The Little Penguin, Eudyptula minor, is a seabird that nests in colonies throughout New Zealand and southern Australia. Individuals from different colonies in southeast Australia differ significantly in morphology and ecology, suggesting that some genetic structuring may exist among colonies. In contrast, the marking of individuals with flipper bands has revealed some, albeit infrequent, movement between colonies. To determine the extent of genetic structuring, we tested the null hypothesis of substantial gene flow within southeast Australia by examining patterns of genetic variation across seven colonies separated by up to 1,500 km. Phylogeographic structuring was absent for mitochondrial control region sequences (2-3 individuals per colony). Microsatellite allele frequencies at five loci and mitochondrial haplotype frequencies (50 individuals per colony) were also homogenous among the majority of colonies sampled, although two colonies at the western periphery of the sampling range were distinct from those to the east. The genetic homogeneity among the majority of colonies can be explained by low but consistent contemporary gene flow among them, or a recent founder event in Bass Strait following the last marine transgression. The genetic break towards the western end of the sampling distribution appears best explained by differences in sea surface temperature and, consequentially breeding phenology, the latter hindering genetically effective migration.

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