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Schematic representation of the phylogenetic parsimony approach (adapted from [ 10 ]) to define species conservation categories and number of species with binding conservation. Briefly, TF binding events were first aligned and compared across species, then divided using parsimony in lineage- and clade-specific binding losses, and lineage- and clade-specific binding gains. Regions with experimentally determined binding in the species were called orthologous bound, and those without binding unbound. Ultra-conserved binding events were defined as those bound across all species. Below, examples of corresponding degrees of species conservation defined by the total number of species that share a TF binding event.

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