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All neighbor-joining trees were finally re-rooted by the diploid node in Matlab (Mathworks).
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The results obtained were supported by the diploid DEFA1: DEFA3 ratio.
In our case, for each polyploid allele, we constrained the subtree formed by the diploid species to the *BEAST diploid species tree.
The mapping population S3 was made by crossing the diploid S. viminalis male clone (81084) with the diploid S. viminalis female clone (78195) to produce 282 F1 offspring.
After verifying mating by microscopy, the diploid strain was patched onto a sporulation medium.
We generated tetraploid individuals by colchicine treatment of the diploid homozygous individuals.
Viability of the scc4 m7 strain was determined by FACS analysis of homozygous diploid cells and during strain construction by sequential sporulation of the diploid imaging strains.
Trees were simulated to approximate true FISH progression trees by expanding from an initial diploid root node by selecting a Poisson number of children of each node (possibly with repetition) and expanding each node selected recursively until the process terminates.
As detailed below, five diploid cytotypes had less than the number of 25S signals presented by the typical diploid cytotype.
The B, E, F, and G genomes are each represented at the diploid level by a single species, Oryza punctata, O. australiensis, O. brachyantha, and O. granulata respectively.
The mean IOD of a non-diploid peak was divided by the mean IOD of the diploid peak to compute DI.
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