IDEAS home Printed from https://ideas.repec.org/a/eee/ecomod/v490y2024ics0304380024000504.html
   My bibliography  Save this article

A Bayesian multi-state model with data augmentation for estimating population size and effect of inbreeding on survival

Author

Listed:
  • Rondon, Diego
  • Mäntyniemi, Samu
  • Aspi, Jouni
  • Kvist, Laura
  • Sillanpää, Mikko J.

Abstract

A joint model framework for estimating population sizes over time and survival probabilities while considering inbreeding and age as covariates in the survival function is elaborated. This methods is tested with data simulated over two small (N≈150) close to extinction open populations, that aims to imitate wild individuals under decline and bottleneck dynamics. A Hidden Markov Model (HMM) perspective with a multi-state formulation that considers young and adult individuals is applied with data augmentation to account for non-seen individuals. The transition probabilities are estimated, and different treatments of the covariates and levels of data seen are compared. Our results suggest that the model framework correctly estimates different population size trends but the parameter estimation is challenging in some cases. The proposed model presents a new way to use the inbreeding coefficient, and further implementations on a real conservation data of wild species can help the decision-making process for the management of small populations.

Suggested Citation

  • Rondon, Diego & Mäntyniemi, Samu & Aspi, Jouni & Kvist, Laura & Sillanpää, Mikko J., 2024. "A Bayesian multi-state model with data augmentation for estimating population size and effect of inbreeding on survival," Ecological Modelling, Elsevier, vol. 490(C).
    • Handle: RePEc:eee:ecomod:v:490:y:2024:i:c:s0304380024000504
    DOI: 10.1016/j.ecolmodel.2024.110662
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0304380024000504
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.ecolmodel.2024.110662?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. J. D. Lebreton & R. Pradel Cefe, 2002. "Multistate recapture models: Modelling incomplete individual histories," Journal of Applied Statistics, Taylor & Francis Journals, vol. 29(1-4), pages 353-369.
    2. Baey, Charlotte & Smith, Henrik G. & Rundlöf, Maj & Olsson, Ola & Clough, Yann & Sahlin, Ullrika, 2023. "Calibration of a bumble bee foraging model using Approximate Bayesian Computation," Ecological Modelling, Elsevier, vol. 477(C).
    3. Ilik Saccheri & Mikko Kuussaari & Maaria Kankare & Pia Vikman & Wilhelm Fortelius & Ilkka Hanski, 1998. "Inbreeding and extinction in a butterfly metapopulation," Nature, Nature, vol. 392(6675), pages 491-494, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Mengmeng Zhang & Fujun Shen & Tao Yang & Han Zhang & Yunfeng Lu & Keliang Wu & Fujun Shen & Yunfeng Lu, 2018. "Genetic Input from Wild Giant Pandas (Ailuropoda melanoleuca) into the Captive Population Simulated by OMPG Rule," JOJ Wildlife & Biodiversity, Juniper Publishers Inc., vol. 1(1), pages 6-13, December.
    2. Timothy J. Miller & Per K. Andersen, 2008. "A Finite-State Continuous-Time Approach for Inferring Regional Migration and Mortality Rates from Archival Tagging and Conventional Tag-Recovery Experiments," Biometrics, The International Biometric Society, vol. 64(4), pages 1196-1206, December.
    3. Roger Pradel, 2005. "Multievent: An Extension of Multistate Capture–Recapture Models to Uncertain States," Biometrics, The International Biometric Society, vol. 61(2), pages 442-447, June.
    4. A Bradley Duthie & Jane M Reid, 2015. "What Happens after Inbreeding Avoidance? Inbreeding by Rejected Relatives and the Inclusive Fitness Benefit of Inbreeding Avoidance," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-22, April.
    5. J. A. Dupuis, 2002. "Prior distributions for stratified capture-recapture models," Journal of Applied Statistics, Taylor & Francis Journals, vol. 29(1-4), pages 225-237.
    6. Dalton J. Hance & Russell W. Perry & John M. Plumb & Adam C. Pope, 2020. "A temporally stratified extension of space‐for‐time Cormack–Jolly–Seber for migratory animals," Biometrics, The International Biometric Society, vol. 76(3), pages 900-912, September.
    7. Gimenez, Olivier & Rossi, Vivien & Choquet, Rémi & Dehais, Camille & Doris, Blaise & Varella, Hubert & Vila, Jean-Pierre & Pradel, Roger, 2007. "State-space modelling of data on marked individuals," Ecological Modelling, Elsevier, vol. 206(3), pages 431-438.
    8. Wohner, Patti J & Duarte, Adam & Wikert, John & Cavallo, Brad & Zeug, Steven C & Peterson, James T, 2022. "Integrating monitoring and optimization modeling to inform flow decisions for Chinook salmon smolts," Ecological Modelling, Elsevier, vol. 471(C).
    9. J Nevil Amos & Andrew F Bennett & Ralph Mac Nally & Graeme Newell & Alexandra Pavlova & James Q Radford & James R Thomson & Matt White & Paul Sunnucks, 2012. "Predicting Landscape-Genetic Consequences of Habitat Loss, Fragmentation and Mobility for Multiple Species of Woodland Birds," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-12, February.
    10. M. Heino & I. Hanski, 2000. "Evolution of Migration Rate in a Spatially Realistic Metapopulation Model," Working Papers ir00044, International Institute for Applied Systems Analysis.
    11. Vortkamp, Irina & Barraquand, Frédéric & Hilker, Frank M., 2020. "Ecological Allee effects modulate optimal strategies for conservation in agricultural landscapes," Ecological Modelling, Elsevier, vol. 435(C).
    12. Blanquart, François, 2014. "The demography of a metapopulation in an environment changing in time and space," Theoretical Population Biology, Elsevier, vol. 94(C), pages 1-9.
    13. Etterson, Matthew A. & Ellis-Felege, Susan N. & Evers, David & Gauthier, Gilles & Grzybowski, Joseph A. & Mattsson, Brady J. & Nagy, Laura R. & Olsen, Brian J. & Pease, Craig M. & van der Burg, Max Po, 2011. "Modeling fecundity in birds: Conceptual overview, current models, and considerations for future developments," Ecological Modelling, Elsevier, vol. 222(14), pages 2178-2190.
    14. Choquet, Rémi & Garnier, Alexandre & Awuve, Edem & Besnard, Aurélien, 2017. "Transient state estimation using continuous-time processes applied to opportunistic capture–recapture data," Ecological Modelling, Elsevier, vol. 361(C), pages 157-163.
    15. Caswell, Hal & Shyu, Esther, 2012. "Sensitivity analysis of periodic matrix population models," Theoretical Population Biology, Elsevier, vol. 82(4), pages 329-339.
    16. Taylor, Rebecca L. & Himes Boor, Gina K., 2012. "Beyond the robust design: Accounting for changing, uncertain states and sparse, biased detection in a multistate mark-recapture model," Ecological Modelling, Elsevier, vol. 243(C), pages 73-80.
    17. Shirley Pledger & Edward Baker & Kim Scribner, 2013. "Breeding Return Times and Abundance in Capture–Recapture Models," Biometrics, The International Biometric Society, vol. 69(4), pages 991-1001, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:ecomod:v:490:y:2024:i:c:s0304380024000504. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/ecological-modelling .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.