Freshwater biodiversity and conservation in mediterranean climate streams of Chile

In Chile, mediterranean climate conditions only occur in the Central Zone (ChMZ). Despite its small area, this mediterranean climate region (med-region) has been recognised as a hotspot for biodiversity. However, in contrast to the rivers of other med-regions, the rivers in the ChMZ have been studied infrequently, and knowledge of their freshwater biodiversity is scarce and fragmented. We gathered information on the freshwater biodiversity of ChMZ, and present a review of the current knowledge of the principal floral and faunal groups. Existing knowledge indicates that the ChMZ has high levels of endemism, with many primitive species being of Gondwanan origin. Although detailed information is available on most floral groups, most faunal groups remain poorly known. In addition, numerous rivers in the ChMZ remain completely unexplored. Taxonomic specialists are scarce, and the information available on freshwater biodiversity has resulted from studies with objectives that did not directly address biodiversity issues. Research funding in this med-region has a strong applied character and is not focused on the knowledge of natural systems and their biodiversity. Species conservation policies are urgently required in this highly diverse med-region, which is also the most severely impacted and most populated region of the country.     

Biodiversity in Mediterranean-climate streams of California

Although the California mediterranean climate region is widely considered a biodiversity hotspot for terrestrial plants and vertebrates, freshwater biodiversity in this region is generally not well known. Using information from museum specimen databases, published literature, biological assessment surveys, and specialist’s knowledge, we review freshwater biodiversity for several groups of stream organisms in the med-climate region of California, which includes 2,220 species in 292 families. The groups with the highest diversity of lotic species are aquatic insects and diatoms, which comprise 39 and 36 % of species in our lists, respectively. Sequential floods and drying periods limit the overall biodiversity of many stream organisms in California mediterranean rivers, and continued climate and land-use change may cause disproportionate biodiversity declines in the region. However, only 4 % of lotic species have been evaluated in the IUCN Red List of Threatened Species, and many assessments are outdated. Future development of online databases for botanical and zoological collections will significantly enhance biodiversity and distribution knowledge. This information will enable us to more accurately and efficiently assess the effects of global change on biodiversity of freshwater organisms, to evaluate conservation status of individual taxa, and to set conservation priorities for stream ecosystems.     

Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups

Identifying geographical areas with the greatest representation of the tree of life is an important goal for the management and conservation of biodiversity. While there are methods available for using a single phylogenetic tree to assess spatial patterns of biodiversity, there has been limited exploration of how separate phylogenies from multiple taxonomic groups can be used jointly to map diversity and endemism. Here, we demonstrate how to apply different phylogenetic approaches to assess biodiversity across multiple taxonomic groups. We map spatial patterns of phylogenetic diversity/endemism to identify concordant areas with the greatest representation of biodiversity across multiple taxa and demonstrate the approach by applying it to the Murray–Darling basin region of southeastern Australia. The areas with significant centers of phylogenetic diversity and endemism were distributed differently for the five taxonomic groups studied (plant genera, fish, tree frogs, acacias, and eucalypts); no strong shared patterns across all five groups emerged. However, congruence was apparent between some groups in some parts of the basin. The northern region of the basin emerges from the analysis as a priority area for future conservation initiatives focused on eucalypts and tree frogs. The southern region is particularly important for conservation of the evolutionary heritage of plants and fishes.     

Can biodiversity hotspots protect more than tropical forest plants and vertebrates?

Conservation International's biodiversity hotspots are areas of high vascular plant endemism combined with high levels of habitat destruction and land use change. Although such hotspots have also been shown to be centres for terrestrial vertebrate endemism, much less is known about how well these areas function as hotspots for other less well‐studied groups, including the hyperdiverse arthropods, other invertebrates and fungi. Because there is a close evolutionary and ecological relationship between insects and plants, we suggest that the potential role of plants as umbrella species for herbivorous insects, potentially herbivorous fungi and nematodes, and parasitic insects should be explored. Finally, we reflect on the increasing social, economic, human conflict and governance issues and the impacts of increasing land use change and global climate change that threaten the biodiversity hotspot system.     

Fungal biodiversity in aquatic habitats

Fungal biodiversity in freshwater, brackish and marine habitats was estimated based on reports in the literature. The taxonomic groups treated were those with species commonly found on submerged substrates in aquatic habitats: Ascomycetes (exclusive of yeasts), Basidiomycetes, Chytridiomycetes, and the non-fungal Saprolegniales in the Class Oomycetes. Based on presence/absence data for a large number and variety of aquatic habitats, about 3,000 fungal species and 138 saprolegnialean species have been reported from aquatic habitats. The greatest number of taxa comprise the Ascomycetes, including mitosporic taxa, and Chytridiomycetes. Taxa of Basidiomycetes are, for the most part, excluded from aquatic habitats. The greatest biodiversity for all groups occurs in temperate areas, followed by Asian tropical areas. This pattern may be an artifact of the location of most of the sampling effort. The least sampled geographic areas include Africa, Australia, China, South America and boreal and tropical regions worldwide. Some species overlap occurs among terrestrial and freshwater taxa but little species overlap occurs among freshwater and marine taxa. We predict that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.     

Concordance of species richness patterns among multiple freshwater taxa: a regional perspective

Geographical gradients in species richness and the degree to which different taxa show congruent patterns remain unknown for many taxonomic groups. Here, I examined broad-scale species richness patterns in five groups of freshwater organisms; macrophytes, dragonflies, stoneflies, aquatic beetles and fishes. The analyses were based on provincial distribution records in Denmark, Norway, Sweden and Finland. In general, variation in species richness across provinces was concordant among the groups, but stoneflies showed weaker negative relationships with the other taxonomic groups. Species richness in most groups decreased with increasing latitude and altitude, and a considerable part of the variation was explained by mean July temperature. However, stoneflies showed a reversed pattern, with species richness correlating positively, albeit more weakly, with mean provincial altitude. Nevertheless, combined species richness of all five taxa showed a strong relationship with mean July temperature, accounting for 74% of variation in provincial species richness alone. Such temperature-controlled patterns suggest that regional freshwater biodiversity will strongly respond to climate change, with repercussions for local community organization in freshwater ecosystems in Fennoscandia.     

The living heart: Climate gradients predict desert mountain endemism

Mountain regions are centers of biodiversity endemism at a global scale but the role of arid‐zone mountain ranges in shaping biodiversity patterns is poorly understood. Focusing on three guilds of taxa from a desert upland refugium in Australia, we sought to determine: (a) the relative extent to which climate, terrain or geological substrate predict endemism, and (b) whether patterns of endemism are complimentary across broad taxonomic guilds. We mapped regional endemism for plants, land snails, and vertebrates using combined Species Distribution Models (SDMs) for all endemic taxa (n = 82). We then modelled predictors of endemism using Generalised Additive Models (GAMs) and geology, terrain, and climate variables. We tested for the presence of inter‐ and intraguild hotspots of endemism. Many individual plant and land snail taxa were tightly linked with geology, corresponding to small distributions. Conversely, most vertebrate taxa were not constrained to specific geological substrates and occurred over larger areas. However, across all three guilds climate was the strongest predictor of regional endemism, particularly for plants wherein discrete hotspots of endemism were buffered from extreme summer temperatures. Land snail and vertebrate endemism peaked in areas with highest precipitation in the driest times of the year. Hotspots of endemism within each guild poorly predicted endemism in other guilds. We found an overarching signal that climatic gradients play a dominant role in the persistence of endemic taxa in an arid‐zone mountain range system. An association with higher rainfall and cooler temperatures indicates that continuing trends toward hotter and drier climates may lead to range contractions in this, and potentially other, arid‐zone mountain biotas. Contrasting patterns of endemism across guilds highlight the need to couple comprehensive regional planning for the protection of climate refugia, with targeted management of more localized and habitat specialist taxa.     

Climate change and freshwater biodiversity: detected patterns, future trends and adaptations in northern regions

Current rates of climate change are unprecedented, and biological responses to these changes have also been rapid at the levels of ecosystems, communities, and species. Most research on climate change effects on biodiversity has concentrated on the terrestrial realm, and considerable changes in terrestrial biodiversity and species’ distributions have already been detected in response to climate change. The studies that have considered organisms in the freshwater realm have also shown that freshwater biodiversity is highly vulnerable to climate change, with extinction rates and extirpations of freshwater species matching or exceeding those suggested for better‐known terrestrial taxa. There is some evidence that freshwater species have exhibited range shifts in response to climate change in the last millennia, centuries, and decades. However, the effects are typically species‐specific, with cold‐water organisms being generally negatively affected and warm‐water organisms positively affected. However, detected range shifts are based on findings from a relatively low number of taxonomic groups, samples from few freshwater ecosystems, and few regions. The lack of a wider knowledge hinders predictions of the responses of much of freshwater biodiversity to climate change and other major anthropogenic stressors. Due to the lack of detailed distributional information for most freshwater taxonomic groups and the absence of distribution‐climate models, future studies should aim at furthering our knowledge about these aspects of the ecology of freshwater organisms. Such information is not only important with regard to the basic ecological issue of predicting the responses of freshwater species to climate variables, but also when assessing the applied issue of the capacity of protected areas to accommodate future changes in the distributions of freshwater species. This is a huge challenge, because most current protected areas have not been delineated based on the requirements of freshwater organisms. Thus, the requirements of freshwater organisms should be taken into account in the future delineation of protected areas and in the estimation of the degree to which protected areas accommodate freshwater biodiversity in the changing climate and associated environmental changes.     

Endemism and diversification in freshwater insects of Madagascar revealed by coalescent and phylogenetic analysis of museum and field collections

The biodiversity and endemism of Madagascar are among the most extraordinary and endangered in the world. This includes the island’s freshwater biodiversity, although detailed knowledge of the diversity, endemism, and biogeographic origin of freshwater invertebrates is lacking. The aquatic immature stages of mayflies (Ephemeroptera) are widely used as bio-indicators and form an important component of Malagasy freshwater biodiversity. Many species are thought to be microendemics, restricted to single river basins in forested areas, making them particularly sensitive to habitat reduction and degradation. The Heptageniidae are a globally diverse family of mayflies (>500 species) but remain practically unknown in Madagascar except for two species described in 1996. The standard approach to understanding their diversity, endemism, and origin would require extensive field sampling on several continents and years of taxonomic work followed by phylogenetic analysis. Here we circumvent this using museum collections and freshly collected individuals in a combined approach of DNA taxonomy and phylogeny. The coalescent-based GMYC analysis of DNA barcode data (mitochondrial COI) revealed 14 putative species on Madagascar, 70% of which were microendemics. A phylogenetic analysis that included African and Asian species and data from two mitochondrial and four nuclear loci indicated the Malagasy Heptageniidae are monophyletic and sister to African species. The genus Compsoneuria is shown to be paraphyletic and the genus Notonurus is reinstalled for African and Malagasy species previously placed in Compsoneuria. A molecular clock excluded a Gondwanan vicariance origin and instead favoured a more recent overseas colonization of Madagascar. The observed monophyly and high microendemism highlight their conservation importance and suggest the DNA-based approach can rapidly provide information on the diversity, endemism, and origin of freshwater biodiversity. Our results underline the important role that museum collections can play in molecular studies, especially in critically endangered biodiversity hotspots like Madagascar where entire species or populations may go extinct very quickly.     

Disproportional risk for habitat loss of high‐altitude endemic species under climate change

The expected upward shift of trees due to climate warming is supposed to be a major threat to range‐restricted high‐altitude species by shrinking the area of their suitable habitats. Our projections show that areas of endemism of five taxonomic groups (vascular plants, snails, spiders, butterflies, and beetles) in the Austrian Alps will, on average, experience a 77% habitat loss even under the weakest climate change scenario (+1.8 °C by 2100). The amount of habitat loss is positively related with the pooled endemic species richness (species from all five taxonomic groups) and with the richness of endemic vascular plants, snails, and beetles. Owing to limited postglacial migration, hotspots of high‐altitude endemics are situated in rather low peripheral mountain chains of the Alps, which have not been glaciated during the Pleistocene. There, tree line expansion disproportionally reduces habitats of high‐altitude species. Such legacies of climate history, which may aggravate extinction risks under future climate change have to be expected for many temperate mountain ranges.     

Climate Change Implications for River Restoration in Global Biodiversity Hotspots

Global biodiversity hotspots contain exceptional concentrations of endemic species in areas of escalating habitat loss. However, most hotspots are geographically constrained and consequently vulnerable to climate change as there is limited ability for the movement of species to less hostile conditions. Predicted changes to rainfall and temperature will undoubtedly further impact on freshwater ecosystems in these hotspots. Southwestern Australia is a biodiversity hotspot and, as one of the first to experience significant climate change, is an example and potentially a global bellwether for issues associated with river restoration. In this hotspot, current and predicted water temperatures may exceed thermal tolerances of aquatic fauna. Gondwanic aquatic fauna, characteristic of southwestern Australia, are typically cold stenotherms and consequently intolerant of elevated temperatures. The hotspot in southwestern Australia is geographically restricted being surrounded by ocean and desert, and many important national parks are located on the extreme south coast, where the landscape is relatively flat. Consequently, fauna cannot change their distribution southwards or with altitude as a response to increasing temperatures. Therefore, any mitigation responses need to be in situ to produce a suitable biophysical envelope to enhance species' resilience. This could be through “over restoration” by increased riparian replanting at a catchment scale. A rule‐of‐thumb of a 10% increase in riparian cover would be required to reduce water temperatures by 1°C. These restoration techniques are considered applicable to other global biodiversity hotspots where geography constrains species' movement and the present condition is the desired restoration endpoint.     

Diversity, endemism and species turnover of millipedes within the south-western Australian global biodiversity hotspot

Aim To examine how current and historical environmental gradients affect patterns of millipede (Diplopoda) endemism and species turnover in a global hotspot of floristic diversity, and to identify regions of high endemism and taxonomic distinctness for conservation management. Location South‐western Australia. Methods Museum database records of millipedes (subclasses Pentazonia and Helminthomorpha), supplemented with extensive fieldwork, were used to map species richness, species turnover (β‐diversity), weighted endemism, average taxonomic distinctness and variation in taxonomic distinctness in half‐degree grid squares (c. 2500 km²). Generalized linear models were used to examine relationships between these parameters with rainfall (present day and historical), topography and human disturbance (clearing for agriculture and urbanization). Results Millipede species richness, particularly within the order Spirostreptida, and millipede endemism were positively associated with large within‐cell differences in elevation (mountainous regions). Large variation in taxonomic distinctness (unevenness in the taxonomic tree) in higher‐rainfall areas was mainly due to speciation within the Spirostreptida genus Atelomastix. Hotspots of millipede endemism and taxonomic distinctness were identified within three categories of importance: primary (Stirling Range East, Cape Le Grand, Cape Arid, Walpole, Porongurups), secondary (Mount Manypeaks, Bremer Bay, Stirling Range West, Duke of Orleans Bay, Ravensthorpe, Albany, Busselton) and tertiary (Nornalup). A species turnover boundary was positively associated with rainfall, broadly located in the transition zone of 300–600 mm year^?1. Main conclusions The current lack of knowledge on the endemism of invertebrates hampers their incorporation into conservation planning. With this knowledge we can identify global biodiversity hotspots and, at a smaller scale, significant conservation areas within a region. Here we have shown that weighted endemism and taxonomic distinctness are useful tools in identifying centres of high endemism and speciation for millipedes within the south‐west Australian hotspot. Moreover, it is unlikely that either vertebrates or vascular plants will be useful surrogates for identifying significant areas for invertebrate conservation. While other workers have shown that vascular plants, mammals and frogs have different centres of endemism within south‐west Australia, our results show that centres of endemism for millipedes encompass all of these plus other areas.     

Assessing the vulnerability of an assemblage of subtropical rainforest vertebrate species to climate change in south‐east Queensland

Global climate change is a threat to ecosystems that are rich in biodiversity and endemism, such as the World Heritage‐listed subtropical rainforests of central eastern Australia. Possible effects of climate change on the biota of tropical rainforests have been studied, but subtropical rainforests have received less attention. We analysed published data for an assemblage of 38 subtropical rainforest vertebrate species in four taxonomic groups to evaluate their relative vulnerability to climate change. Focusing on endemic and/or threatened species, we considered two aspects of vulnerability: (i) resistance, defined by indicators of rarity (geographical range, habitat specificity and local abundance); and (ii) resilience, defined by indicators of a species potential to recover (reproductive output, dispersal potential and climatic niche). Our analysis indicated that frogs are most vulnerable to climate change, followed by reptiles, birds, then mammals. Many species in our assemblage are regionally endemic montane rainforest specialists with high vulnerability. Monitoring of taxa in regenerating rainforest showed that many species with high resilience traits also persisted in disturbed habitat, suggesting that they have capacity to recolonize habitats after disturbance, that is climate change‐induced events. These results will allow us to prioritize adaptation strategies for species most at risk. We conclude that to safeguard the most vulnerable amphibian, reptile and bird species against climate change, climatically stable habitats (cool refugia) that are currently without protection status need to be identified, restored and incorporated in the current reserve system. Our study provides evidence that montane subtropical rainforest deserves highest protection status as habitat for vulnerable taxa.     

Geographic evaluation of conservation status of African forest squirrels (Sciuridae) considering land use change and climate change: the importance of point data

Known occurrences based on natural history museum voucher specimens for three genera of African forest squirrels were used to develop a detailed, fine-scale distributional under- standing of each species. Considerations of species’ autecology, effects of land use change, and effects of global climate change were all included in our analyses, and negative effects of land use and climate change on species’ distributional areas were roughly equivalent across the species surveyed. We describe geographic patterns of distribution and endemism, and identify areas of potential occurrence of unknown species. Comparing with coarse grid-based approaches currently in vogue in African biodiversity conservation efforts, we suggest that the point-based method offers significant advantages in fine resolution and avoiding loss of information, and yet are feasibly implemented for many vertebrate groups.     

Implications of climate change for potamodromous fishes

There is little understanding of how climate change will impact potamodromous freshwater fishes. Since the mid 1970s, a decline in annual rainfall in south‐western Australia (a globally recognized biodiversity hotspot) has resulted in the rivers of the region undergoing severe reductions in surface flows (ca. 50%). There is universal agreement amongst Global Climate Models that rainfall will continue to decline in this region. Limited data are available on the movement patterns of the endemic freshwater fishes of south‐western Australia or on the relationship between their life histories and hydrology. We used this region as a model to determine how dramatic hydrological change may impact potamodromous freshwater fishes. Migration patterns of fishes in the largest river in south‐western Australia were quantified over a 4 year period and were related to a number of key environmental variables including discharge, temperature, pH, conductivity and dissolved oxygen. Most of the endemic freshwater fishes were potamodromous, displaying lateral seasonal spawning migrations from the main channel into tributaries, and there were significant temporal differences in movement patterns between species. Using a model averaging approach, amount of discharge was clearly the best predictor of upstream and downstream movement for most species. Given past and projected reductions in surface flow and groundwater, the findings have major implications for future recruitment rates and population viabilities of potamodromous fishes. Freshwater ecosystems in drying climatic regions can only be managed effectively if such hydro‐ecological relationships are considered. Proactive management and addressing existing anthropogenic stressors on aquatic ecosystems associated with the development of surface and groundwater resources and land use is required to increase the resistance and resilience of potamodromous fishes to ongoing flow reductions.     

Freshwater fish introductions in mediterranean‐climate regions: are there commonalities in the conservation problem?

Aim To compare patterns and drivers of freshwater fish introductions across five climatically similar regions and evaluate similarities and differences in the non‐native species introduced. Location Five mediterranean‐climate regions: California (USA), central Chile, south‐western Australia, the Iberian peninsula (Spain and Portugal) and the south‐western Cape (South Africa). Methods Species presence–absence for native and non‐native fishes were collated across the regions, and patterns of faunal change were examined using univariate and multivariate statistical approaches. Taxonomic patterns in freshwater fish introductions were evaluated by comparing the number of species introduced by order to the numbers expected from binomial probabilities. Factors influencing multiple introductions of freshwater fish species in mediterranean regions were determined using generalized linear modelling. Results High levels of endemism (70–90%) were revealed for south‐western Cape, south‐western Australia and Chile. Despite their high rates of endemism, all regions currently have more non‐native species than endemic species. Taxonomic selection was found for five orders, although this was only significant for Salmoniformes across regions. The average increase in regional compositional similarity of fish faunas resulting from non‐native fish introductions was 8.0%. Important factors predicting multiple introductions of a species include previous introduction success and mean latitude of its distribution Main conclusions The mediterranean‐climate regions of the world, separated by vast distances, originally had a few fish species in common but are now more similar, owing to species introductions, illustrating the extent and importance of taxonomic homogenization. Introductions are largely driven by taxonomically biased human interests in recreational fisheries, aquaculture and ornamental pet species.     

Are indicator groups and cross-taxon congruence useful for predicting biodiversity in aquatic ecosystems?

Resources for biodiversity surveys and conservation planning are limited, and conservation biologists and environmental managers are thus striving to find suitable surrogates for mapping and predicting biodiversity. Among popular surrogates are indicator groups that could be used for predicting variation in the biodiversity of other taxonomic groups. Despite some success at large scales, surveys of multiple taxonomic groups across ecosystems have suggested that no single group can be used effectively to predict variation in the biodiversity of other taxonomic groups. This paper concentrates on indicator groups and cross-taxon congruence in species richness and assemblage composition patterns in inland aquatic ecosystems. As has been found in studies of terrestrial ecosystems, there is low utility for indicator groups in predicting the biodiversity of other taxa in aquatic ecosystems. Even when statistically highly significant correlations between taxonomic groups have been detected, these correlations have been too weak to provide reliable predictions of biodiversity among various taxonomic groups or biodiversity in general. Indicator groups and, more generally, cross-taxon congruence thus do not appear to be particularly relevant for conservation in the freshwater realm.     

Socio-economic drivers of freshwater fish declines in a changing climate: a New Zealand perspective

New Zealand has a freshwater fish fauna characterized by high levels of national and local endemism and which is threatened by anthropogenic stressors including habitat destruction or deterioration, commercial harvest, pollution and interactions with invasive exotic species. Significant expansion of New Zealand's dairy production has recently created further deterioration of lowland water quality and greater pressure for water allocation in drier eastern regions of the South Island. New Zealand has large freshwater resources and its climate is predicted to experience less dramatic changes in mean annual temperature and precipitation than many other regions of the world as a result of anthropogenic climate change. Predicted changes in regional climate and further expansion of the dairy industry, however, will impose similar pressures on freshwater resources in northern New Zealand to those already acting to threaten freshwater biodiversity in the eastern South Island.     

A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south‐eastern Australia

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species‐level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south‐eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range‐wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 521–540.     

A revision of the bioregionalisation of freshwater fish communities in the Australian Monsoonal Tropics

The Australian freshwater fish fauna is very unique, but poorly understood. In the Australian Monsoonal Tropics (AMT) biome of northern Australia, the number of described and candidate species has nearly doubled since the last attempt to analyse freshwater fish species composition patterns and determine a bioregionalisation scheme. Here, we utilise the most complete database of catchment‐scale freshwater fish distributions from the AMT to date to: (a) reanalyze spatial patterns of species richness, endemism and turnover of freshwater fishes; (b) propose a biogeographic regionalisation based on species turnover; (c) assess the relationship between species turnover and patterns of environmental change and historic drainage connectivity; and (d) identify sampling gaps. Biogeographic provinces were identified using an agglomerative cluster analysis of a Simpson's beta (β_sim) dissimilarity matrix. A generalised dissimilarity model incorporating eighteen environmental variables was used to investigate the environmental correlates of species turnover. Observed and estimated species richness and endemism were calculated and inventory completeness was estimated based on the ratio of observed to estimated species richness. Three major freshwater fish biogeographic provinces and 14 subprovinces are proposed. These differ substantially from the current bioregionalisation scheme. Species turnover was most strongly influenced by environmental variables that are interpreted to reflect changes in terrain (catchment relief and confinement), geology and climate (runoff perenniality, stream density), and biotic responses to climate (net primary productivity). Past connectivity between rivers during low sea‐level events is also influential highlighting the importance of historical processes in explaining contemporary patterns of biodiversity in the AMT. The inclusion of 49 newly discovered species and candidate species only reinforced known focal points of species richness and endemism in the AMT. However, a number of key sampling gaps remain that need to be filled to fully characterise the proposed bioregionalisation.