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doi:10.1534/genetics.106.057331
A more recent version of this article appeared on August 1, 2006.
REGULAR RESEARCH PAPERS |
Performance of marker-based relatedness estimators in natural populations of outbred vertebrates
Katalin Csillery 1*, Toby Johnson 1, Dario Beraldi 1, Tim H. Clutton-Brock 2, Dave Coltman 3, Bengt Hansson 4, Goran Spong 2 and Josephine Pemberton 1
1 Institute of Evolutionary Biology, University of Edinburgh
2 Department of Zoology, University of Cambridge
3 Department of Biological Sciences, University of Alberta
4 Department of Animal Ecology, Lund University
* To whom correspondence should be addressed. E-mail: k.m.csillery{at}sms.ed.ac.uk.
Submitted on February 16, 2006
Revised on May 19, 2006
Accepted on 2 June 2006
Knowledge of relatedness between pairs of individuals plays an important role in many research areas including evolutionary biology, quantitative genetics and conservation. Pairwise relatedness estimation methods based on genetic data from highly variable molecular markers are now extensively used as a substitute for pedigrees. Although the sampling variance of the estimators have been intensively studied for for the most common simple genetic relationships, such as unrelated, half- and full-sib or parent-offspring, little attention has been paid to the average performance of the estimators, by which we mean the performance across all pairs of individuals in a sample. Here we apply two measures to quantify the average performance, first, misclassification rates between pairs of genetic relationships and, second, the proportion of variance explained in the pairwise relatedness estimates by the true population relatedness composition (i.e. the frequencies of different relationships in the population). Using simulated data derived from exceptionally good quality marker and pedigree data from five long-term projects of natural populations, we demonstrate that the average performance mainly depends on the population relatedness composition and may only be improved by the marker data quality only within the limits of the population relatedness composition. Our five examples of vertebrate breeding systems suggest that due to the remarkably low variance in relatedness across the population, marker-based estimates may often have low power to address research questions of interest.
Key Words: Long-term projects, Microsatellites, Moment estimators, Pairwise relatedness, Pedigrees
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