Patterns in the co-occurrence of fish species in streams: the role of site suitability, morphology and phylogeny versus species interactions

Sulawesi stream fish communities depend on connectivity and habitat diversity

Streams provide an array of habitat niches that may act as environmental filters for fish communities. The tropical island of Sulawesi in Indonesia is located in the Wallacea, a region isolated by marine barriers from the Asian and Australian faunas. Primary freshwater fishes are naturally absent in the Wallacea, including Sulawesi's numerous coastal streams. Diadromous species are in contrast species-rich in the area. The knowledge available on stream fishes in the Wallacea is largely restricted to taxonomic work and studies targeting single species groups, whereas baseline data on fish ecology remain extremely scarce. Such data and a deeper understanding of stream fish ecology are, however, urgently required for purposes such as informed management. We assumed that the stream fish assemblages are dominated by recruitment from the sea and are structured by macro- and microhabitat diversity. To test this hypothesis, we quantified the occurrence of individual fishes by point abundance electrofishing at 33 streams across Sulawesi. The 4632 fishes obtained represent 58 species out of 24 families. The native fishes recorded are mainly amphidromous (34 species), euryhaline (five species), and catadromous (five species). Gobiiformes make up the vast majority of records, dominated by Oxudercidae (22 species) and Eleotridae (five species). Only two of the species recorded are endemic to Sulawesi, including a single species strictly confined to freshwaters. Ten species, making up 6% of the fishes caught, are not native to Sulawesi. The outlying mean index (OMI) and BIOENV analyses suggest that effects on the scale of macro- and microhabitat shape fish assemblage composition, ranging from pH, conductivity, and temperature to current velocity, substrate, canopy cover, and elevation. Habitat niche use of species along the first two OMI axes is complementary and fine-scaled, covering a wide range of the available habitat space. Juvenile and adult conspecifics share similar habitat niches in most of the cases. Niche breadths overlap, but niche specialization is significant in most of the species. Non-native fishes link into the assemblages at the margins of habitat space, with substantial niche overlaps to native species. The present findings show that the native fish communities in coastal streams of Sulawesi are largely composed of species depending on access to the sea, highlighting the importance of connectivity down to the estuaries and sea. The ichthyofauna shows a rich diversity in habitat use, and the availability of alternative habitats along the altitudinal gradient provides plausible filters for species establishment. Non-native fishes are locally abundant, pose substantial potential for changing communities, but are still stocked intentionally. We stress the need for incorporating the need for connectivity and maintained habitat quality into management decisions, and a critical evaluation of stocking activities.

A network-based approach to identifying correlations between phylogeny, morphological traits and occurrence of fish species in US river basins

The complex network framework has been successfully used to model interactions between entities in Complex Systems in the Biological Sciences such as Proteomics, Genomics, Neuroscience, and Ecology. Networks of organisms at different spatial scales and in different ecosystems have provided insights into community assembly patterns and emergent properties of ecological systems. In the present work, we investigate two questions pertaining to fish species assembly rules in US river basins, a) if morphologically similar fish species also tend to be phylogenetically closer, and b) to what extent are co-occurring species that are phylogenetically close also morphologically similar? For the first question, we construct a network of Hydrologic Unit Code 8 (HUC8) regions as nodes with interaction strengths (edges) governed by the number of common species. For each of the modules of this network, which are found to be geographically separated, there is differential yet significant evidence that phylogenetic distance predicts morphological distance. For the second question, we construct and analyze nearest neighbor directed networks of species based on their morphological distances and phylogenetic distances. Through module detection on these networks and comparing the module-level mean phylogenetic distance and mean morphological distance with the number of basins of common occurrence of species in modules, we find that both phylogeny and morphology of species have significant roles in governing species co-occurrence, i.e. phylogenetically and morphologically distant species tend to co-exist more. In addition, between the two quantities (morphological distance and phylogentic distance), we find that morphological distance is a stronger determinant of species co-occurrences.

Isolation controls reestablishment mechanisms and post-drying community structure in an intermittent stream

Biota in disturbance-prone landscapes have evolved a variety of strategies to persist long term, either locally (resistance) or by regional recolonization (resilience). Habitat fragmentation and isolation can limit the availability of recolonization pathways, and thus the dynamics of post-disturbance community reestablishment. However, empirical studies on how isolation may control the mechanisms that enable community recovery remain scarce. Here, we studied a pristine intermittent stream (Chalone Creek, Pinnacles National Park, California) to understand how isolation (distance from a perennial pool) alters invertebrate community recolonization after drying. We monitored benthic invertebrate reestablishment during the rewetting phase along a ~2-km gradient of isolation, using mesh traps that selected for specific recolonization pathways (i.e., drift, flying, swimming/crawling, and vertical migration from the hyporheic). We collected daily emigration samples, surveyed the reestablished benthic community after 6 weeks, and compared assemblages across trap types and sites. We found that isolation mediated migration dynamics by delaying peak vertical migration from the hyporheic by ca. 1 day on average per 250 m of dry streambed. The relative importance of reestablishment mechanisms varied longitudinally-with more resistance strategists (up to 99.3% of encountered individuals) in the upstream reaches, and increased drift and aerial dispersers in the more fragmented habitats (up to 17.2% and 18%, respectively). Resistance strategists persisting in the hyporheic dominated overall (88.2% of individuals, ranging 52.9%-99.3% across sites), but notably most of these organisms subsequently outmigrated downstream (85.6% on average, ranging 52.1%-96% across sites). Thus, contrary to conventional wisdom, resistance strategists largely contributed to downstream resilience as well as to local community recovery. Finally, increased isolation was associated with a general decrease in benthic invertebrate diversity, and up to a 3-fold increase in the relative abundance of drought-resistant stoneflies. Our results advance the notion that understanding spatial context is key to predicting post-disturbance community dynamics. Considering the interaction between disturbance and fragmentation may help inform conservation in ecosystems that are subject to novel environmental regimes.

A needle in the haystack? Applying species co-occurrence frameworks with fish assemblage data to identify species associations and sharpen ecological hypotheses

Different species can associate or interact in many ways, and methods exist for inferring associations and underlying mechanisms from incidence data (e.g., co-occurrence frameworks). These methods have received criticism despite their recent resurgence in the literature. However, co-occurrence frameworks for identifying nonrandomly associated species pairs (e.g., aggregated or segregated pairs) have value as heuristic tools for sharpening hypotheses concerning fish ecology. This paper provides a case study examining species co-occurrence across 33 stream fish assemblages in southeastern Oklahoma, USA, which were sampled twice (1974 and 2014). This study sought to determine (a) which species were nonrandomly associated, (b) what processes might have driven these associations and (c) how consistent patterns were across time. Associations among most pairs of species (24 species, 276 unique pairs) were not significantly different from random (>80%). Among all significant, nonrandomly associated species pairs (54 unique pairs), 78% (42 pairs) were aggregated and 22% (12 pairs) segregated. Most of these (28 pairs, 52%) were hypothesized to be driven by nonbiotic mechanisms: habitat filtering (20 pairs, 37%), dispersal limitation (two pairs, 0.4%) or both (six pairs, 11%). The remaining 26 nonrandomly associated pairs (48%) had no detectable signal of spatial or environmental factors involved with the association, therefore the potential for biotic interaction was not refuted. Only five species pairs were consistently associated across both sampling periods: stonerollers Campostoma spp. and orangebelly darter Etheostoma radiosum; red shiner Cyprinella lutrensis and bullhead minnow Pimephales vigilax; bluegill sunfish Lepomis macrochirus and redear sunfish Lepomis microlophus; redfin shiner Lythrurus umbratilis and bluntnose minnow Pimephales notatus; and bigeye shiner Notropis boops and golden shiner Notemigonus crysoleucas. Frameworks for identifying nonrandomly associated species pairs can provide insight into broader mechanisms of species assembly and point to potentially interesting species interactions (out of many possible pairs). However, this approach is best applied as a tool for sharpening hypotheses to be investigated further. Rather than a weakness, the heuristic nature is the strength of such methods, and can help guide biologists toward better questions by employing relatively cheap diversity survey data, which are often already in hand, to reduce complex interaction networks down to their nonstochastic parts which warrant further investigation.

Estimated richness and environmental correlates of miniature fish assemblages in the rio Jacundá, Brazil

Abstract South America is home to more miniature fishes (<26 mm in standard length) than any other continent. Despite this diversity, the ecology of miniature fishes is poorly studied. To promote the study of miniature fish ecology, we investigated patterns in total richness, assemblage structure and environmental correlates for miniature fishes in the rio Jacundá drainage of the Lower Amazon River basin, Pará State. Based on multi-pass dip-netting of leaf litter at 20 locations distributed across two sites, we collected miniature species and used rarefaction to estimate 9 to 14 species might be present. The miniature fish assemblage at the upstream site was a nested subset of the downstream site, and water pH and canopy cover, two features known to be altered by deforestation, correlated most strongly with assemblage variation. Our work represents one of the first quantitative assessments of environmental correlates with miniature fish assemblages and highlights research topics that should be investigated further to promote conservation and preservation of the overlooked and understudied Amazonian diminutive freshwater fish fauna.

Biomass of slow life history species increases as local bottom trawl effort decreases in the Celtic sea

Due to its selective removal, fishing pressure has long influenced the dynamics of species based on their life history traits. Sensitivity to fishing increases along a "fast-to-slow" gradient of life history strategies, and the "slow" species (large, long-lived, late-maturing, giving birth to few large offspring) require the most time to recover from fishing. In the North East Atlantic, after having reached extreme levels, fishing pressure has decreased since the 1980's due to management measures such as total allowable catch (TAC) or area closure. An effect on the distribution of species as well as a potential recovery could be expected. However, temporal patterns of life history strategies are rarely linked to management measures. In addition, a larger emphasis is often put on exploited or emblematic sensitive species but rarely on assembly processes at the ecosystem scale (both commercial and non-commercial species). Based on a 17-year time series of 101 taxa (fishes, elasmobranchs, bivalves, cephalopods and crustaceans), we observed a negative relationship between the biomass of taxa sensitive to fishing and bottom trawling pressure, as well as an increase in their total biomass in the Celtic Sea. Over the whole area, stochasticity appeared as the dominant assembly process. Deterministic assembly processes were at play in the centre of the area where significant overdispersion (caused by the presence of both slow and fast taxa) were observed. The absence of sensitive taxa from the rest of the Celtic Sea appeared to be caused mainly by a historical effect of environmental filtering when fishing was high. At the local scale, we related the decrease in fishing pressure to the increase in biomass of five of the most sensitive taxa. This local decrease in fishing pressure, resulting from the implementation of an area closure, highlights the positive effect of such management measures in less than two decades.

Effects of reservoir cascades on diversity, distribution, and abundance of fish assemblages in three Neotropical basins

River systems are characterized by the existence of longitudinal processes structuring fish assemblages. However, the construction of dams, many of them built in cascades, are disrupting these processes worldwide. Here, we analyzed the fish assemblages across reservoir cascades in three Brazilian river basins (Iguaçu, Paranapanema, and São Francisco) to identify whether there is a spatial convergent pattern and to infer the mechanisms structuring metacommunities in these Neotropical rivers. Linear models were used to assess the effect of reservoir cascades, and the associated morphological, spatial and environmental variables, on the species richness and diversity along them. We analyzed if reservoir cascades produce similar species distribution patterns using the elements of metacommunity structure framework and beta diversity and its components. Finally, super-organizing maps were used to find common trends in species abundances and the environmental, morphological, and spatial variables along cascades. The negative relationship between species richness and diversity and the position in the cascade indicated diversity declines along cascades. However, the resulting metacommunities varied in each river basin. They conformed a quasi-Gleasonian structure, a Clementsian structure, and a nested structure with stochastic species loss in the Iguaçu, Paranapanema, and São Francisco River basins, respectively. Generally, total beta-diversity (βsor) and species turnover (βsim) between pairs of reservoirs increased along reservoir cascades, especially at the downstream end, whereas nestedness (βsne) depicted distinct trends in each river basin. By contrast, there were general decreases in species abundances along cascades, especially downstream the fourth reservoir, with very few species benefiting from such situation. In general, species present in the downstream reservoirs were subsets of the species present in the upstream reservoirs (particularly in the São Francisco River Basin), while some had singular responses to the environmental gradient and appeared or disappeared at random. Although the cascade has an effect on fish assemblages, reservoir characteristics and operation also influence them. Our study highlights the impact of such structures and shows general patterns of fish assemblages that should help to mitigate the resulting ecological impacts and assist the process of infrastructure planning.

Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny

Understanding species' roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator-prey interactions in highly diverse ecosystems.

Null model analyses of temporal patterns of bird assemblages and their foraging guilds revealed the predominance of positive and random associations

Patterns of species associations have been commonly used to infer interactions among species. If species positively co-occur, they may form predominantly neutral assemblages, and such patterns suggest a relatively weak role for compensatory dynamics. The main objective of this study was to test this prediction on temporal samples of bird assemblages (n = 19, 10-57 years) by the presence/absence and quantitative null models on assemblage and guild levels. These null model outcomes were further analyzed to evaluate the effects of various data set characteristics on the outcomes of the null models. The analysis of two binary null models in combination with three association indices revealed 20% with significant aggregations, 61% with random associations, and only 19% with significant segregations (n = 95 simulations). The results of the quantitative null model simulations detected more none-random associations: 61% aggregations, 6% random associations, and 33% segregations (n = 114 simulations). Similarly, quantitative analyses on guild levels showed 58% aggregations, 20% segregations, and 22% random associations (n = 450 simulations). Bayesian GLMs detected that the outcomes of the binary and quantitative null models applied to the assemblage analyses were significantly related to census plot size, whereas the outcomes of the quantitative analyses were also related to the mean population densities of species in the data matrices. In guild-level analyses, only 9% of the GLMs showed a significant influence of matrix properties (plot size, matrix size, species richness, and mean species population densities) on the null model outcomes. The results did not show the prevalence of negative associations that would have supported compensatory dynamics. Instead, we assume that a similar response of the majority of species to climate-driven and stochastic factors may be responsible for the revealed predominance of positive associations.

Local habitat features explain the distribution of the imperiled grass pickerel (Esox americanus vermiculatus)

We investigated patterns of grass pickerel (Esox americanus vermiculatus Lesueur, 1846) distribution in three watersheds in Ontario, Canada, using site- and reach-scale habitat variables and fish community assemblage data to determine why this species occurs sporadically throughout watersheds despite abundant seemingly suitable, but unoccupied, habitat. Habitat and fish community data were collected using conventional field sampling methods, and reach-scale habitat data were compiled with the aid of a geographic information system. We found that occupied sites had lower baseflow indices and reach slopes but higher conductivity and agricultural land uses than unoccupied sites. More grass pickerel were detected when conductivity, channel cover, and wetlands in the floodplain were highest and bank slopes lowest; this is consistent with habitat preferences described elsewhere in its range. Habitat features at the site scale appeared more important than reach-scale features suggesting that grass pickerel may be using small habitat patches. This study identifies habitat elements important to grass pickerel and offers insights into management implications.

Effect of preservation on fish morphology over time: Implications for morphological studies

It has long been recognized that the process of preserving biological specimens results in alterations of body shape, though detailed studies examining the degree to which morphological changes occur throughout the preservation process are lacking. We utilize geometric morphometric analyses, an increasingly common tool for examining shape variation in a wide variety of biological disciplines, to examine the effects of formalin and ethanol preservation on the body shape of 10 freshwater fish species over time: from fresh specimens to eight weeks after preservation. We found significant changes in body shape among fresh and formalin fixed specimens. Furthermore, changes in body shape continue to occur after subsequent ethanol preservation. Two fish species collected at multiple localities show significant morphological differences for a limited number of morphometric characters. However, the significance, or lack thereof, often changed inconsistently from one stage of preservation to another. We conclude that morphometric analyses would ideally be performed on fresh specimens. However, recognizing that this is not always feasible, it is important to be aware of the morphometric changes that can occur during preservation.

Unraveling Saproxylic Insect Interactions in Tree Hollows from Iberian Mediterranean Forest

Tree hollows are complex microhabitats in which a variety of abiotic and biotic factors shape the community assembly of saproxylic insects. Detecting non-random species co-occurrence patterns is a fundamental goal in ecology in order to understand the assembly mechanisms of communities. We study association patterns of species of Coleoptera and Diptera (Syrphidae), belonging to different trophic guilds, on 72 tree hollows at a local and regional scale in three protected areas in Mediterranean forests using a fixed-fixed null model. Our matrix-level analysis shows a tendency for segregation in species association (species exclusion) at the regional and site levels. However, the high complexity of tree-hollow habitats, offering different resources for a more or less specialized fauna, makes it difficult to prove competition interactions. Indeed, pairwise analysis shows a dominance of non-random aggregation patterns (species coexistence) at the local and regional levels. Both aggregation and segregation of non-random patterns were more common among species from different trophic guilds than within the same guilds, with predators being a common denominator for a high percentage of the inter-guild pairs. Our results suggest that predation and facilitation interactions, together with habitat segregation, are the main factors shaping tree-hollow assemblages, while competition seems to be less important. We conclude that species interactions take an important part of the process of assemblage structuration and special attention should be paid to 'ecosystem engineers' and threatened species in the conservation of tree hollow assemblages.

Comparing species interaction networks along environmental gradients

Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co-variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant-hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis-based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients.

Parallel body shape divergence in the Neotropical fish genus Rhoadsia (Teleostei: Characidae) along elevational gradients of the western slopes of the Ecuadorian Andes

Neotropical mountain streams are important contributors of biological diversity. Two species of the characid genus Rhoadsia differing for an ecologically important morphological trait, body depth, have been described from mountain streams of the western slopes of the Andes in Ecuador. Rhoadsia altipinna is a deeper-bodied species reported from low elevations in southwestern Ecuador and northern Peru, and Rhoadsia minor is a more streamlined species that was described from high elevations (>1200 m) in the Esmeraldas drainage in northwestern Ecuador. Little is known about these species and their validity as distinct species has been questioned. In this study, we examine how their body shape varies along replicated elevational gradients in different drainages of western Ecuador using geometric morphometrics and the fineness ratio. We also use sequences of the mitochondrial cytochrome oxidase c I gene and the second intron of the S7 nuclear gene to examine whether genetic data are consistent with the existence of two species. We found that body depth varies continuously among populations within drainages as a function of elevation, and that body shape overlaps among drainages, such that low elevation populations of R. minor in the Esmeraldas drainage have similar body depths to higher elevation R. altipinna in southern drainages. Although a common general trend of declining body depth with elevation is clear, the pattern and magnitude of body shape divergence differed among drainages. Sequencing of mitochondrial and nuclear genes failed to meet strict criteria for the recognition of two species (e.g., reciprocal monophyly and deep genetic structure). However, there was a large component of genetic variation for the COI gene that segregated among drainages, indicating significant genetic divergence associated with geographic isolation. Continued research on Rhoadsia in western Ecuador may yield significant insight into adaptation and speciation in Neotropical mountain streams.

Phylogenetic perspectives on reef fish functional traits

Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.

Eco-morphological attributes and feeding habits in coexisting characins

The head morphology and feeding habits of pairs of characin species (family Characidae) that coexist in four different coastal rainforest streams were analysed. Coexisting species differed in size, but were very similar in eco-morphological attributes. Gut analyses revealed differences in feeding preferences for each coexisting species, indicating resource partitioning. A pattern of organization in species pairs that was repeated in the four studied streams was noticed. The pattern consisted of one slightly larger species with a feeding preference for items of allochthonous origin and another smaller species with a preference for autochthonous items. The hypothesis that small morphological differences enable the current coexistence of those species pairs was proposed. Furthermore, the results show ecological equivalence among different species in the studied streams.

Diatom Cooccurrence Shows Less Segregation than Predicted from Niche Modeling

Species cooccurrence patterns give significant insights into the processes shaping communities. While biotic interactions have been widely studied using cooccurrence analyses in animals and larger plants, studies about cooccurrences among micro-organisms are still relatively rare. We examined stream diatom cooccurrences in France through a national database of samples. In order to test the relative influence of environmental, biotic and spatial constraints on species’ incidence distribution, cooccurrence and nestedness patterns of real communities were compared with the patterns generated from a set of standard and environmentally constrained null models. Real communities showed a higher level of segregation than the most conservative standard null models, but a general aggregation of cooccurrences when compared to environmentally constrained null models. We did not find any evidence of limiting similarity between cooccurring species. Aggregations of species cooccurrences were associated with the high levels of nestedness. Altogether, these results suggested that biotic interactions were not structuring cooccurrences of diatom species at our study scale. Instead, the patterns were more likely to be related with colonization patterns, mass effect, and local temporal dynamics of diatom biofilms. We further highlight that the association of standard and environmentally constrained null models may give realistic insight into the cooccurrence patterns of microbial communities.

Lotic cyprinid communities can be structured as nest webs and predicted by the stress-gradient hypothesis

Little is known about how positive biotic interactions structure animal communities. Nest association is a common reproductive facilitation in which associate species spawn in nests constructed by host species. Nest-associative behaviour is nearly obligate for some species, but facultative for others; this can complicate interaction network topology. Nest web diagrams can be used to depict interactions in nesting-structured communities and generate predictions about those interactions, but have thus far only been applied to cavity-nesting vertebrate communities. Likewise, the stress-gradient hypothesis (SGH) predicts that prevalent biotic interactions shift from competition to facilitation as abiotic and biotic stress increase; this model has been hardly applied to animal communities. Here, both of these models were applied to nest-associative fish communities and extended in novel ways to broaden their applicability. A nest web was constructed using spawning observations over 3 years in several streams in south-western Virginia, USA. Structural equation modelling (SEM) was then implemented through an information-theoretic framework to identify the most plausible nest web topology in stream fish communities at 45 sites in the New River basin of the central Appalachian Mountains, USA. To test the SGH, the per-nest reproductive success of 'strong' (nearly obligate) nest associates was used to represent interaction importance. Eigenvectors were extracted from a principal coordinate analysis (PCoA) of proportional species abundances to represent community structure. Both of these metrics were regressed on physical stress, a combination of catchment-scale agricultural land use and stream size (representing spatiotemporal habitat variability). Seventy-one per cent of SEM model evidence supported a parsimonious interaction topology in which strong associates rely on a single host (Nocomis), but not other species. PCoA identified a gradient of community structure dominated by Nocomis and associates, to communities dominated by other reproductive groups. Both metrics of interaction importance responded positively to physical stress. This study demonstrates that nest webs can be useful in a variety of systems and that SEM can be a quantitative extension of this framework. Likewise, the SGH can be used to understand positive interactions in animal communities and can be extended to predict proportional representation of facilitating and beneficiary species in communities.

Ecomorphology and resource use by dominant species of tropical estuarine juvenile fishes

Eleven ecomorphological attributes and diet of seventeen juvenile fish species were examined to test the hypothesis that morphological patterns determine resource uses in estuarine habitats. Species were separated according to the apparatus to food capture and habitat use (benthic or pelagic) in three different groups: (1) a group with depressed fish body, strong caudal peduncle and enlarged pectoral fins; (2) a second group laterally flattened with a wide protruding mouth, and (3) a third group strongly flattened with small pectorals fins. The following six trophic groups were organized based on prey categories: Zooplanktivores, Benthivores, Omnivores, Detritivores, Macrocarnivores and Insectivores. Significant results (PERMANOVA) between ecomorphological indices and habitat and between ecomorphological indices and trophic groups were found. These data indicate that similarity of ecomorphological forms, which minimize the influence of environment and partitioning of food, would help facilitate the co-existence of these fish when they are abundant in this tropical estuary.

The influence of environmental variables on the functional structure of headwater stream fish assemblages: a study of two tropical basins in Central Brazil

We investigated functional patterns of fish assemblages of two adjacent basins (Araguaia and Tocantins) to test whether their headwater stream fish assemblages are more functionally (dis)similar than expected by chance and whether these (dis)similarities are related to differences of environmental conditions between basins. We used an analysis of similarities (ANOSIM) on a functional dissimilarity matrix to test for (dis)similarities between fish assemblages of both basins. We performed RLQ and fourth-corner analyses to determine fish species trait-environment relationship. Our results revealed functional dissimilarities between fish assemblages of both basins and significant species trait-environment relationships, suggesting that environmental conditions are driving such dissimilarities. Inter-basin dissimilarities are mainly driven by altitudinal and water temperature gradients, whereas dissimilarities among streams within the basins are influenced by channel depth, turbidity and conductivity. These five environmental variables mostly affected six fish species traits (body mass, water column position, substrate preference, parental care, foraging locality and migration) in different manners. This study is an attempt to understand functional trends of fish assemblages in a tropical region that remains poorly known but severely threatened.

Importance of regional diversity and environmental conditions on local species richness of aquatic macro-invertebrates in tropical forested streams

We used aquatic macro-invertebrates as a model to investigate the relationship between the regional species richness (RSR) and local species richness (LSR) in Peninsular Malaysia. A total of 38 streams (local scale) in seven catchments (regional scale), were sampled for aquatic macro-invertebrates. Eleven environmental variables (i.e. pH, DO, velocity, temperature, width, depth, TSS, BOD, COD, ammonia and canopy cover) were measured to assess their importance for local species richness. The average species richness was 34.9 species per region and the average abundance was 1380 individual per region. The highest number of species was 41, while the lowest species richness was 31. We applied local-regional richness regression models to explore the nature of the RSR–LSR relationship and then used variation partitioning to determine the relative importance of RSR and environmental conditions on LSR. We found a linear RSR–LSR relationship, which indicates unsaturated communities for macro-invertebrates in Malaysian streams and absence of local control with strong effects of regional processes. Variation in LSR explained by RSR was 43%, while the variation fraction in LSR explained by environmental conditions was low (2%) and not significant. We conclude that the variation in LSR is mainly controlled by the regional diversity pool (i.e. RSR) for aquatic macro-invertebrates in Peninsular Malaysia. However, weak effects of environmental conditions may reflect relatively low variability in the habitat among investigated streams. Further studies at larger scales, and involving different regions in this area, will be useful to draw comprehensive conclusions about determinants of local species diversity for stream invertebrates.

Environmental heterogeneity, dispersal mode, and co-occurrence in stream macroinvertebrates

Both environmental heterogeneity and mode of dispersal may affect species co-occurrence in metacommunities. Aquatic invertebrates were sampled in 20–30 streams in each of three drainage basins, differing considerably in environmental heterogeneity. Each drainage basin was further divided into two equally sized sets of sites, again differing profoundly in environmental heterogeneity. Benthic invertebrate data were divided into three groups of taxa based on overland dispersal modes: passive dispersers with aquatic adults, passive dispersers with terrestrial winged adults, and active dispersers with terrestrial winged adults. The co-occurrence of taxa in each dispersal mode group, drainage basin, and heterogeneity site subset was measured using the C-score and its standardized effect size. The probability of finding high levels of species segregation tended to increase with environmental heterogeneity across the drainage basins. These patterns were, however, contingent on both dispersal mode and drainage basin. It thus appears that environmental heterogeneity and dispersal mode interact in affecting co-occurrence in metacommunities, with passive dispersers with aquatic adults showing random patterns irrespective of environmental heterogeneity, and active dispersers with terrestrial winged adults showing increasing segregation with increasing environmental heterogeneity.

Fish assemblages in floodplain lakes in a Neotropical river during the wet season (Magdalena River, Colombia)

A number of studies have pointed out that abiotic factors and recolonization dynamics appear to be more important than biotic interactions in structuring river–fish assemblages. In this paper, we studied the fish assemblages in 27 floodplain lakes, with perennial connection to the river, in the middle section of the Magdalena River (Colombia), to examine spatial pattern in freshwater fish diversity in relation to some environmental parameters. Our objective was to examine relationships between floodplain-lake fish communities and environmental variables associated with lake morphology, water chemistry and river–floodplain connectivity in a large river–floodplain ecosystem. During the study, a total of 18 237 fish were caught from 50 species (regional richness; 17 were migrants and 33 residents). In the present study, the most diverse order was Characiformes with 20 species, followed by Siluriformes, with 19 species. Characidae and Loricaridae were the richest families. The range of species richness (local richness) varied between five and 39 species. Similarity of local assemblages (using the presence–absence data) depends on the distance between lakes. A positive relationship was observed between the Ln of the total abundance of each species and the number of lakes where they were found. Out of all the environmental parameters taken in the lakes, only the size (Log Area) and relative perimeter length are significantly related to local assemblage species richness. It has not been possible to demonstrate that the connectivity (distance) from lakes to the main river can be considered a predictor of the local richness.

Using directed phylogenetic networks to retrace species dispersal history

Methods designed for inferring phylogenetic trees have been widely applied to reconstruct biogeographic history. Because traditional phylogenetic methods used in biogeographic reconstruction are based on trees rather than networks, they follow the strict assumption in which dispersal among geographical units have occurred on the basis of single dispersal routes across regions and are, therefore, incapable of modelling multiple alternative dispersal scenarios. The goal of this study is to describe a new method that allows for retracing species dispersal by means of directed phylogenetic networks obtained using a horizontal gene transfer (HGT) detection method as well as to draw parallels between the processes of HGT and biogeographic reconstruction. In our case study, we reconstructed the biogeographic history of the postglacial dispersal of freshwater fishes in the Ontario province of Canada. This case study demonstrated the utility and robustness of the new method, indicating that the most important events were south-to-north dispersal patterns, as one would expect, with secondary faunal interchange among regions. Finally, we showed how our method can be used to explore additional questions regarding the commonalities in dispersal history patterns and phylogenetic similarities among species.

Effects of habitat characteristics and interspecific interactions on co-occurrence patterns of saproxylic beetles breeding in tree boles after forest fire: null model analyses

It is often suggested that habitat attributes and interspecific interactions can cause non-random species co-occurrence patterns, but quantifying their contributions can be difficult. Null models that systematically exclude and include habitat effects can give information on the contribution of these factors to community assembly. In the boreal forest, saproxylic beetles are known to be attracted to recently burned forests where they breed in dead and dying trees. We examined whether species co-occurrences of saproxylic beetles that develop in, and emerge from, boles of recently burned trees show non-random patterns. We also estimated the extent to which both the post-fire habitat attributes and interspecific interactions among beetles contribute to such patterns. We sampled tree boles encompassing key attributes (tree species, tree size/dbh and burn severity) that are thought to characterize species-habitat associations of saproxylic beetles, a proposition that we tested using indicator species analysis. Two null models with no habitat constraints ("unconstrained") indicated that a total of 29.4% of the species pairs tested had significant co-occurrence patterns. Habitat-constrained null models indicated that most of the detected species aggregations (72%) and segregations (59%) can be explained by shared and distinct species-habitat relationships, respectively. The assembly pattern was also driven by interspecific interactions, of which some were modulated by habitat; for example, predator and prey species tended to co-occur in large-sized trees (a proxy of available bark/wood food resource primarily for the prey). In addition, some species segregation suggesting antagonistic, competitive, or prey-predator interactions were evident after accounting for the species' affinities for the same tree species. Overall, our results suggest that an intimate link between habitat and interspecific interactions can have important roles for community assembly of saproxylic assemblages even following disturbance by fire. We also show that a systematic application of null models can offer insight into the mechanisms behind the assembly of ecological communities.

Species interactions mediate phylogenetic community structure in a hyperdiverse lizard assemblage from arid Australia

Evolutionary history can exert a profound influence on ecological communities, but few generalities have emerged concerning the relationships among phylogeny, community membership, and niche evolution. We compared phylogenetic community structure and niche evolution in three lizard clades (Ctenotus skinks, agamids, and diplodactyline geckos) from arid Australia. We surveyed lizard communities at 32 sites in the northwestern Great Victoria Desert and generated complete species-level molecular phylogenies for regional representatives of the three clades. We document a striking pattern of phylogenetic evenness within local communities for all groups: pairwise correlations in species abundance across sites are negatively related to phylogenetic similarity. By modeling site suitability on the basis of species' habitat preferences, we demonstrate that phylogenetic evenness generally persists even after controlling for habitat filtering among species. This phylogenetic evenness is coupled with evolutionary lability of habitat-associated traits, to the extent that closely related species are more divergent in habitat use than distantly related species. In contrast, lizard diets are phylogenetically conserved, and pairwise dietary overlap between species is negatively related to phylogenetic distance in two of the three clades. Our results suggest that contemporary and historical species interactions have led to similar patterns of community structure across multiple clades in one of the world's most diverse lizard communities.

Structure and integrity of fish assemblages in streams associated to conservation units in Central Brazil

This study aims to characterize the spatial and seasonal distribution of the fish assemblage and evaluate the integrity of streams in a sustainable use area that includes integral protection conservation units in Distrito Federal, Central Brazil (Cerrado biome). For the study, 12 stretches of 8 streams were sampled in 2008 (dry season) and 2009 (wet season). For that evaluation was estimated the Physical Habitat Index (PHI), vegetation cover (VC), pH, dissolved oxygen, turbidity, and conductivity. We recorded 22 species, about eight undescribed species, by a total of 2,327 individuals. The most representative families in number of species were Characidae (31.8%), Loricariidae (31.8%), and Crenuchidae (13.6%). Knodus moenkhausii was the most abundant species with 1,476 individuals, added to Astyanax sp., Phalloceros harpagos, and Hasemania sp. they represent over 95% of the total abundance. The species Astyanax sp. (occurring in 79.2% of the stretches) and K. moenkhausii (50.0%) were considered constant in both seasons. The longitudinal gradient (River Continuum) exerts a strong influence on the studied assemblage. According to CCA, the variables that structure the fish assemblage are based on aspects related to water volume and habitat complexity. No seasonal variation in richness, diversity, abundance, and mass were detected. A cluster analysis suggests a separation of species composition between the stretches of higher and lower orders, which was not observed for seasonality. The streams were considered well preserved (mean PHI 82.9±7.5%), but in some stretches were observed anthropogenic influence, detected in the water quality and, mainly, on the riparian vegetation integrity. The exotic species Poecilia reticulata was sampled in the two stretches considered most affected by anthropogenic activities by PHI, conductivity, and VC.