Examples of total ion current (TIC) chromatogram mass spectra for selected phylogroups.

<p>Individual slugs are identified with alphabetic characters; <i>m/z</i> values show a retention time of 2.5–17 min.</p

Group membership based on chemical and genetic data.

<p>(<b>a</b>) Multivariate dendrogram (similarity metric  =  correlation coefficient) for 54 individuals of <i>Doris ‘kerguelenensis’</i> based on extracted total chromatogram mass (TCM) spectra for <i>m/z</i> values with a retention time of 2.5–17 min. The correlation is not size dependent, but rather takes the baseline corrected average mass spectrum of a sample so that comparisons of shapes are more important. Groups with similar chemistry are designated and coloured based on an arbitrarily designated cut-off threshold of 0.3 similarity. Letters below the dendrogram refer to individual slugs. Numbers in coloured blocks below dendrogram give the corresponding phylogroups derived from molecular data. (<b>b</b>) Maximum-likelihood (ML) topology for 193 individuals of <i>D. ‘kerguelenensis’</i> based on combined mitochondrial COI, 16S and nuclear ANT data. *indicates bootstrap support of 95 or above <i>and</i> posterior probability of 0.98 or above. Support values less than 60 or 0.90 are not shown. Terminals are coloured to show the distribution and designation of individuals with corresponding chemical data. Scale bar, 0.07 expected changes per site, ML.</p

Geographic distance matrix South Australia

Pairwise geographic distance in km between sample sets, for South Australian sites only. Distance was measured along the coastline but straight-line connections were allowed across Spencer Gulf and Gulf St Vincent

microsatellite genotypes for all individuals

Microsatellite genotypes for 7 loci for all 70 individuals of leafy seadragons (Phycodurus eques) in genepop format

microsatellite genotypes for all sample sets with >5 individuals

Microsatellite genotypes for 7 loci for 49 individuals of leafy seadragons (Phycodurus eques) in genepop format. Sample sets with <5 individuals and individuals of unknown geographic origin were excluded

Geographic distance matrix

Pairwise geographic distance in km between sample sets. Distance was measured along the coastline but straight-line connections were allowed across Spencer Gulf and Gulf St Vincent

Sequences mitochondrial NADH subunit 4 (ND4)

Sequences of the mitochondrial NADH subunit 4 (ND4) for 56 leafy seadragons (Phycodurus eques) in fasta format

Sequences mitochondrial control region

Sequences of the mitochondrial control region for 56 leafy seadragons (Phycodurus eques) in fasta format

Phylogenomic Supermatrices

Translated homologous gene alignments from transcriptome data. There are two datasets with the partition files. The 70% complete supermatrix and the 80% complete supermatrix. See text for more details

Sowhat Constraint Trees

Constriant trees used for SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)