Fewer than half of the haplotypes (25) occurred in more than one individual (Table S1, Fig. 3). The most common haplotype (h1) was within the restricted lineage and occurred in 31 individuals. Thirteen haplotypes belong in the restricted lineage (95 individuals) and 34 haplotypes in the widespread lineage (81 individuals including one from New Caledonia). Trees generated by BEAST provided posterior support probabilities of 1 for the widespread lineage and 0.9988 for the restricted one (data not shown). Figure 1

shows the numbers of representatives of each lineage from each sampled Doxorubicin mw locality in Australia and Table S1 gives details on distribution of each haplotype. The only sequences from Australian waters that did not belong to the widespread or restricted lineages were from two dugongs from Ashmore Reef (Fig. 1, 3), which lies on the edge of the Australian continental shelf almost Smoothened inhibitor 400 km off Western Australia and ~120 km from Timor from which it is separated

by a deepwater trench. A third dugong from Ashmore Reef carried a sequence representative of the widespread lineage. The Australian lineages were represented outside Australia by a single sequence (h44, widespread lineage) from New Caledonia, about 1,500 km east of the closest part of Queensland. All remaining sequences from outside Australia form a loose cluster in Figure 3, but given the diversity they exhibit and the very limited sampling, this cluster may not represent a single lineage (hence we did not present neutrality indices and some other analyses for this lineage alone). Overall, dugongs exhibit high haplotypic diversity (0.946) and rather low nucleotide diversity (0.026) (Table 2). The restricted lineage, despite including Nintedanib (BIBF 1120) a larger number of samples, displays much lower haplotypic diversity and nucleotide diversity than the widespread lineage (Table 2). When the data were explored for evidence of population growth, strikingly different results

were obtained for each lineage. Runs in Beast rejected the hypothesis of constant population size for the widespread lineage but not for the restricted one. The neutrality indices (Fu’s FS and R2; Table 2) did not support population growth for the restricted lineage. However, the highly significant value for Fu’s FS statistic indicates that the widespread lineage has experienced growth. Values for the R2 statistic did not reject the null hypothesis of constant population size in either lineage and was our only evidence against growth in the widespread lineage. The Bayesian skyline plot (Fig. 4a) suggests recent expansion for the widespread lineage after a period of near-stasis. Both median and mean values for effective population size (NE(FEMALE)) through time are shown in Figure 4a, b because they differ from one another more than we had expected and it is not clear which should be preferred.