Ordination of SNPs
An initial PCoA of the stringently-filtered ‘PCoA’ dataset revealed three primary clusters, ultimately referable to the taxon groupings KN, KE/KEm, and KS/KW/KWm, plus a series of 16 admixed individuals which linked the latter two clusters in the first dimension (Fig. 2a). Further targeted PCoAs (Fig. 2b, Fig. S1), supported by all other molecular datasets, consistently demonstrated that these admixed individuals, representing populations from the Bogan and Castlereagh Rivers (Darling River tributaries), the lower Darling River, and Murray River populations downstream from the Darling River junction, mark the presence of at least one hybrid zone between pure KS and pure KE. These additional PCoAs also revealed that pure KS individuals were readily diagnosable from those occurring in the north-western inland rivers (Fig. 1) and further revealed that this latter taxon itself comprised two allied but distinctive lineages, pure KW in the Cooper and Bulloo systems, and KWm in two MDB rivers, the Warrego and Paroo (Figs. 2b, 2c). Although only subtly supported by PCoA (Figs. 2, S1), it became evident across all other analyses that the KE individuals in the upper MDB (Condamine system down to the mid-Darling River) displayed modest levels of introgression with KS. In consequence, we also assigned a unique taxon identifier (KEm) to individuals from these sites.
Strong support for the presence of four primary taxa (KN, KE, KS, and KW) plus three KS-admixed groupings in the MDB (KEm, KSxKE, KWm) is also evident in the fixed difference counts (Table 2). These data clearly demonstrate that the primary taxa are all readily diagnosable at multiple loci (range 38–432 absolute fixed differences; 64–525 near-fixed differences) whereas KSxKE displays no fixed differences from either parental taxon (as expected for recently-admixed populations) and both KEm and KWm display fewer fixed differences from KS than do their pure parental taxa (as typically found for historic admixture/introgression). Additional support is presented by the observed heterozygosity counts for each group (Table 2), which show all pure taxa display comparatively low levels of heterozygosity (range 0.0098–0.0218) when compared to KEm (almost double that of pure KE), KWm (more than double that of pure KW) and most notably KSxKE (more than fourfold higher than either parent).