a–e, Phylostratigraphic enrichment of genes expressed in each cell type (Ar, archaeocyte; Ch, choanocyte; Pi, pinacocyte; ArCh, archaeocyte + choanocyte; ArPi, archaeocyte + pinacocyte; ChPi, choanocyte + pinacocyte; ALL, all three cell types combined) at different expression thresholds. Expressed genes are parsed into quartiles based on transcript abundance in each of the cell types. Quartile 1 (Q1) includes the least abundant transcripts and Q4 the most abundant. a, Phylostratigraphy enrichment of all genes expressed in each of the cell types (Q1–Q4). b, Phylostratigraphy enrichment of genes expressed in the top three quartiles (excluding Q1). c, Phylostratigraphy enrichment of genes expressed in the top 50% (Q3 and Q4). d, Phylostratigraphy enrichment of the most highly expressed genes (Q4). e, For comparison, the evolutionary age of differentially expressed genes identified using differential expression analysis, DESeq2. Heat maps indicate enrichment (log-odds ratio based on a two-sided Fisher’s exact test) of phylostrata contained in each gene list in comparison to the A. queenslandica genome (n = 44,719). Asterisks mark significant (P < 0.05; Fisher’s exact test) overlap between gene lists, indicative of phylostrata enrichment. The heat maps on the far right are collapsed versions of the heat maps on the left, in which the premetazoan category contains phylostrata from cellular to holozoan, and the poriferan category contains phylostrata from poriferan to A. queenslandica. To the left of each heat map is a Venn diagram, showing the number of genes in each cell type and set of cell types. Grey boxes on the heat map indicate that there were no genes in that particular gene list characterized by the given phylostrata. See additional supplementary data on Dryad: /ED_Fig. 3_files and /Fig. 3e. f, Pairwise comparison illustrating the number of overlapping genes for each of the quartiles between the three cell types. The numbers in the cells are the number of genes common between two cell types (for example, there are 1,569 expressed genes in common between Q2 in choanocytes and Q3 in archaeocytes). NE, not expressed. g, The percentage of differentially upregulated genes identified in each of the cell types using DESeq2 in the four quartiles.