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Dietary intake is difficult to measure reliably in humans because approaches typically rely on self-reporting, which can be incomplete and biased. In field studies of animals, DNA sequencing-based approaches such as metabarcoding have been developed to characterize diets, but such approaches have not previously been widely applied to humans. Here, we present data derived from sequencing of a chloroplast DNA marker (the P6 loop of the trnL [UAA] intron) in stool samples collected from 11 individuals consuming both controlled and freely selected diets. The DNA metabarcoding strategy resulted in successful PCR amplification in about 50% of samples, which increased to a 70% success rate in samples from individuals eating a controlled plant-rich diet. Detection of plant taxa among sequenced samples yielded a recall of 0.86 and a precision of 0.55 compared to a written diet record during controlled feeding of plant-based foods. The majority of sequenced plant DNA matched common human food plants, including grains, vegetables, fruits, and herbs prepared both cooked and uncooked. Moreover, DNA metabarcoding data were sufficient to distinguish between baseline and treatment diet arms of the study. Still, the relatively high PCR failure rate and an inability to distinguish some dietary plants at the sequence level using the trnL-P6 marker suggest that future methodological refinements are necessary. Overall, our results suggest that DNA metabarcoding provides a promising new method for tracking human plant intake and that similar approaches could be used to characterize the animal and fungal components of our omnivorous diets.IMPORTANCE Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of human memory. DNA sequencing-based approaches, frequently used for profiling nonhuman diets, do not suffer from the same limitations. Here, we used metabarcoding to broadly characterize the plant portion of human diets for the first time. The majority of sequences corresponded to known human foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between experimental diets and matched individual diet records from controlled settings with high accuracy. Because this method is independent of survey language and timing, it could also be applied to geographically and culturally disparate human populations, as well as in retrospective studies involving banked human stool.

Mammalian gut microbiomes differ within and among hosts. Hosts that occupy a broad range of environments may exhibit greater spatiotemporal variation in their microbiome than those constrained as specialists to narrower subsets of resources or habitats. This can occur if widespread host encounter a variety of ecological conditions that act to diversify their gut microbiomes and/or if generalized host species tend to form large populations that promote sharing and maintenance of diverse microbes. We studied spatiotemporal variation in the gut microbiomes of three co‐occurring rodent species across an environmental gradient in a Kenyan savanna. We hypothesized: (1) the taxonomic, phylogenetic, and functional compositions of gut microbiomes as predicted using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) differ significantly among host species; (2) microbiome richness increases with population size for all host species; and (3) host species exhibit different levels of seasonal change in their gut microbiomes, reflecting different sensitivities to the environment. We evaluated changes in gut microbiome composition according to host species identity, site, and host population size using three years of capture–mark–recapture data and 351 microbiome samples. Host species differed significantly in microbiome composition, though the two species with more specialized diets and higher demographic sensitivities showed only slightly greater microbiome variability than those of a widespread dietary generalist. Total microbiome richness increased significantly with host population size for all species, but only one of the more specialized species also exhibited greater individual‐level microbiome richness in large populations. Across co‐occurring rodent species with diverse diets and life histories, large host population sizes were associated both with greater population‐level microbiome richness (sampling effects) and turnover in the relative abundance of bacterial taxa (environmental effects), but there was no consistent pattern for individual‐level richness (individual specialization). Together, our results show that maintenance of large host populations contributes to the maintenance of gut microbiome diversity in wild mammals. [ABSTRACT FROM AUTHOR]

Many applications in molecular ecology require the ability to match specific DNA sequences from single‐ or mixed‐species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target‐specific enrichment capabilities of CRISPR‐Cas systems may offer advantages in some applications. We identified 54,837 CRISPR‐Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single‐ and mixed‐species samples, which yielded mean chloroplast sequence lengths of 2,530–11,367 bp, depending on the experiment. In comparison to mixed‐species experiments, single‐species experiments yielded more on‐target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed‐species experiments yielded sufficient data to provide ≥48‐fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL‐P6 marker. Prior work developed CRISPR‐based enrichment protocols for long‐read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short‐read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR‐based analyses of mixed‐species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori. [ABSTRACT FROM AUTHOR]

Biological invasions are both a pressing environmental challenge and an opportunity to investigate fundamental ecological processes, such as the role of top predators in regulating biodiversity and food-web structure. In whole-ecosystem manipulations of small Caribbean islands on which brown anole lizards (Anolis sagrei) were the native top predator, we experimentally staged invasions by competitors (green anoles, Anolis smaragdinus) and/or new top predators (curly-tailed lizards, Leiocephalus carinatus). We show that curly-tailed lizards destabilized the coexistence of competing prey species, contrary to the classic idea of keystone predation. Fear-driven avoidance of predators collapsed the spatial and dietary niche structure that otherwise stabilized coexistence, which intensified interspecific competition within predator-free refuges and contributed to the extinction of green-anole populations on two islands. Moreover, whereas adding either green anoles or curly-tailed lizards lengthened food chains on the islands, adding both species reversed this effect--in part because the apex predators were trophic omnivores. Our results underscore the importance of top-down control in ecological communities, but show that its outcomes depend on prey behaviour, spatial structure, and omnivory. Diversity-enhancing effects of top predators cannot be assumed, and non-consumptive effects of predation risk may be a widespread constraint on species coexistence. Whole-ecosystem manipulations of Caribbean islands occupied by brown anoles, involving the addition of competitors (green anoles) and/or top predators (curly-tailed lizards), demonstrate that predator introductions can alter the ecological niches and destabilize the coexistence of competing prey species., Author(s): Robert M. Pringle [sup.1] , Tyler R. Kartzinel [sup.1] [sup.2] , Todd M. Palmer [sup.3] , Timothy J. Thurman [sup.4] [sup.5] [sup.6] , Kena Fox-Dobbs [sup.7] , Charles C. [...]

Understanding how animals succeed in novel environments is critical to predicting the outcomes of species introductions under global change. Variation in exploratory behaviour—the willingness to investigate unfamiliar environments—has potential to influence species' invasion success. The Italian wall lizard, Podarcis siculus , is native to southern Europe and has been introduced across Europe and North America. To compare the exploratory behaviour and bite force of individuals from three non-native populations in the United States, we conducted a laboratory experiment involving wild-caught lizards from New York City, Philadelphia, and Boston. We tested a series of hypotheses concerning the predictions that: (1) exploratory behaviour would be greatest in the most recently established population and (2) bite force—associated with competitive ability—would be greatest in the densest populations. Across populations, exploratory behaviour increased significantly with body size. Contrary to our first prediction, exploratory behaviour was not significantly greater in more recently established populations. Consistent with our second prediction, however, lizards from the low-density Philadelphia population exhibited weaker bites. Results suggest that contemporary behavioural variation reflects differences in local ecological conditions, such as resource abundance, population density, and size structure rather than establishment history. Our findings highlight the need for further research into behavioural and performance drivers of lizard invasion success. [ABSTRACT FROM AUTHOR]

Size‐structured differences in resource use stabilize species coexistence in animal communities, but what behavioral mechanisms underpin these niche differences? Behavior is constrained by morphological and physiological traits that scale allometrically with body size, yet the degree to which behaviors exhibit allometric scaling remains unclear; empirical datasets often encompass broad variation in environmental context and phylogenetic history, which complicates the detection and interpretation of scaling relationships between size and behavior. We studied the movement and foraging behaviors of three sympatric, congeneric spiral‐horned antelope species (Tragelaphus spp.) that differ in body mass—bushbuck (26–40 kg), nyala (57–83 kg), and kudu (80–142 kg)—in an African savanna ecosystem where (i) food was patchily distributed due to ecosystem engineering by fungus‐farming termites and (ii) predation risk was low due to the extirpation of several large carnivores. Because foraging behavior is directly linked to traits that scale allometrically with size (e.g., metabolic rate, locomotion), we hypothesized that habitat use and diet selection would likewise exhibit nonlinear scaling relationships. All three antelope species selected habitat near termitaria, which are hotspots of abundant, high‐quality forage. Experimental removal of forage from termite mounds sharply reduced use of those mounds by bushbuck, confirming that habitat selection was resource driven. Strength of selection for termite mounds scaled negatively and nonlinearly with body mass, as did recursion (frequency with which individuals revisited locations), whereas home‐range area and mean step length scaled positively and nonlinearly with body mass. All species disproportionately ate mound‐associated plant taxa; nonetheless, forage selectivity and dietary composition, richness, and quality all differed among species, reflecting the partitioning of shared food resources. Dietary protein exhibited the theoretically predicted negative allometric relationship with body mass, whereas digestible‐energy content scaled positively. Our results demonstrate cryptic size‐based separation along spatial and dietary niche axes—despite superficial similarities among species—consistent with the idea that body‐size differentiation is driven by selection for divergent resource‐acquisition strategies, which in turn underpin coexistence. Foraging and space‐use behaviors were nonlinearly related to body mass, supporting the hypothesis that behavior scales allometrically with size. However, explaining the variable functional forms of these relationships is a challenge for future research. [ABSTRACT FROM AUTHOR]

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Copyright of Journal of Ecology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi‐quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa‐specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low‐level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population‐level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research. [ABSTRACT FROM AUTHOR]