Approximately Unbiased phylogenetic test results.

BUSCO (microsporidia_odb10, version 5.4.6) (Simão and colleagues 2015) was run on the unpurged genome assemblies of the tetraploid genomes. The haplotypes of each BUSCO locus were aligned to one another using MAFFT (version 7.525) (Katoh and colleagues 2002), and a phylogeny was generated for each alignment using IQ-TREE (version 2.3.4, with ModelFinder enabled and 1,000 bootstrap replicates) (Minh and colleagues 2020; Kalyaanamoorthy and colleagues 2017). The Approximately Unbiased statistical test [90] on the multi-copy BUSCO gene phylogenies for all pairwise combinations of tetraploid microsporidian genomes. The high-level summary of these pairwise tests are included in this text. For each listed pairwise comparison, the “+” sign indicates the number of phylogenies where haplotypes coalesce more recently than species, and the “−” sign indicates the number of phylogenies where species coalesce more recently than haplotypes. (TXT)