These authors contributed equally to this work.
Special Issue: Genotyping by Sequencing
RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
Article first published online: 3 APR 2013
© 2013 John Wiley & Sons Ltd
Special Issue: GENOTYPING BY SEQUENCING IN ECOLOGICAL AND CONSERVATION GENOMICS
Volume 22, Issue 11, pages 3179–3190, June 2013
How to Cite
Arnold, B., Corbett-Detig, R. B., Hartl, D. and Bomblies, K. (2013), RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Molecular Ecology, 22: 3179–3190. doi: 10.1111/mec.12276
- Issue published online: 30 MAY 2013
- Article first published online: 3 APR 2013
- Manuscript Accepted: 25 JAN 2013
- Manuscript Revised: 24 JAN 2013
- Manuscript Received: 21 SEP 2012
- NSF DDIG
- Harvard Prize Fellowship
Fig. S1 True and estimated values of π and θw as a function of the chromosome sampling depth for θ = ρ = 0.01 per bp.
Fig. S2 Mean values of πe (solid red) and θe (solid blue) for loci with different sampling depth cutoffs (i.e. loci that have at least the specified number of sampled chromosomes with intact recognition sequences).
Fig. S3 Chromosome sampling depth proportions for the standard (red) and double digest (blue) RADseq protocols.
Fig. S4 True π (solid lines) and estimated π (dashed lines) vary as a function of chromosome sampling depth for the standard (blue) and double-digest (red) RADseq protocols.
Fig. S5 Mean values of πe (solid red) and θe (solid blue) for loci with different sampling depth cutoffs (CSDC, i.e. loci that have at least the specified number of sampled chromosomes with intact recognition sequences).
Fig. S6 Distribution of estimated FST when all haplotypes are sampled (blue) vs. the true distribution (black), for Nm = 10 (A), Nm = 1 (B), and Nm = 0.1 (C).
Fig. S7 Proportion of estimated π (red), θw (blue), or D (purple) 5% outlier loci that are false positives (solid lines) or false negatives (dashed lines) relative to the true distribution for different chromosome sampling depth cutoffs.
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