Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon’s ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extreme temperatures and salinities. Our genomic and cytogenetic assessments of ten meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and widespread, high heterozygosity, polyploid clones (2n = 40) in all other locations. A single polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clones likely formed in the shallow waters after inundation of Shark Bay < 8,500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.

A de novo ddRAD loci assembly and identification of Single Nucleotide Polymorphisms (SNPs) was performed using the denovo_map pipeline in STACKS v2.52. A minimum distance of three nucleotides was used to identify a stack (-m), a maximum of three nucleotides was permitted between stacks (-M) and a maximum of three mismatches were permitted between loci of different individuals during catalogue construction.