Table 2. Taxon sampling and data sources for genomes and transcriptomes analyzed in this study.

Group	Species	Source
Choanoflagellate proteomes	Diaphanoeca grandis, Acanthoeca spectabilis, Salpingoeca punica, Salpingoeca urceolata, Hartaetosiga gracilis, Salpingoeca macrocollata, Stephanoeca diplocostata, Helgoeca nana, Salpingoeca kvevrii, Didymoeca costata, Choanoeca perplexa, Salpingoeca infusionum, Microstomoeca roanoka, Savillea parva, Hartaetosiga balthica, Salpingoeca dolichothecata, Codosiga hollandica, Salpingoeca helianthica, Mylnosiga fluctuans, Salpingoeca rosetta, Monosiga brevicollis, Barroeca monosierra, Choanoeca flexa	NCBI BioProject PRJNA419411, Figshare DOI: 10.6084 /m9.figshare.5686984.v2 Richter et al., 2018, NCBI BioProject PRJNA37927 Fairclough et al., 2013 ,GenBank GCA_000002865.1 King et al., 2008, Figshare DOI: 10.6084 /m9.figshare.8216291 Brunet et al., 2019, Barroeca monosierra genome-derived proteome Hake et al., 2024, EukProt: https://evocellbio.com/eukprot/
Filasterean proteomes	Pigoraptor vietnamica, Pigoraptor chileana, Capsaspora owczarzaki, Ministeria vibrans	MulticellGenome: https://multicellgenome.com/genomes
Ichthyosporean proteomes	Sphaeroforma arctica, Creolimax fragrantissima, Ichthyophonus hoferi, Abeoforma whisleri, Pirum gemmata, Chromosphaera perkinsii	MulticellGenome: https://multicellgenome.com/genomes
Corallochytrean proteomes	Syssomonas multiformis, Corallochytrium limacisporum	MulticellGenome: https://multicellgenome.com/genomes; https://doi.org/10.5061/dryad.26bv4
Metazoan proteomes	Trichoplax adhaerens, Amphimedon queenslandica, Corticium candelabrum, Dysidea avara, Ephydatia muelleri, Halichondria panicea, Oscarella lobularis, Oopsacas minuta, Tethya wilhelma, Mnemiopsis leidyi, Bolinopsis microptera, Danio rerio, Gallus gallus, Drosophila melanogaster, Ciona intestinalis, Branchiostoma floridae,	UniProt Proteomes: https://www.uniprot.org/
	Nematostella vectensis, Acropora millepora, Caenorhabditis elegans, Mus musculus, Homo sapiens
Holomycota proteomes	Paraphelidium tribonemae, Neurospora crassa, Emericella nidulans, Ustilago maydis, Yarrowia lipolytica, Cryptococcus neoformans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Fonticula alba, Rozella allomycis, Allomyces macrogynus, Conidiobolus coronatus, Batrachochytrium dendrobatidis, Rhizophagus irregularis, Rhizopus delemar	UniProt Proteomes https://www.uniprot.org/
Amoebozoan proteomes	Dictyostelium purpureum, Heterostelium pallidum, Entamoeba histolytica, Dictyostelium discoideum, Cavenderia fasciculata, Acanthamoeba castellanii, Planoprotostelium fungivorum, Polysphondylium violaceum, Dictyostelium firmibasis	UniProt Proteomes: https://www.uniprot.org/
Viridiplantae proteomes	Volvox carteri, Chlamydomonas reinhardtii, Chlorella variabilis, Ostreococcus tauri, Gonium pectorale, Bathycoccus prasinos, Chlamydomonas eustigma, Raphidocelis subcapitata, Chloropicon primus, Chlamydomonas schloesseri, Pycnococcus provasolii, Volvox reticuliferus, Coccomyxa sp., Pleodorina starrii, Arabidopsis thaliana, Ricinus communis, Oryza sativa, Rosa chinensis, Vigna angularis, Rhododendron simsii, Papaver atlanticum, Cryptomeria japonica	UniProt Proteomes: https://www.uniprot.org/
Ciliate proteomes	Paramecium tetraurelia, Ichthyophthirius multifiliis, Tetrahymena thermophila, Stylonychia lemnae, Pseudocohnilembus persalinus, Stentor coeruleus, Halteria grandinella, Euplotes crassus	UniProt Proteomes: https://www.uniprot.org/