Phylogeny of the Lake Tanganyika cichlid species flock and its relationship to the Central and East African haplochromine cichlid fish faunas

Lake Tanganyika, the oldest of the East African Great Lakes, harbors the ecologically, morphologically, and behaviorally most complex of all assemblages of cichlid fishes, consisting of about 200 described species. The evolutionary old age of the cichlid assemblage, its extreme degree of morphological differentiation, the lack of species with intermediate morphologies, and the rapidity of lineage formation have made evolutionary reconstruction difficult. The number and origin of seeding lineages, particularly the possible contribution of riverine haplochromine cichlids to endemic lacustrine lineages, remains unclear. Our phylogenetic analyses, based on mitochondrial DNA sequences of three gene segments of 49 species (25% of all described species, up to 2,400 bp each), yield robust phylogenies that provide new insights into the Lake Tanganyika adaptive radiation as well as into the origin of the Central- and East-African haplochromine faunas. Our data suggest that eight ancient African lineages may have seeded the Tanganyikan cichlid radiation. One of these seeding lineages, probably comprising substrate spawning Lamprologus-like species, diversified into six lineages that evolved mouthbrooding during the initial stage of the radiation. All analyzed haplochromines from surrounding rivers and lakes seem to have evolved within the radiating Tanganyikan lineages. Thus, our findings contradict the current hypothesis that ancestral riverine haplochromines colonized Lake Tanganyika to give rise to at least part of its spectacular endemic cichlid species assemblage. Instead, the early phases of the Tanganyikan radiation affected Central and East African rivers and lakes. The haplochromines may have evolved in the Tanganyikan basin before the lake became a hydrologically and ecologically closed system and then secondarily colonized surrounding rivers. Apparently, therefore, the current diversity of Central and East African haplochromines represents a relatively young and polyphyletic fauna that evolved from or in parallel to lineages now endemic to Lake Tanganyika.     

Consideration of Geography and Wetland Geomorphic Type in the Development of Great Lakes Coastal Wetland Bird Indicators

We examined how geographic distribution of birds and their affinities to three geomorphic wetland types would affect the scale at which we developed indicators based on breeding bird communities for Great Lakes coastal wetlands. We completed 385 breeding bird surveys on 222 wetlands in the US portion of the basin in 2002 and 2003. Analyses showed that wetlands within two ecoprovinces (Laurentian Mixed Forest and Eastern Broadleaf Forest) had different bird communities. Bird communities were also significantly different among five lakes (Superior, Michigan, Huron, Erie, and Ontario) and among three wetland types (lacustrine, riverine, barrier-protected). Indicator values illustrated bird species with high affinities for each group (ecoprovince, lake, wetland type). Species with restricted geographic ranges, such as Alder and Willow Flycatchers (Empidonax alnorum and E. traillii), had significant affinities for ecoprovince. Ten bird species had significant affinities for lacustrine wetlands. Analyses on avian guild metrics showed that Lake Ontario wetlands had fewer long-distant migrants and warblers than other lakes. Numbers of short-distant migrants and total individuals in wetlands were higher in the Eastern Broadleaf Forest ecoprovince. Number of flycatchers and wetland obligate birds were not different among provinces, lakes, or wetland type. One potential indicator for wetland condition in Great Lakes wetlands, proportion of obligate wetland birds, responded negatively to proportion of developed land within 1 km of the wetland. We conclude that, although a guild approach to indicator development ameliorates species-specific geographic differences in distribution, individual species responses to disturbance scale will need to be considered in future indicator development with this approach.     

Use of ecological indicators to assess the quality of Great Lakes coastal wetlands

Over 2000 coastal wetland complexes have been identified in the Laurentian Great Lakes watershed, each providing critical habitat for numerous aquatic and terrestrial species. Research has shown there is a direct link between anthropogenic activities (urbanization and agricultural development) and deterioration in wetland health in terms of water quality and biotic integrity. In this study, we evaluate coastal marshes throughout the Great Lakes basin using a suite of published ecological indices developed specifically for coastal wetlands of the Great Lakes (Water Quality Index (WQI), Wetland Macrophyte Index (WMI), and the Wetland Fish Index (WFI_Basin)). We surveyed 181 wetlands, including 19 in Lake Superior (11%), 11 in Lake Michigan (6%), 13 in Lake Huron (7%), 92 in Georgian Bay and the North Channel (51%), 18 in Lake Erie (10%), and 28 in Lake Ontario (15%), over a 13 year period (1995–2008). Water quality parameters were measured at every site, while paired fyke nets were used to assess the fish community (132 sites) and macrophytes were surveyed and identified to species (174 sites); all of this information was used to calculate the associated index scores. One-way ANOVA results showed that there were significant differences in wetland quality among lakes. According to the WQI, we found that over 50% of marshes in Lakes Michigan, Erie, and Ontario were in degraded condition, while over 70% of marshes in Lakes Superior, Huron, and Georgian Bay were minimally impacted. Georgian Bay had the highest proportion of wetlands in very good and excellent condition and least number of wetlands in a degraded state. The WMI and WFI showed similar results. This is the largest bi-national database of coastal wetlands and the first study to provide a snapshot of the quality of coastal habitats within the Great Lakes basin. We recommend this information be used to guide conservation and restoration efforts within the Laurentian Great Lakes.     

Potential changes to the biology and challenges to the management of invasive sea lamprey Petromyzon marinus in the Laurentian Great Lakes due to climate change

Control programs are implemented to mitigate the damage caused by invasive species worldwide. In the highly invaded Great Lakes, the climate is expected to become warmer with more extreme weather and variable precipitation, resulting in shorter iced‐over periods and variable tributary flows as well as changes to pH and river hydrology and hydrogeomorphology. We review how climate change influences physiology, behavior, and demography of a damaging invasive species, sea lamprey (Petromyzon marinus), in the Great Lakes, and the consequences for sea lamprey control efforts. Sea lamprey control relies on surveys to monitor abundance of larval sea lamprey in Great Lakes tributaries. The abundance of parasitic, juvenile sea lampreys in the lakes is calculated by surveying wounding rates on lake trout (Salvelinus namaycush), and trap surveys are used to enumerate adult spawning runs. Chemical control using lampricides (i.e., lamprey pesticides) to target larval sea lamprey and barriers to prevent adult lamprey from reaching spawning grounds are the most important tools used for sea lamprey population control. We describe how climate change could affect larval survival in rivers, growth and maturation in lakes, phenology and the spawning migration as adults return to rivers, and the overall abundance and distribution of sea lamprey in the Great Lakes. Our review suggests that Great Lakes sea lamprey may benefit from climate change with longer growing seasons, more rapid growth, and greater access to spawning habitat, but uncertainties remain about the future availability and suitability of larval habitats. Consideration of the biology of invasive species and adaptation of the timing, intensity, and frequency of control efforts is critical to the management of biological invasions in a changing world, such as sea lamprey in the Great Lakes.     

Phylogeography and speciation in the <Emphasis Type="Italic">Pseudocrenilabrus philander</Emphasis> species complex in Zambian Rivers

Haplochromine cichlids form the most species-rich lineage of cichlid fishes that both colonized almost all river systems in Africa and radiated to species flocks in several East African lakes. The enormous diversity of lakes is contrasted by a relatively poor albeit biogeographically clearly structured species diversity in rivers. The present study analyzed the genetic structure and phylogeographic history of species and populations of the genus Pseudocrenilabrus in Zambian rivers that span two major African drainage systems, the Congo- and the Zambezi-system. The mtDNA phylogeny identifies four major lineages, three of which occur in the Congo-system and one in the Zambezi system. Two of the Congo-clades (Lake Mweru and Lunzua River) comprise distinct albeit yet undescribed species, while the fish of the third Congo-drainage clade (Chambeshi River and Bangweulu swamps), together with the fish of the Zambezi clade (Zambezi and Kafue River) are assigned to Pseudocrenilabrus philander. Concerning the intraspecific genetic diversity observed in the sampled rivers, most populations are highly uniform in comparison to lacustrine haplochromines, suggesting severe founder effects and/or bottlenecking during their history. Two bursts of diversification are reflected in the structure of the linearized tree. The first locates at about 3.9% mean sequence divergence and points to an almost simultaneous colonization of the sampled river systems. Subsequent regional diversification (with about 1% mean sequence divergence) occurred contemporaneously within the Kafue River and the Zambezi River. The clear-cut genetic biogeographic structure points to the dominance of geographic speciation in this lineage of riverine cichlid fishes, contrasting the importance of in situ diversification observed in lake cichlids.     

The seasonality of phytoplankton in the North American Great Lakes,a comparative synthesis

The phytoplankton and productivity of the North American Great Lakes has been studied extensively by Fisheries and Oceans Canada during the past 15 years to monitor the impact of nutrient and contaminant loading on the plankton of the ecosystem. Lakewide cruises were conducted at monthly intervals mainly during the spring to fall period. This provided extensive biomass, species, size, productivity and nutrient concentration data for the Great Lakes. These data were collected using the Utermöhl inverted microscope technique together with standardized taxonomic, productivity and data-handling procedures. These standardized methodologies were applied to all the Great Lakes which resulted in a comprehensive phycological and ecological data base for the first time. These data form the basis for the evaluation of the complex phenomenon of seasonality.The eutrophic/mesotrophic Lower Great Lakes exhibited well-developed seasonal peaks of high biomass, with inshore-offshore differentiation and spring maxima most pronounced in the inshore region. However, the oligotrophic Upper Great Lakes had low biomass and generally lacked well-developed seasonal patterns. No marked seasonal trends were observed in the ultra-oligotrophic Lake Superior. The seasonality of biomass and various taxonomic groups of phytoplankton showed differentiation between individual lakes and is discussed in detail. The seasonal succession of species provided interesting comparisons between the Lower Great Lakes, which harbour eutrophic and mesotrophic species, and the Upper Great Lakes, which harbour oligotrophic species.Due to the voluminous nature of our data, a general overview has been given for all the Great Lakes with Lake Ontario treated in detail as a case study. The Lake Ontario case study provides the state-of-the-art status ranging from the lakewide surveys of 1970 to the current research with minute organisms such as ultraplankton and picoplankton.     

Pico- and Nanoplankton in Aquatic Ecosystems in the Valley of the Lakes and Great Lakes Depression (Mongolia)

The abundance and biomass of bacterioplankton, phototrophic picoplankton, and heterotrophic nanoflagellates has been determined in lakes, rivers, and reservoirs located in the Valley of the Lakes and Great Lakes Depression (Mongolia). The species richness of the heterotrophic flagellates and their consumption of bacteria are estimated. Pico- and nanoplankton are the most abundant in shallow mineral lakes Orog and Tatsyn and in the freshwater Durgun Reservoir. Heterotrophic nanoflagellates consume 26–92% (on average 66%) of the daily bacterioplankton production. Thus, flagellates are important in the transfer of bacterial carbon to the higher levels of planktonic trophic webs. A total of 30 species and their forms of heterotrophic flagellates from 14 large taxa are identified. The highest species diversity of these protists are found in the Durgun and Taishyr reservoirs.     

Phylogeography of Altai osmans (Oreoleuciscus sp., Cyprinidae, Pisces) based on sequence variation of the mitochondrial DNA cytochrome b gene

Representatives of the genus Oreoleuciscus (Altai osmans) from the water bodies of Western Mongolia were examined for sequence polymorphism of the mitochondrial DNA fragment containing the cytochrome b (Cyt-b) gene. A total of 17 sequence variants (haplotypes) were discovered, which formed two clusters, A and B, with nonoverlapping geographic localization. Cluster A included haplotypes of Altai osmans from the Valley of Lakes water bodies. Cluster B consisted of two subclusters, the first of which (B1) united sequence variants of the populations from Hollow of the Great Lakes and the lakes of the Great Altai Range. The second subcluster (B2) was formed by the haplotypes originating from the Hollow of the Lake Uvs, some isolated lakes of the Northwestern Khangay region, and the water bodies of the Arctic Ocean Basin (basins of Selenga and Orchon rivers). Based on the genetic divergence estimates and the radiation time of genetic geographic groups identified, the existence of three allopatric species of Altaic osmans in the genus Oreoleuciscus was substantiated.     

The conservation of the fishes of Lake Victoria,Africa: an ecological perspective

Synopsis The African Great Lakes are considered to be dynamically fragile ecosystems that are relatively resistant to minor changes with which they have co-evolved but vulnerable to major perturbations such as overfishing, the introduction of alien species and pollution. These lakes are inhabited by large species flocks of cichlid fishes which are characterised by a complex structure of interaction both between and within species, as is typical of mature ecosystems. Major perturbations, such as the disruption of trophic interactions through the introduction of alien fishes, may reverse the domination of relatively precocial, specialised forms and result in the creation of conditions that are conducive to the survival of more altricial, generalised forms with strong colonising abilities. The introduction of Nile perch and Nile tilapia, as well as other alien fishes, into Lake Victoria, combined with overfishing for the indigenous cichlid species, has resulted in marked changes to the fish communities and the fisheries that depend on them. The most important impacts of the Nile perch appear to be predation and aggressive effects whereas those of the tilapias include hybridization, overcrowding, competition for food and possibly the introduction of parasites and diseases. While the three proposed methods of conserving the indigenous flocks of cichlid fishes (captive propagation, reducing Nile perch stocks and closure of the haplochromine trawl fishery) all have merit, the changes that are occurring in Lake Victoria are basically irreversible. The highest priority should be to assist the governments of the riparian countries (Tanzania, Uganda and Kenya) with monitoring and research programmes and to support their policies of non-introduction of further alien fishes into any of the African Great Lakes so as prevent the same cycle of events from occurring, for example, in Lakes Tanganyika and Malawi. The diverse animal and plant communities of the African Great Lakes are a heritage of all mankind and it is the duty of every country to play a role in their conservation. It is therefore proposed that an internationally funded research programme should be mounted on the African Great Lakes on the scale of the tropical forest biome project of the IUCN. Editorial     

Mitochondrial phylogeny and phylogeography of East African squeaker catfishes (Siluriformes: Synodontis)

Background  

Squeaker catfishes (Pisces, Mochokidae, Synodontis) are widely distributed throughout Africa and inhabit a biogeographic range similar to that of the exceptionally diverse cichlid fishes, including the three East African Great Lakes and their surrounding rivers. Since squeaker catfishes also prefer the same types of habitats as many of the cichlid species, we hypothesized that the East African Synodontis species provide an excellent model group for comparative evolutionary and phylogeographic analyses.     

Lake level fluctuations synchronize genetic divergences of cichlid fishes in African lakes

Water level fluctuations are important modulators of speciation processes in tropical lakes, in that they temporarily form or break down barriers to gene flow among adjacent populations and/or incipient species. Time estimates of the most recent major lowstands of the three African Great Lakes are thus crucial to infer the relative timescales of explosive speciation events in cichlid species flocks. Our approach combines geological evidence with genetic divergence data of cichlid fishes from the three Great East African Lakes derived from the fastest-evolving mtDNA segment. Thereby, we show for each of the three lakes that individuals sampled from several populations which are currently isolated by long geographic distances and/or deep water form clusters of equally closely related haplotypes. The distribution of identical or equally closely related haplotypes in a lake basin allows delineation of the extent of lake level fluctuations. Our data suggest that the same climatic phenomenon synchronized the onset of genetic divergence of lineages in all three species flocks, such that their most recent evolutionary history seems to be linked to the same external modulators of adaptive radiation. A calibration of the molecular clock of the control region was elaborated by gauging the age of the Lake Malawi species flock through the divergence among the utaka-cichlid and the mbuna-cichlid lineages to minimally 570,000 years and maximally 1 Myr. This suggests that the low-lake-level period which established the observed patterns of genetic relatedness dates back less than 57,000 years, probably even to 17,000-12,400 years ago, when Lake Victoria dried up and Lakes Malawi and Tanganyika were also low. A rapid rise of all three lakes about 11,000 years ago established the large-scale population subdivisions observed today. Over that period of time, a multitude of species originated in Lakes Malawi and Victoria with an impressive degree of morphological and ecological differentiation, whereas the Tanganyikan taxa that were exposed to the same habitat changes hardly diverged ecologically and morphologically. Our findings also show that patterns of genetic divergences of stenotopic organisms provide valuable feedback on geological and sedimentological time estimates for lake level changes.     

Climate and human water use diminish wetland networks supporting continental waterbird migration

Migrating waterbirds moving between upper and lower latitudinal breeding and wintering grounds rely on a limited network of endorheic lakes and wetlands when crossing arid continental interiors. Recent drying of global endorheic water stores raises concerns over deteriorating migratory pathways, yet few studies have considered these effects at the scale of continental flyways. Here, we investigate the resiliency of waterbird migration networks across western North America by reconstructing long‐term patterns (1984–2018) of terminal lake and wetland surface water area in 26 endorheic watersheds. Findings were partitioned regionally by snowmelt‐ and monsoon‐driven hydrologies and combined with climate and human water‐use data to determine their importance in predicting surface water trends. Nonlinear patterns of lake and wetland drying were apparent along latitudinal flyway gradients. Pervasive surface water declines were prevalent in northern snowmelt watersheds (lakes ?27%, wetlands ?47%) while largely stable in monsoonal watersheds to the south (lakes ?13%, wetlands +8%). Monsoonal watersheds represented a smaller proportion of total lake and wetland area, but their distribution and frequency of change within highly arid regions of the continental flyway increased their value to migratory waterbirds. Irrigated agriculture and increasing evaporative demands were the most important drivers of surface water declines. Underlying agricultural and wetland relationships however were more complex. Approximately 7% of irrigated lands linked to flood irrigation and water storage practices supported 61% of all wetland inundation in snowmelt watersheds. In monsoonal watersheds, small earthen dams, meant to capture surface runoff for livestock watering, were a major component of wetland resources (67%) that supported networks of isolated wetlands surrounding endorheic lakes. Ecological trends and human impacts identified herein underscore the importance of assessing flyway‐scale change as our model depictions likely reflect new and emerging bottlenecks to continental migration.     

Great Lakes coastal wetland habitat use by seven turtle species: influences of wetland type, vegetation, and abiotic conditions

Great Lakes coastal wetlands are important habitats for turtles but few studies have looked at factors driving community structure in these systems. We evaluated the effects of wetland type, vegetation, and abiotic conditions on turtle communities for 56 wetlands in Lakes Huron, Michigan, and Superior with data collected during the summers of 2000–2008. Overall, 1,366 turtles representing seven species were captured using fyke nets. For the majority of species, catches were highest in drowned river mouth wetlands In addition, turtles tended to be more abundant in water lilies, submersed aquatic vegetation, and cattails compared to bulrush. We also found positive correlations between catches of four of the species as well as total turtle catch and turtle species richness with a human disturbance gradient. These correlations suggest that turtles may be able to utilize coastal wetland areas that are inhospitable to fish because of hypoxic conditions. Our results show the importance Great Lakes coastal wetlands to turtles, and stress the need for managers to take into account turtle populations when preparing conservation and restoration strategies.     

Fish communities in the African Great Lakes

Synopsis Ecological conditions in tropical lacustrine systems are considered by focusing on the evolution, maintenance, exploitation and vulnerability of fish communities in the African Great Lakes. The exceptionally high biodiversities in the littoral/sublittoral zones of the very ancient, deep, clear, permanently stratified rift lakes Tanganyika and Malawi, are contrasted with the simpler systems in their pelagic zones, also with biodiversity in the much younger, shallower Victoria, the world's largest tropical lake.Paper from the Canadian Society of Zoologists symposium Great Lakes of the World, organized by David L.G. Noakes     

Unique qualities and special problems of the African Great Lakes

Synopsis The African Great Lakes consist of large, deep rift valley lakes (e.g. Malawi & Tanganyika) and shallower lakes between the Eastern and Western Rifts (e.g. Victoria). They are a group comparable in size to the North American Great Lakes, but are old. Most are seasonally thermally stratified, and wind is the decisive factor that determines the annual cycle of cooling and mixing. Lakes Tanganyika, Malawi and Kivu are meromictic, with deep relict hypolimnia. Large magnitudes and time scales of periodic internal motion, where these have been measured, appear unique among lakes. These lakes harbour the world's richest lacustrine fish faunas, and the family Cichlidae provides the supreme example of geographically circumscribed vertebrate evolution. The lakes provide a unique comparative series of natural laboratories for evolutionary studies. Primary production is generally high, but in the deeper lakes standing stocks of plankton and of small fish species are low. These pelagic populations are characterised by very high P:B ratios. The fisheries are productive and of socio-economic importance. Large-scale mechanised fishing is not compatible with the survival of the diverse fish communities. Cichlids appear especially vulnerable to unselective fishing. Aquatic reserves might offer a means of survival for at least some communities. Various pollution threats exist. Because water retention times are long, extremely long for some deep lakes, and flushing rates are low, the lakes are vulnerable to pollution which would be long-lasting. Introductions of alien fishes have mostly had undesirable or disastrous results. While the faunas are one of the significant natural heritages of mankind, their conservation must realistically be linked to the legitimate development of the lakes for the well-being of the people who live there. Scientific value alone will not protect the lakes. Just as survival of African terrestrial wildlife in extensive reserves depends heavily upon tourism, so also might the cichlid flocks in underwater reserves. Greater interest from the international scientific community is needed to further rational development and conservation of these great lakes.Invited Editorial     

Using SINEs to probe ancient explosive speciation: "hidden" radiation of African cichlids?

Cichlid fishes of the east African Great Lakes represent a paradigm of adaptive radiation. We conducted a phylogenetic analysis of cichlids including pan-African and west African species by using insertion patterns of short interspersed elements (SINEs) at orthologous loci. The monophyly of the east African cichlids was consistently supported by seven independent insertions of SINE sequences that are uniquely shared by these species. In addition, data from four other loci indicated that the genera Tilapia (pan-African) and Steatocranus (west African) are the closest relatives to east African cichlids. However, relationships among Tilapia, Steatocranus, and the east African clade were ambiguous because of incongruencies among topologies suggested by insertion patterns of SINEs at six other loci. One plausible explanation for this phenomenon is incomplete lineage sorting of alleles containing or missing a SINE insertion at these loci during ancestral speciation. Such incomplete sorting may have taken place earlier than 14 MYA, followed by random and stochastic fixation of the alleles in subsequent lineages. These observations prompted us to consider the possibility that cichlid speciation occurred at an accelerated rate during this period when the African Great Lakes did not exist. The SINE method could be useful for detecting ancient exclusive speciation events that tend to remain hidden during conventional sequence analyses because of accumulated point mutations.     

Genetic isolation and morphological divergence mediated by high-energy rapids in two cichlid genera from the lower Congo rapids

Background  

It is hypothesized that one of the mechanisms promoting diversification in cichlid fishes in the African Great Lakes has been the well-documented pattern of philopatry along shoreline habitats leading to high levels of genetic isolation among populations. However lake habitats are not the only centers of cichlid biodiversity - certain African rivers also contain large numbers of narrowly endemic species. Patterns of isolation and divergence in these systems have tended to be overlooked and are not well understood.     

Habitat Use by Migrant Shorebirds in Saline Lakes of the Southern Great Plains

Abstract Shorebirds migrating through the Southern Great Plains of North America use saline lakes as stopovers to rest and replenish energy reserves. To understand how availability of invertebrates, salinity, freshwater springs, vegetation, and water influence the value of saline lakes as migration stopovers, we compared lakes used and not used by migrant shorebirds. Shorebirds used lakes that had freshwater springs, mudflats and standing water, sparse vegetation (≤1% cover), low to moderate salinities (x = 30.87 g/L), and mean invertebrate biomass of 0.79 g/m². Lakes that were not used were generally dry or had hypersaline water (x = 82.56 g/L), lacked flowing springs and vegetation, and had few or no invertebrates (x = 0.007 g/m²). Our results suggest that reduced spring flows and increased salinity negatively affect availability of shorebird habitats and aquatic invertebrates. We recommend preservation of the freshwater springs discharging in the saline lakes. Because the springs are discharged from the Ogallala aquifer, which is recharged through the playa wetlands, the entire complex of wetlands in the Great Plains and the Ogallala aquifer should be managed as an integral system.     

Temporal Changes between Ecological Regimes in a Range of Primary and Secondary Salinised Wetlands

Many rivers and wetlands in south-western Australia are threatened by salinisation due to rising saline watertables, which have resulted from land clearing and the replacement of deep-rooted perennial species with shallow-rooted annual species. A four to six weekly sampling program of water quality, submerged macrophytes and macroinvertebrates was undertaken at six wetlands, from September 2002 to February 2004, to investigate seasonal variation in a range of primary and secondary saline systems. The wetlands dried and filled at different times in response to local rainfall patterns, and salinities varied accordingly with evapoconcentration and dilution. Two types of clear-water wetlands were recognised; those dominated by submerged aquatic macrophytes (Ruppia, Lepilaena and Lamprothamnium) and those dominated by benthic microbial communities. Two types of turbid wetlands were also recognised; those with high concentrations of phytoplankton and those with high concentrations of suspended sediments. A primary saline lake and two lakes that have only recently been affected by secondary salinisation persisted in a clear, macrophyte-dominated regime throughout most of the study period, except during drying and filling. Two lakes with a long history of secondary salinisation (70 years) moved between regimes over the study period. A clear, benthic microbial community – dominated regime only persisted at the wetland which contained permanent water throughout the study period. The turbid regimes were only present during drying and refilling phases. A richer and more abundant macroinvertebrate fauna was associated with the clear, macrophyte- dominated wetlands. Our results suggest that the development of management guidelines that recognise the presence of different ecological regimes and that consider the interactions between water regime, salinity, and primary and secondary production will be more useful in protecting biodiversity and ecological function in these systems than managing salinity as a single factor.