Special Issue: Genotyping by Sequencing
The effect of RAD allele dropout on the estimation of genetic variation within and between populations
Article first published online: 30 OCT 2012
© 2012 John Wiley & Sons Ltd
Special Issue: GENOTYPING BY SEQUENCING IN ECOLOGICAL AND CONSERVATION GENOMICS
Volume 22, Issue 11, pages 3165–3178, June 2013
How to Cite
Gautier, M., Gharbi, K., Cezard, T., Foucaud, J., Kerdelhué, C., Pudlo, P., Cornuet, J.-M. and Estoup, A. (2013), The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Molecular Ecology, 22: 3165–3178. doi: 10.1111/mec.12089
- Issue published online: 30 MAY 2013
- Article first published online: 30 OCT 2012
- Manuscript Accepted: 12 SEP 2012
- Manuscript Revised: 4 SEP 2012
- Manuscript Received: 12 JUL 2012
- Institut National de la Recherche Agronomique
- Agence Nationale de la Recherche. Grant Number: 2010-JCJC-1705-01
- UK Natural Environment Research Council. Grant Number: R8/H10/56
- Medical Research Council. Grant Number: G0900740
|mec12089-sup-0001-AppendixS1.pdf||application/PDF||55K||Appendix S1 Probability of the four RAD loci segregation patterns described in Fig. 1 of the main text.|
|mec12089-sup-0002-AppendixS2.pdf||application/PDF||110K||Appendix S2 Biases in allele frequency estimation within population due to allele drop-out (ADO).|
|mec12089-sup-0003-FigS1.pdf||application/PDF||21K||Fig. S1 Relationship between observed and true minor allele frequencies (MAF) under a scenario of two diverging populations assuming Ne = 105 and tS = 105.|
Table S1 FST false outlier proportions (FOP) at different threshold under a scenario of two diverging populations assuming Ne = 105 and tS = 105.
Table S2 FST false outlier proportions (FOP95% in %) in individual-based RAD analyses.
Table S3 Standard deviation (SD) of the FST–based scores (average over nsnp SNPs) under a scenario of two diverging populations assuming Ne = 105 and tS = 105.
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