Fig. 4: Gene gain and loss and its role in freshwater evolution.

Gene gains (histogram at right) and losses (numbers in circles at nodes) across sponge and metazoan phylogeny, as assessed using a selection of choanoflagellate, sponge, ctenophore, and eumetazoan species with full genome sequence available, assuming sponges (a) or ctenophores (b) are sister to other metazoans, as shown on representative cladograms. Note that the large number of apparent gains in Branchiostoma floridae is largely due to incompletely curated records in that resource. Sponges show a uniformly high rate of gene gain relative to other metazoans. E. muelleri shows considerable gene losses, but this is likely less acute in reality due to incomplete gene models. c Example of a highly duplicated gene in E. muelleri, the mGABA receptor. Here we show the incidence of this gene, as a segmental duplicate dotplot, on scaffold 22. Same strand (forward) matches are represented in green, and reverse strand matches in purple. Boxed is the cluster of extremely high duplication levels of this gene. d Phylogeny of mGluR and mGABAR genes, rooted with Capsaspora owczarzaki sequences. Phylogeny generated in IQTREE v1.6.9 under the WAG + F + R9 model, based on a 1364-position (appx 45% gaps) amino acid alignment generated in MAFFT v7.313 (with -linsi options). Tree visualised in iTOL, with mGluR, vertebrate GABAR1 and GABAR2 genes shaded. Dots on nodes represent nodes with 100% bootstrap support. Colour of branches and outer circle indicates origin of sequences, with Ephydatia muelleri and other species coloured as seen in Legend, bottom right. Note the extreme level of duplication of these genes seen in sponges in general, and in freshwater lineages in particular. Source data are provided as a Source Data file.