Explore the vast range of titles available.

1. In a faunally intact lowland Amazonian rain forest stand, we conducted a long-term multi-species experiment aimed at determining the primary mechanistic basis of seedling establishment patterns. We deployed a total of 1050 experimental seedlings, representing 11 common tree species in mixed compositions and at fixed, highly elevated densities in shaded understorey sites, representing extremes of distance from large conspecific trees. We used mesh exclosures to isolate the effects of distinct classes of natural enemies, and monitored survival for up to 45 months. 2. Final seedling survival of all species pooled represented a 40% increase at sites located far from ('F' sites) versus close to ('N' sites) large conspecific trees, and median seedling lifetime was 75% longer. These differences between N and F sites were significant for all species pooled, and for five out of 11 (survivorship) and four out of nine (lifetime) individual species examined. Survival analysis based on multiple censuses revealed that a 'distance effect' persisted and intensified over time, with the onset of significant distance-related differential mortality differing amongst species. 3. The use of mesh exclosures (<2 mm mesh size) and a factorial experimental design revealed that host-specific organisms <2 mm in size and/or below-ground soil-borne organisms are more strongly distance-responsive and depress seedling establishment primarily in the vicinity of large conspecific adults whereas above-ground organisms >2 mm in size appear to have a negative impact on seedling establishment at all distances. 4. No evidence was found for the effect of intra-cohort resource competition on seedling establishment even though initial density of experimental seedlings at all sites was elevated to c. 25 times the mean natural density of the mixed-species seedling layer in this forest. 5. Synthesis. Our study provides strong, multi-species support for the influence of host-specific distance-responsive natural enemies on seedling establishment, and suggests that negative density-dependent patterns of tree recruitment in tropical rain forests are at least partly produced at early life stages as an outcome of processes described by the classic Janzen-Connell model.

The southwestern Amazon is a biodiversity hotspot home to some of the oldest permanent forest dynamics plots in the basin. Despite the region's abundance of plots, we still know relatively little about how tree diversity and composition change across the region's precipitation gradient, between habitat types, and how disturbed and managed forests compare to protected, old‐growth forests since the majority of forest plots are located in protected forests. In this study, we first described a new 1‐ha permanent forest dynamics plot at the confluence of agricultural land and managed Brazil nut forest. We then compared the plot to others in the region to evaluate the relationship between precipitation and plot diversity, compositional differences between floodplain and terra firme forest, and differences in forest dynamics between our disturbed forest plot and old‐growth forest plots. Contrary to large‐scale patterns in tree diversity, we found no relationship between precipitation and tree alpha diversity for plots in the southwestern Amazon. There were, however, clear compositional differences between floodplain and terra firme forests. Annual change in the aboveground biomass of the new plot was higher than in other plots in the region. Similarly, annual rates of mortality and recruitment were lower and higher, respectively, in the new plot compared to the other plots. The floristic and structural similarities between plots in disturbed or managed forests and plots in old‐growth forests indicate a high resilience of tropical forests to low‐intensity disturbances. Our findings thus provide evidence that low‐intensity logging and low‐impact Brazil nut harvesting in the southwest Amazon do not significantly alter forest structure and composition in the medium to long term. Our new plot bolsters the representation of disturbed and managed forests in plot databases and will be an important resource for future studies of large‐scale patterns of forest diversity, structure, and dynamics. Southwestern Amazon forests are highly diverse, but information on how tree diversity and composition changes between habitat and forest types remains scarce. We conducted floristic analyses to investigate these changes across a precipitation gradient, between habitat types, and between disturbed and old‐growth forest.

To assess how the decimation of large vertebrates by hunting alters recruitment processes in a tropical forest, we compared the sapling cohorts of two structurally and compositionally similar forests in the Rio Manu floodplain in southeastern Peru. Large vertebrates were severely depleted at one site, Boca Manu (BM), whereas the other, Cocha Cashu Biological Station (CC), supported an intact fauna. At both sites we sampled small (≥1 m tall, <1 cm dbh) and large (≥1 cm and <10 cm dbh) saplings in the central portion of 4-ha plots within which all trees ≥10 cm dbh were mapped and identified. This design ensured that all conspecific adults within at least 50 m (BM) or 55 m (CC) of any sapling would have known locations. We used the Janzen-Connell model to make five predictions about the sapling cohorts at BM with respect to CC: (1) reduced overall sapling recruitment, (2) increased recruitment of species dispersed by abiotic means, (3) altered relative abundances of species, (4) prominence of large-seeded species among those showing depressed recruitment, and (5) little or no tendency for saplings to cluster closer to adults at BM. Our results affirmed each of these predictions. Interpreted at face value, the evidence suggests that few species are demographically stable at BM and that up to 28% are increasing and 72% decreasing. Loss of dispersal function allows species dispersed abiotically and by small birds and mammals to substitute for those dispersed by large birds and mammals. Although we regard these conclusions as preliminary, over the long run, the observed type of directional change in tree composition is likely to result in biodiversity loss and negative feedbacks on both the animal and plant communities. Our results suggest that the best, and perhaps only, way to prevent compositional change and probable loss of diversity in tropical tree communities is to prohibit hunting.

Phenology has long been hypothesized as an avenue for niche partitioning or interspecific facilitation, both promoting species coexistence. Tropical plant communities exhibit striking diversity in reproductive phenology, but many are also noted for large synchronous reproductive events. Here we study whether the phenology of seed fall in such communities is nonrandom, the temporal scales of phenological patterns, and ecological factors that drive reproductive phenology. We applied multivariate wavelet analysis to test for phenological synchrony versus compensatory dynamics (i.e., antisynchronous patterns where one species' decline is compensated by the rise of another) among species and across temporal scales. We used data from long‐term seed rain monitoring of hyperdiverse plant communities in the western Amazon. We found significant synchronous whole‐community phenology at multiple timescales, consistent with shared environmental responses or positive interactions among species. We also observed both compensatory and synchronous phenology within groups of species (confamilials) likely to share traits and seed dispersal mechanisms. Wind‐dispersed species exhibited significant synchrony at ~6‐month scales, suggesting these species might share phenological niches to match the seasonality of wind. Our results suggest that community phenology is shaped by shared environmental responses but that the diversity of tropical plant phenology may partly result from temporal niche partitioning. The scale‐specificity and time‐localized nature of community phenology patterns highlights the importance of multiple and shifting drivers of phenology.

Phenology has long been hypothesized as an avenue for niche partitioning or interspecific facilitation, both promoting species coexistence. Tropical plant communities exhibit striking diversity in reproductive phenology, but many are also noted for large synchronous reproductive events. Here we study whether the phenology of seed fall in such communities is nonrandom, the temporal scales of phenological patterns, and ecological factors that drive reproductive phenology. We applied multivariate wavelet analysis to test for phenological synchrony versus compensatory dynamics (i.e., antisynchronous patterns where one species’ decline is compensated by the rise of another) among species and across temporal scales. We used data from long-term seed rain monitoring of hyperdiverse plant communities in the western Amazon. We found significant synchronous whole-community phenology at multiple timescales, consistent with shared environmental responses or positive interactions among species. We also observed both compensatory and synchronous phenology within groups of species (confamilials) likely to share traits and seed dispersal mechanisms. Wind-dispersed species exhibited significant synchrony at ∼6-month scales, suggesting these species might share phenological niches to match the seasonality of wind. Our results suggest that community phenology is shaped by shared environmental responses but that the diversity of tropical plant phenology may partly result from temporal niche partitioning. The scale-specificity and time-localized nature of community phenology patterns highlights the importance of multiple and shifting drivers of phenology.

1. Declines of large vertebrates in tropical forests may reduce dispersal of tree species that rely on them, and the resulting undispersed seedlings might suffer increased distance- and density-dependent mortality. Consequently, extirpation of large vertebrates may alter the composition and spatial structure of plant communities and impair ecosystem functions like carbon storage. 2. We analysed spatial patterns of tree recruitment within six forest plots along a defaunation gradient in western Amazonia. We divided recruits into two size cohorts (\"saplings\": ≤1 m tall and <1 cm diameter at breast height [dbh], and juveniles, 1-2 cm dbh) and examined the spatial organisation of conspecific recruits within each cohort (within-cohort) and around conspecific reproductive-sized trees (between-cohort). We used replicated spatial point pattern analysis to quantify relationships between recruit clustering and cohort, defaunation intensity, each tree species reliance on hunted dispersers and the interactions among these three covariates. 3. Within-cohort clustering of conspecific saplings increased with reliance of tree species on hunted dispersers, and this trend strengthened significantly as defaunation increased, probably because of reduced dispersal. 4. Within-cohort clustering of conspecifics declined from saplings to juveniles, suggesting density-dependent mortality of saplings. However, the positive relationship between sapling clustering and defaunation did not lead to greater reductions in within-cohort clustering during the sapling-juvenile transition, suggesting that higher conspecific densities did not translate into increased mortality. Instead, the increased spatial clustering associated with defaunation was retained for juvenile recruits. 5. Between-cohort clustering was unrelated to defaunation and did not change during the sapling–juvenile transition. 6. Synthesis. Defaunation increased spatial aggregation of saplings of tree species reliant on hunted dispersers. The increase in sapling clustering did not increase density-dependent thinning, and persisted into older recruit cohorts, suggesting that hunting may initiate long-term spatial reorganisation of Amazonian tree communities. The lack of increased density-dependent thinning indicates that reduced dispersal did not increase mortality of large-vertebrate dispersed tree species that contribute disproportionately to forest biomass. We, therefore, caution against the fait accompli acceptance of the prediction by recent modelling studies that overhunting will precipitate a collapse in carbon sequestration by tropical forests.

Liverworts and mosses are a major component of the epiphyte flora of tropical montane forest ecosystems. Canopy access was used to analyse the distribution and vertical stratification of bryophyte epiphytes within tree crowns at nine forest sites across a 3400 m elevational gradient in Peru, from the Amazonian basin to the high Andes. The stable isotope compositions of bryophyte organic material (13C/12C and 18O/16O) are associated with surface water diffusive limitations and, along with C/N content, provide a generic index for the extent of cloud immersion. From lowland to cloud forest δ13C increased from −33‰ to −27‰, while δ18O increased from 16.3‰ to 18.0‰. Epiphytic bryophyte and associated canopy soil biomass in the cloud immersion zone was estimated at up to 45 t dry mass ha−1, and overall water holding capacity was equivalent to a 20 mm precipitation event. The study emphasizes the importance of diverse bryophyte communities in sequestering carbon in threatened habitats, with stable isotope analysis allowing future elevational shifts in the cloud base associated with changes in climate to be tracked.

The keystone plant resources (KPR) concept describes certain plant species in tropical forests as vital to community stability and diversity because they provide food resources to vertebrate consumers during the season of scarcity. Here, we use an 8-y, continuous record of fruit fall from a 1.44-ha mature forest stand to identify potential KPRs in a lowland western Amazonian rain forest. KPRs were identified based on four criteria: temporal non-redundancy; year-to-year reliability; abundance of reproductive-size individuals and inferred fruit crop size; and the variety of vertebrate consumers utilizing their fruit. Overall, seven species were considered excellent KPRs: two of these belong to the genus Ficus, confirming that this taxon is a KPR as previously suggested. Celtis iguanaea (Cannabaceae) – a canopy liana – has also been previously classified as a KPR; in addition, Pseudomalmea diclina (Annonaceae), Cissus ulmifolia (Vitaceae), Allophylus glabratus (Sapindaceae) and Trichilia elegans (Meliaceae) are newly identified KPRs. Our results confirm that a very small fraction (<5%) of the plant community consistently provides fruit for a broad set of consumers during the period of resource scarcity, which has significant implications for the conservation and management of Amazonian forests.

Liverworts and mosses are amajor component of the epiphyte flora of tropical montane forest ecosystems. Canopy access was used to analyse the distribution and vertical stratification of bryophyte epiphytes within tree crowns at nine forest sites across a 3400 m elevational gradient in Peru, from the Amazonian basin to the high Andes. The stable isotope compositions of bryophyte organic material (13C/12C and 18O/16O) are associated with surface water diffusive limitations and, along with C/N content, provide a generic index for the extent of cloud immersion. From lowland to cloud forest δ 13C increased from −33‰to −27‰, while δ 18O increased from 16.3‰ to 18.0‰. Epiphytic bryophyte and associated canopy soil biomass in the cloud immersion zone was estimated at up to 45 t dry mass ha−1, and overall water holding capacity was equivalent to a 20 mm precipitation event. The study emphasizes the importance of diverse bryophyte communities in sequestering carbon in threatened habitats, with stable isotope analysis allowing future elevational shifts in the cloud base associated with changes in climate to be tracked.

Species extinctions in the tropics are accelerating, outpacing documentation efforts. Meanwhile, DNA barcoding is flourishing in the Global North, backed by extensive infrastructure, allowing non-taxonomic experts to identify species from nonlethal, minimally invasive, and environmental samples. However, hyper-diverse regions like Peru make up only 0.52% (n = 93,246) of the Barcode of Life Database (BOLD). To address this, we established three decentralized laboratories with low-cost, portable nanopore sequencers. From 2018–2023, we generated 1,858 barcodes in situ using six genetic markers for 1,097 vertebrates and 76 plants from existing and new biobanks. We present the first genetic barcodes for 30 mammal and 196 bird species from Peruvian specimens, increasing the number of Peruvian mammal and bird species in BOLD by 110% and 36.5% respectively. We also report the first records of the marsupial Marmosops ocellatus and the bat Sturnira lilium for Peru. This dataset represents an effort to go from fresh or museum-preserved samples to barcodes entirely in situ , avoiding the export of samples outside the country, and facilitating local capacity in molecular biodiversity research.