A Sample locations of the sponge <i>Suberites diversicolor</i>: top three maps represent distribution and frequencies of haplotypes for partial Cytochrome Oxidase I (COI) and bottom three maps of genotypes of internal transcribed spacer region (ITS) in Indonesia Singapore and Australia with insets of Berau (East Kalimantan left) and Raja Ampat (West Papua right) in Indonesia; location codes are explained in Table 2; circles represent marine lakes and squares are coastal populations; haplo/genotypes are indicated by number code (COI: C1-4 and ITS: T1-9) and color codes as provided in B. Note that scale differs per map. B Bayesian/maximum likelihood phylogram of 105 COI sequences (right) and 104 ITS sequences (left); each haplo/genotype indicated by specific color followed by location code and total number of samples in squared brackets. Only posterior probabilities of >90 and maximum likelihood values of >70 are indicated. Color blocks represent the same individuals for both molecular m

<p>A Sample locations of the sponge <i>Suberites diversicolor</i>: top three maps represent distribution and frequencies of haplotypes for partial Cytochrome Oxidase I (COI) and bottom three maps of genotypes of internal transcribed spacer region (ITS) in Indonesia Singapore and Australia with insets of Berau (East Kalimantan left) and Raja Ampat (West Papua right) in Indonesia; location codes are explained in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075996#pone-0075996-t002" target="_blank">Table 2</a>; circles represent marine lakes and squares are coastal populations; haplo/genotypes are indicated by number code (COI: C1-4 and ITS: T1-9) and color codes as provided in B. Note that scale differs per map. B Bayesian/maximum likelihood phylogram of 105 COI sequences (right) and 104 ITS sequences (left); each haplo/genotype indicated by specific color followed by location code and total number of samples in squared brackets. Only posterior probabilities of >90 and maximum likelihood values of >70 are indicated. Color blocks represent the same individuals for both molecular markers (i.e. lineage A (pink) and B (green) represented by the same individuals with both COI and ITS markers). Species of the family Halichondriidae were used for the outgroup followed by Genbank accession numbers. Scale bars indicate substitutions/site.</p

Pairwise <i>Φst</i> values between all populations of lineage B based on ITS sequences of <i>Suberites diversicolor</i> (location codes indicated in Table 2).

<p>Values in bold and with asterisk indicate significant values (p<0.05).</p

A <i>Suberites diversicolor</i> purple color morph. B Landlocked marine lakes in Raja Ampat Indonesia.

<p>A <i>Suberites diversicolor</i> purple color morph. B Landlocked marine lakes in Raja Ampat Indonesia.</p

Overview of published genetic variation in populations within anchialine systems.

<p>Overview of published genetic variation in populations within anchialine systems.</p

COI_18SrRNA_28SrRNA_combined_tree

Phylogenetic tree presented in Figure 1: Bayesian phylogenetic tree reconstructed from a combined dataset of the cox1 gene and the 18S and 28S rRNA sequences. Secondary structures were taken into account in the model. Newick format

COI DNA alignment

DNA sequence alignment of the cox1 gene in Nexus forma

18S rDNA alignment

DNA sequence alignment of the 18S rRNA gene in Nexus forma

28S rDNA alignment

DNA sequence alignment of the 28S rRNA gene in Nexus forma

Frequency and distribution of haplotypes in populations of <i>Montastraea cavernosa</i> (A) and <i>Xestospongia muta</i> (B) in the wider Caribbean region.

<p>Haplotype frequencies provided as pie-chart per location, number of samples in brackets. Haplotype network of ITS (A) and I3-M11 (B), baes on all sequences collected throughout the wider Caribbean region. Size of circle reflects the number of individuals with a specific haplotype. Each line represents the genetic distance between haplotypes. Specific haplotype colors match those presented in the pie-charts. White circles (ITS) are haplotypes private to a certain location.</p

COI tree

Phylogenetic tree presented in Figure 2: Bayesian phylogenetic tree reconstructed from the COI gene, in Nexus format