Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diagnosing underdetermination in stable isotope mixing models.

ABSTRACT: Stable isotope mixing models (SIMMs) provide a powerful methodology for quantifying relative contributions of several sources to a mixture. They are widely used in the fields of ecology, geology, and archaeology. Although SIMMs have been rapidly evolved in the Bayesian framework, the underdetermination of mixing space remains problematic, i.e., the estimated relative contributions are incompletely identifiable. Here we propose a statistical method to quantitatively diagnose underdetermination in Bayesian SIMMs, and demonstrate the applications of our method (named β-dependent SIMM) using two motivated examples. Using a simulation example, we showed that the proposed method can rigorously quantify the expected underdetermination (i.e., intervals of β-dependent posterior) of relative contributions. Moreover, the application to the published field data highlighted two problematic aspects of the underdetermination: 1) ordinary SIMMs was difficult to quantify underdetermination of each source, and 2) the marginal posterior median was not necessarily consistent with the joint posterior peak in the case of underdetermination. Our study theoretically and numerically confirmed that β-dependent SIMMs provide a useful diagnostic tool for the underdetermined mixing problem. In addition to ordinary SIMMs, we recommend reporting the results of β-dependent SIMMs to obtain a biologically feasible and sound interpretation from stable isotope data.

SUBMITTER: Osada Y

PROVIDER: S-EPMC8486109 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Quantifying inter- and intra-population niche variability using hierarchical bayesian stable isotope mixing models.

Project description:Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.

| S-EPMC2704373 | biostudies-literature

Exploring source differences on diet-tissue discrimination factors in the analysis of stable isotope mixing models.

Project description:Stable isotope mixing models are regularly used to provide probabilistic estimates of source contributions to dietary mixtures. Whilst Bayesian implementations of isotope mixing models have become prominent, the use of appropriate diet-tissue discrimination factors (DTDFs) remains as the least resolved aspect. The DTDFs are critical in providing accurate inferences from these models. Using both simulated and laboratory-based experimental data, this study provides conceptual and practical applications of isotope mixing models by exploring the role of DTDFs. The experimental study used Mozambique Tilapia Oreochromis mossambicus, a freshwater fish, to explore multi-tissue variations in isotopic incorporation patterns, and to evaluate isotope mixing model outputs based on the experiment- and literature-based DTDFs. Isotope incorporation patterns were variable for both muscle and fin tissues among the consumer groups that fed diet sources with different stable isotope values. Application of literature-based DTDFs in isotope mixing models consistently underestimated the dietary proportions of all single-source consumer groups. In contrast, application of diet-specific DTDFs provided better dietary estimates for single-source consumer groups. Variations in the proportional contributions of the individual sources were, nevertheless, observed for the mixed-source consumer group, which suggests that isotope assimilation of the individual food sources may have been influenced by other underlying physiological processes. This study provides evidence that stable isotope values from different diet sources exhibit large variations as they become incorporated into consumer tissues. This suggests that the application of isotope mixing models requires consideration of several aspects such as diet type and the associated biological processes that may influence DTDFs.

| S-EPMC7519091 | biostudies-literature

Stable isotope mixing models demonstrate the role of an invasive plant in wetland songbird food webs.

Project description:PremiseInvasive plants in wetlands are often ecosystem engineers, mediating changes in ecosystem functions like trophic support. We documented the impacts of Lepidium latifolium, an invasive plant, on the food web of omnivorous birds (Suisun song sparrows, Melospiza melodia maxillaris) in a tidal wetland of northern California, USA.MethodsWe used analysis of natural abundance stable isotopes of 13C and 15N in song sparrow blood, invertebrate food sources, L. latifolium seeds, and other marsh plant seeds to inform Bayesian, concentration-dependent mixing models that predicted average song sparrow diets.ResultsSeason and plant phenology influenced food source incorporation and isotopic signatures. Song sparrows showed higher isotopic variability in the summer. The observed changes in song sparrow diets were driven by altered invertebrate communities related to seasonal L. latifolium presence and by shifts from seeds to consumption of invertebrate food sources during the breeding season in the spring and summer.DiscussionThis study used stable isotope tools and modeling to demonstrate two mechanisms of isotopic influence by L. latifolium on omnivorous song sparrows. This study can inform site- and species-specific management strategies by demonstrating how changes to the plant community can impact entire trophic systems.

| S-EPMC9400394 | biostudies-literature

Coastal complexity: Ancient human diets inferred from Bayesian stable isotope mixing models and a primate analogue.

Project description:An extensive ecological literature applies stable isotope mixing models to derive quantitative dietary reconstructions from isotope ratios of consumer tissues. While this approach works well for some organisms, it is challenging for consumers with complex, varied diets, including humans; indeed, many archaeologists have avoided the use of mixing models because uncertainties in model outputs are sufficiently large that the findings are not helpful in understanding ancient lifeways. Here, we exploit an unparalleled opportunity to evaluate the feasibility of dietary quantification in a nutritionally and isotopically complex context on the Cape Peninsula, South Africa. Delta values (δ13C and δ15N) of 213 indigenous food samples enable us to characterise four food groups: terrestrial plants, terrestrial vertebrates, marine invertebrates and marine vertebrates. A recent study of baboons that consumed marine and terrestrial foods provides insight into the relationship between such foods and consumer tissue isotopes. We use this information to refine our interpretation of δ15N and especially δ13C in bone collagen from 35 archaeological hunter-gatherers, achieving better estimates of the relative importance of marine and terrestrial foods in the diet than has hitherto been possible. Based on Bayesian stable isotope mixing model (SIMM) outputs, we infer that the trophic enrichment factor (TEF) for δ13Cbone collagen in these coastal humans is closer to +3 than +5‰. In the most 13C- and 15N-rich individuals, 65-98% of bone collagen (95% credible intervals) derived from marine foods. Conversely, in 13C and 15N-poor individuals, 7-44% of bone collagen derived from marine foods. The uncertainties discussed here highlight the need for caution when implementing SIMMs in studies of consumers with complex diets. To our knowledge, this work constitutes the most detailed and most tightly constrained study of this problem to date.

| S-EPMC6301609 | biostudies-literature

FRAME—Monte Carlo model for evaluation of the stable isotope mixing and fractionation

Project description:Bayesian stable isotope mixing models are widely used in geochemical and ecological studies for partitioning sources that contribute to various mixtures. However, none of the existing tools allows accounting for the influence of processes other than mixing, especially stable isotope fractionation. Bridging this gap, new software for the stable isotope Fractionation And Mixing Evaluation (FRAME) has been developed with a user-friendly graphical interface (malewick.github.io/frame). This calculation tool allows simultaneous sources partitioning and fractionation progress determination based on the stable isotope composition of sources/substrates and mixture/products. The mathematical algorithm applies the Markov-Chain Monte Carlo model to estimate the contribution of individual sources and processes, as well as the probability distributions of the calculated results. The performance of FRAME was comprehensively tested and practical applications of this modelling tool are presented with simple theoretical examples and stable isotope case studies for nitrates, nitrites, water and nitrous oxide. The open mathematical design, featuring custom distributions of source isotope signatures, allows for the implementation of additional processes that alternate the characteristics of the final mixture and its application for various range of studies.

| S-EPMC9704640 | biostudies-literature

Merging resource availability with isotope mixing models: the role of neutral interaction assumptions.

Project description:BackgroundBayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values.MethodologyWe develop a procedure to incorporate prey availability data into bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates.ConclusionsOur results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

| S-EPMC3131389 | biostudies-literature

Selecting the best stable isotope mixing model to estimate grizzly bear diets in the Greater Yellowstone Ecosystem.

Project description:Past research indicates that whitebark pine seeds are a critical food source for Threatened grizzly bears (Ursus arctos) in the Greater Yellowstone Ecosystem (GYE). In recent decades, whitebark pine forests have declined markedly due to pine beetle infestation, invasive blister rust, and landscape-level fires. To date, no study has reliably estimated the contribution of whitebark pine seeds to the diets of grizzlies through time. We used stable isotope ratios (expressed as δ13C, δ15N, and δ34S values) measured in grizzly bear hair and their major food sources to estimate the diets of grizzlies sampled in Cooke City Basin, Montana. We found that stable isotope mixing models that included different combinations of stable isotope values for bears and their foods generated similar proportional dietary contributions. Estimates generated by our top model suggest that whitebark pine seeds (35±10%) and other plant foods (56±10%) were more important than meat (9±8%) to grizzly bears sampled in the study area. Stable isotope values measured in bear hair collected elsewhere in the GYE and North America support our conclusions about plant-based foraging. We recommend that researchers consider model selection when estimating the diets of animals using stable isotope mixing models. We also urge researchers to use the new statistical framework described here to estimate the dietary responses of grizzlies to declines in whitebark pine seeds and other important food sources through time in the GYE (e.g., cutthroat trout), as such information could be useful in predicting how the population will adapt to future environmental change.

| S-EPMC5426898 | biostudies-literature

Using plant physiological stable oxygen isotope models to counter food fraud.

Project description:Fraudulent food products, especially regarding false claims of geographic origin, impose economic damages of $30-$40 billion per year. Stable isotope methods, using oxygen isotopes (δ18O) in particular, are the leading forensic tools for identifying these crimes. Plant physiological stable oxygen isotope models simulate how precipitation δ18O values and climatic variables shape the δ18O values of water and organic compounds in plants. These models have the potential to simplify, speed up, and improve conventional stable isotope applications and produce temporally resolved, accurate, and precise region-of-origin assignments for agricultural food products. However, the validation of these models and thus the best choice of model parameters and input variables have limited the application of the models for the origin identification of food. In our study we test model predictions against a unique 11-year European strawberry δ18O reference dataset to evaluate how choices of input variable sources and model parameterization impact the prediction skill of the model. Our results show that modifying leaf-based model parameters specifically for fruit and with product-independent, but growth time specific environmental input data, plant physiological isotope models offer a new and dynamic method that can accurately predict the geographic origin of a plant product and can advance the field of stable isotope analysis to counter food fraud.

| S-EPMC8397719 | biostudies-literature

Stable Isotope Models Predict Foraging Habitat of Northern Fur Seals (Callorhinus ursinus) in Alaska.

Project description:We developed models to predict foraging habitat of adult female northern fur seals (Callorhinus ursinus) using stable carbon (?13C) and nitrogen (?15N) isotope values from plasma and red blood cells. Binomial generalized linear mixed models were developed using blood isotope samples collected from 35 adult female fur seals on three breeding colonies in Alaska during July-October 2006. Satellite location and dive data were used to define habitat use in terms of the proportion of time spent or dives made in different oceanographic/bathymetric domains. For both plasma and red blood cells, the models accurately predicted habitat use for animals that foraged exclusively off or on the continental shelf. The models did not perform as well in predicting habitat use for animals that foraged in both on- and off-shelf habitat; however, sample sizes for these animals were small. Concurrently collected scat, fatty acid, and dive data confirmed that the foraging differences predicted by isotopes were associated with diet differences. Stable isotope samples, dive data, and GPS location data collected from an additional 15 females during August-October 2008 validated the effective use of the models across years. Little within year variation in habitat use was indicated from the comparison between stable isotope values from plasma (representing 1-2 weeks) and red blood cells (representing the prior few months). Constructing predictive models using stable isotopes provides an effective means to assess habitat use at the population level, is inexpensive, and can be applied to other marine predators.

| S-EPMC4451762 | biostudies-literature

Global Stable-isotope Tracing Metabolomics Reveals System-wide Metabolic Alternations in Aging Drosophila

Project description:System-wide metabolic homeostasis is crucial for maintaining physiological functions of living organisms. Stable-isotope tracing metabolomics allows to unravel metabolic activity quantitatively by measuring the isotopically labeled metabolites, but has been largely restricted by coverage. Yet, delineating system-wide metabolic homeostasis at the whole-organism level remains non-trivial. Here, we develop a global isotope tracing metabolomics technology to measure labeled metabolites with a metabolome-wide coverage. Using Drosophila as an aging model organism, we probe the in vivo tracing kinetics with quantitative information on labeling patterns, extents and rates on a metabolome-wide scale. We curate a system-wide metabolic network to characterize metabolic homeostasis and disclose a system-wide loss of metabolic coordinations that impacts both intra- and inter-tissue metabolic homeostasis significantly during Drosophila aging. Importantly, we reveal an unappreciated metabolic diversion from glycolysis to serine metabolism and purine metabolism as Drosophila aging. The developed technology facilitates a system-level understanding of metabolic regulation in living organisms.

2022-05-29 | GSE204740 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data