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For the present study, discrete genotypes were analysed and missing alleles resulting from imputation with findhap.
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For the 3598 markers, the total missing rate was 18.9% (total missing alleles divided by 3598 × 277).
In the second step, missing alleles in the U part are then imputed based on the probability derived from the results of the calculation in the first step.
The missing alleles were interpreted as sequences that had been stochastically eliminated from the T. miscellus genome.
Regarding "missing" alleles, we consider missing alleles to be real, rather than an artifact of poor procedure, because of the procedures we outline in Methods.
The remaining missing data points are across isolates and markers and likely represent genuine alleles (null alleles) especially since repeated attempts were made to amplify missing alleles.
However isolates with missing alleles were left in the haplotypic analysis.
Missing alleles in the haplotypes were imputed with BEAGLE 3.3.2 [ 30].
Missing alleles precluded computation of a median-joining network with NETWORK (Technical Appendix Table 1).
Interestingly, most of the distorted loci showed missing alleles in the freshwater grandfather.
Regions heterozygous are shown in black, those homozygous for KSH alleles are shown in white, and those missing alleles are shown in gray.
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