In light of recent alarming trends in human population growth, climate change, and other environmental modifications, a “Warning to humanity” manifesto was published in BioScience in 2017. This call reiterated most of the ideas originally expressed by the Union of Concerned Scientists in 1992, including the fear that we are “pushing Earth's ecosystems beyond their capacities to support the web of life.” As subterranean biologists, we take this opportunity to emphasize the global importance and the conservation challenges associated with subterranean ecosystems. They likely represent the most widespread nonmarine environments on Earth, but specialized subterranean organisms remain among the least documented and studied. Largely overlooked in conservation policies, subterranean habitats play a critical role in the function of the web of life and provide important ecosystem services. We highlight the main threats to subterranean ecosystems and propose a set of effective actions to protect this globally important natural heritage.

The wheatbelt region of Western Australia has been extensively cleared of indigenous vegetation for agriculture and is now severely affected by dryland salinity. Wetlands that were once freshwater are now saline and others are under threat, as are the animals and plants that inhabit them. Rising groundwater is also affecting the many naturally saline playas. To provide a framework for setting conservation priorities in this region a biological survey was undertaken, including sampling of aquatic invertebrates at 230 wetlands. In this paper, we have used data from the survey to summarise occurrence of species in relation to salinity. Total species richness at a wetland showed no response to salinity below 4.

Summary 1. AusRivAS (Australian River Assessment Scheme) models were developed, using macroinvertebrates as indicators, to assess the ecological condition of rivers in Western Australia as part of an Australia‐wide program. The models were based on data from 188 minimally disturbed reference sites and are similar to RIVPACS models used in Britain. The major habitats in the rivers (macrophyte, channel) were sampled separately and macroinvertebrates collected were identified to family level. 2. Laboratory sorting of preserved macroinvertebrate samples recovered about 90% of families present when 150 animals were collected, whereas live picking in the field recovered only 76%. 3. Reference sites clustered into five groups on the basis of macroinvertebrate families present. Using seven physical variables, a discriminant function allocated 73% of sites to the correct classification group. A discriminant function based on seven physical and two chemical variables allocated 81% of sites to the correct group. However, when the same reference sites were re‐sampled the following year, the nine variable discriminant function misallocated more sites than the seven variable function, owing to annual fluctuations in water chemistry that were not accompanied by changes in fauna. 4. In preliminary testing, the wet season channel model correctly assessed 80% of reference sites as undisturbed in the year subsequent to model building (10% of sites were expected to rate as disturbed because the 10th percentile was used as the threshold for disturbance). Nine sites from an independent data set, all thought to be disturbed, were assessed as such by the model. Results from twenty test sites, chosen because they represented a wide range of ecological condition, were less clear‐cut. In its current state the model reliably distinguishes undisturbed and severely disturbed sites. Subtle impacts are either detected inconsistently or do not affect ecological condition.

The landscape of the Pilbara region of Western Australia has been relatively unchanged for 100 million years. The ancient river systems of this region might be expected to be sources of isolation and divergence for aquatic species. Hence, the occurrence of widespread groundwater taxa in this landscape offers the opportunity to examine associations between genetic diversity and drainage patterns. Pilbarus and Chydaekata are two widespread genera of subterranean amphipods endemic to the Pilbara, each occupying multiple tributaries. We used molecular data to examine the roles of drainage patterns in structuring genetic diversity. Gene flow within a tributary may be facilitated by the occasional occurrence of these amphipods in springs, which results in their downstream dispersal during episodic flooding. However, tributary boundaries may form hydrological barriers to gene flow, resulting in localised isolation of populations and divergence. Samples of both genera, collected throughout three river basins, were examined for sequence divergence in the cytochrome c oxidase I mitochondrial gene. There was no evidence of contemporary gene flow among populations of either genus, and each tributary contained highly divergent lineages, which were not associated with similar morphological differentiation. This suggests cryptic speciation has occurred, and similar phylogenetic signals in both taxa imply similar evolutionary histories. Surface populations may have been driven into subterranean refugia by the cessation of flow in the rivers, associated with Tertiary climate change, while morphological evolution may have been constrained by stabilising selection. The lack of congruence between molecular diversity and morphology raises important practical issues for conservation.

Saline water was common in south-west Western Australian aquatic systems prior to land-clearing because most streams and wetlands were ephemeral and evapo-concentrated as they dried, and there were high concentrations of stored salt in groundwater and soil profiles. Nevertheless, a 1998 review of salinity trends in rivers of south-west Western Australia showed that 20-fold increases in salinity concentrations had occurred since clearing in the medium-rainfall zone (300–700 mm). More recent data confirm these trends and show that elevated salinities have already caused substantial changes to the biological communities of aquatic ecosystems. Further substantial changes will occur, despite the flora and fauna of the south-west being comparatively well adapted to the presence of salinity in the landscape. Up to one-third of wetland and river invertebrate species, large numbers of plants and a substantial proportion of the waterbird fauna will disappear from the wheatbelt, a region that has high biodiversity value and endemism. Increased salinities are not the only threat associated with salinisation: increased water volumes, longer periods of inundation and more widespread acidity are also likely to be detrimental to the biota.