Both 74 taxon datasets used for the initial phylogenomic analyses, were subjected to constrained maximum likelihood tree reconstruction in IQtree (LG+C60+F+G) using the same partitioning scheme applied in our initial analyses. The overall topologies published in Mathur et al. [23] (i.e., gregarines are sister to other apicomplexans) and Janouškovec et al. [22] (monophyletic gregarines and Cryptosporidium spp. as sister to other apicomplexans) were used as constraints. Gene concordance factors (gCF) for the best ML tree for our initial phylogenomic analysis and the constrained topologies were calculated using IQtree [29]. Additionally, the approximately unbiased (AU) test [120] was conducted on the maximum likelihood tree, the constrained trees, and 100 distinct local topologies saved during the initial ML analysis (-wt option in IQtree) as implemented by IQtree [115].

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