Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators.

BACKGROUND: A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro). RESULTS: In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43-71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46-273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding. CONCLUSIONS: Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.

Plastic debris and natural food in two commercially important fish species from the coast of Peru.

The aim of this study was to evaluate the presence of plastic debris in the stomach contents of two commercially important species Ethmidium maculatum and Mugil cephalus from Peru and relate their characteristics to their diet. The contents of 1820 stomachs were analyzed visually to detect the presence of plastics and prey. Of the analyzed samples, 0.3% contained nine microplastic fragments (0.72-4.54 mm) and one mesoplastic fragment (6.65 mm). Green and blue plastics of polyethylene and polypropylene were the most common. In E. maculatum, copepods were the main prey, followed by diatoms and decapods, and they exhibited the highest amount of plastics. In M. cephalus, the main prey were diatoms, copepods, and dinoflagellates, and they exhibited only one type of microplastic. Although the characteristics of the plastics and the prey of these species may be related (sizes-colors), more research is required to understand this problem in commercially important fishery resources in Peru.

Frugivorous bat (Chiroptera: Phyllostomidae) community structure and trophic relations in Atlantic Forest fragments

We evaluated the structure of a community of frugivorous bats using composition and abundance patterns, niche amplitude and food overlap of these animals in four Atlantic Forest fragments, each one exposed to different conservation realities. For twelve months, we captured six bat species and found the seeds of 13 species of pioneering plants in 158 fecal samples. The most abundant bat species were Artibeus planirostris (25.4%), Artibeus lituratus (24.1%) and Carollia perspicillata(23.9%). Only one fragment (Fazenda Unida), the most conserved area, exhibited a significantly different composition and abundance of species. We found low trophic niche amplitude values (<0.60), associated to high food overlaps. Our results suggest that bats can adjust their foraging strategy to deal with food availability variations. By favoring pioneering plant species, the fragmentation process noted of the studied areas creates an attractive environment for bats more tolerant to this type of disturbance. The sampled areas represent important secondary forest remnants in southern Brazil that require attention to avoid an even greater loss of bat diversity.(AU)

Frugivorous bat (Chiroptera: Phyllostomidae) community structure and trophic relations in Atlantic Forest fragments

We evaluated the structure of a community of frugivorous bats using composition and abundance patterns, niche amplitude and food overlap of these animals in four Atlantic Forest fragments, each one exposed to different conservation realities. For twelve months, we captured six bat species and found the seeds of 13 species of pioneering plants in 158 fecal samples. The most abundant bat species were Artibeus planirostris (25.4%), Artibeus lituratus (24.1%) and Carollia perspicillata(23.9%). Only one fragment (Fazenda Unida), the most conserved area, exhibited a significantly different composition and abundance of species. We found low trophic niche amplitude values (<0.60), associated to high food overlaps. Our results suggest that bats can adjust their foraging strategy to deal with food availability variations. By favoring pioneering plant species, the fragmentation process noted of the studied areas creates an attractive environment for bats more tolerant to this type of disturbance. The sampled areas represent important secondary forest remnants in southern Brazil that require attention to avoid an even greater loss of bat diversity.

Dietary partitioning promotes the coexistence of planktivorous species on coral reefs.

Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co-occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In particular, the extent to which food partitioning contributes to species coexistence in hyperdiverse tropical ecosystems remains unresolved. Here, we use a molecular approach to investigate inter- and intraspecific dietary partitioning between two species of damselfish (Dascyllus flavicaudus, Chromis viridis) that commonly co-occur in branching corals. Species-level identification of their diverse zooplankton prey revealed significant differences in diet composition between species despite their seemingly similar feeding strategies. Dascyllus exhibited a more diverse diet than Chromis, whereas Chromis tended to select larger prey items. A large calanoid copepod, Labidocera sp., found in low density and higher in the water column during the day, explained more than 19% of the variation in dietary composition between Dascyllus and Chromis. Dascyllus did not significantly shift its diet in the presence of Chromis, which suggests intrinsic differences in feeding behaviour. Finally, prey composition significantly shifted during the ontogeny of both fish species. Our findings show that levels of dietary specialization among coral reef associated species have likely been underestimated, and they underscore the importance of characterizing trophic webs in tropical ecosystems at higher levels of taxonomic resolution. They also suggest that niche redundancy may not be as common as previously thought.

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.

Molecular detection of invertebrate prey in vertebrate diets: trophic ecology of Caribbean island lizards.

Understanding community assembly and population dynamics frequently requires detailed knowledge of food web structure. For many consumers, obtaining precise information about diet composition has traditionally required sacrificing animals or other highly invasive procedures, generating tension between maintaining intact study populations and knowing what they eat. We developed 16S mitochondrial DNA sequencing methods to identify arthropods in the diets of generalist vertebrate predators without requiring a blocking primer. We demonstrate the utility of these methods for a common Caribbean lizard that has been intensively studied in the context of small island food webs: Anolis sagrei (a semi-arboreal 'trunk-ground' anole ecomorph). Novel PCR primers were identified in silico and tested in vitro. Illumina sequencing successfully characterized the arthropod component of 168 faecal DNA samples collected during three field trips spanning 12 months, revealing 217 molecular operational taxonomic units (mOTUs) from at least nine arthropod orders (including Araneae, Blattodea, Coleoptera, Hemiptera, Hymenoptera, Isoptera, Lepidoptera and Orthoptera). Three mOTUs (one beetle, one cockroach and one ant) were particularly frequent, occurring in ≥50% of samples, but the majority of mOTUs were infrequent (180, or 83%, occurred in ≤5% of samples). Species accumulation curves showed that dietary richness and composition were similar between size-dimorphic sexes; however, female lizards had greater per-sample dietary richness than males. Overall diet composition (but not richness) was significantly different across seasons, and we found more pronounced interindividual variation in December than in May. These methods will be generally useful in characterizing the diets of diverse insectivorous vertebrates.

Ecological patterns of blood-feeding by kissing-bugs (Hemiptera: Reduviidae: Triatominae)

Host use by vectors is important in understanding the transmission of zoonotic diseases, which can affect humans, wildlife and domestic animals. Here, a synthesis of host exploitation patterns by kissing-bugs, vectors of Chagas disease, is presented. For this synthesis, an extensive literature review restricted to feeding sources analysed by precipitin tests was conducted. Modern tools from community ecology and multivariate statistics were used to determine patterns of segregation in host use. Rather than innate preferences for host species, host use by kissing-bugs is influenced by the habitats they colonise. One of the major limitations of studies on kissing-bug foraging has been the exclusive focus on the dominant vector species. We propose that expanding foraging studies to consider the community of vectors will substantially increase the understanding of Chagas disease transmission ecology. Our results indicate that host accessibility is a major factor that shapes the blood-foraging patterns of kissing-bugs. Therefore, from an applied perspective, measures that are directed at disrupting the contact between humans and kissing-bugs, such as housing improvement, are among the most desirable strategies for Chagas disease control.

Alimentación del pez insectívoro neotropical Creagrutus bolivari (Pisces: Characidae) según los métodos gráfico y de importancia relativa / The diet of the neotropical insectivorous fish Creagrutus bolivari (Pisces: Characidae) according to the graphic and relative importance methods

The diet ofa neotropical fish species (Creagrutus bolivari) was studied using different methods: the Cortés 1997 graphic method and two relative importance indexes, one designed by George and Hadley in 1979 (% RIi) and another proposed by Cortés in 1997 (% IRIi). Only discrete prey (aquatic and terrestrial invertebrates) were used in the diet analysis. The occurrence (% A), number (% N) and weight (% G) frequencies were estimated for each food item. A total of 240 specimens (size range from 25.3 to 64.7 mm standard length) were analyzed. For values of % A > 50 %, % IRIi was higher than % RIi with an opposite trend (up to 130 times) for values of % A < 50 %. % IRIi overestimated the relative importance of prey for high values of % A, while it underestimated the relative importance of prey for low values of % A, showing a nonlinear relationship to % A. The variables used in the Cortés graphic method are insufficient to evaluate predator feeding strategy (generalization versus specialization). Therefore, we suggest including other variables, such as population and individual trophic niche breadth and a suitable field sampling record. An extended sampling record is necessary to classify prey as rare or dominant according to Cortés' classification. The indexes of relative importance and graphic method are complementary. Compound indexes that comprise mass, number, and occurrence provide a more accurate description of diet and allow comparative studies. The graphic analysis is easy to interpret and helps in the evaluation of prey importance and predator feeding strategy.

Se estudió la alimentación de un pez neotropical (Creagrutus bolivari) usando diferentes métodos: el método gráfico de Cortés (1997) y dos índices de importancia relativa (George y Hadley, 1979 (% RIi) y Cortés, 1997 (% IRIi)). Sólo las presas discretas (invertebrados acuáticos y terrestres) se emplearon en el análisis de dieta. Se estimó para cada ítem, las frecuencias de aparición (% A), numérica (% N) y gravimétrica (% G). Se analizó un total de 240 ejemplares (intervalo de talla desde 25.3 hasta 64.7 mm de longitud estándar). Para valores de % A > 50 %, el % IRIi resultó mayor al obtenido para el % RIi, con una tendencia opuesta (hasta 130 veces) para valores de % A por debajo del 50 %. El % IRIi sobreestimó la importancia relativa de las presas para valores altos de % A, mientras que subestimó la importancia relativa de las presas para valores bajos de % A y mostró un comportamiento no lineal a medida que varió el % A. Las variables empleadas en el método gráfico de Cortés son insuficientes para evaluar la estrategia alimentaria del depredador (generalismo-especialismo). De este modo, se sugiere incluir otras variables como el ancho de nicho trófico poblacional e individual así como un adecuado registro de campo. Es necesario un amplio registro de campo para clasificar a las presas como escasa o dominante de acuerdo a la clasificación de Cortés. Los índices compuestos que incluyen las variables: masa, número y aparición proporcionan una descripción más precisa de la dieta y permiten realizar estudios comparativos. El análisis gráfico es fácil de interpretar y ayuda a evaluar aspectos como la importancia de la presa y la estrategia alimentaria del depredador.