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.     

Trophic resource partitioning drives fine‐scale coexistence in cryptic bat species

Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co‐occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and high‐throughput sequencing to characterize for the first time the trophic ecology of two recently described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected fecal samples from allopatric and sympatric regions and from syntopic and allotopic locations within the sympatric region to describe the diets both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had highly similar diets characterized by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey item level was lower in syntopic populations, supporting trophic shift under fine‐scale co‐occurrence. Furthermore, the diet of M. escalerai had a marginally lower proportion of not nocturnally volant prey in syntopic populations, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine‐scale coexistence mechanisms can have implications for maintaining broad‐scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.     

Habitat selection as a mechanism of resource partitioning in two cryptic bat species Pipistrellus pipistrellus and Pipistrellus pygmaeus

Ecomorphological studies of bat communities often reveal the spatial and temporal coexistence of morphologically similar species, leading to suggestions that these communities are structured by non-deterministic processes. However, the diversification of echolocation call structure in bats allows for considerable morphological similarity while still permitting niche differentiation based on specialisation for prey type and habitat structure. The recent separation of a common Palaearctic bat, the pipistrelle, into Pipistrellus pipistrellus and P. pygmaeus, which are sympatrically distributed throughout their range, raises the question as to whether these two morphologically similar species partition resources in time and space.
To test the hypothesis that the coexistence of these cryptic species is facilitated by differential habitat use, 14 P . pipistrellus , and 12 P. pygmaeus were radio-tracked from adjacent maternity roosts, in northeast Scotland, from May to September 2002/2003. The two species showed distinct habitat partitioning with P. pygmaeus foraging predominantly in riparian woodland and over water, and P. pipistrellus foraging along woodland edges and short isolated tree lines. Inter-specific overlap in habitat use was low and consequently foraging ranges were segregated spatially.
The degree of habitat partitioning revealed in these species, which show considerable overlap in echolocation call parameters and functional morphology, suggests that morphological features, whilst useful in separating chiropteran species into coarse-grained foraging guilds, may not predict fine-grained ecological segregation.     

Trophic niche partitioning of cryptic species of long-eared bats in Switzerland: implications for conservation

Dietary niche partitioning is postulated to play a major role for the stable coexistence of species within a community, particularly among cryptic species. Molecular markers have recently revealed the existence of a new cryptic species of long-eared bat, Plecotus macrobullaris, in the European Alps. We studied trophic niches as well as seasonal and regional variations of diet in eight colonies of the three Plecotus species occurring in Switzerland. Faeces were collected monthly from individuals returning to roost after foraging. Twenty-one arthropod categories were recognized from the faeces. All three species fed predominantly on Lepidoptera, which made up 41%, 87% and 88% (means across colonies) of the diet composition of P. auritus, P. macrobullaris and P. austriacus, respectively. The occurrence of numerous fragments of both diurnal and flightless insects in the diet of P. auritus (but rarely in the diet of the other two species) indicates that this species mostly gleans prey from substrates. P. austriacus and P. macrobullaris are more typical aerial feeders. The latter two species have narrow trophic niches, whilst P. auritus has a much broader diet. Comparison of intraspecific and interspecific niche overlaps in P. auritus and P. macrobullaris in sympatry suggests dietary niche partitioning between these two species. In contrast, the high similarity of the trophic niches of P. austriacus and P. macrobullaris, associated with a typical parapatric distribution, indicates competitive exclusion. The best conservation measures are preservation and restoration of habitats offering a high abundance of moths, the major prey of the three Plecotus species.     

Habitat selection of three cryptic Plecotus bat species in the European Alps reveals contrasting implications for conservation

Assessing the ecological requirements of species coexisting within a community is an essential requisite for developing sound conservation action. A particularly interesting question is what mechanisms govern the stable coexistence of cryptic species within a community, i.e. species that are almost impossible to distinguish. Resource partitioning theory predicts that cryptic species, like other sympatric taxa, will occupy distinct ecological niches. This prediction is widely inferred from eco-morphological studies. A new cryptic long-eared bat species, Plecotus macrobullaris, has been recently discovered in the complex of two other species present in the European Alps, with even evidence for a few mixed colonies. This discovery poses challenges to bat ecologists concerned with planning conservation measures beyond roost protection. We therefore tested whether foraging habitat segregation occurred among the three cryptic Plecotus bat species in Switzerland by radiotracking 24 breeding female bats (8 of each species). We compared habitat features at locations visited by a bat versus random locations within individual home ranges, applying mixed effects logistic regression. Distinct, species-specific habitat preferences were revealed. P. auritus foraged mostly within traditional orchards in roost vicinity, with a marked preference for habitat heterogeneity. P. austriacus foraged up to 4.7 km from the roost, selecting mostly fruit tree plantations, hedges and tree lines. P. macrobullaris preferred patchy deciduous and mixed forests with high vertical heterogeneity in a grassland dominated-matrix. These species-specific habitat preferences should inform future conservation programmes. They highlight the possible need of distinct conservation measures for species that look very much alike.     

Can skull morphology be used to predict ecological relationships between bat species? A test using two cryptic species of pipistrelle.

Can ecological relationships between bat species be predicted largely on the basis of morphology? This question was addressed by investigating skull morphology of two cryptic species of the pipistrelle bat. Since 45 Pipistrellus pipistrellus apparently eats larger prey than 55 P. pipistrellus, we predicted that it would have a larger overall skull size, a larger dentary apparatus, and a larger gape. To test these predictions, variables were measured from skulls of the two cryptic species, and comparisons made between them. In accordance with our predictions, overall skull size was larger in 45 P. pipistrellus than in 55 P. pipistrellus, and 45 P. pipistrellus had a longer lower jaw and the distance between the jaws at maximum gape was larger. In addition, 45 P. pipistrellus had longer upper canines, which may allow it to pierce harder prey items than 55 P. pipistrellus. Only some aspects of dietary differences between the two cryptic species could be explained by differences in skull morphology, and we suggest that empirical data, at least on diet and habitat use, are also required to explain mechanisms of resource partitioning among species in bat communities.     

Cryptic diversity in European bats

Different species of bat can be morphologically very similar. In order to estimate the amount of cryptic diversity among European bats we screened the intra- and interspecific genetic variation in 26 European vespertilionid bat species. We sequenced the DNA of subunit 1 of the mitochondrial protein NADH dehydrogenase (ND1) from several individuals of a species, which were sampled in a variety of geographical regions. A phylogeny based on the mitochondrial (mt) DNA data is in good agreement with the current classification in the family. Highly divergent mitochondrial lineages were found in two taxa, which differed in at least 11% of their ND1 sequence. The two mtDNA lineages in Plecotus austriacus correlated with the two subspecies Plecotus austriacus austriacus and Plecotus austriacus kolombatovici. The two mtDNA lineages in Myotis mystacinus were partitioned among two morphotypes. The evidence for two new bat species within Europe is discussed. Convergent adaptive evolution might have contributed to the morphological similarity among distantly related species if they occupy similar ecological niches. Closely related species may differ in their ecology but not necessarily in their morphology. On the other hand, two morphologically clearly different species (Eptesicus serotinus and Eptesicus nilssonii) were found to be genetically very similar. Neither morphological nor mitochondrial DNA sequence analysis alone can be guaranteed to identify species.     

Conflicting molecular phylogenies of European long-eared bats (Plecotus) can be explained by cryptic diversity

Conflicting phylogenetic signals of two data sets that analyse different portions of the same molecule are unexpected and require an explanation. In the present paper we test whether (i) differential evolution of two mitochondrial genes or (ii) cryptic diversity can better explain conflicting results of two recently published molecular phylogenies on the same set of species of long-eared bats (genus Plecotus). We sequenced 1714bp of three mitochondrial regions (16S, ND1, and D-loop) of 35 Plecotus populations from 10 European countries. A likelihood ratio test revealed congruent phylogenetic signals of the three data partitions. Our phylogenetic analyses demonstrated that the existence of a previously undetected Plecotus lineage caused the incongruities of previous studies. This lineage is differentiated on the species level and lives in sympatry with its sister lineage, Plecotus auritus, in Switzerland and Northern Italy. A molecular clock indicates that all European Plecotus species are of mid or late Pliocene origin. Plecotus indet. was previously described as an intergrade between P. auritus and Plecotus austriacus since it shares morphological characters with both. It is currently known from elevations above 800 m a.s.l. in the Alps, the Dinarian Alps and the Pindos mountains in Greece. Since we could demonstrate that incongruities of two molecular analyses simply arose from the mis-identification of one lineage, we conclude that molecular phylogenetic analyses do not free systematists from a thorough inclusion of morphological and ecological data.     

Specialisation in prey capture drives coexistence among sympatric spider‐hunting wasps

1. Sister taxa that coexist in the same space and time often face competition due to the use of similar resources. However, some closely related species can adopt fine‐grained specialisation in resource use to coexist. This study investigated niche overlap between three sympatric spider‐hunting wasp species of the genus Trypoxylon (Hymenoptera: Crabronidae) known to nest in three of the habitats found in the study area. 2. First, the co‐occurrence of these wasp species in the three habitats was estimated, as a proxy for potential competition. Then, the following hypotheses were tested: (i) niche partitioning is seen more often between species that co‐occur in a habitat, whereas there is niche overlap between species nesting in distinct habitats (prey specialisation hypothesis); and (ii) wasp species capture prey according to their size (physical constraint hypothesis). 3. Two pairs of wasp species were found consistently nesting in the same habitat. Niche partitioning based on prey taxa occurred regardless of the habitat preference. It was also found that differences in the size of wasps reflected distinctions in the size of their prey. 4. These findings were consistent over the years, showing that the significance of specialisation in foraging activities and physical constraints during prey capture can play key roles in the coexistence of sympatric species. The distinctions in the foraging strategies of these wasps are discussed, as well as potential mechanisms driving the evolution in prey specialisation, with insights for future studies.     

Diet reveals links between morphology and foraging in a cryptic temperate reef fish

Predators select prey so as to maximize energy and minimize manipulation time. In order to reduce prey detection and handling time, individuals must actively select their foraging space (microhabitat) and populations exhibit morphologies that are best suited for capturing locally available prey. We explored how variation in diet correlates with habitat type, and how these factors influence key morphological structures (mouth gape, eye diameter, fin length, fin area, and pectoral fin ratio) in a common microcarnivorous cryptic reef fish species, the triplefin Helcogrammoides cunninghami. In a mensurative experiment carried out at six kelp‐dominated sites, we observed considerable differences in diet along 400 km of the Chilean coast coincident with variation in habitat availability and prey distributions. Triplefins preferred a single prey type (bivalves or barnacles) at northern sites, coincident with a low diversity of foraging habitats. In contrast, southern sites presented varied and heterogeneous habitats, where triplefin diets were more diverse and included amphipods, decapods, and cumaceans. Allometry‐corrected results indicated that some morphological structures were consistently correlated with different prey items. Specifically, large mouth gape was associated with the capture of highly mobile prey such as decapods, while small mouth gape was more associated with cumaceans and copepods. In contrast, triplefins that capture sessile prey such as hydroids tend to have larger eyes. Therefore, morphological structures co‐vary with habitat selection and prey usage in this species. Our study shows how an abundant generalist reef fish exhibits variable feeding morphologies in response to the distribution of potential habitats and prey throughout its range.     

Mitochondrial phylogeography of the long-eared bats (Plecotus) in the Mediterranean Palaearctic and Atlantic Islands

Long-eared bats of the genus Plecotus are widespread and common over most of the western Palaearctic. Based on recent molecular evidence, they proved to represent a complex of several cryptic species, with three new species being described from Europe in 2002. Evolutionary relationships among the different lineages are still fragmentary because of the limited geographic coverage of previous studies. Here we analyze Plecotus mitochondrial DNA sequences from the entire Mediterranean region and Atlantic Islands. Phylogenetic reconstructions group these western Palaearctic Plecotus into two major clades which split at least 5 Myr ago and that are each subdivided into further subgroups. An 'auritus group' includes the traditional P. auritus species and its sister taxon P. macrobullaris (=P. alpinus) plus related specimens from the Middle East. P. auritus and P. macrobullaris have broadly overlapping distributions in Europe, although the latter is apparently more restricted to mountain ranges. The other major clade, the 'austriacus group,' includes the European species P. austriacus and at least two other related taxa from North Africa (including P. teneriffae from the Canary Islands), the Balkans and Anatolia (P. kolombatovici). The sister species of this 'austriacus group' is P. balensis, an Ethiopian endemic. Phylogenetic reconstructions further suggest that P. austriacus reached Madeira during its relatively recent westward expansion through Europe, while the Canary Islands were colonized by a North African ancestor. Although colonization of the two groups of Atlantic Islands by Plecotus bats followed very distinct routes, neither involved lineages from the 'auritus group.' Furthermore, the Strait of Gibraltar perfectly segregates the distinct lineages, which confirms its key role as a geographic barrier. This study also stresses the biogeographical importance of the Mediterranean region, and particularly of North Africa, in understanding the evolution of the western Palaearctic biotas.     

Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest

Competing hypotheses explaining species’ use of resources have been advanced. Resource limitations in habitat and/or food are factors that affect assemblages of species. These limitations could drive the evolution of morphological and/or behavioural specialization, permitting the coexistence of closely related species through resource partitioning and niche differentiation. Alternatively, when resources are unlimited, fluctuations in resources availability will cause concomitant shifts in resource use regardless of species identity. Here, we used next‐generation sequencing to test these hypotheses and characterize the diversity, overlap and seasonal variation in the diet of three species of insectivorous bats of the genus Pteronotus. We identified 465 prey (MOTUs) in the guano of 192 individuals. Lepidoptera and Diptera represented the most consumed insect orders. Diet of bats exhibited a moderate level of overlap, with the highest value between Pteronotus parnellii and Pteronotus personatus in the wet season. We found higher dietary overlap between species during the same seasons than within any single species across seasons. This suggests that diets of the three species are driven more by prey availability than by any particular predator‐specific characteristic. P. davyi and P. personatus increased their dietary breadth during the dry season, whereas P. parnellii diet was broader and had the highest effective number of prey species in all seasons. This supports the existence of dietary flexibility in generalist bats and dietary niche overlapping among groups of closely related species in highly seasonal ecosystems. Moreover, the abundance and availability of insect prey may drive the diet of insectivores.     

Niche Differentiation and its Relationship with Food Abundance and Vegetation Complexity in Four Frugivorous Bat Species in Southern Mexico

Species can co‐exist within a community when their use of limiting resources is differentiated. To test whether differentiation facilitates coexistence, we quantified differences and overlap in habitat use, fruit consumption, morphological characteristics, and the relationship with vegetation structure for two pairs of ecologically similar frugivorous bat species, Carollia sowelli and C. perspicillata, and Artibeus jamaicensis and A. lituratus. In Carollia sowelli and C. perspicillata, differences in body mass and wing aspect ratio were not reflected in differences in fruit or habitat use (diet overlap, 96 percent; habitat overlap, 98 percent). However, the capture rate of Carollia sowelli positively correlated with canopy openness, and that of C. perspicillata positively correlated with tree height. Body mass and wing characteristics of Artibeus species suggested a greater maneuverability for A. jamaicensis. Also, more A. jamaicensis individuals were captured feeding on Ficus spp., while Artibeus lituratus preferred fruits of the early successional tree Cecropia. However, both habitat overlap and diet overlap were higher than by chance (diet overlap, 75 percent; habitat overlap, 92 percent). The co‐existence of the four bat species in the study area may be facilitated by the abundance of the food resources forming part of the diets of both Carollia species, by the morphological differences between the Artibeus species, which allow the differentiation of foraging behavior in relation to fruit consumption, and by the structural characteristics of the vegetation.     

Analysis of the diet of Natterer's bat Myotis nattereri and the common long-eared bat Plecotus auritus in the West of Ireland

The diets of Natterer's bat Myotis nattereri and the common long-eared bat Plecotus auritus were investigated at a nursery colony of each species by analysis of droppings collected monthly from May to September. Respectively, 68% and 42% of the diets comprised items presumed to have been gleaned from foliage or other surfaces: diurnal insects, insects which rarely fly, and non-flying arthropods. Such surfaces included the ground: centipedes were eaten by both bats, and the muscid, Scatophaga stercoraria , usually associated with cattle dung, was a common prey. Indeed, the prevalence of cattle-farming around both of the bat roosts almost certainly contributed indirectly, in the form of S. stercoraria , to a significant part of the Diptera consumed. The chief food of M. nattereri was the larger Diptera, but Trichoptera, Hymenoptera and Arachnida were also important. Lepidoptera, Coleoptera and Hemiptera were minor prey, with Dermaptera and Chilopoda taken occasionally. Diptera, closely followed by Lepidoptera, together accounted for nearly two-thirds of the diet of P. auritus. Also taken, in descending order of importance, were Trichoptera, Arachnida, Chilopoda, Coleoptera, Dermaptera, Hymenoptera and Hemiptera. Plecotus auritus , but not M. nattereri , was evidently able to take a few small insects such as aphids and lesser nematoceran Diptera.     

Do the evolutionary interactions between moths and bats promote niche partitioning between bats and birds?

Ecological theory suggests that the coexistence of species is promoted by the partitioning of available resources, as in dietary niche partitioning where predators partition prey. Yet, the mechanisms underlying dietary niche partitioning are not always clear. We used fecal DNA metabarcoding to investigate the diets of seven nocturnal insectivorous bird and bat species. Low diet overlap (2%–22%) supported resource partitioning among all species. Differences in diet corresponded with species identity, prey detection method, and foraging behavior of predators. Insects with ultrasonic hearing capabilities were consumed significantly more often by birds than bats, consistent with an evolved avoidance of echolocating strategies. In turn, bats consumed a greater proportion of noneared insects such as spruce budworms. Overall, our results suggest that evolutionary interactions among bats and moths translate to dietary niche partitioning and coexistence among bats and nocturnal birds.     

Intraspecific evolution of Canary Island Plecotine bats,based on mtDNA sequences

Island differentiation and relationships with congenerics were investigated in the endemic Canary Island bat Plecotus teneriffae, based on approximately 1 kb of mtDNA from the 16S rRNA and cytochrome b genes. P. teneriffae had closer affinities with P. austriacus than with P. auritus. Levels of differentiation between Canary Islands were quite high relative to Pipistrelle-like bats, consistent with philopatric behaviour in the Plecotus genus. Cladogenesis within P. teneriffae appears to have occurred after the emergence of the islands of El Hierro and La Palma during the Pleistocene. An intraspecific network shows that haplotypes from the younger islands of La Palma and El Hierro are connected to the Tenerife haplotype by a similarly large number of mutational steps. This suggests that they were both colonised at a similar time from the much older island of Tenerife. The other Plecotine bat species, Barbastellus barbastellus shows close affinities with B. barbastellus from mainland Spain, with levels of mtDNA divergence being comparable with intraspecific variation within other mammal species.     

Molecular diet analysis of two african free-tailed bats (molossidae) using high throughput sequencing

Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep-sequence uniquely 5' tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI sequences in the GenBank and BOLD databases, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus. Insects identified to families within the orders Lepidoptera and Diptera were widely present among the faecal samples analysed. The two families that were observed most frequently were Noctuidae and Nymphalidae (Lepidoptera). Species-level analysis of the data was accomplished using novel bioinformatics techniques for the identification of molecular operational taxonomic units (MOTU). Based on these analyses, our data provide little evidence of resource partitioning between sympatric M. condylurus and C. pumilus in the Simunye region of Swaziland at the time of year when the samples were collected, although as more complete databases against which to compare the sequences are generated this may have to be re-evaluated.     

Diet and prey selection of sympatric tropical skinks

Most skinks are opportunistic predators, taking available prey from the environment as it is encountered. Variation in their diet composition is thought to reflect differences in prey abundance in the environment. We studied diet composition and prey selection in a community of three sympatric skink species (genus Carlia) in northern Australia by comparing contents of skink stomachs with arthropod prey available in their habitat. Carlia were entirely carnivorous and fed on a range of arthropod prey. We found high overlap in diet and prey size among the three species and between the wet and dry seasons, but found that skinks generally focused their foraging efforts on prey types and prey sizes that were not abundant in the habitat. Spiders (Aranea), orthopterans, blattarians, isopods and termites (Isoptera) were important prey of skinks, but these arthropods were rarely trapped in the environment. Skinks also frequently consumed large‐bodied prey, despite the higher relative abundance of small prey in the environment. Skinks were more selective in their foraging and diet than previously assumed. Selection of prey by consumers is a fundamental ecological process, important to consumers for maintaining energy requirements to grow and reproduce, but equally important to the community dynamics of the prey consumed.     

Local patterns of distribution and resource utilization of four bat species (Myotis brandti, Eptesicus nilssoni, Plecotus auritus and Pipistrellus pipistrellus) in patchy and continuous environments

The local patterns of distribution and resource utilization of four bat species ( Myotis brandti, Eptesicus nilssoni, Plecotus auritus and Pipistrellus pipistrellus ) were examined in patchy and continuous environments, using bat detectors. The effects of two different kinds of open matrix habitats (crop-fields and water) on species occurrence were compared in the patchy areas. A crop-field matrix seemed to have a greater negative influence on species occurrence than a water matrix. Presence and absence of species in the patchy areas were analysed against island area, area of some habitats, and isolation. All species were positively affected by one or more forest habitat parameters. Two species ( M. brandti and P. auritus ) were negatively affected by isolation, which suggests that they may be particularly vulnerable to increased forest patchiness. These species occurred mainly on large islands. Two hypotheses that might explain the habit of open area avoidance in M. brandti and P. auritus were tested: 1. Insect abundance hypothesis; 2. Foraging behaviour hypothesis. Both failed to explain why these two species avoid open habitats and as a consequence are negatively affected by isolation.     

The relative influence of competition and prey defences on the trophic structure of animalivorous bat ensembles

Deterministic filters such as competition and prey defences should have a strong influence on the community structure of animals like animalivorous bats which have life histories characterized by low fecundity, low predation risk, long life expectancy and stable populations. We investigated the relative influence of these two deterministic filters on the trophic structure of animalivorous bat assemblages in South Africa. We used null models to test if patterns of dietary overlap were significantly different from patterns expected by chance and multivariate analyses to test the correlations between diet and phenotype (body size, wing morphology and echolocation). We found little evidence that competition structured the trophic niche of coexisting bats. Contrary to predictions from competition, dietary overlap between bats of ensembles and functional groups (open-air, clutter-edge, and clutter foragers) were significantly higher than expected by chance. Instead, we found support for the predictions of the allotonic frequency hypothesis: there were significant relationships between peak echolocation frequency and the proportion of moths in the diets of bats at local and regional scales, and peak echolocation frequency was the best predictor of diet even after we controlled for the influence of body size and phylogeny. These results suggest that echolocation frequency and prey hearing exert more influence on the trophic structure of sympatric animalivorous bats than competition. Nonetheless, differential habitat use and sensory bias may also be major determinants of trophic structure because these are also correlated with frequencies of bat calls.