RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling
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...However, there might still be some subtle biases in either pipeline, caused by factors such as null alleles [63,64], alignment to the reference, and the use of inbreds only (rather than the full set of samples) to filter SNPs for FIT....
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...Additionally, nextgeneration sequencing data may contain a substantial proportion of missing data that should be accounted for (Arnold et al. 2013; Gautier et al. 2013)....
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References
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"RADseq underestimates diversity and..." refers methods in this paper
...We then used these to calculate typical summaries of the data such as average number of pairwise differences (p, Tajima 1983), Watterson’s h (hw, Watterson 1975), Tajima’s D (Tajima 1989) and FST (Weir & Cockerham 1984)....
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11,521 citations
"RADseq underestimates diversity and..." refers methods in this paper
...We then used these to calculate typical summaries of the data such as average number of pairwise differences (p, Tajima 1983), Watterson’s h (hw, Watterson 1975), Tajima’s D (Tajima 1989) and FST (Weir & Cockerham 1984)....
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11,417 citations
7,853 citations
"RADseq underestimates diversity and..." refers background in this paper
...Though it may seem comparatively rare for a mutation to occur within a recognition sequence, these variants are frequent enough to enable detailed population genetic analyses (e.g. Restriction Fragment Length Polymorphisms, Botstein et al. 1980)....
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3,870 citations
"RADseq underestimates diversity and..." refers methods in this paper
...We then used these to calculate typical summaries of the data such as average number of pairwise differences (p, Tajima 1983), Watterson’s h (hw, Watterson 1975), Tajima’s D (Tajima 1989) and FST (Weir & Cockerham 1984)....
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