MtDNA analyses
The whole and half cytb datasets consisted of 1141 and 601 base
pairs for 267 and 293 individuals respectively. Maximum Likelihood (ML)
was run on the two cytb datasets with RAxML producing trees with
likelihood scores of -3145.296216 and -1595.307571, and the rapid
bootstrap search for both analyses finishing at 650 and 500 replicates
respectively (simplified tree for whole cytb in Fig. 6; detailed
trees for both whole and half cytb in Figs. S3 and S4
respectively).
For the full cytb dataset, the deeper phylogenetic relationships
were moderately well-supported and largely similar to those found for
SNPs. The KN clade was sister to the KE clade and both were sister to a
composite KS/KW clade, comprising three distinctive sub-lineages
referable to taxon KS plus well-supported, sister sub-lineages for KW
and KWm (Figs. 6a, S3). Consistent with their hybrid
status, KSxKE individuals displayed either KS-derived or KE-derived
haplotypes (ratio 14:15, Fig. S4). For the non-hybrid taxa, an
individual’s mtDNA clade membership was concordant with their
SNP/allozyme primary lineage identification in all instances apart from
six KS fish, all from three northern MDB rivers (sites 65, 66, and 68;
Gwydir, Namoi, and Macquarie Rivers).
Mapping the distribution of the major cytb lineages (Fig. 6)
clearly demonstrates that KE-derived haplotypes have intruded into the
KSxKE hybrid zones as identified using our nuclear datasets (Fig. 1 and
shaded in Fig. 6) plus are present in the pure KS populations from some
upper MDB rivers. It also reveals that haplotypes from two rare
KS-lineages, otherwise characteristic of the Border Rivers in the upper
MDB (sites 59, 62, and 63) have also spread across the drainage divide
into the upper Clarence River (site 41) and far downstream into the
KSxKE hybrid zone in the lower Murray.