Sample collection, sex identification
We used samples of 261 Macquarie perch, 68 golden perch, 4 Murray cod
and 4 trout cod (Supplementary Material S1). Of 261 Macquarie perch
individuals, 173 were Snobs Creek hatchery broodstock from Yarra and
Dartmouth populations (see Lutz et al., 2021 for details of the breeding
program), 25 were Narrandera hatchery broodstock from the Abercrombie
River, one was a Snobs Creek hatchery-produced juvenile, and the
remaining 62 were adults sampled from four inland and five coastal
populations. The inland lineage (including Yarra, Dartmouth and
Abercrombie populations) diverged from the coastal one in the
Pleistocene; the two are morphologically distinguishable (Pavlova et
al., 2017). Sex was identified for hatchery broodstock and 21
sampled-and-released fish from inland King Parrot Creek and Holland’s
Creek by observation of mature gametes during the breeding season. For
all but two individuals (exceptions in next section), fin-clip samples
were collected non-lethally and preserved in absolute ethanol at -20°C.
Of the 68 golden perch, one was an adult of unknown sex sampled
non-lethally, one an adult from another population sampled lethally, and
66 were adults from three more populations sampled lethally for another
project. Sex of lethally-sampled fish was identified during dissection
based on presence of maturing or mature gonads. Fin clips from two males
and two females were also used for each of Murray cod and trout cod,
with their sex determined at Snobs Creek hatchery (details of sampling
and sexing in Supplementary Material S1). All procedures employed were
approved by relevant animal care and ethics committees. Field sample
collection was approved by NSW ACEC 14/10, DELWP AEC 14/04 and AEC
15/02, Scientific Collection Permit P01/0059(A)-3.0 and Victorian
Fisheries Research Permit RP827. Hatchery work and sampling were
conducted under approval of VIC DPI Fish AEC Jul09 0067 and NSW
Fisheries ACEC committee 05/06.