identified using Passive Integrated Transponder (PIT) tag technology as potentially lost marks and multi-locus genotypes as 'permanent marks'. 3. Our simulation results revealed that the occurrence of bias and the affected parameters were highly dependent on the study system, making it difficult to establish general rules to predict bias a priori. The model structure and the interdependency among parameters pose challenges in predicting the impact of bias on estimates. 4. Our findings underscore the importance of assessing the effect of mark loss when using AS models. Ignoring such violations of model assumptions can have significant implications for ecological inferences and conservation policies. In general, the use of permanent marks, such as genotypes, should always be preferred when modelling population dynamics. If that is not feasible, an alternative is to combine two independent types of temporary marks, such as PIT tags and bands. 5. Analysis of our empirical dataset on Myotis myotis bats revealed that tag loss is higher in juveniles than in adults during the first year after tagging. The use of surgical glue to close the injection hole reduces tag loss rate from 28% to 19% in juveniles, while it has no effect on the tag loss rate in adults (~10%). The main bias observed in our metapopulation system appears in the survival rate, with up to a 20% underestimation if tag loss is not accounted for.
Type: Research article
CC-BY 4.0
@article{10_24072_pcjournal_348,
author = {Touzalin, Fr\'ed\'eric and Petit, Eric J. and Cam, Emmanuelle and Stagier, Claire and Teeling, Emma C. and Puechmaille, S\'ebastien J.},
title = {Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets},
journal = {Peer Community Journal},
eid = {e122},
publisher = {Peer Community In},
volume = {3},
year = {2023},
doi = {10.24072/pcjournal.348},
language = {en},
url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.348/}
}
TY - JOUR AU - Touzalin, Frédéric AU - Petit, Eric J. AU - Cam, Emmanuelle AU - Stagier, Claire AU - Teeling, Emma C. AU - Puechmaille, Sébastien J. TI - Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets JO - Peer Community Journal PY - 2023 VL - 3 PB - Peer Community In UR - https://peercommunityjournal.org/articles/10.24072/pcjournal.348/ DO - 10.24072/pcjournal.348 LA - en ID - 10_24072_pcjournal_348 ER -
%0 Journal Article %A Touzalin, Frédéric %A Petit, Eric J. %A Cam, Emmanuelle %A Stagier, Claire %A Teeling, Emma C. %A Puechmaille, Sébastien J. %T Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets %J Peer Community Journal %D 2023 %V 3 %I Peer Community In %U https://peercommunityjournal.org/articles/10.24072/pcjournal.348/ %R 10.24072/pcjournal.348 %G en %F 10_24072_pcjournal_348
Touzalin, Frédéric; Petit, Eric J.; Cam, Emmanuelle; Stagier, Claire; Teeling, Emma C.; Puechmaille, Sébastien J. Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets. Peer Community Journal, Volume 3 (2023), article no. e122. doi : 10.24072/pcjournal.348. https://peercommunityjournal.org/articles/10.24072/pcjournal.348/
Peer reviewed and recommended by PCI : 10.24072/pci.ecology.100416
Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.
[1] Laboratory experiment on survival, growth and tag retention following PIT injection into the body cavity of juvenile brown trout (Salmo trutta), Fisheries Research, Volume 86 (2007) no. 2, pp. 280-284 | DOI
[2] Bias and Loss of Precision Due to Tag Loss in Jolly–Seber Estimates for Mark–Recapture Experiments, Canadian Journal of Fisheries and Aquatic Sciences, Volume 38 (1981) no. 9, pp. 1077-1095 | DOI
[3] Parameter estimates from mark-recapture experiments on two populations subject to migration and death, Population Ecology, Volume 13 (1972) no. 2, pp. 97-113 | DOI
[4] The estimation of population size, migration rates and survival in a stratified population, Researches on Population Ecology, Volume 15 (1973) no. 2, pp. 1-8 | DOI
[5] Can Selection by an Ectoparasite Drive a Population of Red Crossbills from Its Adaptive Peak?, Evolution, Volume 59 (2005) no. 9, pp. 2025-2032 | DOI
[6] Modeling survival and mark loss in molting animals: Recapture, dead recoveries, and exuvia recoveries, Ecology, Volume 88 (2007-02) no. 2, pp. 289-295 | DOI
[7] Marks lost in action, biased estimations, Peer Community in Ecology, Volume 100416 (2023) | DOI
[8] General methods for monitoring convergence of iterative simulations, Journal of Computational and Graphical Statistics, Volume 7 (1998) no. 4, pp. 434-455 | DOI
[9] Contribution of Capture-Mark-Recapture Modeling to Studies of Evolution by Natural Selection, Modeling Demographic Processes In Marked Populations (Environmental and Ecological Statistics), Springer US, 2009, pp. 83-129 | DOI
[10] Dispersal and individual quality in a long lived species, Oikos, Volume 106 (2004) no. 2, pp. 386-398 | DOI
[11] U-CARE: Utilities for performing goodness of fit tests and manipulating CApture-REcapture data, Ecography, Volume 32 (2009) no. 6, pp. 1071-1074 | DOI
[12] Program E-Surge: A Software Application for Fitting Multievent Models, Modeling Demographic Processes In Marked Populations (Environmental and Ecological Statistics), Volume 3, Springer US, 2009, pp. 845-865 | DOI
[13] Data gaps and opportunities for comparative and conservation biology, Proceedings of the National Academy of Sciences, Volume 116 (2019) no. 19, pp. 9658-9664 | DOI
[14] A General Model for the Analysis of Mark-Resight, Mark-Recapture, and Band-Recovery Data under Tag Loss, Biometrics, Volume 60 (2004) no. 4, pp. 900-909 | DOI
[15] Estimates of Survival from Sighting of Marked Animals, Biometrika, Volume 51 (1964) no. 3, pp. 429-438 | DOI
[16] The Jolly–Seber Model with Tag Loss, Biometrics, Volume 62 (2006) no. 3, pp. 699-705 | DOI
[17] Modeling and Evaluation of Ear Tag Loss in Black Bears, The Journal of Wildlife Management, Volume 62 (1998) no. 4, pp. 1292-1300 | DOI
[18] Modeling data from double-tagging experiments to estimate heterogeneous rates of tag shedding in lake trout (Salvelinus namaycush), Canadian Journal of Fisheries and Aquatic Sciences, Volume 56 (1999) no. 8, pp. 1409-1419 | DOI
[19] Keeping tabs: Are redundant marking systems needed for rodents?, Wildlife Society Bulletin, Volume 34 (2006) no. 3, pp. 764-771 | DOI
[20] Drivers of longitudinal telomere dynamics in a long-lived bat species, Myotis myotis, Molecular Ecology, Volume 29 (2020) no. 16, pp. 2963-2977 | DOI
[21] Reliable microsatellite genotyping of the Eurasian badger (Meles meles) using faecal DNA, Molecular Ecology, Volume 12 (2003) no. 6, pp. 1649-1661 | DOI
[22] Suitability of passive integrated transponder tags for marking live animals for trade, Wildlife Research, Volume 22 (1995) no. 6, pp. 767-773 | DOI
[23] Individual heterogeneity and capture–recapture models: what, why and how?, Oikos, Volume 127 (2018) no. 5, pp. 664-686 | DOI
[24] R2ucare: An r package to perform goodness-of-fit tests for capture–recapture models, Methods in Ecology and Evolution, Volume 9 (2018) no. 7, pp. 1749-1754 | DOI
[25] MultiBUGS: A Parallel Implementation of the BUGS Modelling Framework for Faster Bayesian Inference, Journal of Statistical Software, Volume 95 (2020), p. 7 | DOI
[26] Estimates of Movement and Site Fidelity Using Mark-Resight Data of Wintering Canada Geese, Ecology, Volume 72 (1991) no. 2, pp. 523-533 | DOI
[27] A Multistate Capture–Recapture Modeling Strategy to Separate True Survival from Permanent Emigration for a Passive Integrated Transponder Tagged Population of Stream Fish, Transactions of the American Fisheries Society, Volume 140 (2011) no. 2, pp. 320-333 | DOI
[28] Evolutionary history and sex are significant drivers of crayfish demography in resource-limited cave ecosystems, Evolutionary Ecology, Volume 34 (2020) no. 2, pp. 235-255 | DOI
[29] State-specific detection probabilities and disease prevalence, Ecological Applications, Volume 17 (2007) no. 1, pp. 154-167 | DOI
[30] The role of heterogeneity in animal population dynamics, Proceedings of the International Biometrics Conference, Volume 13 (1986), p. 5
[31] Multivariate State Hidden Markov Models for Mark-Recapture Data, Statistical Science, Volume 31 (2016) no. 2, pp. 233-244 | DOI
[32] Explicit Estimates from Capture-Recapture Data with Both Death and Immigration-Stochastic Model, Biometrika, Volume 52 (1965), pp. 225-247 | DOI
[33] A Capture–Recapture Model with Double-Marking, Live and Dead Encounters, and Heterogeneity of Reporting Due to Auxiliary Mark Loss, Journal of Agricultural, Biological, and Environmental Statistics, Volume 16 (2011) no. 1, pp. 88-104 | DOI
[34] Effect of Passive Integrated Transponder Tag Implantation Site on Tag Retention, Growth, and Survival of Two Sizes of Juvenile Bluegills and Yellow Perch, North American Journal of Fisheries Management, Volume 31 (2011) no. 4, pp. 726-732 | DOI
[35] jagsUI: A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses, https://CRAN.R-project.org/package=jagsUI, 2016
[36] Estimation of Survival Rates from a Mark-Recapture Study with Tag Loss, Biometrics, Volume 44 (1988) no. 1, pp. 117-130 | DOI
[37] Doing Bayesian Data Analysis: A Tutorial with R, JAGS, and Stan, Academic Press, 2014
[38] Rejecting or Accepting Parameter Values in Bayesian Estimation, Advances in Methods and Practices in Psychological Science, Volume 1 (2018) no. 2, pp. 270-280 | DOI
[39] Hidden Markov Model for Dependent Mark Loss and Survival Estimation, Journal of Agricultural Biological and Environmental Statistics, Volume 19 (2014) no. 4, pp. 524-540 | DOI
[40] An easy way to reduce PIT-tag loss in rodents, Ecological Research, Volume 25 (2010) no. 1, pp. 251-253 | DOI
[41] Modeling Survival and Testing Biological Hypotheses Using Marked Animals - a Unified Approach with Case-Studies, Ecological Monographs, Volume 62 (1992) no. 1, pp. 67-118 | DOI
[42] Estimation by capture-recapture of recruitment and dispersal over several sites, Oikos, Volume 101 (2003) no. 2, pp. 253-264 | DOI
[43] Chapter 3 Modeling Individual Animal Histories with Multistate Capture–Recapture Models, Advances in Ecological Research, Volume Volume 41, Academic Press, 2009, pp. 87-173 | DOI
[44] An Efficient Earth Mover's Distance Algorithm for Robust Histogram Comparison, IEEE Transactions on Pattern Analysis and Machine Intelligence, Volume 29 (2007) no. 5, pp. 840-853 | DOI
[45] WinBUGS - A Bayesian modelling framework: Concepts, structure, and extensibility, Statistics and Computing, Volume 10 (2000) no. 4, pp. 325-337 | DOI
[46] Complete tag loss in capture–recapture studies affects abundance estimates: An elephant seal case study, Ecology and Evolution, Volume 10 (2020) no. 5, pp. 2377-2384 | DOI
[47] Tag loss probabilities are not independent: Assessing and quantifying the assumption of independent tag transition probabilities from direct observations, Journal of Experimental Marine Biology and Ecology, Volume 372 (2009) no. 1, pp. 36-42 | DOI
[48] Informing conservation strategies for the endangered Atlantic sturgeon using acoustic telemetry and multi-state mark-recapture models, Journal of Applied Ecology, Volume 54 (2017) no. 3, pp. 914-925 | DOI
[49] The effect of band loss on estimates of annual survival, Journal of Field Ornithology, Volume 51 (1980) no. 1, p. 9
[50] Annual Survival Rates of Adult and Immature Eastern Population Tundra Swans, The Journal of Wildlife Management, Volume 56 (1992) no. 3, pp. 485-494 | DOI
[51] Survival rate estimation in the presence of tag loss using joint analysis of capture-recapture and resighting data, Marked Individuals in the Study of Bird Population, 1993, pp. 229-243
[52] The use of multi-state capture-recapture models to address questions in evolutionary ecology, Journal of Applied Statistics, Volume 22 (1995) no. 5, pp. 835-846 | DOI
[53] Assessing tag loss and survival probabilities in green turtles (Chelonia mydas) nesting in Malaysia, Journal of the Marine Biological Association of the United Kingdom, Volume 98 (2018) no. 4, pp. 961-972 | DOI
[54] Long Term Retention, Survival, Growth, and Physiological Indicators of Juvenile Salmonids Marked with Passive Integrated Transponder Tags, Advances in Fish Tagging and Marking Technology, Volume 76, Amer Fisheries Soc, 2012, pp. 135-145
[55] JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling, 3rd International Workshop on Distributed Statistical Computing (DSC 2003), K. Hornik, F. Leisch, and A. Zeileis, 2003, pp. 1-10
[56] Empirical evaluation of non-invasive capture–mark–recapture estimation of population size based on a single sampling session, Journal of Applied Ecology, Volume 44 (2007) no. 4, pp. 843-852 | DOI
[57] R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, 2019
[58] Integrated population models: Model assumptions and inference, Methods in Ecology and Evolution, Volume 10 (2019) no. 7, pp. 1072-1082 | DOI
[59] Estimates of Tag Loss from Recoveries of Fish Tagged and Permanently Marked, Transactions of the American Fisheries Society, Volume 95 (1966) no. 1, pp. 56-59 | DOI
[60] Stan Modeling Language Users Guide and Reference Manual, 2.31, 2022
[61] Estimating survival and temporary emigration in the multistate capture-recapture framework, Ecology, Volume 85 (2004) no. 8, pp. 2107-2113 | DOI
[62] A Unified Capture-Recapture Framework, Journal of Agricultural Biological and Environmental Statistics, Volume 13 (2008) no. 4, pp. 458-477 | DOI
[63] Estimating Migration Rates Using Tag-Recovery Data, Biometrics, Volume 49 (1993) no. 1, pp. 177-193 | DOI
[64] The implications of assuming independent tag loss in southern elephant seals, Ecosphere, Volume 3 (2012) no. 9, p. art81 | DOI
[65] A Note on Multiple-Recapture Census, Biometrika, Volume 52 (1965), pp. 249-260 | DOI
[66] Tag loss and the Petersen mark-recapture experiment, Biometrika, Volume 68 (1981) no. 1, pp. 211-219 | DOI
[67] Tagging Methods and Tag Loss, Capture-Recapture: Parameter Estimation for Open Animal Populations (Statistics for Biology and Health), Springer International Publishing, 2019, pp. 13-37 | DOI
[68] Integrating heterogeneity of detection and mark loss to estimate survival and transience in UK grey seal colonies, Journal of Applied Ecology, Volume 48 (2011) no. 2, pp. 364-372 | DOI
[69] Estimating demographic parameters for capture-recapture data in the presence of multiple mark types, Environmental and Ecological Statistics, Volume 18 (2011) no. 2, pp. 331-347 | DOI
[70] Estimating Annual Survival and Movement Rates of Adults within a Metapopulation of Roseate Terns, Ecology, Volume 76 (1995) no. 8, pp. 2415-2428 | DOI
[71] Modelling mortality causes in longitudinal data in the presence of tag loss: application to raptor poisoning and electrocution, Journal of Applied Ecology, Volume 49 (2012) no. 1, pp. 297-305 | DOI
[72] Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets (Version v2) [Data set], Zenodo, 2023 | DOI
[73] Mark loss can strongly bias estimates of demographic rates in multi-state models: a case study with simulated and empirical datasets, Zenodo, 2023 | DOI
[74] Program MARK: survival estimation from populations of marked animals, Bird Study, Volume 46 (1999) no. S, pp. 120-139 | DOI
[75] Analysis and Management of Animal Populations, Academic Press, 2002
[76] Effects of Photo and Genotype-Based Misidentification Error on Estimates of Survival, Detection and State Transition using Multistate Survival Models, PLOS ONE, Volume 11 (2016) no. 1, p. e0145640 | DOI
[77] Programming With Models: Writing Statistical Algorithms for General Model Structures With NIMBLE, Journal of Computational and Graphical Statistics, Volume 26 (2017) no. 2, pp. 403-413 | DOI
[78] Recovery of southern bent-winged bats (Miniopterus orianae bassanii) after PIT-tagging and the use of surgical adhesive, Australian Mammalogy, Volume 42 (2020) no. 2, pp. 216-219 | DOI
Cited by Sources: