Genomic study reveals evolutionary origin of inducible defensive helmets in Daphnia sinensis

Our genomic analyses, focusing on single-nucleotide and genome structural variation, indicate monophyletic origin of this morphotype, which apparently emerged following a pond-to-lake habitat shift.

Daphnia knockout mutants for TM2D2 or ISM1, generated from a helmet-forming clone using CRISPR-Cas9, exhibit much reduced plastic formation of the helmet, demonstrating the polygenic control of this adaptive trait and large effect sizes of the respective genes.

The divergence of the two morphotypes is characterized by signals of positive selection and extensive chromosome structural changes.

ISM1 differs in coding regions and amino acid sequences, indicating protein-level changes; TM2D2 differences primarily involve regulatory regions, as confirmed by different level of expression of this gene between morphotypes despite shared protein sequences.

A signal of hard selective sweep is particularly strong in the tightly linked ISM1 and TM2D2 genes, both involved in morphogenesis, but with contrasting level of divergence between morphotypes.