Low genetic structuring among Pericharax heteroraphis (Porifera: Calcarea) populations from the Great Barrier Reef (Australia), revealed by analysis of nrDNA and nuclear intron sequences

A new nuclear marker system for sponges, the second intron of the nuclear ATP synthetase beta subunit gene (ATPSbeta-iII), was analysed together with nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences aiming to uncover phylogeographic patterns of the coral reef sponge Pericharax heteroraphis in the southwest Pacific, focussing on the Great Barrier Reef (GBR). Variation among ITS sequences was low (< 1.1% p-distance), in contrast to ATPSbeta-iII (< 8.3% p-distance). Single-Stranded Conformation Polymorphism (SSCP) analysis proved to be an effective toot for phasing ATPSbeta-ill alleles of 292 bp length. Although sample sizes were limited for most populations and these results await corroboration by an extended sampling regime, a past population subdivision with subsequent range expansion was indicated by a 'dumb-bell' shaped statistical parsimony network of GBR ATPSbeta-ill alleles. Although no clear phylogeographic break was discovered on the GBR, the northern GBR was genetically differentiated from the central/southern GBR and Queensland Plateau, based on significant pairwise F-st values (0.137-0.275 and p <= 0.05) of pooled regional populations. The ATPSbeta-ill used in this study outperformed the frequently employed nrDNA ITS and might also turn out to be useful for phylogeographic studies of other coral reef taxa.