SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness

Healy, Kevin; Guillerme, Thomas; Kelly, Seán; Inger, Richard; Bearhop, Stuart; Jackson, Andrew L.

doi:10.1111/ecog.03371

Cited by 82 publications

(74 citation statements)

References 27 publications

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“…Additionally, trophic discrimination factors can influence estimates from mixing models (Phillips et al., ), and species‐specific discrimination factors were unavailable for this study. However, our applied enrichment factor has been widely used to estimate carnivore diets (Carlson et al., ; Darimont et al., ; Yeakel et al., ) and falls within the predicted range for martens (Healy et al., ). Despite these nuances, we implemented three independent approaches to quantify dietary overlap and observed equivalent results, thereby reinforcing our conclusions and the power of these complimentary analyses.…”

Section: Discussionmentioning

confidence: 57%

Stable isotopes reveal limited Eltonian niche conservatism across carnivore populations

et al. 2019

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Niche conservatism—the retention of ecological traits across space and time—is an emerging topic of interest because it can predict responses to global change. The conservation of Grinnellian niche characteristics, like species‐habitat associations, has received widespread attention, but the conservation of Eltonian traits such as consumer–resource interactions remains poorly understood. The inability to quantify Eltonian niches through space and time has historically limited the assessment of Eltonian niche conservatism and the dynamics of foraging across populations. Consequently, the relative influence of endogenous factors like phylogeny versus exogenous features like environmental context has rarely been addressed. We tested Eltonian niche conservatism using a paired design to compare foraging among four populations of American martens Martes americana and Pacific martens Martes caurina, morphologically and ecologically similar sister taxa that are allopatrically distributed throughout western North America. We developed a three‐stage isotopic framework and then quantified dietary niche overlap between the sister species and paired island‐mainland sites to assess the relative influence of endogenous (i.e., species) versus exogenous (i.e., environment) factors on Eltonian niches. First, we calculated pairwise dietary overlap in scaled δ‐space using standard ellipses. We then estimated proportional diets (“p‐space”) for individuals using isotopic mixing models and developed a novel utilization distribution overlap approach to quantify proportional dietary overlap. Lastly, we estimated population‐level proportional diets and quantified the differential use of functional prey groups across sites. We detected no pairwise overlap of dietary niches in δ‐space, and distributions of individual diets in p‐space revealed little overlap in core diets across populations. All pairwise comparisons of individuals revealed significant differences in diet, and population‐level comparisons detected contrasting use of functional prey groups. We developed a multi‐faceted isotopic framework to quantify Eltonian niches and found limited evidence of Eltonian niche conservatism across carnivore populations. Our findings are consistent with the growing recognition of dietary plasticity in consumers and suggest that consumer–resource dynamics are largely driven by exogenous environmental factors like land cover and community composition. These results illustrate the context‐dependent nature of foraging and indicate consumer functionality can be dynamic. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13266/suppinfo is available for this article.

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Section: Discussionmentioning

confidence: 57%

Stable isotopes reveal limited Eltonian niche conservatism across carnivore populations

et al. 2019

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“…Isotoperatios were averaged for each dog. Trophic discrimination factors for dogs for δ 15 N (2.75‰ SD 1.19) and δ 13 C (1.64‰ SD 1.43) were obtained using the SIDER package (Healy et al . 2017).…”

Section: Methodsmentioning

confidence: 99%

Ecology of domestic dogs Canis familiaris as an emerging reservoir of Guinea worm Dracunculus medinensis infection

McDonald

Wilson‐Aggarwal

Swan

et al. 2020

Preprint

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AbstractGlobal eradication of human Guinea worm disease (dracunculiasis) has been set back by the emergence of infections in animals, particularly domestic dogs Canis familiaris. The ecology and epidemiology of this reservoir is unknown. We tracked dogs using GPS, inferred diets using stable isotope analysis and analysed correlates of infection in Chad, where numbers of Guinea worm infections are greatest. Dogs had small ranges that varied markedly among villages. Diets consisted largely of human staples and human faeces. A minority of ponds, mostly <200 m from dog-owning households, accounted for most dog exposure to potentially unsafe water. The risk of a dog having had Guinea worm was reduced in dogs living in households providing water for animals but increased with increasing fish consumption by dogs. Provision of safe water might reduce dog exposure to unsafe water, while prioritisation of proactive temephos (Abate) application to the small number of ponds to which dogs have most access is recommended. Fish might have an additional role as transport hosts for Guinea worm, by concentrating copepods infected with worm larvae.Author summaryGuinea worm is a parasite that causes profoundly debilitating disease in humans. An eradication program has been successful in nearly eliminating the disease from people. However, the same worm has now been found in domestic dogs and the frequency of detecting Guinea worm in dogs has been increasing. This means that to eradicate Guinea worm, the infection must be eliminated in dogs as well as in people. However, not much is known about the disease in dogs. This study is the first to investigate dog ecology in relation to Guinea worm infection. We worked in the worst-affected country, Chad. We attached GPS collars to dogs to track their ranging and use of water bodies and analysed their diets using a forensic technique, based on analysing stable isotope compostion of their whiskers and potential food items. We showed that dogs living in households that provided water to their animals had a lower risk of having had Guinea worm and that dogs that ate more fish had an increased risk. These findings suggest there is a classical route for worm transmission in dogs, via drinking contaminated water, as well as a novel route, potentially by eating fish carrying a source of infection.

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“…Prior to running mixing models, we removed δ 15 N terrestrial insect taxa that had substantially higher δ 15 N values than those of Eastern Phoebes and which were unlikely to contribute substantially to insectivore diets (Drosophila spp., Staphylinidae and Scarabaeidae) based on past diet studies (Weeks, 2011) and our foraging observations. We ran mixing models for Eastern Phoebe chicks using trophic discrim- (Healy et al, 2018). For stream fish, we used δ 13 C and δ 15 N TDF and their standard deviations from Post (2002).…”

Section: Resource Usementioning

confidence: 99%

Aquatic and terrestrial resources are not nutritionally reciprocal for consumers

et al. 2019

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Aquatic and terrestrial ecosystems are connected through reciprocal fluxes of energy and nutrients that can subsidize consumers. Past research on reciprocal aquatic–terrestrial subsidies to consumers has generally focused on subsidy quantity while ignoring major differences in the nutritional composition of aquatic and terrestrial resources. Because aquatic resources contain substantially more highly unsaturated omega‐3 fatty acids (HUFAs) than terrestrial resources, aquatic subsidies may play a unique role by supplying these critical compounds to both aquatic and terrestrial consumers. Here, we first characterized nutritional quality in terms of HUFA content in aquatic and terrestrial insect prey. We then used bulk stable isotope analyses to estimate subsidy use by stream and riparian consumers coupled with compound‐specific stable isotope analyses, which allowed us to document consumer HUFA sources. Finally, in order to understand the nutritional importance of aquatic‐derived HUFAs for riparian consumers, we conducted manipulative diet experiments on Eastern Phoebe (Sayornis phoebe) chicks in the laboratory. Aquatic insects were significantly enriched in HUFAs, mainly in terms of eicosapentaenoic acid (EPA), compared with terrestrial insects. Stream fishes relied mainly upon aquatic resources, while insectivorous birds varied in their use of aquatic subsidies across sites. However, like stream fishes, Eastern Phoebe chicks received HUFAs from aquatic insects, even when they were heavily reliant upon terrestrial insects for their overall diet. In the laboratory, dietary HUFAs, such as those supplied by aquatic insects, increased the growth rate and condition of Eastern Phoebe chicks. This study demonstrates that aquatic and terrestrial subsidies are not nutritionally reciprocal from the perspective of consumers because aquatic resources are the main source of critical fatty acids for both stream and riparian consumers. It also confirms previous findings on the nutritional importance of HUFAs for riparian birds, demonstrating that an insectivorous riparian lifestyle influences avian nutritional needs. Finally, our findings raise the possibility that birds and other riparian insectivores may experience nutritional mismatches with terrestrial prey if they do not have access to high‐quality aquatic subsidies as a consequence of aquatic habitat degradation or shifts in consumer and resource phenology. A free Plain Language Summary can be found within the Supporting Information of this article.

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SIDER: an R package for predicting trophic discrimination factors of consumers based on their ecology and phylogenetic relatedness

Cited by 82 publications

References 27 publications

Stable isotopes reveal limited Eltonian niche conservatism across carnivore populations

Stable isotopes reveal limited Eltonian niche conservatism across carnivore populations

Ecology of domestic dogs Canis familiaris as an emerging reservoir of Guinea worm Dracunculus medinensis infection

Aquatic and terrestrial resources are not nutritionally reciprocal for consumers

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