Main 46The last common ancestor of all living animals appears to have possessed epithelial and 47 mesenchymal cell types that could transdifferentiate over an ontogenetic life cycle 48 ( Fig.1a) 1,4 . This capacity to develop and differentiate required a regulatory capacity to 49 control spatial and temporal gene expression, and included a diversified set of signalling 50 pathways, transcription factors, enhancers, promoters and non-coding RNAs (Fig. 1a) [5][6][7][8][9] . 51Recent analyses of the genomes and life cycles of unicellular holozoan relatives of 52 animals have revealed that the regulatory repertoire present in multicellular animals 53 largely evolved first in a unicellular ancestor ( Fig. 1a) 2,5,6 . These insights contrast with a 54 widely-held view that all animals evolved from a stem organism that was a simple ball 55 of ciliated cells 1,3,4 . Implicit in this traditional perspective is that (i) regulatory systems 56 necessary for cell differentiation evolved after the divergence of metazoan and 57 choanoflagellates lineages, and (ii) morphological features shared between 58 choanoflagellate and choanocytes are homologous and were present in the original 59 animal cell. While the former is not supported by recent data -unicellular holozoans 60 can change cell states by environmentally-induced temporal shifts in gene expression 61 ( Fig. 1a) 5,6,10-12 -the latter is contingent upon the still controversial aspect of whether 62 extant choanocytes and choanoflagellates accurately reflect the ancestral animal cell 63
type. 64To test this, we first compared cell type-specific transcriptomes 13 from the sponge 65Amphimedon queenslandica with each other, and with transcriptomes expressed during 66 the life cycles of closely-related unicellular holozoans, the choanoflagellate Salpingoeca 67 rosetta, the filasterean Capsaspora owczarzaki and the ichthyosporean Creolimax 68 fragrantissima (Fig. 1a) 10-12 . We chose three sponge somatic cell types hypothesised to 69 be homologous to cells present in the last common ancestor of contemporary Extended Data Figure 2: Percentage of KEGG cellular processes and 663 environmental information processing (i.e. cell signalling) genes present in each 664 cell type, corresponding to the number of components making up each KEGG 665 category identified. 666 a, Cellular processes genes. b, Environmental information processing (i.e. cell 667 signalling) genes. 668 669 Extended Data Figure 3: Evolutionary age of genes expressed in Amphimedon 670 queenslandica choanocytes, archeocytes and pinacocytes using different 671 expression thresholds. 672 *