Genetic variation in the brooding brittle-star: A global hybrid polyploid complex?

The widespread and abundant brooding brittle-star (Amphipholis squamata) is a simultaneous hermaphrodite with a complex mitochondrial phylogeography of multiple divergent overlapping mtDNA lineages, high levels of inbreeding or clonality and unusual sperm morphology. We use exon-capture and transcriptome data to show that the nuclear genome comprises multiple (>3) divergent (π > 6%) expressed components occurring across samples characterised by highly divergent (~20%)  mitochondrial lineages, and encompassing several other genera, including diploid dioecious species. We report a massive sperm genome size in A. squamata, an order of magnitude larger than that present in other brittlestars, and consistent with our SNP-based measure of greatly elevated ploidy. Similarity of these genetic signatures to well-known animal systems suggests that A. squamata (and related taxa) is a hybrid polyploid asexual complex of variable subgenome origins, ploidy and reproductive mode. We discuss enigmatic aspects of A. squamata biology in this light. This putative allopolyploid complex would be the first to be reported from the phylum Echinodermata.

Methods
Exon capture next-generation DNA sequence data, including mitochondrial genes

Bioinformatic scripts (R and Bash) and data tables