Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades.

Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families— including the complete circadian toolkit—were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction.