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Except for the haplotype file, only one SNP per locus was retained (i.e. the first SNP on each locus) to minimise as much as possible linkage of markers.
Mutation and recombination rates, sequence lengths, and sample sizes were conditioned on each locus individually.
To test further for evidence of recombination, we used the programme SplitsTrees on each locus separately and on the concatenated sequences of all STs.
CIM is done by regressing the trait on each locus in the genome with some markers used as covariates and called background markers.
Thus, we conditioned simulations on each locus individually (including mutation and recombination rates), and explored a continuous range of parameter values rather than restricting our search to a set of predetermined grid coordinates.
The mode and intensity of selection, ω (∼dN/dS, the ratio of non-synonymous to synonymous substitution rates), acting on each locus was estimated using a codon-based substitution model [40] as implemented in PAML's program codeml [41].
Similar(32)
We first conducted a two-sample T-test on methylation of each locus regarding sex difference, and corrected the results with 5% Bonferroni correction.
Genetic distance (cM) of each locus on a consensus map obtained from the Komugi wheat genetic resources database [http://www.shigen.nig.ac.jp/wheat/komugi/top/top.jsp] (Table S2, Figure S1).
Pearson correlations were calculated by weighting the alteration frequency of each locus on a linear scale.
Both parental and recombinant classes illustrate the effects of meiotic drive on the inheritance of each locus.
We undertook χ analyses in CLUMP focusing on the association of each locus with the different phenotypic manifestations (Table 2).
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