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

Gilbert M. Macbeth, Damien Broderick, Jennifer R. Ovenden and Rik C. Buckworth

Theoretical Population Biology, 2011, vol. 80, issue 3, 185-196

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.

Keywords: SHAZA; Missing loci; Genetic tagging; Type I errors; Type II errors; Genotype errors (search for similar items in EconPapers)
Date: 2011
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.sciencedirect.com/science/article/pii/S004058091100058X
Full text for ScienceDirect subscribers only

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:eee:thpobi:v:80:y:2011:i:3:p:185-196

DOI: 10.1016/j.tpb.2011.06.006

Access Statistics for this article

Theoretical Population Biology is currently edited by Jeremy Van Cleve

More articles in Theoretical Population Biology from Elsevier
Bibliographic data for series maintained by Catherine Liu ().