On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs
Article first published online: 10 FEB 2010
© 2010 Blackwell Publishing Ltd
Volume 19, Issue 7, pages 1439–1451, April 2010
How to Cite
SANTURE, A. W., STAPLEY, J., BALL, A. D., BIRKHEAD, T. R., BURKE, T. and SLATE, J. (2010), On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs. Molecular Ecology, 19: 1439–1451. doi: 10.1111/j.1365-294X.2010.04554.x
- Issue published online: 19 MAR 2010
- Article first published online: 10 FEB 2010
- Received 24 September 2009; revision received 19 November 2009; accepted 21 November 2009
Fig. S1 Frequency distribution of the correlation between standardised multilocus heterozygosity (sMLH) and pedigree inbreeding coefficient for 1000 simulated data sets of linked and unlinked markers. Labels represent the lower value of the interval
Fig. S2 Example of a four generation pedigree, with all individuals assumed outbred
Fig. S3 Frequency distribution of linkage disequilibrium between pairs of markers (Rp2) across ten simulated data sets and true zebra finch data. Labels represent the lower value of the interval; the final interval includes Rp2 values between 0.09 and 1.
Table S1 The mean (and standard deviation) of the correlation coefficients between true pedigree relatedness coefficients and relatedness estimators for 125 simulated marker sets with and without linkage information
Table S2 Mean (and standard deviation) of the correlations of marker relatedness estimators with pedigree relatedness as the number of markers are increased. Averages are over ten replicates of random subsets of loci, selected without replacement. Note the change of interval after 125 loci
Table S3 Correlations between relatedness coefficients calculated from the pedigree (rij) and estimated from markers (T – QG) from 20 microsatellite markers alone, and mean correlations and standard deviations from 20 microsatellite markers supplemented with 25, 75, 125 and 250 randomly selected SNPs.
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