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55 results for “Diet diversity”
Code for 'Food-insecure women eat a less diverse diet in a more temporally variable way: Evidence from the US National Health and Nutrition Examination Survey, 2013-4'
<p>Code to reproduce the analyses in the study '<strong>Food-insecure women eat a less diverse diet in a more temporally variable way: Evidence from the US National Health and Nutrition Examination Survey, 2013-4'</strong></p> <p>The analysis requires two R scripts available here, plus original 2013-4 NHANES data files, downloadable from the NHANES website (https://wwwn.cdc.gov/nchs/nhanes/continuousnhanes/default.aspx?BeginYear=2013).</p> <p>The first R script, 'merging script.r' takes the original NHANES files, extracts the variables required for the study, merges them into a single data frame, and saves this in .csv format. The NHANES files it requires are:</p> <p># Demographics, food insecurity and BMI<br> DEMO_H.XPT<br> FSQ_H.XPT<br> BMX_H.XPT</p> <p># Summary files of food recalls<br> DR1TOT_H.XPT<br> DR2TOT_H.XPT</p> <p># Individual foods files from food recalls<br> DR1FF_H.XPT<br> DR2FF_H.XPT</p> <p>The second R script takes the .csv file output by the merging script, and reproduces the analyses and figures described in the paper.</p> <p>Initially uploaded by Daniel Nettle, April 23rd 2019. Slightly revised versions uploaded August 6th 2019 by Daniel Nettle.</p>
Resources from: Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers
<p>Understanding the factors that shape microbiomes can provide insight on the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary, and evolutionary influences on gut microbiome structure. We performed fecal metabarcoding to characterize both the gut microbiome and diet of fifteen wood-warbler species across a four-year period and from two geographic localities. We find host taxonomy generally explained ~10% of the variation between individuals, which is ~6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.</p>
Disentangling relationships between physiology, morphology, diet, and gut microbial diversity in American Kestrel nestlings
<p>Gut microbiota are increasingly recognized as important drivers of host health and fitness across vertebrate taxa. Given that gut microbial composition is directly influenced by the environment, gut microbiota may also serve as an eco-physiological mechanism connecting host ecology, such as diet, and physiology. Although gut microbiota have been well-studied in mammalian systems, little is known about how gut microbial diversity and composition impact morphological and physiological development in wild birds. Here, we characterized both diet and gut microbial diversity of free-living American kestrel (<em>Falco sparverius</em>) nestlings throughout development to test whether gut microbial diversity predicts host morphological and physiological traits in either contemporary or time-lagged manners. Gut microbial alpha diversity on day 21 of nestling development was positively correlated with diet alpha diversity representative of the majority of nestling development (days 5–20). Gut microbial alpha diversity early in development was negatively correlated with body mass in both contemporary and time-lagged manners. Gut microbial alpha diversity early in development was positively correlated with blood glucose later in development. As nestlings experience rapid growth demands in preparation to fledge, these time-lagged associations may indicate that gut microbial diversity at early critical developmental windows may determine the future trajectory of morphological and physiological traits underlying metabolism that ultimately impact fitness.</p>
Disentangling relationships between physiology, morphology, diet, and gut microbial diversity in American Kestrel nestlings
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Resources from: Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers
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Data from: Diet variability among insular populations of Podarcis lizards reveals diverse strategies to face resource-limited environments
Access to resources is a dynamic and multi-causal process that determines the success and survival of a population. It is therefore often challenging to disentangle the factors affecting ecological traits like diet. Insular habitats provide a good opportunity to study how variation in diet originates, in particular in populations of mesopredators such as lizards. Indeed, high levels of population density associated with low food abundance and low predation are selection pressures typically observed on islands. In the present study, the diet of eighteen insular populations of two closely related species of lacertid lizards (Podarcis sicula and Podarcis melisellensis) was assessed. Our results reveal that despite dietary variability among populations, diet taxonomic diversity is not impacted by island area. In contrast, however, diet disparity metrics, based on the variability in the physical (hardness) and behavioral (evasiveness) properties of ingested food items, are correlated with island size. These findings suggest that an increase in intraspecific competition for access to resources may induce shifts in functional components of the diet. Additionally, the two species differed in the relation between diet disparity and island area suggesting that different strategies exist to deal with low food abundance in these two species. Finally, sexual dimorphism in diet and head dimensions is not greater on smaller islands, in contrast to our predictions.
Increasing agricultural habitat reduces solitary bee offspring number and weight in apple orchards through reduced floral diet diversity and increased fungicide risk
<p>1. Threats to bee pollinators such as land use change, high pesticide risk, and reduced floral diet diversity are usually assessed independently, even though they often co-occur to impact bees in agroecosystems.</p> <p>2. We established populations of the non-native mason bee O. cornifrons at 17 NY apple orchards varying in proportion of surrounding agriculture and measured floral diet diversity and pesticide risk levels in the pollen provisions they produced. We used path analysis to test the direct and indirect effects of different habitats, diet diversity, and pesticide risk on emergent female offspring number and weight.</p> <p>3. Our results showed that high proportions of agricultural habitat surrounding bee nests indirectly reduced the number of female offspring produced, by reducing floral diet diversity in pollen.</p> <p>4. When proportion agriculture surrounding bee nests was high, bees collected increased proportions of Rosaceae in their pollen provisions, which marginally (0.05<p<0.1) increased fungicide risk levels in pollen, which, in turn, marginally reduced female offspring weight. In contrast, female offspring weight increased as proportion surrounding open habitat (wildflowers, grassland, pasture) increased, but this effect was not influenced by proportion Rosaceae or fungicide risk levels in pollen.</p> <p>5. Synthesis and Applications: To promote healthy O. cornifrons populations in apple, we must maintain floral resource diversity and open habitats, while reducing fungicide risk levels and agricultural habitats. More broadly, our results show that land use change, in the form of increasing agricultural habitat, can negatively impact bee populations in agroecosystems indirectly through multiple, simultaneous threats. We must strive to understand these complex interactions between simultaneous threats to maintain healthy bee populations in agroecosystems, where we rely on them for pollination.</p>
Diverse ethnic diets in Ireland intake dataset
<p>The diverse ethnic diets in Ireland intake dataset was conducted as part of the FNS-Cloud project (Field Lab 1) in 2020 and 2021. This study aimed to validate the Foodbook24 tool version 2 by comparing 24-hour dietary recalls collected using Foodbook24 against interviewer-led recalls in Irish, Polish, Chinese and Brazilian adults (≥18 years) living in Ireland. Participants completed one self-administered dietary recall using Foodbook24 and one interviewer-led dietary recall with a trained researcher on the same day. Two weeks later the process was repeated in the opposite order. In total n=136 participants were recruited: n=32 Brazilian, n=53 Irish, n=32 Chinese, n=19 Polish. Data are contained in the following files: 1) dietary intake food file containing individual food, beverage and supplement intake for each day of data collection 2) demographic, lifestyle (physical activity (IPAQ), smoking status, alcohol consumption) and anthropometric (self-reported weight/height) file 3) Food choice questionnaire file</p>
Data from: Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity
<p>Microbiome diversity and diet composition concomitantly influence species health, fitness, immunity, and digestion. In environments where diet varies spatially and temporally, microbiome plasticity may promote rapid host adaptation to available resources. For northern ungulates in particular, metabarcoding of noninvasively collected fecal pellets presents unprecedented insights into their diverse ecological requirements and niches by clarifying the interrelationships of microbiomes, key to deriving nutrients, in context of altered forage availability in changing climates. Muskoxen (<em>Ovibos moschatus</em>) are Arctic-adapted species that experience fluctuating qualities and quantities of vegetation. Geography and seasonality have been noted to influence microbiome composition and diversity in muskoxen, yet it is unclear how their microbiomes intersect with diet. Following observations from other species, we hypothesized increasing diet diversity would result in higher microbiome diversity in muskoxen. We assessed diet composition in muskoxen using three common plant metabarcoding markers and explored correlations with microbiome data. Patterns of dietary diversity and composition were not fully concordant among the markers used, yet all reflected the primary consumption of willows and sedges. Individuals with similar diets had more similar microbiomes, yet in contrast to most literature, yielded negative relationships between microbiome and diet alpha diversity. This negative correlation may reflect the unique capacities of muskoxen to survive solely on high-fiber Arctic forage and provide insight into their resiliency to exploit changing dietary resources in a rapidly warming Arctic altering vegetation diversity.</p>
Phylogenetically diverse diets favor more complex venoms in North American pitvipers
<p>The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are traits composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates considerably over evolutionary timescales, with apparent increases and decreases in complexity, yet the evolutionary causes of this variation is unclear. Here, we tested alternative hypotheses for the link between venom complexity and ecological sources of selection related to diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths <em>Crotalus, Sistrurus </em>and <em>Agkistrodon</em>. We generated independent transcriptomic and proteomic measures of venom complexity and then estimated prey diversity using the past century's extensive natural history studies on these snakes. We then conducted comparative tests relating different measures of predator venom complexity and prey community diversity using the first, genome-scale, dated phylogenies for this clade of snakes. Strikingly, phylogenetic diversity of prey was more strongly correlated to venom diversity than was species diversity, implicating prey species divergence, rather than the number of lineages alone, in the evolution of venom complexity. This positive relationship was observed within three of the four largest toxin gene families in viper venom. Given documented examples of taxonomic specificity of venoms spanning several levels of divergence, we suggest that the phylogenetic diversity of prey measures functionally-relevant divergence in the molecular targets of venom, a claim supported by diversity in the coagulation cascade targets of snake venom serine proteases. Our results support the general concept that the evolved diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.</p>
Dietary abundance distributions: Dominance and diversity in vertebrate diets
<p>Diet composition is among the most important yet least understood dimensions of animal ecology. Inspired by the study of species-abundance distributions (SADs), we tested for generalities in the structure of vertebrate diets by characterizing them as dietary-abundance distributions (DADs). We compiled data on 1167 population-level diets, representing >500 species from 6 vertebrate classes, spanning all continents and oceans. DADs near-universally (92.5%) followed a hollow-curve shape, with scant support for other plausible rank-abundance-distribution shapes. This strong generality is inherently related to, yet incompletely explained by, the SADs of available food taxa. By quantifying dietary generalization as the half-saturation point of the cumulative distribution of dietary abundance (<em>sp50</em>, minimum number of foods required to account for 50% of diet), we found that vertebrate populations are surprisingly specialized: in most populations, fewer than three foods accounted for at least half the diet. Variation in <em>sp50</em> was strongly associated with consumer type, with carnivores being more specialized than herbivores or omnivores. Other methodological (sampling method and effort, taxonomic resolution), biological (body mass, frugivory), and biogeographic (latitude) factors influenced <em>sp50</em> to varying degrees. Future challenges include identifying the mechanisms underpinning the hollow-curve DAD, its generality beyond vertebrates, and the biological determinants of dietary generalization.</p>
Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
<p>Conservation strategies centred around species habitat protection rely on species' dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (<i>Tetrao urogallus</i>), which is an indicator species for forest biodiversity conservation. Non-molecular means used to study their diet are time-consuming and at low taxonomic resolution. This delays the implementation of conservation strategies including resource protection due to uncertainty about its diet. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, <i>Pinus</i> and <i>Vaccinium myrtillus</i>, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis pseudo F<sub>5,86</sub>= 11.01, <i>r<sup>2</sup></i> = 0.17, <i>p</i> = 0.001) and seasons (adonis pseudo F<sub>2,03</sub> = 0.64, <i>r<sup>2</sup></i> = 0.01, <i>p</i> = 0.036). Dietary composition also differed between sexes at each location (adonis pseudo F<sub>1,47</sub> = 2.77, <i>r<sup>2</sup></i> = 0.04, <i>p</i> = 0.024), although not significant for all data combined. In total, 35 taxa (36.8% of taxa recorded) were new capercaillie food items compared to existing knowledge from non-molecular means. The non-invasive molecular dietary analysis applied in this study provides new ecological information of capercaillies' diet, improving our understanding of adequate habitat required for their conservation.</p>
What is a mammalian omnivore? Insights into terrestrial mammalian diet diversity, body mass, and evolution
<p>Mammalian omnivores are a broad and diverse group of mammals that are often lumped together in ecological studies. As a result, there are open questions about what macroevolutionary and macroecological information can be gained when omnivorous dietary differences are investigated in ecological and phylogenetic comparative studies. In this study, we investigate the frequency at which vertebrate prey, invertebrate prey, fibrous plant material, and non-fibrous plant material co-occur in the diets of omnivorous species. We quantify the body size distributions and phylogenetic signal of terrestrial mammals that consume different omnivorous diets and using multistate reversible jump MCMC, we assess the transition rates between mammalian diet strategies on the mammalian phylogenetic tree. We find that omnivores that consume all four food types are rare and most omnivorous mammals consume only invertebrate prey and non-fibrous plants. We also find that omnivores that only consume invertebrate prey are on average smaller than omnivores that incorporate vertebrate prey as many are from within Rodentia. Our transition rate models show that there are high transition rates from invertivorous omnivory to herbivory, and from vertebrate predation to prey mixing and ultimately invertivory. Our results suggest that prey type is an important aspect of omnivore macroevolution and macroecology, as it is correlated with body mass, evolutionary history, and diet-related evolutionary transition rates.</p>
Dietary abundance distributions: Dominance and diversity in vertebrate diets
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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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Increasing agricultural habitat reduces solitary bee offspring number and weight in apple orchards through reduced floral diet diversity and increased fungicide risk
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Data from: Diet variability among insular populations of Podarcis lizards reveals diverse strategies to face resource-limited environments
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What is a mammalian omnivore? Insights into terrestrial mammalian diet diversity, body mass, and evolution
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Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
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Data from: Metabarcoding of fecal pellets in wild muskox populations reveals negative relationships between microbiome and diet alpha diversity
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