Tree mode of death and mortality risk factors across Amazon forests

The carbon sink capacity of tropical forests is substantially affected by tree mortality. However, the main drivers of tropical tree death remain largely unknown. Here we present a pan-Amazonian assessment of how and why trees die, analysing over 120,000 trees representing > 3800 species from 189 long-term RAINFOR forest plots. While tree mortality rates vary greatly Amazon-wide, on average trees are as likely to die standing as they are broken or uprooted-modes of death with different ecological consequences. Species-level growth rate is the single most important predictor of tree death in Amazonia, with faster-growing species being at higher risk. Within species, however, the slowest-growing trees are at greatest risk while the effect of tree size varies across the basin. In the driest Amazonian region species-level bioclimatic distributional patterns also predict the risk of death, suggesting that these forests are experiencing climatic conditions beyond their adaptative limits. These results provide not only a holistic pan-Amazonian picture of tree death but large-scale evidence for the overarching importance of the growth-survival trade-off in driving tropical tree mortality.

The Forest Observation System, building a global reference dataset for remote sensing of forest biomass

Forest biomass is an essential indicator for monitoring the Earth's ecosystems and climate. It is a critical input to greenhouse gas accounting, estimation of carbon losses and forest degradation, assessment of renewable energy potential, and for developing climate change mitigation policies such as REDD+, among others. Wall-to-wall mapping of aboveground biomass (AGB) is now possible with satellite remote sensing (RS). However, RS methods require extant, up-to-date, reliable, representative and comparable in situ data for calibration and validation. Here, we present the Forest Observation System (FOS) initiative, an international cooperation to establish and maintain a global in situ forest biomass database. AGB and canopy height estimates with their associated uncertainties are derived at a 0.25 ha scale from field measurements made in permanent research plots across the world's forests. All plot estimates are geolocated and have a size that allows for direct comparison with many RS measurements. The FOS offers the potential to improve the accuracy of RS-based biomass products while developing new synergies between the RS and ground-based ecosystem research communities.

Compositional response of Amazon forests to climate change

Most of the planet's diversity is concentrated in the tropics, which includes many regions undergoing rapid climate change. Yet, while climate-induced biodiversity changes are widely documented elsewhere, few studies have addressed this issue for lowland tropical ecosystems. Here we investigate whether the floristic and functional composition of intact lowland Amazonian forests have been changing by evaluating records from 106 long-term inventory plots spanning 30 years. We analyse three traits that have been hypothesized to respond to different environmental drivers (increase in moisture stress and atmospheric CO₂ concentrations): maximum tree size, biogeographic water-deficit affiliation and wood density. Tree communities have become increasingly dominated by large-statured taxa, but to date there has been no detectable change in mean wood density or water deficit affiliation at the community level, despite most forest plots having experienced an intensification of the dry season. However, among newly recruited trees, dry-affiliated genera have become more abundant, while the mortality of wet-affiliated genera has increased in those plots where the dry season has intensified most. Thus, a slow shift to a more dry-affiliated Amazonia is underway, with changes in compositional dynamics (recruits and mortality) consistent with climate-change drivers, but yet to significantly impact whole-community composition. The Amazon observational record suggests that the increase in atmospheric CO₂ is driving a shift within tree communities to large-statured species and that climate changes to date will impact forest composition, but long generation times of tropical trees mean that biodiversity change is lagging behind climate change.

ZooKeys anniversary: 10 years of leadership toward open-access publishing of zoological data and establishment at Pensoft of like-minded sister journals across the biodiversity spectrum

ZooKeys anniversary: 10 years

Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID

Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.

Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples

The concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XML-tagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workflow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used.

Drought sensitivity of the Amazon rainforest

Amazon forests are a key but poorly understood component of the global carbon cycle. If, as anticipated, they dry this century, they might accelerate climate change through carbon losses and changed surface energy balances. We used records from multiple long-term monitoring plots across Amazonia to assess forest responses to the intense 2005 drought, a possible analog of future events. Affected forest lost biomass, reversing a large long-term carbon sink, with the greatest impacts observed where the dry season was unusually intense. Relative to pre-2005 conditions, forest subjected to a 100-millimeter increase in water deficit lost 5.3 megagrams of aboveground biomass of carbon per hectare. The drought had a total biomass carbon impact of 1.2 to 1.6 petagrams (1.2 x 10(15) to 1.6 x 10(15) grams). Amazon forests therefore appear vulnerable to increasing moisture stress, with the potential for large carbon losses to exert feedback on climate change.

Pattern and process in Amazon tree turnover, 1976-2001

Previous work has shown that tree turnover, tree biomass and large liana densities have increased in mature tropical forest plots in the late twentieth century. These results point to a concerted shift in forest ecological processes that may already be having significant impacts on terrestrial carbon stocks, fluxes and biodiversity. However, the findings have proved controversial, partly because a rather limited number of permanent plots have been monitored for rather short periods. The aim of this paper is to characterize regional-scale patterns of 'tree turnover' (the rate with which trees die and recruit into a population) by using improved datasets now available for Amazonia that span the past 25 years. Specifically, we assess whether concerted changes in turnover are occurring, and if so whether they are general throughout the Amazon or restricted to one region or environmental zone. In addition, we ask whether they are driven by changes in recruitment, mortality or both. We find that: (i) trees 10 cm or more in diameter recruit and die twice as fast on the richer soils of southern and western Amazonia than on the poorer soils of eastern and central Amazonia; (ii) turnover rates have increased throughout Amazonia over the past two decades; (iii) mortality and recruitment rates have both increased significantly in every region and environmental zone, with the exception of mortality in eastern Amazonia; (iv) recruitment rates have consistently exceeded mortality rates; (v) absolute increases in recruitment and mortality rates are greatest in western Amazonian sites; and (vi) mortality appears to be lagging recruitment at regional scales. These spatial patterns and temporal trends are not caused by obvious artefacts in the data or the analyses. The trends cannot be directly driven by a mortality driver (such as increased drought or fragmentation-related death) because the biomass in these forests has simultaneously increased. Our findings therefore indicate that long-acting and widespread environmental changes are stimulating the growth and productivity of Amazon forests.

Increasing biomass in Amazonian forest plots

A previous study by Phillips et al. of changes in the biomass of permanent sample plots in Amazonian forests was used to infer the presence of a regional carbon sink. However, these results generated a vigorous debate about sampling and methodological issues. Therefore we present a new analysis of biomass change in old-growth Amazonian forest plots using updated inventory data. We find that across 59 sites, the above-ground dry biomass in trees that are more than 10 cm in diameter (AGB) has increased since plot establishment by 1.22 +/- 0.43 Mg per hectare per year (ha(-1) yr(-1), where 1 ha = 10(4) m2), or 0.98 +/- 0.38 Mg ha(-1) yr(-1) if individual plot values are weighted by the number of hectare years of monitoring. This significant increase is neither confounded by spatial or temporal variation in wood specific gravity, nor dependent on the allometric equation used to estimate AGB. The conclusion is also robust to uncertainty about diameter measurements for problematic trees: for 34 plots in western Amazon forests a significant increase in AGB is found even with a conservative assumption of zero growth for all trees where diameter measurements were made using optical methods and/or growth rates needed to be estimated following fieldwork. Overall, our results suggest a slightly greater rate of net stand-level change than was reported by Phillips et al. Considering the spatial and temporal scale of sampling and associated studies showing increases in forest growth and stem turnover, the results presented here suggest that the total biomass of these plots has on average increased and that there has been a regional-scale carbon sink in old-growth Amazonian forests during the previous two decades.

Increasing dominance of large lianas in Amazonian forests

Ecological orthodoxy suggests that old-growth forests should be close to dynamic equilibrium, but this view has been challenged by recent findings that neotropical forests are accumulating carbon and biomass, possibly in response to the increasing atmospheric concentrations of carbon dioxide. However, it is unclear whether the recent increase in tree biomass has been accompanied by a shift in community composition. Such changes could reduce or enhance the carbon storage potential of old-growth forests in the long term. Here we show that non-fragmented Amazon forests are experiencing a concerted increase in the density, basal area and mean size of woody climbing plants (lianas). Over the last two decades of the twentieth century the dominance of large lianas relative to trees has increased by 1.7-4.6% a year. Lianas enhance tree mortality and suppress tree growth, so their rapid increase implies that the tropical terrestrial carbon sink may shut down sooner than current models suggest. Predictions of future tropical carbon fluxes will need to account for the changing composition and dynamics of supposedly undisturbed forests.

Role of N-myc in the developing mouse kidney

N-myc is a transcription factor expressed in the developing metanephric kidney and other organs. In mice, complete disruption of the N-myc gene results in fetal death on the first day of renal organogenesis. In addition to the null N-myc allele, others have generated a hypomorphic N-myc allele. In this study, combinations of these mutant genes were used to demonstrate that reduction in N-myc protein levels correlate with fewer developing glomeruli and collecting ducts in embryonic kidney explants. Histological sections revealed that the mutant kidneys were hypoplastic with normal developing structures. The data indicate that the hypoplasia is due to a reduction in proliferation rather than an increase in apoptosis. Thus, N-myc loss causes a decrease in numbers of ureteric bud tips and developing glomeruli in explants and hypoplastic kidneys in vivo, in a dose-dependent manner.