How Can Model Comparison Help Improving Species Distribution Models?

Today, more than ever, robust projections of potential species range shifts are needed to anticipate and mitigate the impacts of climate change on biodiversity and ecosystem services. Such projections are so far provided almost exclusively by correlative species distribution models (correlative SDMs). However, concerns regarding the reliability of their predictive power are growing and several authors call for the development of process-based SDMs. Still, each of these methods presents strengths and weakness which have to be estimated if they are to be reliably used by decision makers. In this study we compare projections of three different SDMs (STASH, LPJ and PHENOFIT) that lie in the continuum between correlative models and process-based models for the current distribution of three major European tree species, Fagussylvatica L., Quercusrobur L. and Pinussylvestris L. We compare the consistency of the model simulations using an innovative comparison map profile method, integrating local and multi-scale comparisons. The three models simulate relatively accurately the current distribution of the three species. The process-based model performs almost as well as the correlative model, although parameters of the former are not fitted to the observed species distributions. According to our simulations, species range limits are triggered, at the European scale, by establishment and survival through processes primarily related to phenology and resistance to abiotic stress rather than to growth efficiency. The accuracy of projections of the hybrid and process-based model could however be improved by integrating a more realistic representation of the species resistance to water stress for instance, advocating for pursuing efforts to understand and formulate explicitly the impact of climatic conditions and variations on these processes.     

Do Butterfly Activity Data from Mark-Recapture Surveys Reflect Temporal Patterns?

Temporal patterns in butterfly behavior should reflect diurnal, seasonal and population-level changes in mate availability. Investment into mating should peak at times when potential mates are at a maximum; at other times, individuals should save energy and focus on maintenance activities. To explore these assumptions, we re-analyzed mark-recapture data containing records of behavior for each handled individual: 15 species, 21 separate datasets, total of 20,828 activity records (13,223 males and 7605 females). We used ordination analysis, with activity categories as response variables and controls for dataset identity and weather effects. Across species, basking and nectaring were prevailing morning activities, while mating peaked at afternoons. With the progressing season, males switched from maintenance behavior to mating activities, whereas opposite trend applied to females. Density predictors (sex ratio, daily population size) revealed that mating concentrated to high densities of the opposite sex and that female oviposition, resting and nectaring increased under low density of males. Exploring mark-recapture data for studying behavioral patterns proved to be fruitful but cannot replace focused observations or experiments.     

Do Correlation Patterns Reflect the Role of Development in Morphological Evolution?

Correlation patterns have been widely used in evolutionary studies for exploring the role of development in channelling morphological evolution. The approach was firstly introduced by Olson and Miller in the 1950s, but it did not gain prominence until the 1980s, due to some extent to Gould and Lewontin’s (Proc R Soc Lond B 205:581–598, 1979) assertion of the importance of considering organisms as integrated entities, where the internal organization of a structure, and not only the selective regime acting upon it, would play a fundamental role in its evolution. Here we show that this approach, mainly focused on the study of small, quantitative shape changes of existing structures, does not deal with a fundamental aspect of developmental systems, that is, their intrinsic capacity of originating morphological novelties. We show that only when the physicochemical processes underlying morphogenesis and pattern formation are taken into account, would the causal role of development be fully incorporated into the evolutionary view.     

Species Diversity and Life-Form Patterns in Steppe Vegetation along a 3000 m Altitudinal Gradient in the Alborz Mountains, Iran

Biodiversity pattern and life-form spectra were studied along a 3,000 m altitudinal gradient from a semi-desert area to the alpine peak of Tochal Mountain. The gradient is located on the southern slopes of Central Alborz with a Mediterranean continental climate. DCA ordination was applied to 1,069 relevés and 7 quantitative variables to discover the relation of diversity and altitude. A biodiversity pattern was obtained by relating values for species richness and Shannon-Wiener’s index to 100-m altitudinal sections. Altitude was determined as the major ecological gradient. Both diversity indices are negatively correlated with altitude and show a decreasing trend beyond a peak in species richness at 1,800–1,900 m a.s.l. towards a very low diversity in the high alpine zone. The biodiversity peak does not match with the potential tree line in the area (2,500–3,000 m a.s.l.). The high diversity in foothills can be related to habitat heterogeneity, longer suitable climatic conditions, and diverse disturbance factors, while unfavorable conditions at high-altitude alpine and low-altitude desert areas reduce the number of species at both extremes. Life-form patterns clearly change along altitudinal gradient. Annuals with decreasing trend, and hemicryptophytes and chamaephytes with increasing trend along the altitudinal gradient are notable patterns of life form in the area. Temperature, soil moisture and nutrients are the main factors that explain the ecological influence of altitude on species diversity and life-form patterns in the semi-arid steppe vegetation of the area.     

Diversity Patterns in the Flora of the Campo-Ma’an Rain Forest, Cameroon: Do Tree Species Tell it All?

This study describes diversity patterns in the flora of the Campo-Ma’an rain forest, in south Cameroon. In this area, the structure and composition of the forests change progressively from the coastal forest on sandy shorelines through the lowland evergreen forest rich in Caesalpinioideae with Calpocalyx heitzii and Sacoglottis gabonensis, to the submontane forest at higher elevations and the mixed evergreen and semi-deciduous forest in the drier Ma’an area. We tested whether there is a correlation between tree species diversity and diversity of other growth forms such as shrubs, herbs, and lianas in order to understand if, in the context of African tropical rain forest, tree species diversity mirrors the diversity of other life forms or strata. Are forests that are rich in tree species also rich in other life forms? To answer this question, we analysed the family and species level floristic richness and diversity of the various growth forms and forest strata within 145 plots recorded in 6 main vegetation types. A comparison of the diversity within forest layers and within growth forms was done using General Linear Models. The results showed that tree species accounted for 46% of the total number of vascular plant species with DBH ≥1 cm, shrubs/small trees 39%, climbers 14% and herbs less than 1%. Only 22% of the diversity of shrubs and lianas could be explained by the diversity of large and medium sized trees, and less than 1% of herb diversity was explained by tree diversity. The shrub layer was by far the most species rich, with both a higher number of species per plot, and a higher Shannon diversity index, than the tree and the herb layer. More than 82% of tree species, 90% of shrubs, 78% of lianas and 70% of herbaceous species were recorded in the shrub layer. Moreover, shrubs contributed for 38% of the 114 strict and narrow endemic plant species recorded in the area, herbs 29%, trees only 20% and climbers 11%. These results indicate that the diversity of trees might not always reflect the overall diversity of the forest in the Campo-Ma’an area, and therefore it may not be a good indicator for the diversity of shrubs and herbaceous species. Furthermore, this suggests that biodiversity surveys based solely on large and medium sized tree species (DBH ≥0cm) are not an adequate method for the assessment of plant diversity because other growth form such as shrubs, climbers and herbs are under-represented. Therefore, inventory design based on small plots of 0.1 ha, in which all vascular plants with DBH ≥1 cm are recorded, is a more appropriate sampling method for biodiversity assessments than surveys based solely on large and medium sized tree species.     

Do Online Voting Patterns Reflect Evolved Features of Human Cognition? An Exploratory Empirical Investigation

Online votes or ratings can assist internet users in evaluating the credibility and appeal of the information which they encounter. For example, aggregator websites such as Reddit allow users to up-vote submitted content to make it more prominent, and down-vote content to make it less prominent. Here we argue that decisions over what to up- or down-vote may be guided by evolved features of human cognition. We predict that internet users should be more likely to up-vote content that others have also up-voted (social influence), content that has been submitted by particularly liked or respected users (model-based bias), content that constitutes evolutionarily salient or relevant information (content bias), and content that follows group norms and, in particular, prosocial norms. 489 respondents from the online social voting community Reddit rated the extent to which they felt different traits influenced their voting. Statistical analyses confirmed that norm-following and prosociality, as well as various content biases such as emotional content and originality, were rated as important motivators of voting. Social influence had a smaller effect than expected, while attitudes towards the submitter had little effect. This exploratory empirical investigation suggests that online voting communities can provide an important test-bed for evolutionary theories of human social information use, and that evolved features of human cognition may guide online behaviour just as it guides behaviour in the offline world.     

Do Patterns of Bacterial Diversity along Salinity Gradients Differ from Those Observed for Macroorganisms?

It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns.     

Invasion Success and Community Resistance in Single and Multiple Species Invasion Models: Do the Models Support the Conclusions?

Elton's concept of community-level resistance to invasion has derived significant theoretical support from community assembly models in which species invade (colonize) singly at low densities. Several theoretical models have provided support to this concept and are frequently cited as providing evidence that invasion resistance occurs in nature. The underlying assumptions of these models however, are derived from island or island-like systems in which species invade infrequently at low abundances. We suggest that these island-like models cannot be generalized to systems in which species arrive in greater frequencies and densities. To investigate the effects of altering the basic assumptions of these original models, we utilized assembly algorithms similar to those used in previous studies, but allowed either two species to invade per time step or single species invasions at relatively high inoculation densities. In these models, invasion resistance only occurred when the invasion process was restricted to single species invading at low densities (as in previous models). When two species were allowed to invade per time step, invasion resistant states did not occur in any of 20 simulated communities, even after 10,000 invasion events. Relaxation of the assumption of invasion at low density also resulted in a lack of invasion resistance. These results may explain why the strict concept of complete invasion resistance appears only to operate in island and island-like systems.     

Do American Dippers Obtain a Survival Benefit from Altitudinal Migration?

Studies of partial migrants provide an opportunity to assess the cost and benefits of migration. Previous work has demonstrated that sedentary American dippers (residents) have higher annual productivity than altitudinal migrants that move to higher elevations to breed. Here we use a ten-year (30 period) mark-recapture dataset to evaluate whether migrants offset their lower productivity with higher survival during the migration-breeding period when they occupy different habitat, or early and late-winter periods when they coexist with residents. Mark-recapture models provide no evidence that apparent monthly survival of migrants is higher than that of residents at any time of the year. The best-supported model suggests that monthly survival is higher in the migration-breeding period than winter periods. Another well-supported model suggested that residency conferred a survival benefit, and annual apparent survival (calculated from model weighted monthly apparent survival estimates using the Delta method) of residents (0.511 ± 0.038SE) was slightly higher than that of migrants (0.487 ± 0.032). Winter survival of American dippers was influenced by environmental conditions; monthly apparent survival increased as maximum daily flow rates increased and declined as winter temperatures became colder. However, we found no evidence that environmental conditions altered differences in winter survival of residents and migrants. Since migratory American dippers have lower productivity and slightly lower survival than residents our data suggests that partial migration is likely an outcome of competition for limited nest sites at low elevations, with less competitive individuals being forced to migrate to higher elevations in order to breed.     

Are Tree Species Diversity and Genotypic Diversity Effects on Insect Herbivores Mediated by Ants?

Plant diversity can influence predators and omnivores and such effects may in turn influence herbivores and plants. However, evidence for these ecological feedbacks is rare. We evaluated if the effects of tree species (SD) and genotypic diversity (GD) on the abundance of different guilds of insect herbivores associated with big-leaf mahogany (Swietenia macrophylla) were contingent upon the protective effects of ants tending extra-floral nectaries of this species. This study was conducted within a larger experiment consisting of mahogany monocultures and species polycultures of four species and –within each of these two plot types– mahogany was represented by either one or four maternal families. We selected 24 plots spanning these treatment combinations, 10 mahogany plants/plot, and within each plot experimentally reduced ant abundance on half of the selected plants, and surveyed ant and herbivore abundance. There were positive effects of SD on generalist leaf-chewers and sap-feeders, but for the latter group this effect depended on the ant reduction treatment: SD positively influenced sap-feeders under ambient ant abundance but had no effect when ant abundance was reduced; at the same time, ants had negative effects on sap feeders in monoculture but no effect in polyculture. In contrast, SD did not influence specialist stem-borers or leaf-miners and this effect was not contingent upon ant reduction. Finally, GD did not influence any of the herbivore guilds studied, and such effects did not depend on the ant treatment. Overall, we show that tree species diversity influenced interactions between a focal plant species (mahogany) and ants, and that such effects in turn mediated plant diversity effects on some (sap-feeders) but not all the herbivores guilds studied. Our results suggest that the observed patterns are dependent on the combined effects of herbivore identity, diet breadth, and the source of plant diversity.     

Is the Climate Right for Pleistocene Rewilding? Using Species Distribution Models to Extrapolate Climatic Suitability for Mammals across Continents

Species distribution models (SDMs) are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial “Pleistocene rewilding” proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion) was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of organisms in response to climate change.     

Predicting the Fate of Biodiversity Using Species�� Distribution Models: Enhancing Model Comparability and Repeatability

Species distribution modeling (SDM) is an increasingly important tool to predict the geographic distribution of species. Even though many problems associated with this method have been highlighted and solutions have been proposed, little has been done to increase comparability among studies. We reviewed recent publications applying SDMs and found that seventy nine percent failed to report methods that ensure comparability among studies, such as disclosing the maximum probability range produced by the models and reporting on the number of species occurrences used. We modeled six species of Falco from northern Europe and demonstrate that model results are altered by (1) spatial bias in species’ occurrence data, (2) differences in the geographic extent of the environmental data, and (3) the effects of transformation of model output to presence/absence data when applying thresholds. Depending on the modeling decisions, forecasts of the future geographic distribution of Falco ranged from range contraction in 80% of the species to no net loss in any species, with the best model predicting no net loss of habitat in Northern Europe. The fact that predictions of range changes in response to climate change in published studies may be influenced by decisions in the modeling process seriously hampers the possibility of making sound management recommendations. Thus, each of the decisions made in generating SDMs should be reported and evaluated to ensure conclusions and policies are based on the biology and ecology of the species being modeled.     

Do Intensive Care Data on Respiratory Infections Reflect Influenza Epidemics?

Objectives

Severe influenza can lead to Intensive Care Unit (ICU) admission. We explored whether ICU data reflect influenza like illness (ILI) activity in the general population, and whether ICU respiratory infections can predict influenza epidemics.

Methods

We calculated the time lag and correlation between ILI incidence (from ILI sentinel surveillance, based on general practitioners (GP) consultations) and percentages of ICU admissions with a respiratory infection (from the Dutch National Intensive Care Registry) over the years 2003–2011. In addition, ICU data of the first three years was used to build three regression models to predict the start and end of influenza epidemics in the years thereafter, one to three weeks ahead. The predicted start and end of influenza epidemics were compared with observed start and end of such epidemics according to the incidence of ILI.

Results

Peaks in respiratory ICU admissions lasted longer than peaks in ILI incidence rates. Increases in ICU admissions occurred on average two days earlier compared to ILI. Predicting influenza epidemics one, two, or three weeks ahead yielded positive predictive values ranging from 0.52 to 0.78, and sensitivities from 0.34 to 0.51.

Conclusions

ICU data was associated with ILI activity, with increases in ICU data often occurring earlier and for a longer time period. However, in the Netherlands, predicting influenza epidemics in the general population using ICU data was imprecise, with low positive predictive values and sensitivities.     

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.What evolutionary forces maintain genetic diversity in natural populations? How do diversity levels relate to census population sizes (Box 1)? Do low levels of diversity limit adaptation to novel selective pressures? Efforts to address such questions spurred the rise of modern population genetics and contributed to the development of the neutral theory of molecular evolution—the null hypothesis for much of evolutionary genetics and comparative genomics [1]–[3]. Yet these questions remain wide open and, for close to two decades, have been neglected [4]. Most notably, little progress has been made to resolve a riddle first pointed out 40 years ago on the basis of allozyme data: the mysteriously narrow range of genetic diversity levels seen across taxa that vary markedly in their census population sizes [5]. This gap in our understanding is glaring, and may hamper efforts at conservation (e.g., [6]).

Box 1. Glossary

Allozymes: Allelic variants of a protein, often detected by differences in gel electrophoresis. Balancing selection: Natural selection that maintains variation longer than expected from genetic drift alone. Census population size: The actual number of individuals in a population; methods to estimate this number vary depending on the species and may involve aerial, transect, or capture/recapture counts. Diversity levels: The measure used here is the probability that a pair of randomly chosen haplotypes differ at a site. Effective population size: The size of an idealized population with some of the same properties as the actual one, e.g., the same rate of genetic drift. Under simplifying assumptions, notably a constant population size and no population structure, this parameter can be estimated from observed diversity levels, given an independent estimate of the mutation rate. Fluctuating selection: When the fitness of an allele changes over time or over space. Genetic draft: A dramatic loss of genetic variation due to strong, frequent selection at nearby sites [8]. Genetic drift: In a finite population, the loss of genetic variation due to the random sampling of gametes at each generation. Local adaptation: Adaptation to a particular environment that is not shared by the entire species. Nearly neutral theory of molecular evolution: A modification of the neutral theory, in which many mutations are slightly deleterious, rather than strictly neutral or strongly deleterious [75]. Neutral theory of molecular evolution: The theory that most genetic variation seen within populations and between species is neutral, and most mutations are either neutral or strongly deleterious [11]. Panmixia: Random mating among individuals, and hence no population structure. Phylogenetically independent contrasts: A statistical method that allows one to compare properties of species controlling for their evolutionary relationship. Purifying (negative) selection: Natural selection that favors the common, fitter allele against rare, deleterious alleles. Selection at linked sites: Selection at sites linked to the locus under consideration, which can affect the population dynamics of alleles at that locus. Silent sites: A general term for synonymous, intronic, and intergenic sites—all sites at which mutations do not change an amino acid. Variation-reducing selection: Selection that leads to a decrease in diversity at linked sites.With the recent technological revolution in sequencing, the data needed to address questions about the determinants of genetic diversity levels are now within reach. As a first step towards reviving these questions, we compile existing estimates of nuclear sequence diversity. These data are highly preliminary, but they underscore how little is known about the narrow span of diversity levels across species or why some species maintain more genetic variation than others [5],[7],[8], and they offer a glimpse of trends that may be worth pursuing.     

How Well Do Clinical Pain Assessment Tools Reflect Pain in Infants?

Background

Pain in infancy is poorly understood, and medical staff often have difficulty assessing whether an infant is in pain. Current pain assessment tools rely on behavioural and physiological measures, such as change in facial expression, which may not accurately reflect pain experience. Our ability to measure cortical pain responses in young infants gives us the first opportunity to evaluate pain assessment tools with respect to the sensory input and establish whether the resultant pain scores reflect cortical pain processing.

Methods and Findings

Cortical haemodynamic activity was measured in infants, aged 25–43 wk postmenstrual, using near-infrared spectroscopy following a clinically required heel lance and compared to the magnitude of the premature infant pain profile (PIPP) score in the same infant to the same stimulus (n = 12, 33 test occasions). Overall, there was good correlation between the PIPP score and the level of cortical activity (regression coefficient = 0.72, 95% confidence interval [CI] limits 0.32–1.11, p = 0.001; correlation coefficient = 0.57). Of the different PIPP components, facial expression correlated best with cortical activity (regression coefficient = 1.26, 95% CI limits 0.84–1.67, p < 0.0001; correlation coefficient = 0.74) (n = 12, 33 test occasions). Cortical pain responses were still recorded in some infants who did not display a change in facial expression.

Conclusions

While painful stimulation generally evokes parallel cortical and behavioural responses in infants, pain may be processed at the cortical level without producing detectable behavioural changes. As a result, an infant with a low pain score based on behavioural assessment tools alone may not be pain free.     

Searching for Altitudinal Zonation: Species Distribution and Vegetation Composition in the Superpáramo of Volcán Iliniza, Ecuador

Altitudinal variation of the zonal superpáramo vegetation was studied between 4300 and 4630 m to test a possible occurrence of a fine altitudinal zonation within the superpáramo belt. A rectangular grid of 1 m² sample plots was established; 25 replicate plots separated by a 3 m space were located along a 100 m long transect parallel to the contours, and there were 17 such transects separated by 20 m of altitude. Species were scored using a 7-grade cover scale and basic environmental data were gathered for each sample. Major changes occur over a short altitudinal range, at around 4400 m, which corresponds to a transition between the lower and upper superpáramo. Species richness sharply declines but species turnover (per altitude) increases along the altitudinal gradient. The correlation between richness and bare ground or rock cover is negative, but the correlation to rocks becomes positive above 4500 m. Species from lower altitudes tend to have narrower altitudinal range, although a large number of species appear to be indifferent to altitude. Direct ordination analyses indicate that high-altitude species show stronger correlation to environmental variables, especially rock, than species from lower altitudes. TWINSPAN cluster analysis delimited 15 groups of samples. There is a change in the clustering pattern along the altitudinal gradient from a horizontal (i.e., within altitude) to vertical (i.e., across altitude) arrangement of the cluster groups, although this pattern is partly obscured at the highest altitudes due to a large number of empty samples. MANOVA tests for samples from adjacent altitudinal levels indicate two distinct altitudinal breaks at lower altitudes, corresponding to the Loricaria-belt in lower superpáramo and the transition between lower and upper superpáramo, while no indication of a zonation was found in upper superpáramo.     

Cryptic Diversity in the Ubiquist Species Parisotoma notabilis (Collembola,Isotomidae): A Long-Used Chimeric Species?

Parisotoma notabilis is the most common species of Collembola in Europe and is currently designated as ubiquist. This species has been extensively used in numerous studies and is considered as well characterized on a morphological ground. Despite the homogeneity of its morphology, the sequencing of the barcoding fragment (5′ end of COI) for several populations throughout Europe and North America revealed four distinct genetic lineages. The divergence found between these lineages was similar to the genetic distance among other species of the genus Parisotoma included in the analysis. All four lineages have been confirmed by the nuclear gene 28S. This congruence between mitochondrial and nuclear signals, as well as the geographical distribution pattern of lineages observed in Europe, supports the potential specific status of these lineages. Based on specimens from the type locality (Hamburg), the species name was successfully assigned to one of these lineages. This finding raises several problems as Parisotoma notabilis has been widely used in many ecological studies. Accumulation of new data for the different lineages detected, especially ecological information and life history traits, is needed to help resolve this situation.     

Spatial and Temporal Patterns of Diversity and Distribution of the Upper Juruá River Fish Community (Brazilian Amazon)

We studied spatial and temporal patterns in fish species composition and diversity at the upper Juruá River located in the west Brazilian Amazon. We collected with gillnet 822 fishes belonging to 90 species in the main Juruá River, its tributaries and the floodplain lakes during wet and dry seasons. Fish abundance and species richness were greater in the dry season. During that season, fishes may be concentrated due to the low water level, being caught more easily by gillnets. There has been a trend towards a greater fish biomass caught in lakes. This might be associated with a greater environmental stability as lakes may be less subject to large variations in water level. The fish communities differed between the two seasons and between lakes and the lotic environments (main river and tributaries). Fish species from the family Curimatidae were most abundant in the lakes, while Pimelodus spp. and Hypostomus spp. predominated in the main Juruá River. Seasonal variations in fish communities may be related to differences in the migratory behavior among fish species. Such spatial and temporal patterns influencing fish community structure at the Upper Juruá Extractive Reserve must be accounted for in management and conservation strategies.