Can an original be found? Mitochondrial species identity does not predict nuclear genome similarity in the photosymbiotic jellyfish Cassiopea andromeda and C. xamachana

The Upside-Down Jellyfish, Cassiopea , has become a mainstay of cnidarian photosymbiosis research. Two nominal sister species, C. xamachana and the globally introduced C. andromeda , supply most of the medusae used in American and European laboratory research within this genus. As founder identity can shape experimental outcomes, here we utilize whole genome resequencing of 21 Cassiopea medusae spanning the Florida Keys, Bocas del Toro (Panama), and a European laboratory line, to ask whether mitochondrial species assignment predicts nuclear genome identity. Across multiple population structure analyses using the nuclear genome, Floridian Cassiopea carrying C. xamachana or C. andromeda mitotypes are indistinguishable, and geography is the dominant axis of nuclear genetic structure. A population tree that groups the two Floridian mitotypes as a single interbreeding unit is strongly supported (Patterson’s D ≈ 0.0, Z = 0.02), whereas a tree that respects mitochondrial species boundaries is rejected ( D = 0.42, Z = 20.8). Strikingly, the European “true” C. andromeda line clusters with Panamanian C. xamachana rather than with Floridian C. andromeda -mitotype animals. From the same sequencing effort, we recover evidence of symbiont variability ( Cladocopium ) in Panama and assemble two near-complete Tenacibaculum and Endozoicomonas metagenomically-assembled genomes from Floridian host tissue. Together these results indicate that the C. andromeda/C. xamachana hybridization zone may extend across ocean basins, and that a “pure” original of either species may be difficult to find. We urge Cassiopea researchers to establish new European lines with described genomes.