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Nock, CJ 2009, 'Conservation genetics of the endangered eastern freshwater cod, Maccullochella ikei', PhD thesis, Southern Cross University, Lismore, NSW.

Copyright CJ Nock 2009


Fragmentation over evolutionary time scales following vicariant and dispersal events has long been recognised as a dominant process in biological diversification and speciation; while anthropogenic habitat fragmentation in recent times is considered a threat to the long-term persistence of species and ecosystems. The eastern freshwater cod Maccullochella ikei is Australia’s largest endangered freshwater fish species. Abundant in the Clarence and Richmond River systems at the time of European settlement, populations crashed in the early 1900s causing local extinctions and range reduction. Recovery efforts, including a prohibition on fishing for M. ikei and hatchery breeding programs, were initiated in an attempt to re-establish locally extirpated populations and to support the remnant population. This thesis aims to fill critical gaps in the knowledge of M. ikei by examining genetic diversity over a broad range of evolutionary scales. Microsatellite and mitochondrial markers and a DNA extraction method were developed and applied to address issues of conservation concern including taxonomy, hybridisation, genetic variation, population structure, effective population size and genetic stocking impact. Mitochondrial sequence and nuclear genotypic data were used to infer the evolutionary relationships among the Murray cod Maccullochella peelii peelii from the inland Murray-Darling Basin and taxa from eastern coastal drainages, M. ikei and Mary River cod M. peelii mariensis. Phylogenetic analyses provide strong support for a more recent common ancestry between M. ikei and M. p. mariensis. This finding conflicts with the existing taxonomy and suggests that ancestral cod crossed the Great Dividing Range around 1 million years ago and subsequently colonised east coast drainages during Pleistocene glacial periods. The eastern taxa, persisting in isolated drainages at the periphery of the historical coastal distribution of Maccullochella are estimated to have diverged around 300 thousand years ago. Mary River cod are morphologically and genetically distinct and may warrant recognition as a separate species. High levels of population structure (global FST = 0.13) and a pattern of isolation by distance in M. ikei from the Clarence system are indicative of fragmentation and restricted dispersal. Genetically-distinct upstream populations are small and isolated with effective population sizes below 30. Cluster analysis and assignment tests suggest that gene flow to and among these populations is limited. Bayesian and frequency-based analysis of hatchery progeny suggest population admixture in the hatchery, with most parental stock sourced from upstream sites with reduced genetic variation. Analysis of temporal samples from the largest remnant population showed a significant loss in genetic variation (>20%) since the commencement of stocking, consistent with genetic swamping with hatchery-bred fish. These findings are relevant to the conservation of M. ikei and to captive breeding programs generally as they show that genetic homogeneity across a species’ range cannot be assumed; and the selection of parental stock for supportive breeding programs from anthropogenically-fragmented populations could have detrimental genetic effects on the recipient wild population. This thesis illustrates the importance of incorporating genetic information into conservation and management plans for threatened species, and the implications of fragmentation over different time scales for the proliferation and loss of biological diversity.