The effect of RAD allele dropout on the estimation of genetic variation within and between populations
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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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"The effect of RAD allele dropout on..." refers background or methods in this paper
...(K2P) model of DNA evolution (Kimura 1980) with a fraction of constant sites (those that do not mutate)...
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...…rate per nucleotide (l) was sampled from a uniform distribution [10 9–10 8], and we assumed a Kimura two-parameters (K2P) model of DNA evolution (Kimura 1980) with a fraction of constant sites (those that do not mutate) fixed to 10% and the shape parameter of the Gamma distribution of…...
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...When an SNP was present, its genetic variation was summarized within population by computing the expected heterozygosity (He; Nei 1977) for each population and between populations by computing unbiased estimates of FST as described by Weir & Cockerham (1984) (see also Weir 1996, eqn 5.2)....
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"The effect of RAD allele dropout on..." refers background or methods in this paper
...Deep sequencing of restriction site associated DNA (RAD-seq) borrows from the RRL strategy (Baird et al. 2008)....
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...across a wide range of organisms and questions ranging from genetic map construction and mapping of genes underlying traits of interest (Baird et al. 2008; Baxter et al. 2011) to population genomics (Hohenlohe et al....
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...…2012 John Wiley & Sons Ltd across a wide range of organisms and questions ranging from genetic map construction and mapping of genes underlying traits of interest (Baird et al. 2008; Baxter et al. 2011) to population genomics (Hohenlohe et al. 2010) and phylogeography (Emerson et al. 2010)....
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...We considered an RAD locus as generated by the standard protocol of Baird et al. (2008): such a RAD locus includes a sequence of L bp long associated with a single restriction site of length S bp....
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