Assessing seasonal changes in animal diets with stable-isotope analysis of amino acids: a migratory boreal songbird switches diet over its annual cycle

The effects of diet-shifting from invertebrates towards fruit on the condition of autumn-migrant Catharus thrushes

Migration is an energetically challenging and risky life history stage for many animals, but could be supported by dietary choices en route, which may create opportunities to improve body and physiological condition. However, proposed benefits of diet shifts, such as between seasonally available invertebrates and fruits, have received limited investigation in free-living animals. We quantified diet composition and magnitude of autumn diet shifts over two time periods in two closely-related species of migratory songbirds on stopover in the northeastern U.S. (Swainson's thrush [Catharus ustulatus], long-distance migrant, N = 83; hermit thrush [C. guttatus], short-distance migrant, N = 79) and used piecewise structural equation models to evaluate the relationships among (1) migration timing, (2) dietary behavior, and (3) morphometric and physiological condition indices. Tissue isotope composition indicated that both species shifted towards greater fruit consumption. Larger shifts in recent weeks corresponded to higher body condition in Swainson's, but not hermit thrushes, and condition was more heavily influenced by capture date in Swainson's thrushes. Presence of "high-antioxidant" fruits in fecal samples was unrelated to condition in Swainson's thrushes and negatively related to multiple condition indices in hermit thrushes, possibly indicating the value of fruits during migration is related more to their energy and/or macronutrient content than antioxidant content. Our results suggest that increased frugivory during autumn migration can support condition, but those benefits might depend on migration strategy: a longer-distance, more capital-dependent migration strategy could require stricter regulation of body condition aided by increased fruit consumption.

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.

Isotopic niches do not follow the expectations of niche conservatism in the bird genus Cinclodes

Phenotypic traits are expected to be more similar among closely related species than among species that diverged long ago (all else being equal). This pattern, known as phylogenetic niche conservatism, also applies to traits that are important to determine the niche of species. To test this hypothesis on ecological niches, we analysed isotopic data from 254 museum study skins from 12 of the 16 species of the bird genus Cinclodes and measured stable isotope ratios for four different elements: carbon, nitrogen, hydrogen and oxygen. We find that all traits, measured individually, or as a composite measurement, lack any phylogenetic signal, which in turn suggests a high level of lability in ecological niches. We compared these metrics to the measurements of morphological traits in the same genus and found that isotopic niches are uniquely evolutionarily labile compared to other traits. Our results suggest that, in Cinclodes, the realized niche evolves much faster than expected by the constraints of phylogenetic history and poses the question of whether this is a general pattern across the tree of life.

Assessment of Compound-Specific Fatty Acid δ13C and δ2H Values to Track Fish Mobility in a Small Sub-alpine Catchment

Methods for identifying origin, movement, and foraging areas of animals are essential for understanding ecosystem connectivity, nutrient flows, and other ecological processes. Telemetric methods can provide detailed spatial coverage but are limited to a minimum body size of specimen for tagging. In recent years, stable isotopes have been increasingly used to track animal migration by linking landscape isotope patterns into movement (isoscapes). However, compared to telemetric methods, the spatial resolution of bulk stable isotopes is low. Here, we examined a novel approach by evaluating the use of compound-specific hydrogen and carbon stable isotopes of fatty acids (δ²H_FA and δ¹³C_FA) from fish liver, muscle, brain, and eye tissues for identifying site specificity in a 254 km² sub-alpine river catchment. We analyzed 208 fish (European bullhead, rainbow trout, and brown trout) collected in 2016 and 2018 at 15 different sites. δ¹³C_FA values of these fish tissues correlated more among each other than those of δ²H_FA values. Both δ²H_FA and δ¹³C_FA values showed tissue-dependent isotopic fractionation, while fish taxa had only small effects. The highest site specificity was for δ¹³C_DHA values, while the δ²H isotopic difference between linoleic acid and alpha-linolenic acid resulted in the highest site specificity. Using linear discrimination analysis of FA isotope values, over 90% of fish could be assigned to their location of origin; however, the accuracy dropped to about 56% when isotope data from 2016 were used to predict the sites for samples collected in 2018, suggesting temporal shifts in site specificity of δ²H_FA and δ¹³C_FA. However, the predictive power of δ²H_FA and δ¹³C_FA over this time interval was still higher than site specificity of bulk tissue isotopes for a single time point. In summary, compound-specific isotope analysis of fatty acids may become a highly effective tool for assessing fine and large-scale movement and foraging areas of animals.

Winter locations of red-throated divers from geolocation and feather isotope signatures

Migratory species have geographically separate distributions during their annual cycle, and these areas can vary between populations and individuals. This can lead to differential stress levels being experienced across a species range. Gathering information on the areas used during the annual cycle of red‐throated divers (RTDs; Gavia stellata) has become an increasingly pressing issue, as they are a species of concern when considering the effects of disturbance from offshore wind farms and the associated ship traffic. Here, we use light‐based geolocator tags, deployed during the summer breeding season, to determine the non‐breeding winter location of RTDs from breeding locations in Scotland, Finland, and Iceland. We also use δ¹⁵N and δ¹³C isotope signatures, from feather samples, to link population‐level differences in areas used in the molt period to population‐level differences in isotope signatures. We found from geolocator data that RTDs from the three different breeding locations did not overlap in their winter distributions. Differences in isotope signatures suggested this spatial separation was also evident in the molting period, when geolocation data were unavailable. We also found that of the three populations, RTDs breeding in Iceland moved the shortest distance from their breeding grounds to their wintering grounds. In contrast, RTDs breeding in Finland moved the furthest, with a westward migration from the Baltic into the southern North Sea. Overall, these results suggest that RTDs breeding in Finland are likely to encounter anthropogenic activity during the winter period, where they currently overlap with areas of future planned developments. Icelandic and Scottish birds are less likely to be affected, due to less ship activity and few or no offshore wind farms in their wintering distributions. We also demonstrate that separating the three populations isotopically is possible and suggest further work to allocate breeding individuals to wintering areas based solely on feather samples.

Amino acid nitrogen and carbon isotope data: Potential and implications for ecological studies

Explaining food web dynamics, stability, and functioning depend substantially on understanding of feeding relations within a community. Bulk stable isotope ratios (SIRs) in natural abundance are well‐established tools to express direct and indirect feeding relations as continuous variables across time and space. Along with bulk SIRs, the SIRs of individual amino acids (AAs) are now emerging as a promising and complementary method to characterize the flow and transformation of resources across a diversity of organisms, from microbial domains to macroscopic consumers. This significant AA‐SIR capacity is based on empirical evidence that a consumer's SIR, specific to an individual AA, reflects its diet SIR coupled with a certain degree of isotopic differences between the consumer and its diet. However, many empirical ecologists are still unfamiliar with the scope of applicability and the interpretative power of AA‐SIR. To fill these knowledge gaps, we here describe a comprehensive approach to both carbon and nitrogen AA‐SIR assessment focusing on two key topics: pattern in AA‐isotope composition across spatial and temporal scales, and a certain variability of AA‐specific isotope differences between the diet and the consumer. On this basis we review the versatile applicability of AA‐SIR to improve our understanding of physiological processes as well as food web functioning, allowing us to reconstruct dominant basal dietary sources and trace their trophic transfers at the specimen and community levels. Given the insightful and opportunities of AA‐SIR, we suggest future applications for the dual use of carbon and nitrogen AA‐SIR to study more realistic food web structures and robust consumer niches, which are often very difficult to explain in nature.

Biofilm and invertebrate consumption by western sandpipers (Calidris mauri) and dunlin (Calidris alpina) during spring migratory stopover: insights from tissue and breath CO2 isotopic (δ 13C, δ 15N) analyses

Shorebirds use key migratory stopover habitats in spring and fall where body proteins are replenished and lipids stored as fuel for the remaining journey. The Fraser River estuary, British Columbia, Canada, is a critical spring stopover site for hundreds of thousands of migrating western sandpiper, Calidris mauri, and dunlin, Calidris alpina. Intertidal biofilm in spring is an important nutritional source for western sandpiper, with previous isotopic research predicting 45-59% of total diet and 50% of total energy needs. However, these studies relied on isotopic mixing models that did not consider metabolic routing of key dietary macromolecules. Complexity arises due to the mixed macromolecular composition of biofilm that is difficult to characterize isotopically. We expanded on these earlier findings by considering a protein pathway from diet to the body protein pool represented by liver tissue, using a Bayesian mixing model based on δ ¹³C and δ ¹⁵N. We used δ ¹³C measurements of adipose tissue and breath CO₂ to provide an estimate of the carbohydrate and protein δ ¹³C values of microphytobenthos and used these derived values to better inform the isotopic mixing models. Our results reinforce earlier estimates of the importance of biofilm to staging shorebirds in predicting that assimilated nutrients from biofilm contribute ~35% of the protein budgets for staging western sandpipers (n = 13) and dunlin (n = 11) and at least 41% of the energy budget of western sandpiper (n = 69). Dunlin's ingestion of biofilm appeared higher than anticipated given their expected reliance on invertebrate prey compared to western sandpiper, a biofilm specialist. Isotopic analyses of bulk tissues that consider metabolic routing and that make use of breath CO₂ and adipose lipid assays can provide new insights into avian physiology. We advocate further isotopic research to better understand biofilm use by migratory shorebirds in general and as a critical requirement for more effective conservation.

Interactions at surface-subterranean ecotones: structure and function of food webs within spring orifices

Spring orifices are ecotones between surface and subterranean aquatic ecosystems. Invertebrates of different origins (e.g., surface, spring obligate, and subterranean) coexist in these spatially restricted environments, potentially competing for resources. However, processes that allow for population coexistence in these presumably low resource environments are not well understood. We examined invertebrate communities at two spring complexes in Texas, USA and assessed resource use and food web structure at spring orifices using stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N). Using bulk δ¹³C and δ¹⁵N of organisms and potential food sources, we elucidated dietary sources and found that invertebrate communities exhibited resource partitioning and contained two main food chains (periphyton versus terrestrial organic matter [OM]). In both spring complexes, several endemic spring orifice associated and subterranean taxa derived most of their diet from terrestrial OM. Analysis of compound-specific stable isotopes (i.e., δ¹³C of essential amino acids, EAAs) from two co-occurring elmid species indicated that the endemic spring orifice-associated species (Heterelmis comalensis) derived > 80% of its EAAs from bacteria, whereas the widespread surface species (Microcylloepus pusillus) derived its EAAs from a more equitable mix of bacteria, fungi, and algae. We additionally calculated niche overlap among of several taxonomically related groups (aquatic beetles and amphipods) that co-occur in spring ecotones and posterior probability estimates indicated little to no niche overlap among related species. Results indicate that invertebrates at subterranean-surface aquatic ecotones are partitioning food resources and highlight the importance of connections to riparian zones for persistence of several endemic invertebrates.

Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses

Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ¹⁵N and δ¹³C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ¹⁵N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.

Elucidating stygofaunal trophic web interactions via isotopic ecology

Subterranean ecosystems host highly adapted aquatic invertebrate biota which play a key role in sustaining groundwater ecological functioning and hydrological dynamics. However, functional biodiversity studies in groundwater environments, the main source of unfrozen freshwater on Earth, are scarce, probably due to the cryptic nature of the systems. To address this, we investigate groundwater trophic ecology via stable isotope analysis, employing δ¹³C and δ¹⁵N in bulk tissues, and amino acids. Specimens were collected from a shallow calcrete aquifer in the arid Yilgarn region of Western Australia: a well-known hot-spot for stygofaunal biodiversity. Sampling campaigns were carried out during dry (low rainfall: LR) and the wet (high rainfall: HR) periods. δ¹³C values indicate that most of the stygofauna shifted towards more ¹³C-depleted carbon sources under HR, suggesting a preference for fresher organic matter. Conversion of δ¹⁵N values in glutamic acid and phenylalanine to a trophic index showed broadly stable trophic levels with organisms clustering as low-level secondary consumers. However, mixing models indicate that HR conditions trigger changes in dietary preferences, with increasing predation of amphipods by beetle larvae. Overall, stygofauna showed a tendency towards opportunistic and omnivorous habits—typical of an ecologically tolerant community—shaped by bottom-up controls linked with changes in carbon flows. This study provides baseline biochemical and ecological data for stygofaunal trophic interactions in calcretes. Further studies on the carbon inputs and taxa-specific physiology will help refine the interpretation of the energy flows shaping biodiversity in groundwaters. This will aid understanding of groundwater ecosystem functioning and allow modelling of the impact of future climate change factors such as aridification.

The Importance of Isotopic Turnover for Understanding Key Aspects of Animal Ecology and Nutrition

Stable isotope-based methods have proved to be immensely valuable for ecological studies ranging in focus from animal movements to species interactions and community structure. Nevertheless, the use of these methods is dependent on assumptions about the incorporation and turnover of isotopes within animal tissues, which are oftentimes not explicitly acknowledged and vetted. Thus, the purpose of this review is to provide an overview of the estimation of stable isotope turnover rates in animals, and to highlight the importance of these estimates for ecological studies in terrestrial, freshwater, and marine systems that may use a wide range of stable isotopes. Specifically, we discuss 1) the factors that contribute to variation in turnover among individuals and across species, which influences the use of stable isotopes for diet reconstructions, 2) the differences in turnover among tissues that underlie so-called ‘isotopic clocks’, which are used to estimate the timing of dietary shifts, and 3) the use of turnover rates to estimate nutritional requirements and reconstruct histories of nutritional stress from tissue isotope signatures. As we discuss these topics, we highlight recent works that have effectively used estimates of turnover to design and execute informative ecological studies. Our concluding remarks suggest several steps that will improve our understanding of isotopic turnover and support its integration into a wider range of ecological studies.

Dynamics of Individual Fatty Acids in Muscle Fat Stores and Membranes of a Songbird and Its Functional and Ecological Importance

Although tissue fatty acid (FA) composition has been linked to whole-animal performance (e.g., aerobic endurance, metabolic rate, postexercise recovery) in a wide range of animal taxa, we do not adequately understand the pace of changes in FA composition and its implications for the ecology of animals. Therefore, we used a C₄ to C₃ diet shift experiment and compound-specific δ¹³C analysis to estimate the turnover rates of FAs in the polar and neutral fractions of flight muscle lipids (corresponding to membranes and lipid droplets) of exercised and sedentary zebra finches (Taeniopygia guttata). Turnover was fastest for linoleic acid (LA; 18:2n6) and palmitic acid (PA; 16:0), with 95% replacement times of 10.8-17.7 d in the polar fraction and 17.2-32.8 d in the neutral fraction, but was unexpectedly slow for the long-chain polyunsaturated FAs (LC-PUFAs) arachidonic acid (20:4n6) and docosahexaenoic acid (22:6n3) in the polar fraction, with 95% replacement in 64.9-136.5 d. Polar fraction LA and PA turnover was significantly faster in exercised birds (95% replacement in 8.5-13.3 d). Our results suggest that FA turnover in intramuscular lipid droplets is related to FA tissue concentrations and that turnover does not change in response to exercise. In contrast, we found that muscle membrane FA turnover is likely driven by a combination of selective LC-PUFA retention and consumption of shorter-chain FAs in energy metabolism. The unexpectedly fast turnover of membrane-associated FAs in muscle suggests that songbirds during migration could substantially remodel their membranes within a single migration stopover, and this may have substantial implications for how the FA composition of diet affects energy metabolism of birds during migration.

A long winter for the Red Queen: rethinking the evolution of seasonal migration

This paper advances an hypothesis that the primary adaptive driver of seasonal migration is maintenance of site fidelity to familiar breeding locations. We argue that seasonal migration is therefore principally an adaptation for geographic persistence when confronted with seasonality - analogous to hibernation, freeze tolerance, or other organismal adaptations to cyclically fluctuating environments. These ideas stand in contrast to traditional views that bird migration evolved as an adaptive dispersal strategy for exploiting new breeding areas and avoiding competitors. Our synthesis is supported by a large body of research on avian breeding biology that demonstrates the reproductive benefits of breeding-site fidelity. Conceptualizing migration as an adaptation for persistence places new emphasis on understanding the evolutionary trade-offs between migratory behaviour and other adaptations to fluctuating environments both within and across species. Seasonality-induced departures from breeding areas, coupled with the reproductive benefits of maintaining breeding-site fidelity, also provide a mechanism for explaining the evolution of migration that is agnostic to the geographic origin of migratory lineages (i.e. temperate or tropical). Thus, our framework reconciles much of the conflict in previous research on the historical biogeography of migratory species. Although migratory behaviour and geographic range change fluidly and rapidly in many populations, we argue that the loss of plasticity for migration via canalization is an overlooked aspect of the evolutionary dynamics of migration and helps explain the idiosyncratic distributions and migratory routes of long-distance migrants. Our synthesis, which revolves around the insight that migratory organisms travel long distances simply to stay in the same place, provides a necessary evolutionary context for understanding historical biogeographic patterns in migratory lineages as well as the ecological dynamics of migratory connectivity between breeding and non-breeding locations.