The ancient lakes of Indonesia: towards integrated research on speciation

Ancient lakes have provided considerable insights into the drivers of speciation and adaptive radiation in aquatic organisms. Most studies of species-flocks, however, focus only on a single group of organisms, and few have attempted to integrate geological, limnological, ecological, and genetic drivers of speciation on multiple species-flocks at various trophic levels. As such, there is a need for a comprehensive model system for research on speciation in aquatic environments where multiple radiations are investigated at various levels of biological organization (e.g., individual, population, and ecosystem) and placed in light of geographical and geological setting. The ancient Malili Lakes of Sulawesi, Indonesia, are ideal candidates for such a model, and represent the only hydrologically connected ancient lakes in the world. These lakes are characterized by ultra-oligotrophy and unique physicochemical conditions that govern the composition and production of planktonic communities. At higher trophic levels, there are three recurring trends: (1) low taxonomic richness and simple community structures, (2) adaptive radiations with trophic specialization, and (3) remarkably high endemism with evolutionary innovations throughout the lakes and species-flocks. Furthermore, the restricted geographic distributions of species-flocks within the Malili Lakes indicate that each lake constitutes a unique environment, and dispersal among lakes is limited, despite close contemporary connectivity. These observations suggest that ecological and evolutionary processes are regulated from the bottom up, and speciation is primarily facilitated by interspecific and intraspecific competition for limited resources. The Malili Lakes represent an outstanding natural model for integrative research into speciation as they offer the opportunity to explore the roles of geography, dispersal, and selection in the radiation of aquatic organisms.     

A New Species of Muscicapa Flycatcher from Sulawesi,Indonesia

The Indonesian island of Sulawesi, a globally important hotspot of avian endemism, has been relatively poorly studied ornithologically, to the extent that several new bird species from the region have been described to science only recently, and others have been observed and photographed, but never before collected or named to science. One of these is a new species of Muscicapa flycatcher that has been observed on several occasions since 1997. We collected two specimens in Central Sulawesi in 2012, and based on a combination of morphological, vocal and genetic characters, we describe the new species herein, more than 15 years after the first observations. The new species is superficially similar to the highly migratory, boreal-breeding Gray-streaked Flycatcher Muscicapa griseisticta, which winters in Sulawesi; however, the new species differs strongly from M. griseisticta in several morphological characters, song, and mtDNA. Based on mtDNA, the new species is only distantly related to M. griseisticta, instead being a member of the M. dauurica clade. The new species is evidently widely distributed in lowland and submontane forest throughout Sulawesi. This wide distribution coupled with the species'' apparent tolerance of disturbed habitats suggests it is not currently threatened with extinction.     

Herpetofaunal Richness and Community Structure of Offshore Islands of Sulawesi,Indonesia1

We examined the distribution and broad habitat associations of the herpetofauna on three offshore islands of southeast Sulawesi, Indonesia. A total of 74 amphibian and reptile taxa were recorded, comprising 13 frogs, 29 lizards, 29 snakes, 1 freshwater turtle, and 1 crocodile. Of the total taxa, 38 percent were endemic to Sulawesi, 13 were new undescribed taxa. Range extensions were also recorded for one taxon previously not known from Sulawesi. Herpetofauna of these islands is largely derived from that of mainland Sulawesi, and as for Sulawesi generally, is depauperate compared with herpetofaunal assemblages in Borneo, Java, and Thailand. Taxon richness was much higher in minimally disturbed forest and forest habitats with only moderate disturbance levels than in highly modified or disturbed habitats, such as secondary forests, plantations, and villages. Disturbed habitats were characterized by widespread, habitat generalists and human commensals. Forests were characterized by endemic and habitat‐specialist taxa. Little discrimination of taxon composition or endemism was found between minimally and moderately disturbed forest habitats. These results reaffirm the need for more general biological survey and research in this region. Taxa most likely to be displaced by human impacts tend to be endemic taxa, for which there exists little or no ecological information. The similarity in the herpetofaunal community structure between habitats with minimal and moderate disturbance levels has important implications for our understanding of ecological resilience in tropical herpetofaunal communities.     

Salmon‐derived nutrients drive diatom beta‐diversity patterns

1. Pacific salmon are a textbook example of migratory animals that transfer nutrients between ecosystems, but little is known about how salmon‐derived nutrients (SDN) affect the biodiversity of recipient freshwater ecosystems. We examined paleolimnological records from six Alaskan lakes to define how changes in SDN from sockeye salmon (Oncorhynchus nerka) influenced sedimentary diatom community structure and beta‐diversity among lakes and through time. 2. Using an isotopic mixing model, we showed that SDN loading could account for >80% of the lake total nitrogen budgets and strongly regulated diatom community composition. Spatial dissimilarity in diatom communities was positively related to differences in SDN among lakes (r² = 0.69, P < 0.01, n = 10). Likewise, temporal dissimilarity in diatom communities was positively related to differences in SDN in a sediment core with substantial variation in salmon spawner dynamics between 1700 and 1950 AD (r² = 0.34, P < 0.01, n = 19). Finally, beta‐diversity metrics quantifying temporal turnover within each lake’s sediment record were also positively related to the variance in SDN loading among lakes (r² = 0.88, P < 0.05, n = 5). Mean SDN was only negatively correlated to temporal diatom beta‐diversity. 3. Spatially subsidised systems often receive temporally variable resource inputs, and thus, it is not surprising that, unlike previous studies, we found that resource variability was the key driver of community composition and beta‐diversity. In habitats that receive strongly fluctuating external nutrient loads, environment heterogeneity may overweigh stochastic community processes. In addition, freshwater diatoms are characterised by great dispersal capabilities and short life cycles and therefore may be a more sensitive indicator for evaluating the role of resource variability than previously used model organisms. These results suggest that productivity–diversity relationship vary with the nature of nutrient loading and the life history of the community studied. 4. Overall, our study highlights that the transport of nutrients by sockeye salmon across ecosystem boundaries is a significant driver of algal community and biodiversity in nursery lakes, mainly through changing the magnitude of nutrient variation. As such, freshwater species diversity in regions like the U.S. Pacific Northwest may become impoverished where there have been long‐term declines in salmon populations and decreases in nutrient variability among lakes.     

Speciation patterns and processes in the zooplankton of the ancient lakes of Sulawesi Island,Indonesia

Although studies of ancient lake fauna have provided important insights about speciation patterns and processes of organisms in heterogeneous benthic environments, evolutionary forces responsible for speciation in the relatively homogenous planktonic environment remain largely unexplored. In this study, we investigate possible mechanisms of speciation in zooplankton using the freshwater diaptomids of the ancient lakes of Sulawesi, Indonesia, as a model system. We integrate phylogenetic and population genetic analyses of mitochondrial and nuclear genes with morphological and genome size data. Overall, our results support the conclusion that colonization order and local adaptation are dominant at the large, island scale, whereas at local and intralacustrine scales, speciation processes are regulated by gene flow among genetically differentiated and locally adapted populations. In the Malili lakes, the diaptomid populations are homogenous at nuclear loci, but show two highly divergent mitochondrial clades that are geographically restricted to single lakes despite the interconnectivity of the lake systems. Our study, based on coalescent simulations and population genetic analyses, indicates that unidirectional hybridization allows gene flow across the nuclear genome, but prevents the introgression of mitochondria into downstream populations. We suggest that hybridization and introgression between young lineages is a significant evolutionary force in freshwater plankton.     

Determinants of Benthic Diatom Community Structurein Boreal Streams: the Role of Environmental and Spatial Factors at Different Scales

Benthic diatoms were sampled at 197 sites in Finnish boreal streams. The diatom distribution patterns were related to environmental and spatial factors at three spatial scales using Canonical Correspondence Analysis (CCA). The results emphasized the predominance of chemical‐constituent concentration and ion composition on structuring benthic diatom communities in running waters. Within a river system, physical factors had notable influence on diatom community structure reflecting mainly only minor changes in water chemistry within a watershed. Partial CCA revealed that pure spatial component explained ca. 20% of explainable variation in diatom data at each of the three scales. Environmental factors captured 53–78% of explained variation in species data at ecoregion and river system level. According to Procrustean Randomization Test, spatial coordinates of the study sites and patterns in diatom community structure were strongly concordant (m² = 0.862, p = 0.001) across the largest spatial scale. Similarly, at smaller spatial scales in southern and central Finland, congruence was significant. These data support the view that diatom communities exhibit a rather strong spatial component especially at largest, national scale.     

Ancient lakes as hotspots of diversity: a morphological review of an endemic species flock of <Emphasis Type="Italic">Tylomelania</Emphasis> (Gastropoda: Cerithioidea: Pachychilidae) in the Malili lake system on Sulawesi,Indonesia

The viviparous freshwater gastropod Tylomelania (Caenogastropoda: Cerithioidea: Pachychilidae) endemic to the Indonesian island Sulawesi has radiated extensively in two ancient lake systems. We here present the first systematic species-level review of taxa in the five lakes of the Malili lake system, which contains the most diverse and best studied freshwater fauna on Sulawesi. Our results indicate a significantly higher diversity of Tylomelania in these lakes than previously perceived based on morphological evidence for delimiting the taxa. We describe nine new species, thus increasing the number of taxa known from the Malili lakes to 25. Tylomelania species are inhabiting all available substrates in the lakes, and the diversity of habitats is reflected in an unparalleled range of radula types in this closely related group. Several species show a high intraspecific variability in some characters, and their closer investigation will probably lead to the discovery of more cryptic species. As it is, this species flock on Sulawesi is among the largest freshwater mollusc radiations known. Since the Malili lake system also contains other large endemic species flocks of e.g. crustaceans and fishes, it is a major hotspot of freshwater biodiversity in Asia to become a conservation priority. Handling editor: K. Martens     

Shifts in taxonomical and guild composition of littoral diatom assemblages along environmental gradients

Diatoms are commonly and frequently used as water quality indicators, but only a few studies have been done to evaluate the importance of littoral, contemporary diatoms as bioindicators. This study aims to determine the main predictors of diatom community composition from 73 Swedish lakes. Canonical correspondence analysis (CCA) revealed pH, phosphate, nitrite/nitrate levels, longitude and percentage of forest in the catchment to be the most important factors of 51 environmental variables for structuring diatom assemblages. Cluster analysis separated the lakes into three groups based on the diatom community composition. Lakes belonging to these groups were characterised as: (1) acidic, nutrient-poor; (2) circumneutral, nutrient-poor and (3) alkaline, nutrient-rich, according to the results of a discriminant function analysis and dominant diatom taxa revealed by similarity percentage analysis. Ecological guilds according to growth morphology and the ability of nitrogen-fixation were assigned to all diatom taxa. All three lake groups exhibited a distinct guild composition. Nitrogen-fixing diatoms were found in nutrient-rich lakes, only. Our results indicate that taxonomical composition of littoral diatom assemblages can be applied in the assessment of nutrient and acidity status of Swedish lakes. Differences in distribution of the ecological guilds were connected to several environmental factors such as nutrients, light and grazing; their application in assessment of trophic status of lakes is therefore precarious.     

Floristics of forests across low nutrient soils in Sulawesi,Indonesia

The island of Sulawesi formed from the joining of proto-islands roughly three million years ago. Regions of zoological endemism, corresponding to the proto-islands, have been reported. Sulawesi's tree communities, however, remain poorly documented. In better-studied tropical regions, soil types similar to those found in Sulawesi often have distinctive tree communities. To gather data on Sulawesi's tree communities, we established ten (0.25 ha) plots on four soil types across three regions. We documented diversity, endemism, dominance, and species composition. Linear models of species composition showed greater influence of geographic distance rather than soil, and no relationship with climate. This suggests that the legacy of Sulawesi's formation may have influenced tree communities more so than the soil types we sampled. Most of our plots were on stressful soil types making it difficult to conclude on the importance of edaphic specialization in the Sulawesi tree flora. The lack of climatic effects reflects Sulawesi's position within the wet tropics where the small climatic differences are unlikely to have large influence on tree communities.     

The diversity and distribution of diatoms: from cosmopolitanism to narrow endemism

It has been claimed that microbial taxa will not exhibit endemism because their enormous populations remove dispersal as an effective constraint on geographical range. Here we review evidence that challenges this ubiquity hypothesis for the most speciose group of microbial eukaryotes, the diatoms. Detailed taxonomic inventories using fine-grained morphological characteristics, molecular markers, and crossing experiments have revealed that the geographic distribution of diatoms ranges from global to narrow endemic. Records of human-mediated introductions of exotic species further provide a strong indication that geographic dispersal was limiting in the past. Finally, recent studies have revealed that diatom community structure and diversity are influenced by geographical factors independent of environmental conditions. Diatom communities are thus regulated by the same processes that operate in macro-organisms, although possibly to a different degree, implying that dispersal limitation is significant and the endemism observed in isolated areas is real. These results underscore the pressing need to (1) continue research into diatom biology, ecology and the factors driving diatom species diversity and geographic distributions, and (2) protect relatively isolated areas against further introductions of exotic species. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

The use of diatoms in monitoring the development of created wetlands at a sandmining site in Western Australia

Former sand-mining pits at Capel, 200 km south of Perth in Western Australia, have been rehabilitated into artificial wetlands since 1975–1979. A chain of fresh water lakes was created as a potential waterbird refuge and an area for passive recreation. Initially, the lakes had low pH, high ammonium, iron and manganese levels and low phosphorus concentration. The lakes were characterised by low diversity of diatoms dominated by acidophilous species. Following an increase in pH in the effluent water discharged into the lake from the mining process plant and landscaping of the lakes since 1988, the diversity of diatoms gradually increased. The system is now dominated by periphytic diatom communities, preferring high conductivity. There has been a marked transition in the diatom community from acidophilous to alkaliphilous species. Planktonic diatom blooms replaced dinoflagellate blooms. Concomitantly, there has been a dramatic increase in the diversity of invertebrates and waterbirds in these lakes. The value of diatoms in assessing the progressive development of created wetlands as self-sustaining ecosystems at sand mines in Australia is discussed.     

Broad‐scale environmental response and niche conservatism in lacustrine diatom communities

Aim (1) To resolve theoretical debates regarding the role of environment versus dispersal limitation, the conservatism of niches across distances and the prevalence of environmental specialists in diatom communities. (2) To provide guidance on the use of diatom communities and other microbial analogues to analyse ecological response to environmental change. Location Eight hundred and ninety‐one lakes in five regional datasets from north‐western Europe and four regional datasets from north‐eastern North America. Methods Lacustrine diatom communities were analysed at three scales: inter‐continental, intra‐continental and regional. Nested partial redundancy analyses (RDAs) were used to determine spatial versus environmental components of community variation. Weighted‐averaging (WA) regression and calibration, as well as logistic and quadratic regressions, were used to detect niche conservatism and the prevalence of environmental specialists. Results Community patterns indicate that dispersal limitation acts predominantly at the inter‐continental scale, while at the regional (less than c. 1,000,000 km²) scale, a single environmental variable (pH) explains more than five times the community variation as spatial (dispersal‐related) variables. In addition, pH niche components appear to be conserved at the inter‐continental scale, and environmental specialization does not impose relative rarity, as specialists apparently readily disperse to suitable environments. Main conclusions Analysis at multiple scales is clearly important in determining the influences of community variation. For diatom communities, dispersal limitation acts most strongly at the broadest scales, giving way to environment at the scales considered by most analyses. The availability of a wide variety of propagules with consistent niches across regions indicates that diatom communities reflect the succession of taxa according to local environmental conditions, rather than disequilibrium with the environment or adaptation of local populations. While multi‐scale analyses must be undertaken for other groups to resolve debates over community drivers and determine appropriate scales for prediction, for diatoms (and probably other microbial communities), responses to environmental change can be inferred using analogue datasets from large geographic areas.     

The effect of land use on the diatom communities in lakes

Data on recenr diatom community structure and relevant environmental characteristics from the lakes and their catchments have been collected from 151 oligotrophic lakes in eastern Finland. The pattern of frequency distribution of diatoms as a function of environmental variables, including land use in the catchment, differs between diatom taxa and indicates the optimum conditions and amplitude of occurrence for particular species. This kind of study should lead to increased understanding of the environmental requirements of diatom species and will be useful in the interpretation of historical changes in lakes as well as in forecasting possible future changes.     

Correlation of surface sediment diatoms with the present lake water pH in 28 Algoma lakes,Ontario, Canada

The surface sediment diatom analysis of 28 Algoma lakes (pH 4.40–8.13) indicates that even though each lake has a widely different aquatic environment and characteristic diatom assemblage, a definite relationship exists between the lake water pH and their diatom assemblages. In the acidic lakes acidobiontic and acidophilous diatom species predominate whereas in circumneutral and alkaline lakes circumneutral and alkaliphilous diatoms were most common. Cluster analysis of the pH indicator diatom assemblages grouped the study lakes into three distinct cluster groups. These groups also closely corresponded to lake water pH. On the basis of published ecological information as well as their presence in our study lakes, the pH indicator status of a number of diatom taxa have been discussed. A detailed listing of the diatom taxa identified and their pH indicator status is provided in order to facilitate their use in future diatom-inferred pH studies.     

Beta diversity of stream diatoms at two hierarchical spatial scales: implications for biomonitoring

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Importance of scalar and riparian habitat effects for assessment of ecological status using littoral diatoms

The classification of waterbodies under the Water Framework Directive is dependent on the ability of monitoring programmes to reflect habitat quality using biotic elements including benthic diatom communities. This study investigated the influence of specific riparian habitats, of mixed woodland, grassland and lake artificial structures such as jetties and slipways, on benthic diatom assemblages in nine lakes across gradients of total phosphorus, alkalinity and in the presence or absence of Dreissena polymorpha. The heterogeneity of the benthic diatom assemblages at riparian and lake scale was assessed by taking three replicates per site category per lake, following standard European Union protocols. Canonical correspondence analysis (CCA) and mixed effect modelling was used to investigate the main environmental controls on assemblage structure. Non-metric Multidimensional Scaling (NMDS) was used to examine patterns in assemblage structure. No single environmental gradient was found to control benthic diatom composition, with differences among assemblages influenced both by riparian habitat type within lakes and interaction of multiple environment gradients, including presence of D. polymorpha. Greater control was exerted on community structure at the lake than local riparian scale. The influence of scalar factors on diatom assemblages increased with increasing scale. We recommend that for effective monitoring and assessment of ecological status, standard sampling protocols should include localised littoral habitats with individual samples pooled across riparian habitat types, thereby accounting for both multiple environmental and spatial controls on community structure.     

长江中下游湖群大型底栖动物群落结构及影响因素

长江中下游地区是我国淡水湖泊分布最为密集的区域,其中面积大于10 km²的湖泊总面积占相同级别中国淡水湖泊总面积的51.3%。目前对本地区湖泊大型底栖动物研究主要是关于单个湖泊或几个湖泊之间的比较,将区域内湖泊作为一个整体来分析的研究较少。为揭示现阶段长江中下游浅水湖泊底栖动物群落现状及其主要影响因素,于2008年和2009年夏季对本地区5个湖群69个湖泊大型底栖动物和水化学进行了调查,并分析区域过程和局域环境条件在决定该地区底栖群落结构中的相对重要性。结果表明水体矿化度、电导率及氮磷指标在不同湖群间具有显著差异,而高锰酸盐指数、叶绿素a及营养状态指数无显著差异。密度方面,以寡毛类和摇蚊幼虫为优势类群的湖泊共46个,占总数量的66.7%,以螺类为优势类群之一的湖泊16个,占总数量的23.2%;生物量方面,以螺类为优势的湖泊数量最多(33个),占总数量的46.4%,但以寡毛类和摇蚊幼虫占优势的湖泊亦有27个,占总数量的39.1%,双壳类仅在9个湖泊占据优势。典范对应分析结果表明该地区底栖动物群落结构是局域环境条件和区域过程共同作用的结果,两类因子共解释了33.9%的底栖动物群落变异,其中局域环境因子占被解释量的48.1%,空间变量占35.4%。空间变量较高的解释量表明对整个长江中下游地区湖泊而言,区域过程对底栖动物的分布也起着非常重要的作用。     

Lake regionalization and diatom metacommunity structuring in tropical South America

Lakes and their topological distribution across Earth's surface impose ecological and evolutionary constraints on aquatic metacommunities. In this study, we group similar lake ecosystems as metacommunity units influencing diatom community structure. We assembled a database of 195 lakes from the tropical Andes and adjacent lowlands (8°N–30°S and 58–79°W) with associated environmental predictors to examine diatom metacommunity patterns at two different levels: taxon and functional (deconstructed species matrix by ecological guilds). We also derived spatial variables that inherently assessed the relative role of dispersal. Using complementary multivariate statistical techniques (principal component analysis, cluster analysis, nonmetric multidimensional scaling, Procrustes, variance partitioning), we examined diatom–environment relationships among different lake habitats (sediment surface, periphyton, and plankton) and partitioned community variation to evaluate the influence of niche‐ and dispersal‐based assembly processes in diatom metacommunity structure across lake clusters. The results showed a significant association between geographic clusters of lakes based on gradients of climate and landscape configuration and diatom assemblages. Six lake clusters distributed along a latitudinal gradient were identified as functional metacommunity units for diatom communities. Variance partitioning revealed that dispersal mechanisms were a major contributor to diatom metacommunity structure, but in a highly context‐dependent fashion across lake clusters. In the Andean Altiplano and adjacent lowlands of Bolivia, diatom metacommunities are niche assembled but constrained by either dispersal limitation or mass effects, resulting from area, environmental heterogeneity, and ecological guild relationships. Topographic heterogeneity played an important role in structuring planktic diatom metacommunities. We emphasize the value of a guild‐based metacommunity model linked to dispersal for elucidating mechanisms underlying latitudinal gradients in distribution. Our findings reveal the importance of shifts in ecological drivers across climatic and physiographically distinct lake clusters, providing a basis for comparison of broad‐scale community gradients in lake‐rich regions elsewhere. This may help guide future research to explore evolutionary constraints on the rich Neotropical benthic diatom species pool.     

Sensitivity and responses of diatoms to climate warming in lakes heavily influenced by humans

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Testing of the applicability of European diatom indices in the tropical rift valley lake,Lake Hawassa,in Ethiopia

Quantitative ecological monitoring of African lakes is needed to understand growing human pressures on ecosystems. Diatom-based indices are routinely used for this purpose elsewhere in the world, but have not yet been produced for the flora of African freshwater lakes. Here we tested the applicability of the European diatom indices on the biomonitoring system of Lake Hawassa, Ethiopia. Physico-chemical and benthic diatom sampling was done at nine sites with different degrees of human disturbance along the lakeshore area from February to November 2015 and 2016. A percentage disturbance score (PDS) was calculated at each site and categorised from no evident disturbance (0–25%) to high disturbance (75–100%). Based on this criterion and selected physico-chemical parameters, the sampling sites categorized into minimal, moderate and high disturbance. Seventeen diatom indices were calculated using Omnidia software version 5.3. Out of a total of 17 indices that were calculated using the Omnidia software, six were selected as potential metrics. The diatom indices had a high discrimination efficiency and were significantly correlated with most the environmental parameters (r > 0.6; p < 0.05). Among these, the trophic diatom index (TDI) and generic diatom index (IDG) showed the best potential to discriminate the three clustered sites, based on their ecological classification. Accordingly, although robust locally based indices are needed, the TDI and IDG diatom indices could be used in monitoring of water quality in tropical African rift lakes.