IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v80y2011i3p185-196.html
   My bibliography  Save this article

Likelihood-based genetic mark–recapture estimates when genotype samples are incomplete and contain typing errors

Author

Listed:
  • Macbeth, Gilbert M.
  • Broderick, Damien
  • Ovenden, Jennifer R.
  • Buckworth, Rik C.

Abstract

Genotypes produced from samples collected non-invasively in harsh field conditions often lack the full complement of data from the selected microsatellite loci. The application to genetic mark–recapture methodology in wildlife species can therefore be prone to misidentifications leading to both ‘true non-recaptures’ being falsely accepted as recaptures (Type I errors) and ‘true recaptures’ being undetected (Type II errors). Here we present a new likelihood method that allows every pairwise genotype comparison to be evaluated independently. We apply this method to determine the total number of recaptures by estimating and optimising the balance between Type I errors and Type II errors. We show through simulation that the standard error of recapture estimates can be minimised through our algorithms. Interestingly, the precision of our recapture estimates actually improved when we included individuals with missing genotypes, as this increased the number of pairwise comparisons potentially uncovering more recaptures. Simulations suggest that the method is tolerant to per locus error rates of up to 5% per locus and can theoretically work in datasets with as little as 60% of loci genotyped. Our methods can be implemented in datasets where standard mismatch analyses fail to distinguish recaptures. Finally, we show that by assigning a low Type I error rate to our matching algorithms we can generate a dataset of individuals of known capture histories that is suitable for the downstream analysis with traditional mark–recapture methods.

Suggested Citation

  • Macbeth, Gilbert M. & Broderick, Damien & Ovenden, Jennifer R. & Buckworth, Rik C., 2011. "Likelihood-based genetic mark–recapture estimates when genotype samples are incomplete and contain typing errors," Theoretical Population Biology, Elsevier, vol. 80(3), pages 185-196.
  • Handle: RePEc:eee:thpobi:v:80:y:2011:i:3:p:185-196
    DOI: 10.1016/j.tpb.2011.06.006
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S004058091100058X
    Download Restriction: Full text for ScienceDirect subscribers only

    File URL: https://libkey.io/10.1016/j.tpb.2011.06.006?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. Janine A. Wright & Richard J. Barker & Matthew R. Schofield & Alain C. Frantz & Andrea E. Byrom & Dianne M. Gleeson, 2009. "Incorporating Genotype Uncertainty into Mark–Recapture-Type Models For Estimating Abundance Using DNA Samples," Biometrics, The International Biometric Society, vol. 65(3), pages 833-840, September.
    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. Richard J. Barker & Matthew R. Schofield & Janine A. Wright & Alain C. Frantz & Chris Stevens, 2014. "Closed-population capture–recapture modeling of samples drawn one at a time," Biometrics, The International Biometric Society, vol. 70(4), pages 775-782, December.
    2. R. M. Fewster, 2017. "Some applications of genetics in statistical ecology," AStA Advances in Statistical Analysis, Springer;German Statistical Society, vol. 101(4), pages 349-379, October.
    3. Simon J Bonner & Jason Holmberg, 2013. "Mark-Recapture with Multiple, Non-Invasive Marks," Biometrics, The International Biometric Society, vol. 69(3), pages 766-775, September.
    4. Xinyi Lu & Mevin B. Hooten & Andee Kaplan & Jamie N. Womble & Michael R. Bower, 2022. "Improving Wildlife Population Inference Using Aerial Imagery and Entity Resolution," Journal of Agricultural, Biological and Environmental Statistics, Springer;The International Biometric Society;American Statistical Association, vol. 27(2), pages 364-381, June.
    5. Matthew R. Schofield & Richard J. Barker & Nicholas Gelling, 2018. "Continuous†time capture–recapture in closed populations," Biometrics, The International Biometric Society, vol. 74(2), pages 626-635, June.
    6. Ben C. Stevenson & David L. Borchers & Rachel M. Fewster, 2019. "Cluster capture‐recapture to account for identification uncertainty on aerial surveys of animal populations," Biometrics, The International Biometric Society, vol. 75(1), pages 326-336, March.
    7. Li‐Chun Zhang & Tiziana Tuoto, 2021. "Linkage‐data linear regression," Journal of the Royal Statistical Society Series A, Royal Statistical Society, vol. 184(2), pages 522-547, April.
    8. Matthew R. Schofield & Richard J. Barker, 2020. "Rejoinder to “On continuous‐time capture‐recapture in closed populations”," Biometrics, The International Biometric Society, vol. 76(3), pages 1034-1035, September.
    9. R. T. R. Vale & R. M. Fewster & E. L. Carroll & N. J. Patenaude, 2014. "Maximum likelihood estimation for model M t,α for capture–recapture data with misidentification," Biometrics, The International Biometric Society, vol. 70(4), pages 962-971, 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:thpobi:v:80:y:2011:i:3:p:185-196. 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: https://www.journals.elsevier.com/intelligence .

    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.