Philip Manlick

Exploring the causes of species extirpation can provide insights into mitigating the ongoing extinction. The Japanese otter Lutra lutra whiteleyi had extincted around 1970s, but their extinction causes remain unknown. To elucidate the ecological relationship among their foraging ecology, habitat degradation, and the extinction, we assessed dependency of Japanese otters on marine- or freshwater-derived resources using sulfur stable isotopes ( δ ³⁴ S: ³⁴ S/ ³² S) of the museum specimens which were collected on the brink of extinction. Our results clearly showed that the otters strongly depended on marine-derived resources, indicating anthropogenic activities led to depletion of freshwater prey and a potential extinction factor of the last population of otters in Japan. Protecting freshwater habitats was crucial for preventing otter extinction in Japan, and for safeguarding the extant otter species.

Legacies of land use can persist for decades, thereby impacting populations, communities, and ecosystems long after the original disturbance has concluded. The coastal rainforests of western North America were fundamentally transformed by commercial logging throughout the 20th century, resulting in depauperate second‐growth forests that provide limited understory production and foraging habitat for herbivores. The Tongass National Forest in Alaska, USA, is the largest contiguous tract of coastal temperate rainforest in the world, but nearly 200,000 ha of second‐growth forest have created a need to restore understory plant communities and foraging habitat for ungulates like Sitka black‐tailed deer ( Odocoileus hemionus sitkensis ), a regional indicator of forest health and key subsistence resource for local and Indigenous communities. We leveraged a 16‐year adaptive management experiment—the Tongass‐Wide Young Growth Studies (TWYGS) program—to test the effects of precommercial thinning on forage availability and use by deer in second‐growth forests. We measured plant communities, presence–absence of browse, and slash debris in 14,908 quadrats across 730 plots and found that plant community composition, understory forage biomass, digestible energy, and digestible protein were all significantly higher in thinned plots versus controls. Precommercial thinning also doubled browse probabilities relative to unthinned stands, and plots treated within 35 years of stand initiation experienced the highest gains. Deer selected for both plant quantity and plant quality, as browse was positively associated with both digestible energy and digestible protein. Conversely, slash debris generated by precommercial thinning reduced browse probability by an average of 11.3%, but these effects attenuated as slash decomposed over the course of the study. We found no effects of landscape composition on relative browse probability, indicating that fine‐scale resource quality and accessibility were the strongest drivers of habitat use by deer over nearly two decades of sampling. Collectively, our results show that precommercial thinning is a valuable management tool that increases forage and deer habitat use in second‐growth coastal rainforests. This study highlights the enduring legacies of forest disturbance and underscores the value of adaptive management experiments with long‐term monitoring to optimize habitat management for wildlife.

The repatriation of species is common, especially in conservation efforts aimed at restoring trophic interactions. Whether the Eltonian niches of restored species are conserved in reassembled ecological communities is largely unknown. Within mammalian carnivores, we hypothesized that the Eltonian niches of sympatric competitors would be structured by trophic facilitation from subsidies provided by large carnivores (i.e. carrion) and humans (i.e. food subsidies). Using stable isotopes (δ¹³C, δ¹⁵N), we quantified the Eltonian niches of an apex predator, the grey wolf Canis lupus and two subordinate guild members, coyotes Canis latrans and red foxes Vulpes vulpes, from Michigan, USA across three periods that differed in community composition: a ‘historical' carnivore community (1910–1930), a ‘reduced' community which lacked wolves (1950–1970), and a ‘reassembled' carnivore community featuring wolves as well as human food subsidies (2000–2020). In historical and reassembled communities, wolves constrained the niche space of coyotes via resource facilitation, regardless of human presence, such that the consumption of deer by coyotes increased by an average of 1.4–1.8‐fold in the presence of wolves. Without wolves, coyotes exhibited an isotopic (dietary) niche breadth ~ 2–5× greater (3.33 ± 0.74‰²) than in the historical (0.64 ± 0.11‰²) and reassembled (1.66 ± 0.63‰²) communities. Conversely, we found that the niche breadth of foxes was conserved across the historical (1.91 ± 0.41‰²) and reduced (1.98 ± 0.75‰²) communities but increased ~ 4‐fold in the presence of human resource subsidies (7.52 ± 1.95‰²). Notably, we found that trophic facilitation by wolves and resource subsidies from humans altered the foraging strategies of individuals, resulting in disparate foraging strategies for foxes in the reassembled community. Our results highlight that Eltonian niche conservatism in carnivore communities is driven by resource subsidies, both from the provisioning of carrion by large carnivores to meso‐carnivores and from human foods subsidizing small carnivores. More broadly, our work suggests that large carnivore repatriation can restore some species interactions, while human resource subsidies can decouple others.

Intraspecific diet variation is widespread, but the causes and consequences of individual foraging strategies are unclear. Interactions between competition and resources dictate foraging strategies, but classical paradigms like optimal foraging and niche theory offer contrasting predictions for individual consumers. Further, both paradigms assume that individual foraging strategies optimize fitness, yet this prediction is rarely tested. We used over 3,500 stable isotope measurements and six years of capture-mark-recapture data to quantify the relationship between environmental variation, individual foraging, and consumer fitness in four desert rodent species. Consistent with niche theory, we found that individuals contracted their dietary niches and increased specialisation in response to both intraspecific and interspecific competition, but the effect was mediated by resource abundance. However, individual specialists obtained no apparent fitness benefit from dietary niche contractions and exhibited lower survival than generalists. These results suggest diet-mediated fitness consequences can regulate population and community dynamics in stochastic resource environments.

Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope analysis, we estimated the proportional contributions of essential amino acids (AA_ESS) synthesized by gut microbes to five co‐occurring desert rodents representing herbivorous, omnivorous and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (Dipodomys spp.) routed a substantial proportion (~40%–50%) of their AA_ESS from gut microbes, while higher trophic level omnivores (Peromyscus spp.) and insectivores (Onychomys arenicola) obtained most of their AA_ESS (~58%) from plant‐based energy channels but still received ~20% of their AA_ESS from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals.

Food web ecology has revolutionized our understanding of ecological processes, but the drivers of food web properties like trophic position (TP) and food chain length are notoriously enigmatic. In terrestrial ecosystems, above‐ and belowground systems were historically compartmentalized into “green” and “brown” food webs, but the coupling of these systems by animal consumers is increasingly recognized, with potential consequences for trophic structure. We used stable isotope analysis (δ¹³C, δ¹⁵N) of individual amino acids to trace the flow of essential biomolecules and jointly measure multichannel feeding, food web coupling, and TP in a guild of small mammals. We then tested the hypothesis that brown energy fluxes to aboveground consumers increase terrestrial food chain length via cryptic trophic transfers during microbial decomposition. We found that the average small mammal consumer acquired nearly 70% of their essential amino acids (69.0% ± 7.6%) from brown food webs, leading to significant increases in TP across species and functional groups. Fungi were the primary conduit of brown energy to aboveground consumers, providing nearly half the amino acid budget for small mammals on average (44.3% ± 12.0%). These findings illustrate the tightly coupled nature of green and brown food webs and show that microbially mediated energy flow ultimately regulates food web structure in aboveground consumers. Consequently, we propose that the integration of green and brown energy channels is a cryptic driver of food chain length in terrestrial ecosystems.