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1. Ecogeographical rules and the macroecology of food webs

   https://doi.org/10.1111/geb.12925  

   Baiser, Benjamin ; Gravel, Dominique ; Cirtwill, Alyssa R. ; Dunne, Jennifer A. ; Fahimipour, Ashkaan K. ; Gilarranz, Luis J. ; Grochow, Joshua A. ; Li, Daijiang ; Martinez, Neo D. ; McGrew, Alicia ; et al ( May 2019 , Global Ecology and Biogeography)

   How do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ecology and macroecology. Here, we integrate macroecology and food web ecology by focusing on how ecogeographical rules [the latitudinal diversity gradient (LDG), Bergmann's rule, the island rule and Rapoport's rule] are associated with the architecture of food webs.

   Global.

   Current.

   All taxa.

   We discuss the implications of each ecogeographical rule for food webs, present predictions for how food web structure will vary with each rule, assess empirical support where available, and discuss how food webs may influence ecogeographical rules. Finally, we recommend systems and approaches for further advancing this research agenda.

   We derived testable predictions for some ecogeographical rules (e.g. LDG, Rapoport's rule), while for others (e.g., Bergmann's and island rules) it is less clear how we would expect food webs to change over macroecological scales. Based on the LDG, we found weak support for both positive and negative relationships between food chain length and latitude and for increased generality and linkage density at higher latitudes. Based on Rapoport's rule, we found support for the prediction that species turnover in food webs is inversely related to latitude.

   The macroecology of food webs goes beyond traditional approaches to biodiversity at macroecological scales by focusing on trophic interactions among species. The collection of food web data for different types of ecosystems across biogeographical gradients is key to advance this research agenda. Further, considering food web interactions as a selection pressure that drives or disrupts ecogeographical rules has the potential to address both mechanisms of and deviations from these macroecological relationships. For these reasons, further integration of macroecology and food webs will help ecologists better understand the assembly, maintenance and change of ecosystems across space and time.

    

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2. The precautionary principle and dietary DNA metabarcoding: commonly used abundance thresholds change ecological interpretation

   https://doi.org/10.5061/dryad.kwh70rz4s  

   Littleford-Colquhoun, Bethan ; Freeman, Patrick ; Sackett, Violet ; Tulloss, Camille ; McGarvey, Lauren ; Geremia, Chris ; Kartzinel, Tyler ( January 2021 , Dryad)

   Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and lab. One of the earliest and most common strategies for dealing with such sensitivities has been to filter resulting sequence data to remove low-abundance sequences before conducting ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be both necessary and sufficient for cleaning up datasets, evidence to support this perception is lacking and more attention needs to be paid to the related risk of introducing other undesirable errors. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream dietary inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of individual dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and niche partitioning. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address a subset of research questions that focus on a subset of relatively abundant food resources, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data—or similar data such as environmental DNA, microbiomes, or pathobiomes—should be aware of potential drawbacks and consider alternative bioinformatic, experimental, and statistical solutions. We used fecal DNA metabarcoding to characterize the diets of bison and bighorn sheep in winter and summer. Our analyses are based on 35 samples (median per species per season = 10) analyzed using the P6 loop of the chloroplast trnL(UAA) intron together with publicly available plant reference data (Illumina sequence read data are available at NCBI (BioProject: PRJNA780500)). Obicut was used to trim reads with a minimum quality threshold of 30, and primers were removed from forward and reverse reads using cutadapt. All further sequence identifications were performed using obitools; forward and reverse sequences were aligned using the illuminapairedend command using a minimum alignment score of 40, and only joined sequences retained. We used the obiuniq command to group identical sequences and tally them within samples, enabling us to quantify the relative read abundance (RRA) of each sequence. Sequences that occurred ≤2 times overall or that were ≤8 bp were discarded. Sequences were considered to be likely PCR artifacts if they were highly similar to another sequence (1 bp difference) and had a much lower abundance (0.05%) in the majority of samples in which they occurred; we discarded these sequences using the obiclean command. Overall, we characterized 357 plant sequences and a subset of 355 sequences were retained in the dataset after rarefying samples to equal sequencing depth. We then applied relative read abundance thresholds from 0% to 5% to the fecal samples. We compared differences in the inferred dietary richness within and between species based on individual samples, based on average richness across samples, and based on the total richness of each population after accounting for differences in sample size. The readme file contains an explanation of each of the variables in the dataset. Information on the methodology can be found in the associated manuscript referenced above.  

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3. What's going to be on the menu with global environmental changes?

   https://doi.org/10.1111/gcb.16866  

   Hallam, Jane ; Harris, Nyeema C. ( July 2023 , Global Change Biology)

   Ongoing anthropogenic change is altering the planet at an unprecedented rate, threatening biodiversity, and ecosystem functioning. Species are responding to abiotic pressures at both individual and population levels, with changes affecting trophic interactions through consumptive pathways. Collectively, these impacts alter the goods and services that natural ecosystems will provide to society, as well as the persistence of all species. Here, we describe the physiological and behavioral responses of species to global changes on individual and population levels that result in detectable changes in diet across terrestrial and marine ecosystems. We illustrate shifts in the dynamics of food webs with implications for animal communities. Additionally, we highlight the myriad of tools available for researchers to investigate the dynamics of consumption patterns and trophic interactions, arguing that diet data are a crucial component of ecological studies on global change. We suggest that a holistic approach integrating the complexities of diet choice and trophic interactions with environmental drivers may be more robust at resolving trends in biodiversity, predicting food web responses, and potentially identifying early warning signs of diversity loss. Ultimately, despite the growing body of long‐term ecological datasets, there remains a dearth of diet ecology studies across temporal scales, a shortcoming that must be resolved to elucidate vulnerabilities to changing biophysical conditions.

    

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4. Reconstructing hyperdiverse food webs: Gut content metabarcoding as a tool to disentangle trophic interactions on coral reefs

   https://doi.org/10.1111/2041-210X.13206  

   Casey, Jordan M. ; Meyer, Christopher P. ; Morat, Fabien ; Brandl, Simon J. ; Planes, Serge ; Parravicini, Valeriano ; Mahon, ed., Andrew ( June 2019 , Methods in Ecology and Evolution)

   Anthropogenic stressors have strong impacts on ecosystems. To understand their influence, detailed knowledge about trophic relationships among species is critical. However, this requires both exceptional resolution in dietary assessments and sampling breadth within communities, especially for highly diverse, tropical ecosystems.

   We used gut content metabarcoding across a broad range of coral reef fishes (8 families, 22 species) in Mo'orea, French Polynesia, to test whether this technique has the potential to capture the structure of a hyperdiverse marine food web. Moreover, we explored whether taxonomic groups (families) and traditional, broad‐scale trophic assignments explained fish diet across four different metrics of quantifying predator–prey interactions.

   Metabarcoding yielded a large number (4,341) of unique operational taxonomic units (i.e. prey) with high‐resolution taxonomic assignments (i.e. often to the level of genus or species). We demonstrate that across multiple metrics, taxonomic group at the family level is a consistently better, albeit still weak, predictor of empirical trophic relationships than frequently used, broad‐scale functional assignments. Our method also reveals a complex trophic network with fine‐scale partitioning among species, further emphasizing the importance of examining fish diets beyond broad trophic categories.

   We demonstrate the capacity of metabarcoding to reconstruct diverse and complex food webs with exceptional resolution, a significant advancement from traditional food web reconstruction. Furthermore, this method allows us to pinpoint the trophic niche of species with niche‐based modelling, even across hyperdiverse species assemblages such as coral reefs. In conjunction with complementary techniques such as stable isotope analysis, applying metabarcoding to whole communities will provide unparalleled information about energy and nutrient fluxes and inform their susceptibility to disturbances even in the world's most diverse ecosystems.

    

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5. Importance of interaction rewiring in determining spatial and temporal turnover of tritrophic ( Piper ‐caterpillar‐parasitoid) metanetworks in the Yucatán Península, México

   https://doi.org/10.1111/btp.12946  

   Campos‐Moreno, Diego F. ; Dyer, Lee A. ; Salcido, Danielle ; Massad, Tara Joy ; Pérez‐Lachaud, Gabriela ; Tepe, Eric J. ; Whitfield, James B. ; Pozo, Carmen ( May 2021 , Biotropica)

   Natural history studies documenting spatial and temporal variation of species assemblages and their interactions are critical for understanding biodiversity and community ecology. We characterized caterpillar–parasitoid assemblages on shrubs in the genusPiperacross remnants of semi‐evergreen forest in the Yucatán Península during the rainy and rainy–dry seasons. We collected caterpillars feeding onPiperleaves and reared them to adults or parasitoids to: (i) describe tritrophic interactions betweenPiper, caterpillars, and parasitoids, (ii) compare empirical metanetworks among sites and seasons, and (iii) investigate patterns in species and interaction turnover across spatial and temporal scales to understand the contribution of species composition and interaction rewiring to overall interaction turnover. We found sixPiperspecies supporting 79 species of caterpillars, which in turn hosted 20 species of parasitoids. In total, there were 116 realized trophic interactions. Species and interactions exhibited substantial turnover at temporal and spatial scales. Total interaction turnover was more pronounced across seasons in all sites (>93%), than it was between sites (<91%). We also found that interaction rewiring contributed more to overall interaction turnover than species turnover. The spatial and temporal variation in metanetworks documented here contribute to understanding fine‐scale temporal and spatial turnover in tropical species and interactions and raise important questions about the lability of consumer specialization and the short‐term effects of interaction rewiring on the stability of biotic communities. Our results highlight the importance of tropical food web studies that are based on natural history using consistent field methods to document bi‐ and tripartite interactions.

   Abstract in Spanish is available with online material.

    

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