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These aberrant sites are of interest, either because; they were polymorphic in an ancestral species and arisen due to lineage sorting, or they have arisen due to recent introgression, or are true homoplastic double mutations.
Forty eight percent of the monomorphic markers within S. lycopersicum still were useful because they were polymorphic within tomato wild relatives or between wild relatives and cultivated tomato.
The eight mitochondrial microsatellite markers reported here are highly polymorphic, making them useful for differentiating between genetic individuals as well as for investigating the population genetic structure of Laccaria sp. A. Mitochondrial markers were not deliberately sought; the markers were selected because they were polymorphic and amplified consistently.
In particular, the panels chosen specifically because they were polymorphic in either the Bavarian or Norwegian populations alter the scatter of the data with respect to the whole data set panels (all 306 and random 104 SNPs), with the difference being most noticeable in the Norwegian data set, where the variability in Norway is dramatically inflated versus the other populations.
These markers were chosen because they were polymorphic (an average of 16 alleles per locus and observed heterozygosity 0.65 - 0.7) and because significant deviation from Hardy-Weinberg equilibrium across all loci and populations (assessed using Arlequin [[ 77] ]) was only observed in a few loci and was not consistent across populations.
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The first three genes were chosen because they are polymorphic among various groups of the Cryptococcus species complex [3], [9], [10], [17].
A further 725 markers were removed from analysis because they were not polymorphic between our 37 selected strains.
Of the 768 SNPs genotyped, 29 were excluded because they were not polymorphic, or had heterozygous or missing genotypes for many samples, including parent strains (Fungal Genetics Stock Centre A4 and A91), leaving a total of 739 markers.
A total of 1,712 SNP markers were excluded from analysis because they were not polymorphic.
While several of the SNPs could not be used because they were non-polymorphic or provided low quality data, 326 SNPs were available for diversity analysis.
We excluded 15 SNPs from any subsequent analyses either because they were non-polymorphic in this study, had a call rate of <80% or as they showed deviation from Hardy-Weinberg equilibrium expectations in the control population (p < 0.001).
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