Identifying environmental correlates of intraspecific genetic variation.

Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

Variable stocking effect and endemic population genetic structure in Murray cod Maccullochella peelii.

Microsatellite markers were utilized to examine the genetic structure of Murray cod Maccullochella peelii throughout its distribution in the Murray--Darling Basin (MDB) of eastern Australia, and to assess the genetic effects of over three decades of stocking hatchery-reared fingerlings. Bayesian analysis using the programme Structure indicated that the species is largely genetically panmictic throughout much of its extensive range, most probably due to the high level of connectivity between catchments. Three catchments with terminal wetlands (the Lachlan, Macquarie and Gwydir), however, contained genetically distinct populations. No stocking effects were detected in the catchments that were genetically panmictic (either because of low genetic power or lack of effects), but the genetically differentiated Gwydir and Macquarie catchment populations were clearly affected by stocking. Conversely, there was no genetic evidence for survival and reproduction of stocked fish in the Lachlan catchment. Therefore, stocking of M. peelii throughout the MDB has resulted in a range of genetic effects ranging from minimal detectable effect, to substantial change in wild population genetic structure.