Abstract. 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.

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (−9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth’s climate.

In 1980 the State of Connecticut began a tidal marsh restoration program targeting systems degraded by tidal restrictions and impoundments. Such marshes become dominated by common reed grass ( Phragmites australis ) and cattail ( Typha angustifolia and T. latifolia ), with little ecological connection to Long Island Sound. The management and scientific hypothesis was that returning tidal action, reconnecting marshes to Long Island Sound, would set these systems on a recovery trajectory. Specific restoration targets (i.e., predisturbance conditions or particular reference marshes) were considered unrealistic. However, it was expected that with time restored tides would return ecological functions and attributes characteristic of fully functioning tidal salt marshes. Here we report results of this program at nine separate sites within six marsh systems along 110 km of Long Island Sound shoreline, with restoration times of 5 to 21 years. Biotic parameters assessed include vegetation, macroinvertebrates, and use by fish and birds. Abiotic factors studied were soil salinity, elevation and tidal flooding, and soil water table depth. Sites fell into two categories of vegetation recovery: slow, ca. 0.5%, or fast, more than 5% of total area per year. Although total cover and frequency of salt marsh angiosperms was positively related to soil salinity, and reed grass stand parameters negatively so, fast versus slow recovery rates could not be attributed to salinity. Instead, rates appear to reflect differences in tidal flooding. Rapid recovery was characterized by lower elevations, greater hydroperiods, and higher soil water tables. Recovery of other biotic attributes and functions does not necessarily parallel those for vegetation. At the longest studied system (rapid vegetation recovery) the high marsh snail Melampus bidentatus took two decades to reach densities comparable with a nearby reference marsh, whereas the amphipod Orchestia grillus was well established on a slow-recovery marsh, reed grass dominated after 9 years. Typical fish species assemblages were found in restoration site creeks and ditches within 5 years. Gut contents of fish in ditches and on the high marsh suggest that use of restored marsh as foraging areas may require up to 15 years to reach equivalence with reference sites. Bird species that specialize in salt marshes require appropriate vegetation; on the oldest restoration site, breeding populations comparable with reference marshland had become established after 15 years. Use of restoration sites by birds considered marsh generalists was initially high and was still nearly twice that of reference areas even after 20 years. Herons, egrets, and migratory shorebirds used restoration areas extensively. These results support our prediction that returning tides will set degraded marshes on trajectories that can bring essentially full restoration of ecological functions. This can occur within two decades, although reduced tidal action can delay restoration of some functions. With this success, Connecticut...

Background In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). Findings Using a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. Conclusions Sequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities.

Summary1. In a faunally intact lowland Amazonian rain forest stand, we conducted a long-term multispecies 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 densitydependent 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.