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).