Testing the River Continuum Concept with geostatistical stream-network models

The River Continuum Concept (RCC) provided one of the first unifying frameworks in fluvial ecosystem theory. While the RCC predictions held in many empirical tests, other research highlighted how the model overlooked sources of heterogeneity at different scales e.g. the effects of tributaries. Disentangling these effects requires an assessment of variation in key ecosystem variables over the longitudinal and lateral dimension of river networks. However, so far, no empirical tests have employed a spatially explicit statistical approach to this assessment.Here, we show how recently-developed spatially-explicit models for river networks can be used to test predictions of the RCC whilst taking into account cross-scale sources of heterogeneity. We used macroinvertebrate data from 195 monitoring sites from 1^st to 4^th order streams spread across the Adige River network (NE Italy). We compared theoretical expectations with empirical semivariograms that incorporated network topology to assess the continuity and patchiness in the proportion of invertebrates functional feeding groups (FFG) over Euclidean and in-stream distances. Geostatistical stream-network models were then used to quantify the influence of the longitudinal gradient relative to local-scale water quality and land-use drivers, while accounting for network spatial autocorrelation.Patterns in the semivariograms based on flow-connected relationships were characterised by a nested structure associated with heterogeneity at multiple scales. Therefore, the longitudinal variation in FFG was better described by a patchy discontinuum rather than a gradient, implying that both in-stream processes and landscape factors influenced stream ecosystem function. The overall shift in FFG along the longitudinal profile was generally consistent with the RCC predictions, although the best models often included water quality and local land-use predictors. Stream-network models further indicated that up to 90% of residual variation (mean=50%) was accounted for by spatial autocorrelation, especially among flow-connected communities. Accounting for such autocorrelation not only improved model performance relative to non-spatial approaches, but indicated that most flow-connected communities were spatially correlated to some extent. This has clear implications for the assessment of the RCC tenets. This is the first test of the river continuum model that explicitly accounted for stream network topology and autocorrelation. Results indicated that in the Adige River, macroinvertebrates feeding groups exhibited heterogeneity along the longitudinal gradient, which appeared punctuated by local habitat transitions. Such transitions could be associated with artificial impoundments that alter the natural continuity of river processes, and we advocate the use of spatially explicit network models to test the RCC in more natural contexts.     

Geomorphology and fish assemblages in a Piedmont river basin, U.S.A.

1. We investigated linkages between fishes and fluvial geomorphology in 31 wadeable streams in the Etowah River basin in northern Georgia, U.S.A. Streams were stratified into three catchment sizes of approximately 15, 50 and 100 km², and fishes and geomorphology were sampled at the reach scale (i.e. 20–40 times stream width). 2. Non‐metric multidimensional scaling (NMDS) identified 85% of the among‐site variation in fish assemblage structure and identified strong patterns in species composition across sites. Assemblages shifted from domination by centrarchids, and other pool species that spawn in fine sediments and have generalised food preferences, to darter‐cyprinid‐redhorse sucker complexes that inhabit riffles and runs, feed primarily on invertebrates, and spawn on coarser stream beds. 3. Richness and density were correlated with basin area, a measure of stream size, but species composition was best predicted (i.e. |r| between 0.60–0.82) by reach‐level geomorphic variables (stream slope, bed texture, bed mobility and tractive force) that were unrelated to stream size. Stream slope was the dominant factor controlling stream habitat. Low slope streams had smaller bed particles, more fines in riffles, lower tractive force and greater bed mobility compared with high slope streams. 4. Our results contrast with the ‘River Continuum Concept’ which argues that stream assemblages vary predictably along stream size gradients. Our findings support the ‘Process Domains Concept’, which argues that local‐scale geomorphic processes determine the stream habitat and disturbance regimes that influence stream communities.     

Parallels and contrasts between intermittently freezing and drying streams: From individual adaptations to biodiversity variation

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Functional diversity and trait–environment relationships of stream fish assemblages in a large tropical catchment

1. The species composition of stream fish assemblages changes across the longitudinal fluvial gradient of large river basins. These changes may reflect both zonation in species distributions and environmental filtering of fish traits as stream environments change from the uplands to the lowlands of large catchments. Previous research has shown that taxonomic diversity generally increases in larger, lowland streams, and the River Continuum Concept, the River Habitat Template and other frameworks have provided expectations for what functional groups of fishes should predominate in certain stream types. However, studies addressing the functional trait composition of fish assemblages across large regions are lacking, particularly in tropical river basins. 2. We examined functional trait–environment relationships and functional diversity of stream fish assemblages in the Río Grijalva Basin in southern Mexico. Traits linked to feeding, locomotion and life history strategy were measured in fishes from streams throughout the catchment, from highland headwaters to broad, lowland streams. Relationships between functional traits and environmental variables at local and landscape scales were examined using multivariate ordination, and the convex hull volume of trait space occupied by fish assemblages was calculated as a measure of functional diversity. 3. Although there were a few exceptions, functional diversity of assemblages increased with species richness along the gradient from uplands to lowlands within the Grijalva Basin. Traits related to swimming, habitat preference and food resource use were associated with both local (e.g. substratum type, pool availability) and landscape‐scale (e.g. forest cover) environmental variables. 4. Along with taxonomic structure and diversity, the functional composition of fish assemblages changed across the longitudinal fluvial gradient of the basin. Trait–environment relationships documented in this study partially confirmed theoretical expectations and revealed patterns that may help in developing a better understanding of general functional responses of fish assemblages to environmental change.     

Concordance among stream assemblages and spatial autocorrelation along a fragmented gradient

Patterns of spatial autocorrelation of biota and distributional similarity (concordance) between assemblages of different organism groups have important implications in both theoretical ecology and biodiversity conservation. Here we report environmental gradients and spatial distribution patterns of taxonomic composition among stream fish, benthic macroinvertebrate, and diatom assemblages along a fragmented stream in south‐western France. We quantified spatial patterns of lotic assemblage structure along this stream, and we tested for concordance in distribution patterns among the three taxonomic groups. Our results showed that both environmental characteristics and stream assemblages were spatially autocorrelated. For stream fish and diatom assemblages, these patterns reflected assemblage changes along the longitudinal stream gradient, whereas environmental variables and benthic macroinvertebrates exhibited a more patchy spatial pattern. Cross‐taxa concordance was significant between stream fish and diatoms, and between stream fish and benthic macroinvertebrates. The assemblage concordance between stream fish and diatoms could be attributed to similar responses along the longitudinal gradient, whereas those between stream fish and benthic macroinvertebrates may result from biotic interactions. Based on potential dispersal capacities of taxa, our results validated the hypotheses that weakly dispersing taxa exhibit greater concordance than highly dispersing ones and that dispersal capacities affect how taxonomic groups respond to their local environment. Both diatoms and highly dispersing stream fish were affected by stream fragmentation (i.e. the number of dams between sites), while the effect of fragmentation was not significant for invertebrates that fly well in their adult stage, thus emphasizing the importance of the way of dispersal. These results suggest that addressing the effects of dispersal capacity on stream assemblage patterns is crucial to identifying mechanisms behind patterns and to better understanding the determinants of stream biodiversity.     

Scale‐dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks; and (ii) testing for genetic isolation by distance along stream corridors vs. overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. amova identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in‐stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.     

Genetic population structure of the net-winged midge, Elporia barnardi (Diptera: Blephariceridae) in streams of the south-western Cape, South Africa: implications for dispersal

SUMMARY 1. The net‐winged midges (Diptera: Blephariceridae), with highly specific habitat requirements and specialised morphological adaptations, exhibit high habitat fidelity and a limited potential for dispersal. Given the longitudinal and hierarchical nature of lotic systems, along with the geological structure of catchment units, we hypothesise that populations of net‐winged midge should exhibit a high degree of population sub‐structuring. 2. Sequence variation in the cytochrome c oxidase subunit I (COI) region of the mitochondrial DNA (mtDNA) was examined to determine patterns of genetic variation and infer historical and contemporary processes important in the genetic structuring of populations of Elporia barnardi. The DNA variation was examined at sites within streams, between streams in the same range, and between mountain ranges in the south‐western Cape of South Africa. 3. Twenty‐five haplotypes, 641 bp in length, were identified from the 93 individuals sampled. A neighbour‐joining tree revealed two highly divergent clades (～5%) corresponding to populations from the two mountain ranges. A number of monophyletic groups were identified within each clade, associated with individual catchment units. 4. The distribution of genetic variation was examined using analysis of molecular variance (amova ). This showed most of the variation to be distributed among the two ranges (～80%), with a small percentage (～15%) distributed among streams within each range. Similarly, variation among streams on Table Mountain was primarily distributed among catchment units (86%). A Mantel's test revealed a significant relationship between genetic differentiation and geographical distance, suggesting isolation by distance (P < 0.001). 5. Levels of sequence divergence between the two major clades, representing the two mountain ranges, are comparable with those of some intra‐generic species comparisons. Vicariant events, such as the isolation of the Peninsula mountain chain and Table Mountain, may have been important in the evolution of what is now a highly endemic fauna. 6. The monophyletic nature of the catchment units suggests that dispersal is confined to the stream environment and that mountain ridges provide effective physical barriers to dispersal of E. barnardi.     

Colonization of an artificial stream by fishes and aquatic macro-invertebrates

We examined colonization by fishes and macro-invertebrates from permanent streams into an artificial freshwater stream simulating lotic temporary bodies of water that exist for only a limited period each year. After introducing water, invertebrates such as chironomid larvae in mud increased in numbers rapidly in the experimental stream, although they were rare in mud in the permanent streams. Eleven of 12 fish species present in the permanent streams colonized the experimental stream and preyed upon invertebrates, although fish composition differed significantly between the two streams. About 100 days after the initiation of the experiment, both species richness and diversity in the experimental stream reached almost the same level as that in the permanent streams. More diverse fishes colonized the complex section where habitat diversity was high compared to the simple section in the experimental stream. Our study strongly suggests that lotic temporary waters such as temporary streams around main rivers have unique ecological characteristics and serve as valuable foraging sites for fish.     

Variability and convergence in benthic communities along the longitudinal gradients of four physically similar Rocky Mountain streams

1. High‐gradient mountain streams are ideal for studying longitudinal biological patterns, although the degree of similarity in the biological gradient among physically similar streams in a region is poorly known. Our first objective was to evaluate variability in benthic communities along four streams in the central Rocky Mountains of Colorado. We analysed the relative influence of longitudinal position versus reach‐scale physical variables on community structure and measured community similarity at comparable longitudinal positions on the four streams. 2. Our second objective was to evaluate the relative utility of taxonomically versus functionally defined communities to characterise assemblage structure: are taxonomic patterns more predictable along the gradient than are patterns of ecologically important species traits? 3. Redundancy analyses (RDA), including measures of both reach‐scale environmental variables (substratum properties, periphytic cover, local channel slope) and longitudinal position (altitude, stream size), confirmed that the longitudinal position of a site was most important in determining taxonomic composition. Functional community structure was also influenced by longitudinal position, but reach‐scale variables (especially periphyton and median particle size) were of greater importance. 4. Redundancy analyses explained 29.3% of total taxonomic variance and 26.0% of functional variance, indicating that defining assemblages functionally provides no greater understanding of community patterns given several known environmental variables. Strict longitudinal limits of taxa, the presumably identical regional species pool across our sites, and/or trade‐offs among different types of species traits probably explain this result. 5. Redundancy analyses did suggest, however, that traits related to longer life (semivoltinism, long‐lived adults, and slow larval development) were more common downstream, while long‐distance dispersal ability and high fecundity were associated with higher altitude and its associated harsher conditions. 6. When sampling sites were grouped into three ecological zones defined by altitude, mean community similarity (measured both taxonomically and functionally) was lowest across streams at the highest altitude. This pattern could be driven by increased insularity of alpine‐zone streams, resulting from a combination of harsh terrestrial environment, lack of hydrological connectivity, and limited species ranges along the longitudinal continuum.     

Ecotones and fluvial regimes in arctic lotic environments

The fluvial regime in arctic streams is influenced by size of stream, the presence and storage capacity of lakes in the drainage basin, groundwater, and permafrost. Exchange of material with terrestrial environments depends on the season and is more or less suspended in winter. Permafrost and water storage in ice and snow control run off and erosion. Damage to vegetation by flooding, fire, animal or human activity can affect the permafrost and result in rapid erosion. Living space and conditions in lotic environments are modified by ice and during break up are very labile. Fish and benthic organisms in streams have behavioural and physiological adaptations which allow them to benefit from the wide range of river and stream environments found in the arctic and to tolerate the range of seasonal conditions. Ecotones are weakly developed in arctic streams and are of minor functional significance. Only farther south does riparian vegetation begin to play a role in regulating stream processes and not until south of the tree line can ecotones be considered important modulators of fluvial environments.     

Fish faunal ‘breaks’ and stream order in the eastern and central United States

Synopsis The distribution of fishes within 23 streams in the eastern and central United States was analyzed for evidence of distinct longitudinal faunal breaks, and to compare location of the breaks to stream order and longitudinal position of stations within watersheds. On the basis of presence-absence data for fish species, distinct faunal breaks were found in only 8 of the 23 streams. Qualitative faunal breaks were not significantly more common in any particular reach of streams, and the breaks did not correspond to changes in stream order. In 11 of 14 streams for which data on fish abundance were available, quantitative faunal breaks were found, but the locations of these breaks were unrelated to stream order or longitudinal position of stations in streams. Earlier studies have postulated that stream orders may represent distinct biological units for fishes. In contrast, this analysis shows that local fish faunas differ as much within as between adjacent stream orders, and suggests that stream order alone is not a pervasive organizer of lotic fish communities.     

Longitudinal Distribution of the Functional Feeding Groups of Aquatic Insects in Streams of the Brazilian Cerrado Savanna

We demonstrate that the distribution of the functional feeding groups of aquatic insects is related to hierarchical patch dynamics. Patches are sites with unique environmental and functional characteristics that are discontinuously distributed in time and space within a lotic system. This distribution predicts that the occurrence of species will be based predominantly on their environmental requirements. We sampled three streams within the same drainage basin in the Brazilian Cerrado savanna, focusing on waterfalls and associated habitats (upstream, downstream), representing different functional zones. We collected 2,636 specimens representing six functional feeding groups (FFGs): brushers, collector–gatherers, collector–filterers, shredders, predators, and scrapers. The frequency of occurrence of these groups varied significantly among environments. This variation appeared to be related to the distinct characteristics of the different habitat patches, which led us to infer that the hierarchical patch dynamics model can best explain the distribution of functional feeding groups in minor lotic environments, such as waterfalls.     

Biodiversity: towards a unifying theme for river ecology

1. A broadened concept of biodiversity, encompassing spatio‐temporal heterogeneity, functional processes and species diversity, could provide a unifying theme for river ecology. 2. The theoretical foundations of stream ecology often do not reflect fully the crucial roles of spatial complexity and fluvial dynamics in natural river ecosystems, which has hindered conceptual advances and the effectiveness of efforts at conservation and restoration. 3. Inclusion of surface waters (lotic and lentic), subsurface waters (hyporheic and phreatic), riparian systems (in both constrained and floodplain reaches), and the ecotones between them (e.g. springs) as interacting components contributing to total biodiversity, is crucial for developing a holistic framework of rivers as ecosystems. 4. Measures of species diversity, including alpha, beta and gamma diversity, are a result of disturbance history, resource partitioning, habitat fragmentation and successional phenomena across the riverine landscape. A hierarchical approach to diversity in natural and altered river‐floodplain ecosystems will enhance understanding of ecological phenomena operating at different scales along multidimensional environmental gradients. 5. Re‐establishing functional diversity (e.g. hydrologic and successional processes) across the active corridor could serve as the focus of river conservation initiatives. Once functional processes have been reconstituted, habitat heterogeneity will increase, followed by corresponding increases in species diversity of aquatic and riparian biota.     

Fishpond dams affect leaf‐litter processing and associated detritivore communities along intermittent low‐order streams

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Patch occupancy of North American mammals: is patchiness in the eye of the beholder?

Aim Intraspecific variation in patch occupancy often is related to physical features of a landscape, such as the amount and distribution of habitat. However, communities occupying patchy environments typically exhibit non‐random distributions in which local assemblages of species‐poor patches are nested subsets of assemblages occupying more species‐rich patches. Nestedness of local communities implies interspecific differences in sensitivity to patchiness. Several hypotheses have been proposed to explain interspecific variation in responses to patchiness within a community, including differences in (1) colonization ability, (2) extinction proneness, (3) tolerance to disturbance, (4) sociality and (5) level of adaptation to prevailing environmental conditions. We used data on North American mammals to compare the performance of these ‘ecological’ hypotheses and the ‘physical landscape’ hypothesis. We then compared the best of these models against models that scaled landscape structure to ecologically relevant attributes of individual species. Location North America. Methods We analysed data on prevalence (i.e. proportion of patches occupied in a network of patches) and occupancy for 137 species of non‐volant mammals and twenty networks consisting of four to seventy‐five patches. Insular and terrestrial networks exhibited significantly different mean levels of prevalence and occupancy and thus were analysed separately. Indicator variables at ordinal and family levels were included in models to correct for effects caused by phylogeny. Akaike's information criterion was used in conjunction with ordinary least squares and logistic regression to compare hypotheses. Results A patch network's physical structure, indexed using patch area and isolation, received the greatest support among models predicting the prevalence of species on insular networks. Niche breadth (diet and habitat) received the greatest support for predicting prevalence of species occupying terrestrial networks. For both insular and terrestrial systems, physical features (patch area and isolation) received greater support than any of the ecological hypotheses for predicting species occupancy of individual patches. For terrestrial systems, scaling patch area by its suitability to a focal species and by individual area requirements of the species, and scaling patch isolation by species‐specific dispersal ability and niche breadth, resulted in models of patch occupancy that were superior to models relying solely on physical landscape features. For all selected models, unexplained levels of variation were high. Main conclusions Stochasticity dominated the systems we studied, indicating that random events are probably quite important in shaping local communities. With respect to deterministic factors, our results suggest that forces affecting species prevalence and occupancy may differ between insular and terrestrial systems. Physical features of insular systems appeared to swamp ecological differences among species in determining prevalence and occupancy, whereas species with broad niches were disproportionately represented in terrestrial networks. We hypothesize that differential extinction over long time periods in highly variable networks has driven nestedness of mammalian communities on islands, whereas differential colonization over shorter time‐scales in more homogeneous networks probably governed the local structure of terrestrial communities. Our results also demonstrate that integration of a species' ecological traits with physical features of a patch network is superior to reliance on either factor separately when attempting to predict the species' probability of patch occupancy in terrestrial systems.     

Riverine landscape diversity

1. This review is presented as a broad synthesis of riverine landscape diversity, beginning with an account of the variety of landscape elements contained within river corridors. Landscape dynamics within river corridors are then examined in the context of landscape evolution, ecological succession and turnover rates of landscape elements. This is followed by an overview of the role of connectivity and ends with a riverine landscape perspective of biodiversity. 2. River corridors in the natural state are characterised by a diverse array of landscape elements, including surface waters (a gradient of lotic and lentic waterbodies), the fluvial stygoscape (alluvial aquifers), riparian systems (alluvial forests, marshes, meadows) and geomorphic features (bars and islands, ridges and swales, levees and terraces, fans and deltas, fringing floodplains, wood debris deposits and channel networks). 3. Fluvial action (erosion, transport, deposition) is the predominant agent of landscape evolution and also constitutes the natural disturbance regime primarily responsible for sustaining a high level of landscape diversity in river corridors. Although individual landscape features may exhibit high turnover, largely as a function of the interactions between fluvial dynamics and successional phenomena, their relative abundance in the river corridor tends to remain constant over ecological time. 4. Hydrological connectivity, the exchange of matter, energy and biota via the aqueous medium, plays a major though poorly understood role in sustaining riverine landscape diversity. Rigorous investigations of connectivity in diverse river systems should provide considerable insight into landscape‐level functional processes. 5. The species pool in riverine landscapes is derived from terrestrial and aquatic communities inhabiting diverse lotic, lentic, riparian and groundwater habitats arrayed across spatio‐temporal gradients. Natural disturbance regimes are responsible for both expanding the resource gradient in riverine landscapes as well as for constraining competitive exclusion. 6. Riverine landscapes provide an ideal setting for investigating how complex interactions between disturbance and productivity structure species diversity patterns.     

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

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Patterns of macroinvertebrate traits along three glacial stream continuums

1. Glacier‐fed streams are characterised by low spatial but high temporal heterogeneity, manifested in seasonal and diurnal discharge and suspended sediment peaks induced by glacial runoff. These streams shelter macroinvertebrate communities adapted to such harsh environmental conditions. Studies relating macroinvertebrate traits to environmental conditions in glacial streams could provide important insights into the structure and function of glacial stream communities. 2. From data collected in three glacial streams from the central Swiss and southern French Alps, we analysed the relationships among six biological traits to define five groups of macroinvertebrate taxa with similar suites of traits. 3. The longitudinal distribution of the five groups and of individual traits was analysed, as well as their variation according to a glaciality index combining water temperature, conductivity, suspended solids and substrate stability. 4. The trait diversity along the three streams showed a strong upstream‐downstream gradient. The upper reaches were dominated by a single group of taxa characterised by small, crawling, deposit feeders. The other trait‐based groups appeared progressively downstream. 5. Changes in the relative frequency of trait‐based groups along the glaciality gradient highlighted the dominance of all‐rounder resistant/resilient traits in the three streams and confirmed that environmental conditions in the glacial streams are too harsh or uniform to allow macroinvertebrate communities to develop alternative suites of traits. The findings are discussed in relation to the question of trait coding in the available literature.     

Re‐building brown trout populations in dredged boreal forest streams: in‐stream restoration combined with stocking of young trout

1. Rivers in boreal forested areas were often dredged to facilitate the transport of timber resulting in channels with simplified bed structure and flow fields and reduced habitat suitability for stream organisms, especially lotic fishes. Currently, many streams are being restored to improve their physical habitat, by replacing boulders and gravel and removing constraining embankments. The most compelling justification behind stream restoration of former floatways has been the enhancement of native fish populations, specifically salmonids. 2. We examined the success of a stream management programme aimed at re‐building diminished brown trout (Salmo trutta) populations by monitoring densities of young‐of‐year and older trout in 18 managed and three reference streams during 2000–2005. Rehabilitation included in‐stream restoration combined with a 5‐year post‐restoration period of stocking young brown trout. Our space‐for‐time substitution design comprised four pre‐management, four under‐management, 10 post‐management and three reference streams. 3. Densities of young‐of‐year brown trout, indicating population establishment, were significantly higher in post‐ compared with pre‐management streams. However, density of young‐of‐year brown trout in post‐management streams was significantly lower compared with near‐pristine reference streams. Furthermore, success of managed brown trout population re‐building varied, indicating stream‐specific responses to management measures. Density of burbot (Lota lota), a native generalist predator, was associated with low recruitment of brown trout. 4. Stream‐specific responses imply that rehabilitation of brown trout populations cannot be precisely predicted thereby limiting application. Our findings support the importance of adaptive stream restoration and management, with focus on identifying factor(s) limiting the establishment of target fish populations.     

Phylogeography and population genomics of a lotic water beetle across a complex tropical landscape

The habitat template concept applied to a freshwater system indicates that lotic species, or those which occupy permanent habitats along stream courses, are less dispersive than lentic species, or those that occur in more ephemeral aquatic habitats. Thus, populations of lotic species will be more structured than those of lentic species. Stream courses include both flowing water and small, stagnant microhabitats that can provide refuge when streams are low. Many species occur in these microhabitats but remain poorly studied. Here, we present population genetic data for one such species, the tropical diving beetle Exocelina manokwariensis (Dytiscidae), sampled from six localities along a ~300 km transect across the Birds Head Peninsula of New Guinea. Molecular data from both mitochondrial (CO1 sequences) and nuclear (ddRAD loci) regions document fine‐scale population structure across populations that are ~45 km apart. Our results are concordant with previous phylogenetic and macroecological studies that applied the habitat template concept to aquatic systems. This study also illustrates that these diverse but mostly overlooked microhabitats are promising study systems in freshwater ecology and evolutionary biology. With the advent of next‐generation sequencing, fine‐scale population genomic studies are feasible for small nonmodel organisms to help illuminate the effect of habitat stability on species’ natural history, population structure and geographic distribution.