Intrapopulation variability in wolf diet revealed using a combined stable isotope and fatty acid approach

Effects of lipid extraction on stable isotope ratios of carbon and nitrogen in muscles of freshwater fish

The extraction of lipids by the Folch method from the muscles of all the fish studied led to statistically significant differences in the values of δ15N. At the same time, lipid extraction led to a statistically significant increase in δ13C in pike and roach, and to a statistically insignificant decrease in δ13C in perch and bream. Thus, lipid extraction cannot serve as a universal method of sample preparation for the analysis of the isotopic composition of carbon (13C/12C) and nitrogen (15N/14N) in fish muscles. The differences between the δ13C values in the samples before and after lipid extraction were statistically investigated by different models. It is shown that mathematical correction method models can be used, but the results are depending on the fish types.

Stable isotopes and a changing world

The measurement of naturally occurring stable isotope ratios of the light elements (C, N, H, O, S) in animal tissues and associated organic and inorganic fractions of associated environments holds immense potential as a means of addressing effects of global change on animals. This paper provides a brief review of studies that have used the isotope approach to evaluate changes in diet, isotopic niche, contaminant burden, reproductive and nutritional investment, invasive species and shifts in migration origin or destination with clear links to evaluating effects of global change. This field has now reached a level of maturity that is impressive but generally underappreciated and involves technical as well as statistical advances and access to freely available R-based packages. There is a need for animal ecologists and conservationists to design tissue collection networks that will best answer current and anticipated questions related to the global change and the biodiversity crisis. These developments will move the field of stable isotope ecology toward a more hypothesis driven discipline related to rapidly changing global events.

Multi-isotope (δ2H, δ13C, δ15N) feather profiles and morphometrics inform patterns of migratory connectivity in three species of North American swallows

Aerial insectivorous birds have suffered steep population declines in North America over the last 60 years. A lack of information on migratory connectivity between breeding and non-breeding grounds for these species limits our ability to interpret factors affecting their population-specific trends. We determined likely Latin American non-breeding regions of Bank (Riparia riparia), Barn (Hirundo rustica) and Cliff (Petrochelidon pyrrhonota) swallow from populations across their breeding ranges. We used predicted feather hydrogen (δ²H_f) and carbon (δ¹³C_f) isoscapes for winter-grown feathers to indicate areas of highest probability of moult origin and incorporated these results into a cluster analysis to determine likely broad non-breeding regions. We also assessed variation in wing length among populations to determine the potential for this metric to differentiate population moult origins. We then investigated patterns of multi-isotopic (δ²H_f, δ¹³C_f, δ¹⁵N_f) and wing-length niche occupancy by quantifying niche size and overlap among populations under the assumption that broad niches were consistent with low within-species migratory connectivity and narrow and non-overlapping niches with higher connectivity. Multivariate assignment identified different non-breeding regions and potential clusters of moult origin generally corresponding to Central America and northern South America, eastern and south-central South America, and the western and southern part of that continent, with variation within and among populations and species. Separate niche space indicated different wintering habitat or areas used by species or populations whereas niche overlap indicated only potential spatial similarity. Wing length varied significantly among populations by species, being longer in the west and north for Bank and Cliff Swallow and longer in eastern Canadian Barn Swallow populations. Barn Swallow occupied consistently larger isotopic and wing length niche space than the other species. Comparisons among populations across species showed variable isotopic and wing-length niche overlap generally being greater within breeding regions and lower between western and eastern breeding populations supporting a general North American continental divide for all species with generally low migratory connectivity for all species. We present a novel approach to assessing connectivity using inexpensive and broad isotopic approaches that provides the basis for hypothesis testing using more spatially explicit expensive techniques.

Parental care contributes to vertical transmission of microbes in a skin-feeding and direct-developing caecilian

BACKGROUND

Our current understanding of vertebrate skin and gut microbiomes, and their vertical transmission, remains incomplete as major lineages and varied forms of parental care remain unexplored. The diverse and elaborate forms of parental care exhibited by amphibians constitute an ideal system to study microbe transmission, yet investigations of vertical transmission among frogs and salamanders have been inconclusive. In this study, we assess bacteria transmission in Herpele squalostoma, an oviparous direct-developing caecilian in which females obligately attend juveniles that feed on their mother's skin (dermatophagy).

RESULTS

We used 16S rRNA amplicon-sequencing of the skin and gut of wild caught H. squalostoma individuals (males, females, including those attending juveniles) as well as environmental samples. Sourcetracker analyses revealed that juveniles obtain an important portion of their skin and gut bacteria communities from their mother. The contribution of a mother's skin to the skin and gut of her respective juveniles was much larger than that of any other bacteria source. In contrast to males and females not attending juveniles, only the skins of juveniles and their mothers were colonized by bacteria taxa Verrucomicrobiaceae, Nocardioidaceae, and Erysipelotrichaceae. In addition to providing indirect evidence for microbiome transmission linked to parental care among amphibians, our study also points to noticeable differences between the skin and gut communities of H. squalostoma and that of many frogs and salamanders, which warrants further investigation.

CONCLUSION

Our study is the first to find strong support for vertical bacteria transmission attributed to parental care in a direct-developing amphibian species. This suggests that obligate parental care may promote microbiome transmission in caecilians.

Integrating DNA-based Prey Occurrence Probability Into Stable Isotope Mixing Models

The introduction of laboratory methods to animal dietary studies has allowed researchers to obtain results with accuracy and precision not possible with observational techniques. For example, DNA barcoding, or the identification of prey with taxon-specific DNA sequences, allows researchers to classify digested prey tissues to the species-level, while stable isotope analysis paired with Bayesian mixing models can quantify dietary contributions by comparing a consumer's isotopic values to those derived from their prey. However, DNA-based methods are currently only able to classify, but not quantify, the taxa present in a diet sample, while stable isotope analysis can only quantify dietary taxa that are identified a priori as prey isotopic values are a result of life history traits, not phylogenetic relatedness. Recently, researchers have begun to couple these techniques in dietary studies to capitalize on the reciprocal benefits and drawbacks offered by each approach, with some even integrating DNA-based results directly into Bayesian mixing models as informative priors. As the informative priors used in these models must represent known dietary compositions (e.g., percentages of prey biomasses), researchers have scaled the DNA-based frequency of occurrence of major prey groups so that their normalized frequency of occurrence sums to 100%. Unfortunately, such an approach is problematic as priors stemming from binomial, DNA-based data do not truly reflect quantitative information about the consumer's diet and may skew the posterior distribution of prey quantities as a result. Therefore, we present a novel approach to incorporate DNA-based dietary information into Bayesian stable isotope mixing models that preserves the binomial nature of DNA-based results. This approach uses community-wide frequency of occurrence or logistic regression-based estimates of prey occurrence to dictate the probability that each prey group is included in each mixing model iteration, and, in turn, the probability that each iteration's results are included in the posterior distribution of prey composition possibilities. Here, we demonstrate the utility of this method by using it to quantify the prey composition of nestling Louisiana waterthrush (Parkesia motacilla).

Summer/fall diet and macronutrient assimilation in an Arctic predator

Free-ranging predator diet estimation is commonly achieved by applying molecular-based tracers because direct observation is not logistically feasible or robust. However, tracers typically do not represent all dietary macronutrients, which likely obscures resource use as prey proximate composition varies and tissue consumption can be specific. For example, polar bears (Ursus maritimus) preferentially consume blubber, yet diets have been estimated using fatty acids based on prey blubber or stable isotopes of lipid-extracted prey muscle, neither of which represent both protein and lipid macronutrient contributions. Further, additional bias can be introduced because dietary fat is known to be flexibly routed beyond short-term energy production and storage. We address this problem by simultaneously accounting for protein and lipid assimilation using carbon and nitrogen isotope compositions of lipid-containing prey muscle and blubber to infer summer/fall diet composition and macronutrient proportions from Chukchi Sea polar bear guard hair (n = 229) sampled each spring between 2008 and 2017. Inclusion of blubber (85-95% lipid by dry mass) expanded the isotope mixing space and improved separation among prey species. Ice-associated seals, including nutritionally dependent pups, were the primary prey in summer/fall diets with lower contributions by Pacific walruses (Odobenus rosmarus) and whales. Percent blubber estimates confirmed preferential selection of this tissue and represented the highest documented lipid assimilation for any animal species. Our results offer an improved understanding of summer/fall prey macronutrient usage by Chukchi Sea polar bears which likely coincides with a nutritional bottleneck as the sea ice minimum is approached.

Environmental and life-history factors influence inter-colony multidimensional niche metrics of a breeding Arctic marine bird

Human industrialization has resulted in rapid climate change, leading to wide-scale environmental shifts. These shifts can modify food web dynamics by altering the abundance and distribution of primary producers (ice algae and phytoplankton), as well as animals at higher trophic levels. Methylmercury (MeHg) is a neuro-endocrine disrupting compound which biomagnifies in animals as a function of prey choice, and as such bioavailability is affected by altered food web dynamics and adds an important risk-based dimension in studies of foraging ecology. Multidimensional niche dynamics (MDND; δ¹³C, δ¹⁵N, THg; total mercury) were determined among breeding common eider (Somateria mollissima) ducks sampled from 10 breeding colonies distributed across the circumpolar Arctic and subarctic. Results showed high variation in MDND among colonies as indicated by niche size and ranges in δ¹³C, δ¹⁵N and THg values in relation to spatial differences in primary production inferred from sea-ice presence and colony migratory status. Colonies with higher sea-ice cover during the pre-incubation period had higher median colony THg, δ¹⁵N, and δ¹³C. Individuals at migratory colonies had relatively higher THg and δ¹⁵N, and lower δ¹³C, suggesting a higher trophic position and a greater reliance on phytoplankton-based prey. It was concluded that variation in MDND exists among eider colonies which influenced individual blood THg concentrations. Further exploration of spatial ecotoxicology and MDND at each individual site is important to examine the relationships between anthropogenic activities, foraging behaviour, and the related risks of contaminant exposure at even low, sub-lethal concentrations that may contribute to deleterious effects on population stability over time. Overall, multidimensional niche analysis that incorporates multiple isotopic and contaminant metrics could help identify those populations at risk to rapidly altered food web dynamics.

Patterns and processes of pathogen exposure in gray wolves across North America

The presence of many pathogens varies in a predictable manner with latitude, with infections decreasing from the equator towards the poles. We investigated the geographic trends of pathogens infecting a widely distributed carnivore: the gray wolf (Canis lupus). Specifically, we investigated which variables best explain and predict geographic trends in seroprevalence across North American wolf populations and the implications of the underlying mechanisms. We compiled a large serological dataset of nearly 2000 wolves from 17 study areas, spanning 80° longitude and 50° latitude. Generalized linear mixed models were constructed to predict the probability of seropositivity of four important pathogens: canine adenovirus, herpesvirus, parvovirus, and distemper virus-and two parasites: Neospora caninum and Toxoplasma gondii. Canine adenovirus and herpesvirus were the most widely distributed pathogens, whereas N. caninum was relatively uncommon. Canine parvovirus and distemper had high annual variation, with western populations experiencing more frequent outbreaks than eastern populations. Seroprevalence of all infections increased as wolves aged, and denser wolf populations had a greater risk of exposure. Probability of exposure was positively correlated with human density, suggesting that dogs and synanthropic animals may be important pathogen reservoirs. Pathogen exposure did not appear to follow a latitudinal gradient, with the exception of N. caninum. Instead, clustered study areas were more similar: wolves from the Great Lakes region had lower odds of exposure to the viruses, but higher odds of exposure to N. caninum and T. gondii; the opposite was true for wolves from the central Rocky Mountains. Overall, mechanistic predictors were more informative of seroprevalence trends than latitude and longitude. Individual host characteristics as well as inherent features of ecosystems determined pathogen exposure risk on a large scale. This work emphasizes the importance of biogeographic wildlife surveillance, and we expound upon avenues of future research of cross-species transmission, spillover, and spatial variation in pathogen infection.

Evaluating the performance of the Bayesian mixing tool MixSIAR with fatty acid data for quantitative estimation of diet

We test the performance of the Bayesian mixing model, MixSIAR, to quantitatively predict diets of consumers based on their fatty acids (FAs). The known diets of six species, undergoing controlled-feeding experiments, were compared with dietary predictions modelled from their FAs. Test subjects included fish, birds and mammals, and represent consumers with disparate FA compositions. We show that MixSIAR with FA data accurately identifies a consumer's diet, the contribution of major prey items, when they change their diet (diet switching) and can detect an absent prey. Results were impacted if the consumer had a low-fat diet due to physiological constraints. Incorporating prior information on the potential prey species into the model improves model performance. Dietary predictions were reasonable even when using trophic modification values (calibration coefficients, CCs) derived from different prey. Models performed well when using CCs derived from consumers fed a varied diet or when using CC values averaged across diets. We demonstrate that MixSIAR with FAs is a powerful approach to correctly estimate diet, in particular if used to complement other methods.

The critical importance of experimentation in biomarker-based trophic ecology

Fatty acids are commonly used as biomarkers for making inferences about trophic relationships in aquatic and soil food webs. However, researchers are often unaware of the physiological constraints within organisms on the trophic transfer and modification of dietary biomarkers in consumers. Fatty acids are bioactive molecules, which have diverse structures and functions that both complicate and enhance their value as trophic tracers. For instance, consumers may synthesize confounding non-dietary sourced markers from precursor molecules, and environmental conditions also affect fatty acid composition. There is a vital need for more research on the uptake and transfer of trophic biomarkers in individual organisms in order to advance the field and make meaningful use of these tools at the scale of populations or ecosystems. This special issue is focused on controlled feeding experiments on a diverse taxonomic breadth of model consumers from freshwater, marine and soil ecosystems with a goal of creating a more integrated understanding of the connection between consumer physiology and trophic ecology. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.

Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers

Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free-ranging animals with distinct foraging preferences.We used stable isotopes, morphological, and molecular analyses to investigate the diet of free-ranging consumers with two distinct diet types, that is, carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates.Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population.Although we used free-ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free-ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.

Unlocking the power of fatty acids as dietary tracers and metabolic signals in fishes and aquatic invertebrates

Determining the transfer and transformation of organic matter in food webs is a fundamental challenge that has implications for sustainable management of ecosystems. Fatty acids (FA) offer a potential approach for resolving complex diet mixtures of organisms because they provide a suite of molecular tracers. Yet, uncertainties in the degree of their biochemical modification by consumers, due to selective retention or metabolism, have limited their application. Here, we consolidated 316 controlled feeding studies of aquatic ectotherms (fishes and invertebrates) involving 1404 species-diet combinations to assess the degree of trophic modification of FA in muscle tissue. We found a high degree of variability within and among taxa in the %FA in consumer muscle tissue versus %FA in diet regression equations. Most saturated FA had weak relationships with the diet (r² < 0.30) and shallow slopes (m < 0.30), suggesting a lack of retention in muscle when fed in increasing amounts. Contrarily, several essential FA, including linoleic (18:2n-6) and α-linolenic acid (18:3n-3), exhibited significant relationships with the diet (m > 0.35, r² > 0.50), suggesting supply limitations and selective retention in muscle by consumers. For all FA, relationships strengthened with increasing taxonomic specificity. We also demonstrated the utility of new correction equations by calculating the potential contributions of approximately 20 prey items to the diet of selected species of generalist fishes using a FA mixing model. Our analyses further reveal how a broad range of fishes and invertebrates convert or store these compounds in muscle tissue to meet physiological needs and point to their power in resolving complex diets in aquatic food webs. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.