Invertebrate biodiversity is still commonly assessed using families and morphospecies, approaches developed before genetic tools were widely applied. Molecular methods are now revealing hidden diversity and reshaping how we understand freshwater evolution, monitoring and conservation.
We examined the taxonomy, distribution and conservation status of Austrogammarus amphipods across the Port Phillip and Western Port region using mitochondrial COI, nuclear H3A, morphology and environmental DNA. The study confirmed some species boundaries, challenged others and identified several highly localised lineages likely to represent undescribed species. Diversity within the genus was more finely structured across catchments, and ecological variation among lineages was greater than previously recognised.
Contrasting patterns emerged. Austrogammarus haasei had a comparatively broad distribution with little genetic differentiation, whereas A. australis occupied a much smaller range but showed strong genetic structure among nearby populations. Austrogammarus ‘sp. B’ was widespread and occurred in streams affected by low flows, urbanisation and agricultural impacts, while several close relatives were confined to cool, shaded headwaters with intact riparian vegetation and abundant organic matter. Closely related taxa therefore differed markedly in distribution, habitat association and vulnerability.
Environmental DNA detected lineages that were not consistently recovered by physical sampling. Conversely, some apparently suitable reaches lacked target taxa, potentially reflecting low detectability, patchy occupancy or local loss. One tiny headwater supported three narrow-range lineages, while another stream may support four Austrogammarus species, concentrating substantial evolutionary diversity at very fine spatial scales.
These findings expose a broad conservation challenge: recorded species richness increases as hidden lineages are recognised, even while some may already face a high risk of extinction. Family-level monitoring and broad ecological classifications can therefore overlook the diversity most in need of protection. Integrating molecular methods and fine-scale habitat assessments into monitoring is essential for detecting and protecting this diversity.