Assessing niche partitioning of co‐occurring sibling bat species by DNA metabarcoding

Niche partitioning through foraging is a mechanism likely involved in facilitating the coexistence of ecologically similar and co‐occurring animal species by separating their use of resources. Yet, this mechanism is not well understood in flying insectivorous animals. This is particularly true of bats, where many ecologically similar or cryptic species coexist. The detailed analysis of the foraging niche in sympatric, cryptic sibling species provides an excellent framework to disentangle the role of specific niche factors likely involved in facilitating coexistence. We used DNA metabarcoding to determine the prey species consumed by a population of sympatric sibling Rhinolophus euryale and Rhinolophus mehelyi whose use of habitat in both sympatric and allopatric ranges has been well established through radio tracking. Although some subtle dietary differences exist in prey species composition, the diet of both bats greatly overlapped (O_jk = 0.83) due to the consumption of the same common and widespread moths. Those dietary differences we did detect might be related to divergences in prey availabilities among foraging habitats, which prior radio tracking on the same population showed are differentially used and selected when both species co‐occur. This minor dietary segregation in sympatry may be the result of foraging on the same prey‐types and could contribute to reduce potential competitive interactions (e.g., for prey, acoustic space). Our results highlight the need to evaluate the spatial niche dimension in mediating the co‐occurrence of similar insectivorous bat species, a niche factor likely involved in processes of bat species coexistence.     

Multispecies coexistence of trees in tropical forests: spatial signals of topographic niche differentiation increase with environmental heterogeneity

Neutral and niche theories give contrasting explanations for the maintenance of tropical tree species diversity. Both have some empirical support, but methods to disentangle their effects have not yet been developed. We applied a statistical measure of spatial structure to data from 14 large tropical forest plots to test a prediction of niche theory that is incompatible with neutral theory: that species in heterogeneous environments should separate out in space according to their niche preferences. We chose plots across a range of topographic heterogeneity, and tested whether pairwise spatial associations among species were more variable in more heterogeneous sites. We found strong support for this prediction, based on a strong positive relationship between variance in the spatial structure of species pairs and topographic heterogeneity across sites. We interpret this pattern as evidence of pervasive niche differentiation, which increases in importance with increasing environmental heterogeneity.     

Concurrent niche and neutral processes in the competition-colonization model of species coexistence

The importance of neutral dynamics is contentiously debated in the ecological literature. This debate focuses on neutral theory's assumption of fitness equivalency among individuals, which conflicts with stabilizing fitness that promotes coexistence through niche differentiation. I take advantage of competition-colonization trade-offs between species of aquatic micro-organisms (protozoans and rotifers) to show that equalizing and stabilizing mechanisms can operate simultaneously. Competition trials between species with similar colonization abilities were less likely to result in competitive exclusion than for species further apart. While the stabilizing mechanism (colonization differences) facilitates coexistence at large spatial scales, species with similar colonization abilities also exhibited local coexistence probably due to fitness similarities allowing weak stabilizing mechanisms to operate. These results suggest that neutral- and niche-based mechanisms of coexistence can simultaneously operate at differing temporal and spatial scales, and such a spatially explicit view of coexistence may be one way to reconcile niche and neutral dynamics.     

Ecological traits influence the phylogenetic structure of bird species co‐occurrences worldwide

The extent to which species’ ecological and phylogenetic relatedness shape their co‐occurrence patterns at large spatial scales remains poorly understood. By quantifying phylogenetic assemblage structure within geographic ranges of >8000 bird species, we show that global co‐occurrence patterns are linked – after accounting for regional effects – to key ecological traits reflecting diet, mobility, body size and climatic preference. We found that co‐occurrences of carnivorous, migratory and cold‐climate species are phylogenetically clustered, whereas nectarivores, herbivores, frugivores and invertebrate eaters tend to be more phylogenetically overdispersed. Preference for open or forested habitats appeared to be independent from the level of phylogenetic clustering. Our results advocate for an extension of the tropical niche conservatism hypothesis to incorporate ecological and life‐history traits beyond the climatic niche. They further offer a novel species‐oriented perspective on how biogeographic and evolutionary legacies interact with ecological traits to shape global patterns of species coexistence in birds.     

Can host‐range allow niche differentiation of invasive polyphagous fruit flies (Diptera: Tephritidae) in La Réunion?

Abstract.  1. Biological invasions bring together formerly isolated insect taxa and allow the study of ecological interactions between species with no coevolutionary history. Among polyphagous insects, such species may competitively exclude each other unless some form of niche partitioning allows them to coexist.
2. In the present study, we investigate whether the ability to exploit different fruits can increase the likelihood of coexistence of four species of polyphagous Tephritidae, one endemic and three successive invaders, in the island of La Réunion. In the laboratory, we studied the performances of all four species on the four most abundant fruit resources in the island, as well as the relative abundances of fly species on these four fruit species in the field. We observe no indication of niche partitioning for any of the four abundant fruits.
3. Analyses of an extensive field data series suggest that: (i) the four fly species largely overlap in fruit exploitation, once climatic effects are accounted for; (ii) however, one species ( Ceratitis capitata ) can exploit rare fruit species that are not exploited by others present in the same climatic niche; and (iii) the endemic species C. catoirii , now nearly extinct in La Réunion, has no private niche with respect to either climatic range or fruit use.
4. On the whole, with the possible exception of C. capitata , the results point to a limited role of fruit diversity in encouraging coexistence among polyphagous tephritids recently brought into contact by accidental introductions.     

Testing the divergent adaptation of two congeneric tree species on a rainfall gradient using eco‐physio‐morphological traits

In tropical Africa, evidence of widely distributed genera transcending biomes or habitat boundaries has been reported. The evolutionary processes that allowed these lineages to disperse and adapt into new environments are far from being resolved. To better understand these processes, we propose an integrated approach, based on the eco‐physio‐morphological traits of two sister species with adjacent distributions along a rainfall gradient. We used wood anatomical traits, plant hydraulics (vulnerability to cavitation, wood volumetric water content, and hydraulic capacitance), and growth data from the natural habitat, in a common garden, to compare species with known phylogeny, very similar morphologically, but occupying contrasting habitats: Erythrophleum ivorense (wet forest) and Erythrophleum suaveolens (moist forest and forest gallery). We identified some slight differences in wood anatomical traits between the two species associated with strong differences in hydraulics, growth, and overall species distribution. The moist forest species, E. suaveolens, had narrower vessels and intervessel pits, and higher vessel cell‐wall reinforcement than E. ivorense. These traits allow a high resistance to cavitation and a continuous internal water supply of the xylem during water shortage, allowing a higher fitness during drought periods, but limiting growth. Our results confirm a trade‐off between drought tolerance and growth, controlled by subtle adaptations in wood traits, as a key mechanism leading to the niche partitioning between the two Erythrophleum species. The generality of this trade‐off and its importance in the diversification of the African tree flora remains to be tested. Our integrated eco‐physio‐morpho approach could be the way forward.     

The roles of morphological traits,resource variation and resource partitioning associated with the dietary niche expansion in the fish‐eating bat Myotis pilosus

Niche expansion and shifts are involved in the response and adaptation to environmental changes. However, it is unclear how niche breadth evolves and changes toward higher‐quality resources. Myotis pilosus is both an insectivore and a piscivore. We examined the dietary composition and seasonality in M. pilosus and the closely related Myotis fimbriatus using next‐generation DNA sequencing. We tested whether resource variation or resource partitioning help explain the dietary expansion from insects to fish in M. pilosus. While diet composition and diversity varied significantly between summer and autumn, the proportion of fish‐eating individuals did not significantly change between seasons in M. pilosus. Dietary overlap between M. pilosus and M. fimbriatus during the same seasons was much higher than within individual species across seasons. We recorded a larger body size, hind foot length, and body mass in M. pilosus than in M. fimbriatus and other insectivorous trawling bats from China. Similar morphological differences were found between worldwide fishing bats and nonfishing trawling bats. Our results suggest that variation in insect availability or interspecific competition may not play important roles in the dietary expansion from insects to fish in M. pilosus. Myotis pilosus has morphological advantages that may help it use fish as a diet component. The morphological advantage promoting dietary niche evolution toward higher quality resources may be more important than variation in the original resource and the effects of interspecific competition.     

Effects of species co‐occurrence on the trophic‐niche breadth of characids in Amazon forest streams

This study assessed the width of the trophic niche of four characid species (Bryconops giacopinii, Bryconops inpai, Hyphessobrycon aff. melazonatus and Iguanodectes geisleri) found under different co‐occurrence circumstances in Amazonian upland streams. The study was conducted during the rainy season of 2011 at eight sites of two micro‐basins of the Ducke Reserve, Manaus, Amazonas, Brazil. The four species were studied in the following circumstances: only one of the species occurring in the stream; two species co‐occurring; three species co‐occurring. The relative volume of the food items in the fish stomachs was used to calculate Hurlbert's trophic‐niche breadth for the individuals of each species in the different co‐occurrence circumstances. Hyphessobrycon aff. melazonatus changed their diet when occurring in syntopy with other characid species of similar feeding habits, as shown by a significant narrowing of its trophic niche. The opportunistic habits and great feeding flexibility of these characid species make the partitioning of food resources possible and act as an important ecological mechanism that facilitates the coexistence of different species, possibly by attenuating the effects of direct competition for food. In addition, the low carrying capacity of these upland forest streams may be an important environmental factor influencing the results of this study.     

How do similarities in spatial distributions and interspecific associations affect the coexistence of Quercus species in the Baotianman National Nature Reserve,Henan, China

Congeneric species often have similar ecological characteristics and use similar resources. These similarities may make it easier for them to co‐occur in a similar habitat but may also lead to strong competitions that limit their coexistence. Hence, how do similarities in congeneric species affect their coexistence exactly? This study mainly used spatial point pattern analysis in two 1 hm² plots in the Baotianman National Nature Reserve, Henan, China, to compare the similarities in spatial distributions and interspecific associations of Quercus species. Results revealed that Quercus species were all aggregated under the complete spatial randomness null model, and aggregations were weaker under the heterogeneous Poisson process null model in each plot. The interspecific associations of Quercus species to non‐Quercus species were very similar in Plot 1. However, they can be either positive or negative in different plots between the co‐occurring Quercus species. The spatial distributions of congeneric species, interspecific associations with non‐Quercus species, neighborhood richness around species, and species diversity were all different between the two plots. We found that congeneric species did have some similarities, and the closely related congeneric species can positive or negative associate with each other in different plots. The co‐occurring congeneric species may have different survival strategies in different habitats. On the one hand, competition among congenerics may lead to differentiation in resource utilization. On the other hand, their similar interspecific associations can strengthen their competitive ability and promote local exclusion to noncongeneric species to obtain more living space. Our results provide new knowledge for us to better understand the coexistence mechanisms of species.     

Latitudinal variation in the competition‐colonisation trade‐off reveals rate‐mediated mechanisms of coexistence

Theories of species coexistence often describe a trade‐off between colonising and competitive abilities. In sessile marine invertebrates, this trade‐off can manifest as trends in species distributions relative to the size of isolated patches of substrate. Based on their abilities to find available substrate and competitively exclude neighbours, good colonisers tend to dominate smaller patches, whereas better competitors tend to monopolise larger patches. In theory, species with equivalent colonising and competitive abilities should display similar distributions across patch sizes. We used patch size to observe this manifestation of the competition‐colonisation trade‐off over 20° of latitude. The trade‐off was more readily observed at lower latitudes and was proportional to the ‘ecological age’ of communities (i.e. the degree of resource acquisition and likelihood of species interactions). Results suggest that ecological age may mediate the prominence of stochastic or deterministic coexistence mechanisms and will depend on the rate of ecological processes.     

Habitat filtering drives the local distribution of congeneric species in a Brazilian white‐sand flooded tropical forest

The investigation of ecological processes that maintain species coexistence is revealing in naturally disturbed environments such as the white‐sand tropical forest, which is subject to periodic flooding that might pose strong habitat filtering to tree species. Congeneric species are a good model to investigate the relative importance of ecological processes that maintain high species diversity because they tend to exploit the same limiting resources and/or have similar tolerance limits to the same environmental conditions due to their close phylogenetic relationship. We aim to find evidence for the action and relative importance of different processes hypothesized to maintain species coexistence in a white‐sand flooded forest in Brazil, taking advantage of data on the detailed spatial structure of populations of congeneric species. Individuals of three Myrcia species were tagged, mapped, and measured for diameter at soil height in a 1‐ha plot. We also sampled seven environmental variables in the plot. We employed several spatial point process models to investigate the possible action of habitat filtering, interspecific competition, and dispersal limitation. Habitat filtering was the most important process driving the local distribution of the three Myrcia species, as they showed associations, albeit of different strength, to environmental variables related to flooding. We did not detect spatial patterns, such as spatial segregation and smaller size of nearby neighbors, that would be consistent with interspecific competition among the three congeneric species and other co‐occurring species. Even though congeners were spatially independent, they responded to differences in the environment. Last, dispersal limitation only led to spatial associations of different size classes for one of the species. Given that white‐sand flooded forests are highly threatened in Brazil, the preservation of their different habitats is of utmost importance to the maintenance of high species richness, as flooding drives the distribution of species in the community.     

Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder

Aim Species distribution models (SDMs) or, more specifically, ecological niche models (ENMs) are a useful and rapidly proliferating tool in ecology and global change biology. ENMs attempt to capture associations between a species and its environment and are often used to draw biological inferences, to predict potential occurrences in unoccupied regions and to forecast future distributions under environmental change. The accuracy of ENMs, however, hinges critically on the quality of occurrence data. ENMs often use haphazardly collected data rather than data collected across the full spectrum of existing environmental conditions. Moreover, it remains unclear how processes affecting ENM predictions operate at different spatial scales. The scale (i.e. grain size) of analysis may be dictated more by the sampling regime than by biologically meaningful processes. The aim of our study is to jointly quantify how issues relating to region and scale affect ENM predictions using an economically important and ecologically damaging invasive species, the Argentine ant (Linepithema humile). Location California, USA. Methods We analysed the relationship between sampling sufficiency, regional differences in environmental parameter space and cell size of analysis and resampling environmental layers using two independently collected sets of presence/absence data. Differences in variable importance were determined using model averaging and logistic regression. Model accuracy was measured with area under the curve (AUC) and Cohen's kappa. Results We first demonstrate that insufficient sampling of environmental parameter space can cause large errors in predicted distributions and biological interpretation. Models performed best when they were parametrized with data that sufficiently sampled environmental parameter space. Second, we show that altering the spatial grain of analysis changes the relative importance of different environmental variables. These changes apparently result from how environmental constraints and the sampling distributions of environmental variables change with spatial grain. Conclusions These findings have clear relevance for biological inference. Taken together, our results illustrate potentially general limitations for ENMs, especially when such models are used to predict species occurrences in novel environments. We offer basic methodological and conceptual guidelines for appropriate sampling and scale matching.     

Signatures of competition and strain structure within the major blood‐stage antigen of Plasmodium falciparum in a local community in Ghana

The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency‐dependent selection in response to intraspecific competition for host immune space. The malaria parasite Plasmodium falciparum presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity. The parasite's major blood‐stage antigen, PfEMP1, is encoded by the hyperdiverse var genes. With a dataset that includes thousands of var DBLα sequence types sampled from asymptomatic cases within an area of high endemicity in Ghana, we address how var diversity is distributed within isolates and compare this to the distribution of microsatellite allelic diversity within isolates to test whether antigenic and neutral regions of the genome are structured differently. With respect to var DBLα sequence types, we find that on average isolates exhibit significantly lower overlap than expected randomly, but that there also exists frequent pairs of isolates that are highly related. Furthermore, the linkage network of var DBLα sequence types reveals a pattern of nonrandom modularity unique to these antigenic genes, and we find that modules of highly linked DBLα types are not explainable by neutral forces related to var recombination constraints, microsatellite diversity, sampling location, host age, or multiplicity of infection. These findings of reduced overlap and modularity among the var antigenic genes are consistent with a role for immune selection as proposed by strain theory. Identifying the evolutionary and ecological dynamics that are responsible for the nonrandom structure in P. falciparum antigenic diversity is important for designing effective intervention in endemic areas.