Ecology and Evolution最新文献

We record two new predation events and one new kleptoparasitic Andean Gull (Chroicocephalus serranus) behavior, interactions that directly link to the Titicaca Grebe (Rollandia microptera) and Titicaca Water Frog (Telmatobius culeus). Our reports expand the understanding of the gull's ecological niche and reveal previously overlooked interactions between it and two endemic and endangered Lake Titicaca species which act as indicators of Lake Titicaca's ecosystem health.

Environmental DNA (eDNA) analysis depends critically on high-quality reference databases. However, widely used public repositories (e.g., NCBI) frequently suffer from annotation error, species misidentification, and sequence contamination, leading to unreliable biodiversity assessments. To address these issues, we introduce PhyloRef, a Snakemake-based, semi-automated phylogeny-guided workflow for reference library curation. PhyloRef improves scalability via taxonomic grouping, detects problematic records using clustering-based anomaly detection rather than rigid monophyly requirements, and conservatively flags ambiguous cases using a "similar_to=" annotation. PhyloRef leverages complete mitochondrial genomes while flexibly incorporating single-gene sequences to maximize taxonomic coverage when complete genomes are scarce. The workflow categorizes anomalies into three types: (1) single-sequence outliers, (2) inconsistent sequence pairs, and (3) minority deviations within multi-sequence clusters, flagging them for manual review via convenient visualizations or deleting them automatically by option. Importantly, sequences with ambiguous phylogenetic placement are annotated with a "similar_to=" label to alert users to potential uncertainty. We validated PhyloRef using mitochondrial genome datasets for Chondrichthyes (cartilaginous fishes) and Actinopterygii (ray-finned fishes) extracted from NCBI. The tool identified and removed nine anomalous chondrichthyan sequences and 401 Actinopterygian sequences (~2.3% and ~5.2% of the initial datasets, respectively), yielding curated databases of 380 sequences (266 species) and 7258 sequences (4887 species), respectively. In addition, nine sequences were flagged with "similar_to=" label in chondrichthyan fishes and 597 in Actinopterygian fishes, to reduce the risk of misidentification in downstream eDNA analyses. This resource enhances the reliability of eDNA-based biodiversity and ecological studies. Future directions include integrating machine learning for anomaly detection, incorporating nuclear markers for improved taxonomic resolution, and developing automated updating modules.

In Europe, large carnivore populations have faced a history of persecution and habitat alteration, varying in magnitude across their distribution. Individual animals have developed diverse adaptations to these anthropogenic activities, in most cases to avoid them but in some cases to exploit novel resources in the human-modified environments they inhabit. Here, we used long-term GPS-telemetry data from 108 brown bears Ursus arctos collared across three European countries - Finland, Slovakia and Romania-to assess whether the behavioural movement patterns of brown bears are consistent across their range or vary regionally in response to local environmental and anthropogenic influences. We calculated speed, movement direction and daily displacement, and used mixed-effects models to analyse whether human infrastructure affected brown bear movement behaviour across the study areas. To examine whether the impact of these features varied by study area, and to capture contextual differences that may have affected the movement patterns of bears, we included interactions between environmental predictors and area in the regression models. Our results showed that Finnish bears exhibited consistently higher movement speeds and longer daily displacements than Slovak and Romanian bears, regardless of the proximity to roads, railways, or human settlements. In addition, in proximity to transport infrastructures, Finnish and Slovak bears increased speed, directionality and distance travelled whereas Romanian bears showed the opposite pattern. Conversely, near human settlements, Romanian bears showed higher speeds and less tortuous movements, whereas Finnish and Slovak bears reduced their speed and daily displacements. These contrasting responses suggest that bear movements in multi-use, human-modified landscapes are shaped by complex interactions between animal needs and local environmental conditions.

Pampus species play a significant role in offshore food webs and are regarded as representative economically important fish. Owing to variations in their geographical distribution, distinct differences in feeding habits exist among pomfret species. However, the presence of an esophageal sac in pomfrets complicates accurate identification of their dietary composition through conventional stomach content analysis. Consequently, research on the feeding ecology of pomfrets remains limited and imprecise. This study employed environmental DNA (eDNA) high-throughput sequencing technology to analyze the composition and relative abundance of gastric contents in three Pampus species (P. argenteus, P. punctatissimus, and P. cinereus) collected from Qingdao, Shandong Province and Wenchang, Hainan Province. Key findings include: (1) Analysis revealed 21, 7, and 2 fish species in the gastric contents of P. argenteus, P. punctatissimus, and P. cinereus respectively, with anchovy (Engraulis japonicus) demonstrating the highest relative abundance in the former two species, while Thryssa hamiltonii predominated in P. cinereus. (2) Crustacean communities comprised 49, 42, and 26 species across the respective species, constituting over 60% of total identified taxa and indicating their trophic importance. Acetes japonicus exhibited maximal relative abundance in P. argenteus and P. punctatissimus, whereas Acetes chinensis dominated in P. cinereus. (3) Cephalopod analysis identified 8 and 6 species in P. argenteus and P. punctatissimus respectively, with Loligo beka and Sepiola birostrata showing peak abundance in each species, while no cephalopod species were detected in P. cinereus. Comparative analysis with traditional dissection methods and stable carbon-nitrogen isotope techniques confirmed crustaceans as the most diverse dietary component across Pampus species. This investigation demonstrates the efficacy of eDNA metabarcoding for elucidating feeding ecology in Pampus spp., providing critical insights into their trophic interactions and ecological significance within marine food webs.

Spodoptera frugiperda (fall armyworm; FAW) is a major agricultural pest native to the Americas, with the first reported invasion of Africa in early 2016. Since then, FAW has spread rapidly across Africa and Asia before invading Australia (2020) and first being detected in Aotearoa New Zealand in February 2022. Here, we assessed the whole genomes of 34 novel FAW individuals along the invasion front (representing three new invasive populations from Cambodia, Australia, and New Zealand) with the largest publicly available global FAW genome dataset (n = 173), resulting in a dataset of 112 and 99 samples from the invasive and native range, respectively, to: (1) place the new invasive populations within the global invasion; (2) identify the potential geographic origin of the New Zealand invasion, including from a single or multiple incursion event; and (3) assess pre-existing insecticide resistance potential at the invasion front. We confirm that these new invasions conform to the broad population structure of the initial invasive populations identified in Benin (West Africa), all of which belong to the invasive corn strain, as defined through previous triosephosphate isomerase (TPI) analysis and associated isolation from specific host plants. While we could not confidently assign the source population of the New Zealand invasion, we find preliminary support for a multiple introduction hypothesis in our data, which could contribute to increased genetic diversity within the New Zealand population. Further sampling is therefore required to fully characterise the origins of the New Zealand invasion. In novel samples, we detected putative insecticide resistance alleles previously reported in other invasive populations. These resistant loci should be tracked over time to understand the mechanisms enabling the invasion success of FAW in the Asia-Pacific region. We emphasise that sharing of genomic resources between institutions and consortia is an essential first step in the control of this global invader.

Body size is the principal determinant of acoustic variation in anemonefish, reflecting both the mechanics of sound production and the size-based structure of their social hierarchies. In Amphiprion percula, the absence of a reported size-frequency relationship has led to the interpretation that small acoustic differences are rank-specific. We show that this outcome stems from analytical choices that obscure natural size variation, including pooling individuals across groups and removing size-rank covariance. Because behavioural categories correspond to distinct size classes, morphology must be explicitly accounted for.

Large terrestrial herbivores play crucial roles in shaping ecosystem structure and function through their foraging activities. Still, the dietary ecology of elusive tropical species remains poorly understood. We investigated the diet composition of lowland tapirs (Tapirus terrestris), the largest terrestrial herbivore in the Neotropics, using DNA metabarcoding of fecal samples from 31 latrines in Carlos Botelho State Park, Brazil. We characterized local plant communities through vegetation plots and analyzed five leaf economic spectrum (LES) traits from both consumed and surrounding vegetation to assess selective feeding patterns. Lowland tapirs consumed 61 plant species from 69 genera and 46 families, predominantly those from the Melastomataceae, Asteraceae, and Myrtaceae families. Beta-diversity analysis revealed high compositional turnover among latrines, with a high dissimilarity index, indicating that the samples being compared are distinct in species composition. The plant composition in tapir diets differed significantly from that of the surrounding vegetation, suggesting that this species forages on distinct plant species across its extensive home range rather than consuming locally abundant species. Finally, the functional trait analysis revealed no significant differences between the dietary species and the surrounding vegetation in LES traits. Tapirs consumed plants that spanned both "fast" (high specific leaf area and high nitrogen content) and "slow" (high leaf dry matter content and thick leaves) strategies, indicating a broad dietary tolerance rather than trait-based selectivity. This suggests that tapirs can adapt to diverse plant textures and nutritional profiles, browsing on leaves ranging from tough to softer and more digestible. Our findings demonstrate that lowland tapirs exhibit generalist feeding strategies, which promote high plant species turnover, potentially contributing to the maintenance of tropical forest diversity, as observed in the Atlantic forest. Given the critical threats facing this endangered megafauna, understanding their generalist diet is essential for developing effective conservation strategies.

Humans are changing habitat for wildlife in myriad ways and for populations to persist, they must adapt to this change. In parts of the world that experience snow and ice, road salts are often used to make driving safer in the winter. Runoff from these roads increases the salinity in nearby bodies of water, which has been shown to have detrimental physiological and ecological effects in freshwater ecosystems; however, the evolutionary consequences of salinization remain unclear. Tetrahymena are microbial eukaryotes that live in freshwater habitats and serve as an important link in the microbial food loop. In this study, we tested how T. thermophila can evolve in response to increasing concentrations of road salts in their environment. Using experimental evolution, we found that T. thermophila populations adapted to survive and grow in concentrations of up to 18 g/L of NaCl and 17 g/L MgCl₂, approximately twice the salinity tolerance of ancestral populations. However, populations adapted to the highest salt concentrations experience fitness trade-offs of reduced survival and growth rate and longer lag times when grown in salt-free environments. These results demonstrate the rapidity with which microbial populations can respond to anthropogenic changes to their environment, yet highlight the potential costs associated with this adaptation.

A detailed understanding of how protected species use their habitats can guide management interventions in areas of high human use. For marine turtles, different food availability and physical habitat characteristics can underpin turtle presence at anthropogenically modified compared to unmodified sites. We develop telemetry-based habitat models with boosted regression trees to identify the environmental characteristics underpinning foraging habitat suitability for green turtles in the Great Barrier Reef region. We fit models to green turtle Fastloc GPS tracks from both modified and unmodified inshore foraging sites and using pseudo-absences (simulated correlated random walks). We assess model performance by the ability to predict known foraging areas, true skill statistic, explanatory power (percent deviance explained) and predictive skill (AUC) of the models. We then predict potentially suitable foraging areas for green turtles in the Great Barrier Reef region using the model for unmodified habitats. Our model highlights shallow nearshore environments and midshelf reefs as important foraging areas for green turtles. These areas are likely affected by dynamic floods, development, and turbidity. In 2022, 46.6% of predicted suitable habitat fell within habitat protection zones, and 16.5% in Marine National Park Zones of the Great Barrier Reef Marine Park. A detailed foraging distribution of the species has not previously been compiled at this regional scale. Identifying biophysical drivers of habitat suitability can inform identification of possible foraging habitat in less data rich regions in Australia and overseas. Evaluating changes over time in habitat distribution provides insights into the degree to which broad-scale environmental changes and anthropogenic activities influence the condition and function of habitats, even within protected area boundaries.

Diet composition is a crucial yet understudied, dimension of animal ecology, with seasonal dietary shifts being a key factor in the population dynamics of large herbivores. However, characterizing these variations and their drivers in free-ranging animals has been challenging due to their high mobility and the diverse plant species in their diet. According to optimal foraging theory, animals select their diet to maximize energy intake, a decision process that involves evaluating the abundance and quality of potential food sources. We determined the seasonal dietary shifts and food network in high-altitude grazing yaks using DNA metabarcoding targeting the trnL region of fecal samples. Seasonal shifts in yak diet composition were structured by resource heterogeneity and influenced by plant community diversity and aboveground biomass. Dietary diversity and richness were greater in winter than summer, while plant community diversity and species richness exhibited opposite trends. This pattern indicated that yaks exhibited the strongest dietary selection during the summer with high resource abundance. Less selection in winter led to more diet dissimilarities, possibly reflecting a compensatory strategy to mitigate energetic deficits by broadening dietary niche breadth and maximizing resource availability under food limitation conditions. The proportion of forbs consumed by yaks was highest in both summer and winter, while the intake of sedges and grasses increased significantly in winter, suggesting that yaks selected high-protein forbs over grasses or sedges. Our results support the predictions from optimal foraging theory, demonstrating that the energetic basis of dietary selection governs niche width in seasonal environments. Consistent with predictions from optimal foraging theory, our study shows that the energetic drivers of diet selection determine niche breadth in seasonal environments.