Phylogenetic analysis of SNPs
Our initial ‘phylo’ dataset comprised all individuals except for the 16 hybrid KSxKE fish. Surprisingly, the presence of the nine admixed KEm individuals caused considerable distortion of the relationships among populations and taxa in the resultant ML tree (Fig. 3a), reflecting the reality that reticulate evolution often leads to data that do not exhibit tree-like behaviour (Unmack et al., 2022). Removal of these KEm individuals followed by refiltering resulted in a final ‘phylo’ dataset of 179 individuals for 7419 polymorphic SNP loci.
ML recovered one tree with a -ln score of -72522.995738 and the rapid bootstrap search finished at 450 replicates (Fig. 3b; full tree in Fig. S2). Support across most of the deeper nodes of the tree was strong, with once again four principal lineages recognised, namely KN and KE (as sister clades), with both being sister to clades KS and KW. Taxon KN represents northern coastal populations from the Burdekin, Fitzroy, and the coastal Boyne rivers (note there are two Boyne rivers in our study, the second being a tributary to the Burnett River). Apart from its presence in the Condamine and Darling (as lineage KEm), taxon KE consists of populations from eastern coastal rivers from Baffle Creek south to the Clarence River, plus a recently introduced population in the Barron River in far north Queensland (site 1). Taxon KS contains individuals from three coastal New South Wales rivers (Macleay, Hunter and Shoalhaven) along with non-introgressed populations from the MDB, except those in the Warrego and Paroo rivers (lineage KWm) which, along with Bulloo River and Cooper Creek populations, are referable to taxon KW. Outside of the MDB, most individuals tend to group closely with others from the same or adjacent river and there is obvious phylogeographic structure at the regional level in all taxa except KS.