Cryptic whole-genome duplication in bryozoans

Whole-genome duplications (WGDs) have long been proposed as evolutionary facilitators of biological complexity and diversification. Ancient WGDs occurred deep in the evolutionary history of both plants and vertebrates, but appear to be rare in invertebrates. However, it is unclear whether this reflects genuine scarcity or inadequate detection methodologies, and current methods may be insufficient to detect very old WGDs where extensive gene loss has followed. Here, we used a combination of paralogous and orthologous synteny-based methods incorporating bilaterian ancestral linkage groups (ALGs) to search for genomic signatures of WGD in members of the invertebrate phylum Bryozoa. This revealed strong evidence for an ancient WGD in the freshwater bryozoan Cristatella mucedo, Class Phylactolaemata, with duplicated paralogous regions across every chromosome. Only ~10% of duplicated genes are retained, including a Hox cluster duplication. All eight genomes from the bryozoan class Gymnolaemata also show signatures of ancient WGD in the form of 2:1 ratios in orthologous synteny comparisons, which remain detectable despite only ~5% duplicate retention. Gene trees support a scenario in which all extant bryozoans share an ancient WGD and much of the genome rediploidised independently in the two clades. Duplicates retained after bryozoan WGD are enriched in cilia genes and are preferentially expressed in the lophophore, the tentacular feeding organ covered in highly specialised cilia. We argue that cryptic WGD in bryozoan evolution facilitated adaptation to a sessile, filter-feeding lifestyle, and propose that incorporation of ALGs adds to the power of synteny-based WGD-detection methods.