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255 results for “Diet Analysis”
Otterly delicious: Spatiotemporal variation in the diet of a recovering population of Eurasian otters (Lutra lutra) revealed through DNA metabarcoding and morphological analysis of prey remains
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Meta-analysis and critical review of trophic discrimination factors (Δ13C and Δ15N): importance of tissue, trophic level, and diet source
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Diet composition based on stable isotopic analysis of fecal samples revealed the preference of Black-faced Spoonbill (Platalea minor) for natural wetlands and fishponds
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Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
<p>Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package <i>mvtweedie</i> that extends capabilities of widely used packages in R (<i>mgcv</i> and <i>ggplot2</i>) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted puffins (<i>Fratercula cirrhata</i>) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980-2000) and then Pacific herring and capelin (2000-2020), while wolves (<i>Canis lupus ligoni</i>) in Southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. </p>
Maternal Mediterranean diet in pregnancy and newborn DNA methylation: a meta-analysis in the PACE Consortium
<p>Higher adherence to the Mediterranean diet during pregnancy may be related to offspring cord blood DNA methylation. In a meta-analysis of epigenome-wide association studies (EWAS) in 2802 mother-child pairs from 5 cohorts we calculated the relative Mediterranean diet (rMED) score and an adjusted rMED excluding alcohol (rMEDp). rMEDp was associated with cord blood DNA methylation at cg23757341.</p>
Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians
<p><span>T</span><span>he </span><span>dental system of ceratops</span><span>ids is among the most specialized structure in Dinosauria</span><span>, and includes high angled wear surfaces, split tooth roots, and multiple teeth in each tooth family. However, the early evolution of this unique dental system is generally poorly understood due to a lack of knowledge of the dental morphology and development in early-diverging ceratopsians.</span><span> Here we study the dental system of </span><span>three</span><span> of the earliest-diverging Chinese ceratopsians</span><span>: </span><em><span>Yinlong</span></em><span> and <em>Hualianceratops</em> from the early Late Jurassic of Xinjiang</span><span>,</span><span> and <em>Chaoyangsaurus</em> from the Late Jurassic of Liaoning. By using micro-computed tomographic analyses, our study has revealed significant new information regarding the dental system of these early ceratopsians, including </span><span>no</span><span> more than five replacement teeth in each jaw quadrant; at most one generation of replacement teeth in each alveolus; nearly full resorption of the functional tooth root during tooth replacement; and occlusion with low-angled, concave wear facets that differs significantly from the shearing occlusal system seen in ceratopsids. <em>Yinlong</em> displays an increase in the number of maxillary tooth alveoli and a decrease in the number of replacement teeth during ontogeny as well as the retention of remnants of functional teeth in the largest individual.</span> <span>Early-diverging ceratopsians thus display a relatively slow tooth replacement rate compared to late-diverging ceratopsians.</span> <span>Combined with paleobotany and palaeoenvironment data, <em>Yinlong</em> likely uses gastroliths to triturate foodstuffs, and t</span><span>he difference in diet strategy might have influenced the pattern of tooth replacement in later-diverging ceratopsians.</span></p>
DNA metabarcoding sequence data for diet analysis of caribou
<p>Woodland caribou (<em>Rangifer tarandus caribou</em>) are threatened in Canada due to the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast <em>trnL </em>region, which was only successful on island samples, revealed primary consumption of yew based on relative read abundance (<em>Taxus spp.</em>; 83.68%) with dogwood (<em>Cornus spp</em>.; 9.67%) and maple (<em>Acer spp.</em>; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change.</p>
Diet analysis of David's deer (Elaphurus davidianus) based on stable isotope technology
<p>Faecal stable isotopic analysis is now commonly used to investigate diets of mammal herbivores as samples are easy to obtain and reveal short-term dietary trends. In the Jiangsu Dafeng David's Deer National Nature Reserve, supplemental feed has been provided year round for free-ranging deer (Elaphurus davidianus) to survive from food shortages. Plant species are isotopically distinct in the free-ranging area. We assessed the plant species utilization by deer under supplemental feed condition. Diet-faeces trophic shift of deer was obtained in the semi-captive area. Faeces in both areas were collected and faecal δ<sup>13</sup>C values revealed more variable diets of free-ranging deer than semi-captive deer in different months. Mixing model showed that C4 plants were important food source for free-ranging deer when supplemental feed was provided. We suggest that efficiency and impacts of long-term supplemental feed should be considered for degraded habitat restoration.</p>
Gut microbiome analysis of high fat diet- and control-fed on PXR-KO mice
<p>Nonalcoholic fatty liver disease (NAFLD) is the most prevalent chronic liver disease due to the current epidemics of obesity and diabetes. The pregnane X receptor (PXR) is a xenobiotic-sensing nuclear receptor known for trans-activating liver genes involved in drug metabolism and transport, and more recently implicated in energy metabolism. The gut microbiota can modulate the host xenobiotic biotransformation and contribute to the development of obesity. While the male sex confers a higher risk for NAFLD than women before menopause, the mechanism remains unknown. We hypothesized that the presence of PXR promotes obesity by modifying the gut-liver axis in a sex-specific manner. Male and female C57BL/6 (wild-type/WT) and PXR-knockout (PXR-KO) mice were fed control or high fat diet (HFD) for 16-weeks. Serum parameters, liver histopathology, transcriptomic profiling, 16S-rDNA sequencing, and bile acid (BA) metabolomics were performed. PXR enhanced HFD-induced weight gain, hepatic steatosis and inflammation especially in males, accompanied by PXR-dependent up-regulation in hepatic genes involved in microbial response, inflammation, oxidative stress, and cancer; PXR-dependent increase in intestinal Firmicutes/Bacteroides ratio (hallmark of obesity) and the pro-inflammatory Lactobacillus, as well as a decrease in the anti-obese Allobaculum and the anti-inflammatory Bifidobacterum, with a PXR-dependent reduction of beneficial BAs in liver. The resistance to NAFLD in females may be explained by PXR-dependent decrease in pro-inflammatory bacteria (<em>Ruminococcus gnavus and Peptococcaceae</em>). In conclusion, PXR exacerbates hepatic steatosis and inflammation accompanied by obesity- and inflammation-prone gut microbiome signature, suggesting that gut microbiome may contribute to PXR-mediated exacerbation of NAFLD.</p>
Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
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Data from: Diversity and plasticity in mosquito feeding patterns: a meta-analysis of ‘universal’ DNA diet studies
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Data from: Delineating seasonal shifts in Reindeer habitat and diet selection by integrating GPS telemetry and stable Isotope analysis
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Gut microbiome analysis of high fat diet- and control-fed on PXR-KO mice
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Data from: Computed tomographic analysis of dental system of three Jurassic ceratopsians: implications for the evolution of the tooth replacement pattern and diet in early-diverging ceratopsians
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Optimizing DNA extraction protocols for the diet analysis of a baleen whale (Eubalaena australis)
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Diet analysis of David’s deer (Elaphurus davidianus) based on stable isotope analysis
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DNA metabarcoding sequence data for diet analysis of caribou
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Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the 'all at once' taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing 'chirosurveillance' and conservation strategies.
Data from: A combined mesowear analysis of Mexican Bison antiquus shows a generalist diet with geographical variation
Bison antiquus was one of the largest and most widely distributed megafaunal species during the Late Pleistocene in North America, giving rise to the modern plains bison in the middle Holocene. Despite the importance of the ancient bison, little is known about its feeding ecology. We employed a combination of extended mesowear, and mesowear III to infer the diet preference and habitat use of three Mexican samples of B. antiquus. Two northern samples from the Transmexican Volcanic Belt morphotectonic Province: La Piedad-Santa Ana and La Cinta-Portalitos, as well as one southern sample from the Sierra Madre del Sur morphotectonic province: Viko Vijin. We found that the northern Mexican samples were primarily non-strict grazers, while the southern sample displays a pattern consistent with mixer feeder habits. This suggests variability among the diets of these bison samples, caused by different paleoenvironments. This evidence complements the paleoenvironmental reconstructions in the studied localities; for the northern samples, open prairies composed of patches of woodland or shrubland and for the southern locality a fluvial floodplain with short-lived vegetation. In both scenarios, grasses (Poaceae) were non-dominant. The dietary habits of our samples of ancient bison in Mexico are the southernmost dietary inference for the species in North America and expand our knowledge of the dietary habits of Bison antiquus during the late Pleistocene.
Data from: DNA-based analysis of regurgitates: a noninvasive approach to examine the diet of invertebrate consumers
DNA-based gut content analysis has become an important tool for unravelling feeding interactions in invertebrate communities under natural conditions. It usually implies killing of the consumer and extracting the DNA from its food, either using the whole animal or its dissected gut. This post-mortem approach, however, is not suitable for investigating the diet of rare or protected species and also prohibits tracking individual dietary preferences as each consumer can provide trophic information only once. Moreover, removing large numbers of consumers from a habitat for analysis might critically change population densities and affect species interactions. Here, we present DNA-based analysis of invertebrate regurgitates, a novel approach to overcome these limitations. Conducting feeding experiments where adult Poecilus cupreus (Coleoptera: Carabidae) were fed with larvae of Amphimallon solstitiale (Coleoptera: Scarabaeidae), we show that detection success in regurgitates compared to samples prepared from whole beetles was similar or significantly enhanced for small/medium and large prey DNA fragments, respectively. Prey DNA detection success remained high in regurgitates stored in ethanol for 21 months at room temperature prior to DNA extraction. We conclude that in those invertebrates where regurgitates can be obtained, examination of food DNA in regurgitates offers many advantages over conventional post-mortem gut content analysis.
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