Fig. 5: Cell type evolution of the lung and gill.

a Pairwise cell type similarities of the zebrafish swim bladder, lungfish lung, mouse lung, and human lung by sankey plot. The top 5% highest Kullback–Leibler divergence (KDL) values are indicated as arches connecting cell types for each pair. b Conserved expression in alveolar cells of the human lung, lungfish lung, and mouse lung. Violin plots are including 57 orthologous genes (>1.3 log2 fold-change). Each dot represents a gene, and normalized average expression values are shown. c Enriched biological processes of 57 orthologous genes in b. The enrichment analysis was generated via the Enrichr web server using Fisher exact test, and the Benjamini-Hochberg (BH) was used for correction for multiple hypotheses testing. P values are indicated on the x-axis. d The expression of selected DEGs in lungfish-zebrafish-human-mouse comparisons in the lungfish lung. Circle size reflects the percentage of cells within a cell type that expresses the specific genes. The color of circles indicates the average expression of a DEG. e The expression of lung cell type DEGs in lungfish compared to human. Mean values are shown. DEGs with a q-value ≤ 0.05 and fold change ≥3 are shown. f Cell–cell similarities between the gills of the lungfish and Atlantic salmon. The top 5% highest Kullback–Leibler divergence (KDL) values are indicated as arches connecting cell types. g Violin plots of 40 orthologous genes (>1.3 log2 fold-change) with conserved expression in MRCs of the salmon gills, lungfish gills.Annotated as in (b). h The expression of DEGs of lungfish-Atlantic salmon gill comparisons in the lungfish gill. The x-axis of volcano plot shows the log2 fold-change, the y-axis represents the percent of lungfish and salmon gill cells that express each gene (calculating the Δ percentage difference). Source data are provided as a Source Data file.