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12 results for “diet reconstruction”
Experimental assessment of the relationship between diet and mandibular morphology: new insights for the paleodietary reconstructions of early hominins
<p>Code R.txt : R script containing all the analyses (can be open in R or RStudio or any text reader)</p> <p>landmark_coordinates: Raw coordinates for all specimens</p> <p>diet-scrach.csv : CSV file containing all the information of the specimens</p>
Reevaluating trophic discrimination factors (Δδ13C and Δδ15N) for diet reconstruction
<p>Stable isotope analysis is increasingly used to assess diet and trophic positions of animals. Such assessments require estimates of trophic discrimination factors (TDF — offset between the isotopic composition of diet and animal tissues), with imprecise applications of TDFs leading to biased conclusions in resource use. Because TDFs are unavailable for most species, ecologists often apply values from taxonomically similar species or use trophic step increases of about 1‰ for carbon (TDF-δ<sup>13</sup>C) and 3‰ for nitrogen (TDF-δ<sup>15</sup>N). Such practices may be inaccurate since TDFs vary greatly, even within a species. To better understand the factors that influence TDFs, we conducted a meta-analysis of TDF-δ<sup>13</sup>C and TDF-δ<sup>15</sup>N for mammals and quantified variation in relation to consumer type (herbivore, omnivore, carnivore) and diet source (C3-based, C4-based, marine-based, mixture). Additionally, to guide TDF choice, we used an isotopic dataset of small mammal tissues and diet items to assess how predicted dietary contributions vary with TDFs estimated using (1) taxonomic relatedness, (2) consumer type and diet source, or (3) values derived from wild animals eating natural diets. Our meta-analysis revealed that metabolic routing and interactions between consumer class, dietary source, and the protein versus energy content of diets best explained variation in TDF-δ<sup>13</sup>C values (-1.5 to 7.3‰), whereas consumer class best explained variation in TDF-δ<sup>15</sup>N values (-0.5 to 7.1‰). Our test of methods to estimate TDFs indicated that ecologists should avoid relying on taxonomic relatedness when selecting TDF-δ<sup>13</sup>C, as mixed-diet lab studies may cause misleading results for herbivores and omnivores. Additionally, field-derived estimates could help fill TDF gaps where diets within a consumer class are absent. Overall, we suggest that using standard TDF trophic step values should be abandoned, as feeding studies are often poor proxies for natural diets, particularly for herbivores and omnivores. Instead, we provide recommendations on how to select TDFs, along with a range of TDF-δ<sup>13</sup>C and TDF-δ<sup>15</sup>N values depending on diet source, consumer class, and tissue type. Use of these more refined recommendations and TDF values in isotopic assessments will improve estimates of diets and trophic interactions in natural systems, leading to a better understanding of ecological interactions and communities.</p>
Reevaluating trophic discrimination factors (Δδ13C and Δδ15N) for diet reconstruction
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Metagenomics: A viable tool for reconstructing herbivore diet
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Data from: A fish-focused menu: An interdisciplinary reconstruction of Ancestral Tsleil-Waututh diets
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gapseq reconstructions for representative MAGs from the Diet-Microbiome-Study, Kiel, Germany
<p>The archive contains the gapseq (<a href="https://doi.org/10.1186/s13059-021-02295-1">https://doi.org/10.1186/s13059-021-02295-1</a>) output files from the reconstruction of genome-scale metabolic network models for 182 representative (species-level) metagenome-assembled genomes from the manuscript:</p> <p>A Troci, P Rausch, s Waschina, W Lieb, C Bang, A Franke (in preparation) "Long-term dietary effects on human gut microbiota composition employing shotgun metagenomics data analysis"</p> <p> </p>
Data from: Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers
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Data from: Moa diet fits the bill: virtual reconstruction incorporating mummified remains and prediction of biomechanical performance in avian giants
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Secondary predation constrains DNA-based diet reconstruction in two threatened shark species
<p>Increasing fishing effort, including bycatch and discard practices, are impacting marine biodiversity, particularly among slow-to-reproduce taxa such as elasmobranchs, and specifically sharks. While some fisheries involving sharks are sustainably managed, collateral mortalities continue, contributing towards > 35% of species being threatened with extinction. To effectively manage shark stocks, life-history information, including resource use and feeding ecologies is pivotal, especially among those species with wide-ranging distributions. Two cosmopolitan sharks bycaught off eastern Australia are the common blacktip shark (<i>Carcharhinus limbatus</i>; globally classified as Near Threatened) and great hammerhead (<i>Sphyrna mokarran</i>; Critically Endangered). We opportunistically sampled the digestive tracts of these two species (and also any whole prey; termed the 'Russian-doll' approach), caught in bather-protection gillnets off northern New South Wales, to investigate the capacity for DNA metabarcoding to simultaneously determine predator and prey regional feeding ecologies. While sample sizes were small, <i>S. mokkaran</i> fed predominantly on stingrays and skates (Myliobatiformes and Rajiformes), but also teleosts, while <i>C. limbatus</i> mostly consumed teleosts. Metabarcoding assays showed extensive intermixing of taxa from the digestive tracts of predators and their whole prey, likely via the predator's stomach chyme, negating the opportunity to distinguish between primary and secondary predation. This Russian-doll effect requires further investigation in DNA metabarcoding studies focusing on dietary preferences and implies that any outcomes will need to be interpreted concomitant with traditional visual approaches.</p>
Secondary predation constrains DNA-based diet reconstruction in two threatened shark species
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Tree and sequence alignment used for diet reconstruction of Laurasiatheria
<p><b>Background:</b> Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear.</p> <p><b>Results:</b> In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, <i>APOB</i>, across carnivorous taxa.</p> <p><b>Conclusions: </b>Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets. </p>
Tree and sequence alignment used for diet reconstruction of Laurasiatheria
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International Brain Laboratory public data
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OpenNeuro
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