Effects of selective logging on tree species diversity and composition of Bornean tropical rain forests at different spatial scales

Reduced-impact logging (RIL) is known to be beneficial in biodiversity conservation, but its effects on tree diversity remain unknown. Pattern of tree diversity following disturbance usually varies with spatial scale of sampling (i.e., plot size). We examined the impacts of RIL on species richness and community composition of tree species at different spatial scales, and the scale (plot size) dependency of the two metrics; species richness versus community similarity. One 2-ha and three to four 0.2-ha plots were established in each of primary, RIL, and conventionally logged (CL) forest in Sabah, Malaysia. Species richness (the number of species per unit number of stems) was higher in the RIL than in the CL forest at both scales. The relationship between species richness and logging intensity varied with plot size. Species richness was greater in the RIL than in the primary forest at the 2-ha scale, while it was similar between the two forests at 0.2-ha scale. Similarly, species richness in the CL forest demonstrated a greater value at the 2-ha scale than at the 0.2-ha scale. Greater species richness in the two logged forests at the 2-ha scale is attributable to a greater probability of encountering the species-rich, small patches that are distributed heterogeneously. Community composition of the RIL forest more resembled that of the primary forest than that of the CL forest, regardless of plot size. Accordingly, species richness is a scale-dependent metric, while community similarity is a more robust metric to indicate the response of tree assemblage to anthropogenic disturbance.     

Drought impacts and recovery are driven by local variation in species turnover

In forest systems, drought acts as a disturbance that can generate impacts on community structure and composition at multiple scales. This study focused on a 2-month drought event within an early successional forest system to determine the mechanism(s) of community response to, and recovery from, drought. Drought induced a 28% decline in neighborhood species richness and cover as a result of decreased colonization and increased extinction rates. Following drought, neighborhood richness quickly recovered via increased colonization rates while extinction rates were unaltered. Drought had little long-term effect on neighborhood structure (species richness and cover) and generated only subtle changes in neighborhood composition. Ruderal (annual and biennial) species were more likely to change (increase or decrease) in cover and frequency than the more stress tolerant perennial and woody species. However, population dynamics appeared to be generally driven by stochastic species turnover among fields and not by uniform shifts in species performance across the site. Although drought impacts and recovery appeared predictable at the neighborhood scale, population responses to drought within the site were rather unpredictable. Our findings suggest that stochastic fine-scale processes can generate predictable course-scale dynamics within a disturbed system. The scale-specific mechanisms of community change presented here should be explored in other systems to determine the extent of their generality in driving disturbance impacts on communities.     

Partitioning the impact of abiotic factors and spatial patterns on species richness and community structure of ground ant assemblages in four Bornean rainforests

Contrasting theories have been proposed to explain the structure of ecological communities. Here, we studied the impact of environmental factors and spatial patterns on ground‐foraging ant communities in four different forest types of Gunung Mulu National Park in Sarawak, Borneo, Malaysia. Forest types differed in their environmental parameters and were inhabited by distinct ant communities, with various indicator species characteristic for single forest types. Three environmental parameters, soil volume, number of trees and amount of leaf litter, had the most influence on ant communities. Spatial patterns were correlated with environmental parameters and also influenced ant communities. Environmental parameters influenced community composition only moderately (r²=0.14), but had a high impact on species richness (r²=0.44). Spatial patterns explained only a small fraction of the total variance in species patterns, while much of the residual space in the ordination space of ant community patterns remained unexplained. We conclude that environmental parameters shape the number of niches within a tropical soil habitat, but identities of species that occupy those niches are accounted for by other factors like competition, traits and neutral processes that may further reduce unexplained variance in species ordination.     

Historic variability in fire‐generated landscape heterogeneity of subalpine forests in the Canadian Rockies

Question: This study evaluates historical changes in landscape structure and heterogeneity in subalpine forests. We use response to severe fires in 2001 and 2003, along with historical reconstructions to examine crown‐fire effects on landscape heterogeneity and to assess, comparatively, effects of fire exclusion management in the 20th century. Location: Subalpine forests of Kootenay National Park (KNP), Canadian Rockies. Methods: Using a landscape‐level model based on a fire‐origin stand age map, we reconstructed decadal burned areas within the landscape for 1750‐2000 (forming reconstructed landscapes). Landscape pattern was analysed for each reconstructed landscape map, and we compared landscape pattern indices (total area, number of patches, mean patch area, patch area variation, largest patch index, edge density, perimeter–area ratio, landscape shape index) with those in 2005 after recent large fires. Results: After large fires in 1926, connectivity of the KNP landscape increased and its diversity was quite low. After 2001 and 2003 fires, the post‐fire landscape of 2005 was highly heterogeneous in terms of size, variation, edge density and perimeter–area ratio of the remnant forest patches. Since the decline in occurrence of large fires after 1926 reflected a period of wet weather, fuel build‐up resulting from landscape homogenization within the 20th century landscape could not be attributed solely to fire exclusion. This period without fires greatly enhanced connectivity of late‐successional forests that finally burned in 2001/2003, but connectivity was within the historical range for these forests. The gradual increase in stand connectivity before recent large fires may indicate that fire exclusion was less responsible than often believed for fuel build‐up in these fire‐susceptible older forests. Conclusions: The large fires at the beginning of the 21st century are within the natural range of disturbances for this landscape, and do not stand out as “human‐induced disasters” in their effects on landscape patterns. Such stochastic large disturbances contribute to maintenance of highly heterogeneous landscape structure, which is important for many taxa and natural ecological processes. Identifying future probability of such large disturbances and their ecological roles should be incorporated into management of these dynamic, disturbance‐prone systems.     

Co‐ and post‐translational modifications of the 26S proteasome in yeast

The yeast (Saccharomyces cerevisiae) 26S proteasome consists of the 19S regulatory particle (19S RP) and 20S proteasome subunits. We detected comprehensively co‐ and post‐translational modifications of these subunits using proteomic techniques. First, using MS/MS, we investigated the N‐terminal modifications of three 19S RP subunits, Rpt1, Rpn13, and Rpn15, which had been unclear, and found that the N‐terminus of Rpt1 is not modified, whereas that of Rpn13 and Rpn15 is acetylated. Second, we identified a total of 33 Ser/Thr phosphorylation sites in 15 subunits of the proteasome. The data obtained by us and other groups reveal that the 26S proteasome contains at least 88 phospho‐amino acids including 63 pSer, 23 pThr, and 2 pTyr residues. Dephosphorylation treatment of the 19S RP with λ phosphatase resulted in a 30% decrease in ATPase activity, demonstrating that phosphorylation is involved in the regulation of ATPase activity in the proteasome. Third, we tried to detect glycosylated subunits of the 26S proteasome. However, we identified neither N‐ and O‐linked oligosaccharides nor O‐linked β‐N‐acetylglucosamine in the 19S RP and 20S proteasome subunits. To date, a total of 110 co‐ and post‐translational modifications, including N^α‐acetylation, N^α‐myristoylation, and phosphorylation, in the yeast 26S proteasome have been identified.     

Environmental heterogeneity,species diversity and co‐existence at different spatial scales

The positive relationship between spatial environmental heterogeneity and species diversity is a widely accepted concept, generally associated with niche limitation. However, niche limitation cannot account for negative heterogeneity–diversity relationships (HDR) revealed in several case studies. Here we explore how HDR varies at different spatial scales and provide novel theories for small‐scale species co‐existence that explain both positive and negative HDR. At large spatial scales of heterogeneity (e.g. landscape level), different communities co‐exist, promoting large regional species pool size and resulting in positive HDR. At smaller scales within communities, species co‐existence can be enhanced by increasing the number of different patches, as predicted by the niche limitation theory, or alternatively, restrained by heterogeneity. We conducted meta‐regressions for experimental and observational HDR studies, and found that negative HDRs are significantly more common at smaller spatial scales. We propose three theories to account for niche limitation at small spatial scales. (1) Microfragmentation theory: with increasing spatial heterogeneity, large homogeneous patches lose area and become isolated, which in turn restrains the establishment of new plant individuals and populations, thus reducing species richness. (2) Heterogeneity confounded by mean: when heterogeneity occurs at spatial scales smaller than the size of individual plants, which forage through the patches, species diversity can be either positively or negatively affected by a change in the mean of an environmental factor. (3) Heterogeneity as a separate niche axis: the ability of species to tolerate heterogeneity at spatial scales smaller than plant size varies, affecting HDR. We conclude that processes other than niche limitation can affect the relationship between heterogeneity and diversity.     

Predictability of early stages of primary succession in post‐mining landscapes of Lower Lusatia,Germany

Abstract. The predictability of early primary succession in post‐mining landscapes of eastern Germany was studied at sites 5–70 yr following dumping. This chronosequence was investigated using indirect ordination methods. The position of the vegetation types in the ordination diagram was found not to infer any temporal sequence. Independent observations show that the change of vegetation type is slow and does not necessarily occur among types adjacent in the ordination diagram. Furthermore, direct ordination revealed that environmental parameters such as pH, the levels of available phosphate and organic carbon as well as the age of the study sites do not significantly account for the variance. Instead, attention needs to be paid to the influence of spatial aspects and also what recultivation measures have been carried out. A detailed account of the vegetation dynamics of individual sample plots showed ‐ depending on the respective vegetation type ‐ divergence, convergence, and fluctuation at the smallest spatial scale. While the species richness of the sample plots remained more or less constant after initial colonization, mean vegetation cover continuously increases with age, although some sites still remain free of vegetation after as long as 70 yr. No general trend in dominant life forms was indicated. A conceptual model of early succession mechanisms is outlined and five basic mechanisms are identified (i.e. site availability, site suitability, availability of diaspores, strategies of colonizing species and biotic interactions). Their respective importance in three different stages of early succession is estimated and compared. The predictability of vegetation dynamics at each stage is rated differently.     

Patterns of species richness and turnover along the pH gradient in deciduous forests: testing the continuum hypothesis

Question: (i) How do species richness and species turnover change along a pH gradient? (ii) What are possible driving factors behind these patterns? (iii) Can the observed patterns be explained by an individualistic continuum concept that postulates independence of species responses and constant turnover rates? Location: Semi‐natural, deciduous hardwood forests in NW Germany (558 plots). Methods: The instantaneous rate of compositional turnover is measured by the sum of slope angles of modelled response curves (119 understorey species) at any point along the pH gradient. Total turnover rate, positive turnover rate (species increasing in probability of occurrence) and negative turnover rate (species decreasing in probability of occurrence) are calculated separately. Species richness is modelled using Poisson regression and by calculating the sum of predicted probabilities at any gradient point. Turnover rates are compared with those calculated from a null model based on a Gaussian community model. Soil chemical analyses of 49 plots are used to interpret biodiversity patterns. Results: Species richness shows a hump‐shaped relation to pH(CaCl₂) with a minor decline at approximately pH>5.0. The decline is possibly due to the confounding influence of water regime and local species pool effects. Increasing richness from pH 2.5 to 4.7 can be traced back to positive turnover exceeding negative turnover. Peaks in turnover rates, dominated by positive turnover, are located at pH 3.7 and 2.8, where turnover rates considerably exceed rates derived from the null model. The turnover pattern can be related to soil chemical conditions, e.g. decreasing base saturation, Al and H⁺ toxicity and the occurrence of mor. Conclusions: The high turnover rates and the massive imbalance in positive and negative turnover rates found in deciduous forests cannot be explained by the individualistic continuum concept. Physiological constraints at the gradient limits and species pool effects could be responsible for this. Their role should be considered more explicitly in vegetation concepts dealing with the continuum‐discontinuum controversy. The presented approach can be regarded as a comprehensive analytical tool for a better understanding of biodiversity patterns along environmental gradients by linking species richness, turnover and response curve types.     

Histone deacetylases: salesmen and customers in the post‐translational modification market

HDACs (histone deacetylases) are enzymes that remove the acetyl moiety from N‐?‐acetylated lysine residues in histones and non‐histone proteins. In recent years, it has turned out that HDACs themselves are also subject to post‐translational modification. Such structural alterations can determine the stability, localization, activity and protein—protein interactions of HDACs. This subsequently affects the modification of their substrates and the co‐ordination of cellular signalling networks. Intriguingly, physiologically relevant non‐histone proteins are increasingly found to be deacetylated by HDACs, and aberrant deacetylase activity contributes to several severe human diseases. Targeting the catalytic activity of these enzymes and their post‐translational modifications are therefore attractive targets for therapeutical intervention strategies. To achieve this ambitious goal, details on the molecular mechanisms regulating post‐translational modifications of HDACs are required. This review summarizes aspects of the current knowledge on the biological role and enzymology of the phosphorylation, acetylation, ubiquitylation and sumoylation of HDACs.     

Short-term movements and strong dependence on figs of binturongs (<Emphasis Type="Italic">Arctictis binturong</Emphasis>) in Bornean rainforests

We evaluated short-term movements of three radio-collared binturongs in relation to food distribution in Bornean rainforests, in addition to the basic ecological information on their home-range size and diet. Mean 95% fixed kernel and 95% MCP home-range size were 4.24?±?0.79 km² and 1.54?±?0.89 km², respectively (mean ± SD). We recorded 13 fig Ficus species and four non-fig species as their foods. Fig trees accounted for 87.5% of the feeding sites of the three collared binturongs, and 87.9% including uncollared individuals. Our results suggested that binturongs’ short-term movements were strongly affected by food distribution, especially figs. They feed on various fig species and may remember the location and fruiting periods of fig trees. They may use the biggest fig species, F. punctata, as a fallback food when other foods are scarce. Although this is the first systematic study to describe movement and feeding habits of binturongs, further studies are needed to understand their ecology so that proper measures can be designed for their conservation.     

Effects of pre‐ and post‐dispersal temperature on primary and secondary dormancy dynamics in contrasting genotypes of A rabidopsis thaliana (Brassicaceae)

Germination is determined by the depth of primary dormancy and the dynamics of secondary dormancy induction. We assess how dark imbibition at cool temperatures influences primary dormancy breakage and secondary dormancy induction, and how the depth of primary dormancy influences secondary dormancy induction. We manipulated primary dormancy by maturing seeds at two temperatures (‘pre‐dispersal’) known to induce different levels of primary dormancy, and by employing genotypes that differ in primary dormancy. To assess primary dormancy breakage and secondary dormancy induction, seeds of each genotype and maturation treatment were imbibed in the dark at one of four temperatures (‘post‐dispersal’) for one of three durations. Germination proportions were recorded. Seed ‐ maturation condition and genotype influenced the degree of primary dormancy breakage in response to dark stratification and in the optimal temperature for dormancy breakage. Secondary dormancy induction was strongest in cool‐matured seeds and seeds stratified at warmer temperatures for longer durations. These effects were consistent across genotypes. Maturation temperature influenced the expression of genetic variation for primary but not secondary dormancy, which showed little genetic variation. Seed‐maturation temperature influenced primary and secondary dormancy induction by dark imbibition, and it also influenced the expression of genetic variation for temperature‐dependent dormancy breakage. Cool seed‐maturation induced primary dormancy in a genotype‐specific manner and enhanced secondary dormancy induction. Post‐dispersal temperature also influenced primary dormancy breakage and secondary dormancy induction. The observed interactions between primary and secondary dormancy, and between pre‐ and post‐dispersal temperature, are expected to influence life‐history expression in nature.     

Yuyanapaq no entra: ritual dimensions of post‐transitional justice in Peru

The anthropology of transitional justice has emphasized the ritual aspects of truth commissions but offered less analysis of the conventions through which narratives produced by such institutions come to be viewed over time. A controversy in Peru that centred on a new national museum's possible incorporation of a photo exhibit (Yuyanapaq) created by the Peruvian Truth and Reconciliation Commission (2001‐3) provides an opportunity to explore this problematic. Documenting the disagreements that ultimately led to Yuyanapaq's exclusion from the museum, I suggest that an emphasis on ritual outcomes – including perceived shortcomings and failures – is useful for understanding the long‐term trajectory of national reconciliation initiatives.     

Functional lifespans of xylem vessels: Development,hydraulic function,and post‐function of vessels in several species of woody plants

Premise of the Study

Xylem vessels transition through different stages during their functional lifespan, including expansion and development of vessel elements, transition to vessel hydraulic functionality, and eventual transition to post‐functionality. We used information on vessel development and function to develop a model of vessel lifespan for woody plants.

Methods

We examined vessel functional lifespan using repeated anatomical sampling throughout the growing season, combined with active‐xylem staining to evaluate vessel hydraulic transport functionality. These data were combined with a literature review. The transitions between vessel functional lifespans for several species are illustrated, including grapevine (Vitis vinifera L., Vitaceae), English oak (Quercus robur L., Fagaceae), American chestnut [Castanea dentata (Marshall) Borkh.; Fagaceae], and several arid and semi‐arid shrub species.

Key Results

In intact woody plants, development and maturation of vessel elements may be gradual. Once hydraulically functional, vessel elements connect to form a vessel network that is responsible for bulk hydraulic flow through the xylem. Vessels become nonfunctional due to the formation of gas emboli. In some species and under some conditions, vessel functionality of embolized conduits may be restored through refilling. Blockages, such as tyloses, gels, or gums, indicate permanent losses in hydraulic functional capacity; however, there may be some interesting exceptions to permanent loss of functionality for gel‐based blockages.

Conclusions

The gradual development and maturation of vessel elements in woody plants, variation in the onset of functionality between different populations of vessels throughout the growing season, and differences in the timing of vessel transitions to post‐functionality are important aspects of plant hydraulic function.     

Bryophyte species richness and composition in young forests regenerated after clear-cut logging versus after wildfire and spruce budworm outbreak

The disturbance regime in mixed-wood forests of eastern Canada is characterized by both natural disturbances including wildfires and insect outbreaks as well as forestry. The understanding of how understorey plant assemblages respond to different disturbances is mostly limited to short-term wildfire-logging comparisons of vascular plants. Here, we compare patterns of species richness and composition of four bryophyte guilds in young forests (approx. 40 years old) regenerating after clear-cut logging, wildfire, and spruce budworm outbreak. In addition, young forests were compared with mature spruce-fir dominated stands (approx. 90 years old). Although similar in overall species richness at the scale of 1,000 m² all young forest types were compositionally distinct with fewer species than mature forests. Stands developed after spruce budworm outbreaks had the highest canopy cover values and the highest surface area of coarse woody debris. These stands had similar numbers of woody debris species as mature forests and were closest to mature forests in species composition. Wildfire-disturbed sites were dominated by deciduous trees and a high number of treebase species. Finally, young managed forest had the highest number of forest floor bryophytes at the scale of 100 m² among the three young forest types, but was compositionally far from mature forests in their woody debris flora. In conclusion, young forests regenerating after natural disturbances are distinctly different from young forests regenerated after clear-cutting and if natural disturbances are eliminated certain species (e.g., epixylic and treebase species) might become more restricted to older stands in the landscape.     

Effects of climate‐driven primary production change on marine food webs: implications for fisheries and conservation

Climate change is altering the rate and distribution of primary production in the world's oceans. Primary production is critical to maintaining biodiversity and supporting fishery catches, but predicting the response of populations to primary production change is complicated by predation and competition interactions. We simulated the effects of change in primary production on diverse marine ecosystems across a wide latitudinal range in Australia using the marine food web model Ecosim. We link models of primary production of lower trophic levels (phytoplankton and benthic producers) under climate change with Ecosim to predict changes in fishery catch, fishery value, biomass of animals of conservation interest, and indicators of community composition. Under a plausible climate change scenario, primary production will increase around Australia and generally this benefits fisheries catch and value and leads to increased biomass of threatened marine animals such as turtles and sharks. However, community composition is not strongly affected. Sensitivity analyses indicate overall positive linear responses of functional groups to primary production change. Responses are robust to the ecosystem type and the complexity of the model used. However, model formulations with more complex predation and competition interactions can reverse the expected responses for some species, resulting in catch declines for some fished species and localized declines of turtle and marine mammal populations under primary productivity increases. We conclude that climate‐driven primary production change needs to be considered by marine ecosystem managers and more specifically, that production increases can simultaneously benefit fisheries and conservation. Greater focus on incorporating predation and competition interactions into models will significantly improve the ability to identify species and industries most at risk from climate change.     

Fine‐scale patterns of species and phylogenetic turnover in a global biodiversity hotspot: Implications for climate change vulnerability

Question: What is the relative importance of environmental and spatial factors for species compositional and phylogenetic turnover? Location: High‐rainfall zone of the Southwest Australian Floristic Region (SWAFR). Methods: Correlates of species compositional turnover were assessed using quadrat‐based floristic data, and establishing relationships with environmental and spatial factors using canonical correspondence analyses and Mantel tests. Between‐quadrat phylogenetic distance measures were computed and examined for correlations with environmental and spatial attributes. Processes structuring pa2t2terns of beta diversity were also evaluated within four broad floristic assemblages defined a priori. Results: Floristic diversity was strongly related to environmental attributes. A low significance of spatial variables on assemblage patterns suggested no evident effect of dispersal limitations. Species compositional turnover was especially high within the swamp and outcrop assemblage. Phylogenetic turnover was closely coupled to species compositional turnover, implying the occurrence of many locally endemic and phylogenetically relict taxa. Beta diversity patterns within assemblages were also significantly correlated with the local environment, and relevant correlates differed between floristic assemblage types. Conclusion: Phylogenetic diversity in the SWAFR high‐rainfall zone is clustered within edaphic microhabitats in a generally subdued landscape. A clustered rather than dispersed distribution of phylogenetic diversity increases the probability of significant plant diversity loss during periods of climate change. Climate change susceptibility of the region's flora is accordingly estimated to be high. We highlight the conservation significance of swamp and outcrops that are characterized by distinct hydrological properties and may provide refugial habitat for plant diversity during periods of moderate climate change.     

Law and the architecture of social repair: gacaca days in post‐genocide Rwanda

In this article, I examine post‐genocide Rwanda's gacaca process, in which genocide suspects were tried among their neighbours before locally elected judges. I suggest two limitations in how anthropologists have typically studied post‐conflict legal institutions. Measuring the cultural relevance of law obscures contemporary imbrications of African custom and universal legal principles, and distracts from analysis of the politicized uses of culture. Analysing structural constraints and coercive dimensions, while crucial, can blind us to the very real social work that happens in these forums. Instead, I argue, what differentiated gacaca was how deeply it was contextualized – embedded in daily life, public, participatory, routinized, and based on oral testimony – and this contextualization formed the basis of its situated relevance to people's efforts to shape forms of sociality. People used gacaca sessions to negotiate the micro‐politics of reconciliation, which included debating definitions of ‘genocide citizenship’, guilt, innocence, exchange, and material loyalty. I argue for moving beyond the underlying assumption in critical transitional justice studies that law and reconciliation are mutually exclusive, to acknowledge that the instrumental and often divisive dynamics in gacaca do not merely reflect institutional failures but, rather, reflect the inherent violence of social repair.