Changes in the diet and body size of a small herbivorous mammal (hispid cotton rat, \u3ci\u3eSigmodon hispidus\u3c/i\u3e) following the late Pleistocene megafauna extinction

The catastrophic loss of large-bodied mammals during the terminal Pleistocene likely led to cascading effects within communities. While the extinction of the top consumers probably expanded the resources available to survivors of all body sizes, little work has focused on the responses of the smallest mammals. Here, we use a detailed fossil record from the southwestern United States to examine the response of the hispid cotton rat Sigmodon hispidus to biodiversity loss and climatic change over the late Quaternary. In particular, we focus on changes in diet and body size. We characterize diet through carbon (δ13C) and nitrogen (δ15N) isotope analysis of bone collagen in fossil jaws and body size through measurement of fossil teeth; the abundance of material allows us to examine population level responses at millennial scale for the past 16 ka. Sigmodon was not present at the cave during the full glacial, first appearing at ~16 ka after ice sheets were in retreat. It remained relatively rare until ~12 ka when warming tempera­tures allowed it to expand its species range northward. We find variation in both diet and body size of Sigmodon hispidus over time: the average body size of the population varied by ~20% (90–110 g) and mean δ13C and δ15N values ranged between −13.5 to −16.5‰ and 5.5 to 7.4‰ respectively. A state–space model suggested changes in mass were influenced by diet, maximum temperature and community structure, while the modest changes in diet were most influenced by community structure. Sigmodon maintained a fairly similar dietary niche over time despite contemporaneous changes in climate and herbivore community composition that followed the megafauna extinc­tion. Broadly, our results suggest that small mammals may be as sensitive to shifts in local biotic interactions within their ecosystem as they are to changes in climate and large-scale biodiversity loss

Meta-analysis of primary producer amino acid δ\u3csup\u3e15\u3c/sup\u3eN values and their influence on trophic position estimation

Compound-specific stable isotope analysis of individual amino acids (CSIA-AA) has emerged as a transformative approach to estimate consumer trophic positions (TPCSIA) that are internally indexed to primary producer nitrogen isotope baselines. Central to accurate TPCSIA estimation is an understanding of beta (β) values—the differences between trophic and source AA δ15N values in the primary producers at the base of a consumers’ food web. Growing evidence suggests higher taxonomic and tissue-specific β value variability than typically appreciated. This meta-analysis fulfills a pressing need to comprehensively evaluate relevant sources of β value variability and its contribution to TPCSIA uncertainty. We first synthesized all published primary producer AA δ15N data to investigate ecologically relevant sources of variability (e.g., taxonomy, tissue type, habitat type, mode of photosynthesis). We then reviewed the biogeochemical mechanisms underpinning AA δ15N and β value variability. Lastly, we evaluated the sensitivity of TPCSIA estimates to uncertainty in mean βGlx-Phe values and Glx-Phe trophic discrimination factors (TDFGlx-Phe). We show that variation in βGlx-Phe values is two times greater than previously considered, with degree of vascularization, not habitat type (terrestrial vs. aquatic), providing the greatest source of variability (vascular autotroph = –6.6 ± 3.4‰; non-vascular autotroph = +3.3 ± 1.8‰). Within vascular plants, tissue type secondarily contributed to βGlx-Phe value variability, but we found no clear distinction among C3, C4, and CAM plant βGlx-Phe values. Notably, we found that vascular plant βGlx-Lysvalues (+2.5 ± 1.6‰) are considerably less variable than βGlx-Phe values, making Lys a useful AA tracer of primary production sources in terrestrial systems. Our multi-trophic level sensitivity analyses demonstrate that TPCSIA estimates are highly sensitive to changes in both βGlx-Phe and TDFGlx-Phe values but that the relative influence of β values dissipates at higher trophic levels. Our results highlight that primary producer β values are integral to accurate trophic position estimation. We outline four key recommendations for identifying, constraining, and accounting for β value variability to improve TPCSIA estimation accuracy and precision moving forward. We must ultimately expand libraries of primary producer AA δ15N values to better understand mechanistic drivers of β value variation

Isotopic and genetic methods reveal the role of the gut microbiome in mammalian host essential amino acid metabolism.

Intestinal microbiota perform many functions for their host, but among the most important is their role in metabolism, especially the conversion of recalcitrant biomass that the host is unable to digest into bioavailable compounds. Most studies have focused on the assistance gut microbiota provide in the metabolism of carbohydrates, however, their role in host amino acid metabolism is poorly understood. We conducted an experiment on Mus musculus using 16S rRNA gene sequencing and carbon isotope analysis of essential amino acids (AAESS) to quantify the community composition of gut microbiota and the contribution of carbohydrate carbon used by the gut microbiome to synthesize AAESS that are assimilated by mice to build skeletal muscle tissue. The relative abundances of Firmicutes and Bacteroidetes inversely varied as a function of dietary macromolecular content, with Firmicutes dominating when mice were fed low-protein diets that contained the highest proportions of simple carbohydrates (sucrose). Mixing models estimated that the microbial contribution of AAESS to mouse muscle varied from less than 5% (threonine, lysine, and phenylalanine) to approximately 60% (valine) across diet treatments, with the Firmicute-dominated microbiome associated with the greatest contribution. Our results show that intestinal microbes can provide a significant source of the AAESS their host uses to synthesize structural tissues. The role that gut microbiota play in the amino acid metabolism of animals that consume protein-deficient diets is likely a significant but under-recognized aspect of foraging ecology and physiology

Dietary Protein Content and Digestibility Influences Discrimination of Amino Acid Nitrogen Isotope Values in a Terrestrial Omnivorous Mammal

RATIONALE: Ecologists increasingly determine the δ15N values of amino acids (AA) in animal tissue; source AA typically exhibit minor variation between diet and consumer, while trophic AA have increased δ15N values in consumers. Thus, trophic-source δ15N offsets (i.e., Δ15NT-S) reflect trophic position in a food web. However, even minor variation in δ15Nsource AA values may influence the magnitude of offset that represents a trophic step, known as the trophic discrimination factor (i.e., TDFT-S). Diet digestibility and protein content can influence the δ15N values of bulk animal tissue, but the effects on AA Δ15NT-S and TDFT-S in mammals are unknown. METHODS: We fed captive mice (Mus musculus) either (A) a low-fat, high-fiber diet with low, intermediate, or high protein; or (B) a high-fat, low-fiber diet with low or intermediate protein. Mouse muscle and dietary protein were analyzed for bulk tissue δ15N using elemental analyzer-isotope ratio mass spectrometry (EA-IRMS), and were also hydrolyzed into free AA that were analyzed for δ15N using EA-IRMS. RESULTS: As dietary protein increased, Δ15NConsumer-Diet slightly declined for bulk muscle tissue in both experiments, increased for AA in the low-fat, high-fiber diet (A), and remained the same or decreased for AA in the high-fat, low-fiber diet (B). The effects of dietary protein on Δ15 NT-S and on TDFT-S varied by AA but were consistent between variables. CONCLUSIONS: Diets were less digestible and included more protein in Experiment A than in Experiment B. As a result, the mice in Experiment A probably oxidized more AA, resulting in greater Δ15 NConsumer-Diet values. However, the similar responses of Δ15 NT-S and of TDFT-S to diet variation suggest that if diet samples are available, Δ15 NT-S accurately tracks trophic position. If diet samples are not available, the patterns presented here provide a basis to interpret Δ15 NT-S values The trophic-source offset of Pro-Lys did not vary across diets, and therefore may be more reliable for omnivores than other offsets (e.g., Glu-Phe)

The sensitivity of Neotoma to climate change and biodiversity loss over the late Quaternary

The late Quaternary in North America was marked by highly variable climate and considerable biodiversity loss including a megafaunal extinction event at the terminal Pleistocene. Here, we focus on changes in body size and diet in Neotoma (woodrats) in response to these ecological perturbations using the fossil record from the Edwards Plateau (Texas) across the past 20,000 years. Body mass was estimated using measurements of fossil teeth and diet was quantified using stable isotope analysis of carbon and nitrogen from fossil bone collagen. Prior to ca. 7,000 cal yr BP, maximum mass was positively correlated to precipitation and negatively correlated to temperature. Independently, mass was negatively correlated to community composition, becoming more similar to modern over time. Neotoma diet in the Pleistocene was primarily sourced from C3 plants, but became progressively more reliant on C4 (and potentially CAM) plants through the Holocene. Decreasing population mass and higher C4/CAM consumption was associated with a transition from a mesic to xeric landscape. Our results suggest that Neotoma responded to climatic variability during the terminal Pleistocene through changes in body size, while changes in resource availability during the Holocene likely led to shifts in the relative abundance of different Neotoma species in the community

Reductions in the dietary niche of southern sea otters (Enhydra lutris nereis) from the Holocene to the Anthropocene.

The sea otter (Enhydra lutris) is a marine mammal hunted to near extinction during the 1800s. Despite their well-known modern importance as a keystone species, we know little about historical sea otter ecology. Here, we characterize the ecological niche of ancient southern sea otters (E. lutris nereis) using δ13C analysis and δ15N analysis of bones recovered from archaeological sites spanning ~7,000 to 350 years before present (N = 112 individuals) at five regions along the coast of California. These data are compared with previously published data on modern animals (N = 165) and potential modern prey items. In addition, we analyze the δ15N of individual amino acids for 23 individuals to test for differences in sea otter trophic ecology through time. After correcting for tissue-specific and temporal isotopic effects, we employ nonparametric statistics and Bayesian niche models to quantify differences among ancient and modern animals. We find ancient otters occupied a larger isotopic niche than nearly all modern localities; likely reflecting broader habitat and prey use in prefur trade populations. In addition, ancient sea otters at the most southerly sites occupied an isotopic niche that was more than twice as large as ancient otters from northerly regions. This likely reflects greater invertebrate prey diversity in southern California relative to northern California. Thus, we suggest the potential dietary niche of sea otters in southern California could be larger than in central and northern California. At two sites, Año Nuevo and Monterey Bay, ancient otters had significantly higher δ15N values than modern populations. Amino acid δ15N data indicated this resulted from shifting baseline isotope values, rather than a change in sea otter trophic ecology. Our results help in better understanding the contemporary ecological role of sea otters and exemplify the strength of combing zooarchaeological and biological information to provide baseline data for conservation efforts

Amino acid isotope discrimination factors for a carnivore: physiological insights from leopard sharks and their diet

Stable isotopes are important ecological tools, because the carbon and nitrogen isotopic composition of consumer tissue reflects the diet. Measurements of isotopes of individual amino acids can disentangle the effects of consumer physiology from spatiotemporal variation in dietary isotopic values. However, this approach requires knowledge of assimilation patterns of dietary amino acids. We reared leopard sharks (Triakis semifasciata) on diets of squid (Loligo opalescens; 1250 days; control sharks) or squid then tilapia (Oreochromis sp.; switched at 565 days; experimental sharks) to evaluate consumer-diet discrimination factors for amino acids in muscle tissue. We found that control sharks exhibited lower nitrogen isotope discrimination factors (∆15N) than most previous consumer studies, potentially because of urea recycling. Control sharks also had large carbon isotope discrimination factors (∆13C) for three essential amino acids, suggesting microbial contributions or fractionation upon assimilation. Compared to controls, experimental sharks exhibited higher ∆13C values for four amino acids and ∆15N values for seven amino acids, corresponding with differences between diets in δ13C and δ15N values. This suggests that not all amino acids in experimental sharks had reached steady state, contrary to the conclusion of a bulk isotope study of these sharks. Our results imply that (1) the magnitude of a shift in dietary δ13C and δ15N values temporarily influences the appearance of discrimination factors; (2) slow turnover of amino acid isotopes in elasmobranch muscle precludes inferences about seasonal dietary changes; (3) elasmobranch discrimination factors for amino acids may be affected by urea recycling and microbial contributions of amino acids

Can The Carbon and Nitrogen Isotope Values of Offspring be Used as a Proxy for Their Mother\u27s Diet? Using Foetal Physiology to Interpret Bulk Tissue and Amino Acid \u3ci\u3eδ\u3c/i\u3e\u3csup\u3e15\u3c/sup\u3eN Values

The measurement of bulk tissue nitrogen (δ15N) and carbon isotope values (δ13C) chronologically along biologically inert tissues sampled from offspring can provide a longitudinal record of their mothers\u27 foraging habits. This study tested the important assumption that mother-offspring stable isotope values are positively and linearly correlated. In addition, any change in the mother-offspring bulk tissues and individual amino acids that occurred during gestation was investigated. Whiskers sampled from southern elephant seal pups (Mirounga leonina) and temporally overlapping whiskers from their mothers were analyzed. This included n = 1895 chronologically subsampled whisker segments for bulk tissue δ15N and δ13C in total and n = 20 whisker segments for amino acid δ15N values, sampled from recently weaned pups (n = 17), juvenile southern elephant seals (SES) \u3c 2 years old (n = 23) and adult female SES (n = 17), which included nine mother-offspring pairs. In contrast to previous studies, the mother-offspring pairs were not in isotopic equilibrium or linearly correlated during gestation: the Δ15N and Δ13C mother-offspring offsets increased by 0.8 and 1.2‰, respectively, during gestation. The foetal bulk δ15N values were 1.7 ± 0.5‰ (0.9-2.7‰) higher than mothers\u27 δ15N values before birth, while the foetal δ13C increased by ~1.7‰ during gestation and were 1.0 ± 0.5‰ (0.0-1.9‰) higher than their mothers\u27 δ13C at the end of pregnancy. The mother-offspring serine and glycine Δ15N differed by ~4.3‰, while the foetal alanine δ15N values were 1.4‰ lower than that of their mothers during the third trimester of pregnancy. The observed mother-offspring δ15N differences are likely explained by shuttling of glutamate-glutamine and glycine-serine amongst skeletal muscle, liver, placenta and foetal tissue. Foetal development relies primarily on remobilized endogenous maternal proteinaceous sources. Researchers should consider foetal physiology when using offspring bulk tissue isotope values as biomarkers for the mother\u27s isotopic composition as part of monitoring programmes