A table of the identified SCOs between B. mori and P. napi, including their start locations and chromosomal location, was filtered to remove potential false positives (i.e., any translocated SCO that appeared once within a given collinear block set of four genes) and then collapsed to remove any local chromosome inversions, so that we would detect only the evolutionary dynamics among the collinear blocks. We then further simplified the dataset to have only one gene represent each collinear block (again, to ensure that we were only detecting the large-scale events). The resulting table was then used as input for the software GRIMM v.2.01 (66) to detect an optimal scenario of rearrangements between the two genomes with genes unsigned (options “-s -u”). We also generated predictions of gene signs using an approximation algorithm with a range of iterations from 1000 to 200,000 (option “-U”) and then ran analyses on the resulting datasets.

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