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 the Yarra River and Lake Dartmouth (see Lutz et al., 2020 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, Beheregaray, 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 from three populations, 66 were sampled lethally for another project, and their sex 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.