Direct versus indirect facilitation (herbivore mediated) among woody plants in a semiarid Chaco forest: A spatial association approach

In arid environments, direct facilitation (microhabitat amelioration) and indirect facilitation (‘associational resistance’ via protection from herbivory) among plants of different species may act simultaneously. Little is known about their relative effects. One way to disentangle the effects is by evaluating spatial associations. We examined the relative importance of these two mechanisms of facilitation in the semiarid Chaco vegetation of north‐central Argentina, through an eight‐way observational study in which we quantified the degree of spatial association between saplings of each of two key tree species, Schinopsis lorentzii (Anacardiaceae) and Aspidosperma quebracho‐blanco (Apocynaceae), with shrub neighbours either possessing spines or without spines and in both an ungrazed site and a site with a long history of cattle grazing. We analysed data across 400 subparcels at each site with spatial analysis by distance indices. Saplings of both tree species showed positive spatial associations with spiny shrubs in the grazed site but not in the ungrazed site, and never with non‐spiny shrubs. This result suggests that spiny shrubs may indeed provide associational resistance for saplings of key tree species in grazed habitats in these dry subtropical forests, that is, that indirect facilitation may predominate over direct facilitation. If confirmed by experimental studies, this result can have implications for the silvopastoral management of rapidly expanding ranches in the semiarid Chaco, where current practice includes the near elimination of native shrubs.     

Tasmanian lentic wetland lawns are maintained by grazing rather than inundation

Vertebrate grazers have been shown to be a critical element in maintaining lawns, although lawns can also form in places without such herbivores. In Tasmania lawns are widespread in lentic wetlands. We used environmental observations and exclosure experiments at two altitudinally contrasting lentic wetland lawns, and waterlogging experiments, to test the hypotheses that their structure is maintained (i) periodic inundation; and (ii) grazing. Waterlogging experiments and field observations demonstrated that the two main invading shrubs were indifferent to immersion for several months and that the distribution of the lawns was independent of inundation period, results inconsistent with the first hypothesis. The exclosure experiments showed that both woody and non‐woody plants became taller in the lawns when marsupial grazers and rabbits were excluded. It therefore seems that the lawn structure is maintained by grazing and that alternative structural states result from exclusion of grazing pressure in less than 2 years.     

Protein family clustering for structural genomics

A major goal of structural genomics is the provision of a structural template for a large fraction of protein domains. The magnitude of this task depends on the number and nature of protein sequence families. With a large number of bacterial genomes now fully sequenced, it is possible to obtain improved estimates of the number and diversity of families in that kingdom. We have used an automated clustering procedure to group all sequences in a set of genomes into protein families. Bench-marking shows the clustering method is sensitive at detecting remote family members, and has a low level of false positives. This comprehensive protein family set has been used to address the following questions. (1) What is the structure coverage for currently known families? (2) How will the number of known apparent families grow as more genomes are sequenced? (3) What is a practical strategy for maximizing structure coverage in future? Our study indicates that approximately 20% of known families with three or more members currently have a representative structure. The study indicates also that the number of apparent protein families will be considerably larger than previously thought: We estimate that, by the criteria of this work, there will be about 250,000 protein families when 1000 microbial genomes have been sequenced. However, the vast majority of these families will be small, and it will be possible to obtain structural templates for 70-80% of protein domains with an achievable number of representative structures, by systematically sampling the larger families.     

The comparison of the confidence regions in phylogeny

In this paper, several different procedures for constructing confidence regions for the true evolutionary tree are evaluated both in terms of coverage and size without considering model misspecification. The regions are constructed on the basis of tests of hypothesis using six existing tests: Shimodaira Hasegawa (SH), SOWH, star form of SOWH (SSOWH), approximately unbiased (AU), likelihood weight (LW), generalized least squares, plus two new tests proposed in this paper: single distribution nonparametric bootstrap (SDNB) and single distribution parametric bootstrap (SDPB). The procedures are evaluated on simulated trees both with small and large number of taxa. Overall, the SH, SSOWH, AU, and LW tests led to regions with higher coverage than the nominal level at the price of including large numbers of trees. Under the specified model, the SOWH test gives accurate coverage and relatively small regions. The SDNB and SDPB tests led to the small regions with occasional undercoverage. These two procedures have a substantial computational advantage over the SOWH test. Finally, the cutoff levels for the SDNB test are shown to be more variable than those for the SDPB test.     

Species composition and correlation of understory woody plants in Chinese fir plantation in the lower subtropical area

There are 71 species in the shrub layer of the Cunninghamia lanceolata plantation after natural succession. The species richness and diversity have increased with slight anthropogenic disturbance. The status and function of understory woody species were judged by the analysis of the important value (IV). x ² statistics and r test were used for testing the significance of interspecific association and correlation among 25 main understory woody plants selected from the woody population. The results clearly showed their interspecific relationships and their differences in resource utilization. Species-pairs of positive association were in the majority. Most species were accommodated in the shady habitat. There was a positive correlation between the IV of the species and the interspecific association. The higher the IV of the species, the closer and more significant was the interspecific association. Based on analytical results of interspecific association and correlation, 25 woody plants in the shrub layer could be divided into four ecological species groups: I. Ficus hispida + Antidesma bunius + Mallotus barbatus + Ficus cunia + Saurauia tristyla + Mallotus philippinensis + Maesa japonica + Ficus hirta + Alchornea rugosa + Ficus fulva + Mallotus apelta; II. Cudrania tricuspidata + Schefflera octophylla; III. Cunninghamia lanceolata + Clerodendron cytophyllum + Millettia semicastrata + Randia spinosa + Litsea cubeba + Litsea pungens; IV. Ardisia japonica + Psychotria rubra + Vitex quinata + Cephalanthus occidentalis + Pithecellobium lucidum + Mycetia sinensis. If species group III or II is the advantaged species in the shrub layer, the community would change from a coniferous forest to a sparse evergreen broad-leaved forest. For group IV, the community would be relatively stable. For group I, the coniferous forest would be mixed with coniferous-broad leaved forest. The classification of ecological species groups would provide a theoretical basis on judging its ecological function, adjusting the stand structure of the plantation and directing the suitable natural vegetation type through the close-natural restoration process. __________ Translated from Acta Ecologica Sinica, 2005, 25(9): 2173–2179 [译自: 生态学报, 2005, 25(9): 2173–2179]     

Compensatory growth of Phanerochaete velutina mycelial systems grazed by Folsomia candida (Collembola)

Phanerochaete velutina is a major agent of wood decomposition in temperate forests. It grows out of woody resources in search of other resources and is then vulnerable to grazing by invertebrates. The aim of this study was to determine how continuous grazing and grazing for only 2 days by different densities of collembola, Folsomia candida, affect mycelial development (radial extension, hyphal coverage and fractal dimension) of P. velutina growing across non-sterile soil. High density (80 collembola) continuous grazing resulted in different mycelial foraging patterns compared to controls and lower density (20 and 40 collembola) continuous grazing: radial extension rate was reduced from 8.4 mm day(-1) (control) to 6.9 mm day(-1) (80 collembola), hyphal coverage was reduced to 81% of controls and mass fractal dimension increased from 1.68 (control) to 1.72 (80 collembola). There was evidence of over-compensatory growth: when high density grazing ceased the new growth was considerably greater (38%) than in controls. Grazing also resulted in growth stimulation: at low density continuous grazing (20 collembola) hyphal coverage was 15.6% greater than in controls. The ecological implications of compensatory and stimulatory growth in fungal-invertebrate interactions are considered.     

Aeolian process effects on vegetation communities in an arid grassland ecosystem

Many arid grassland communities are changing from grass dominance to shrub dominance, but the mechanisms involved in this conversion process are not completely understood. Aeolian processes likely contribute to this conversion from grassland to shrubland. The purpose of this research is to provide information regarding how vegetation changes occur in an arid grassland as a result of aeolian sediment transport. The experimental design included three treatment blocks, each with a 25 × 50 m area where all grasses, semi-shrubs, and perennial forbs were hand removed, a 25 × 50 m control area with no manipulation of vegetation cover, and two 10 × 25 m plots immediately downwind of the grass-removal and control areas in the prevailing wind direction, 19° north of east, for measuring vegetation cover. Aeolian sediment flux, soil nutrients, and soil seed bank were monitored on each treatment area and downwind plot. Grass and shrub cover were measured on each grass-removal, control, and downwind plot along continuous line transects as well as on 5 × 10 m subplots within each downwind area over four years following grass removal. On grass-removal areas, sediment flux increased significantly, soil nutrients and seed bank were depleted, and Prosopis glandulosa shrub cover increased compared to controls. Additionally, differential changes for grass and shrub cover were observed for plots downwind of vegetation-removal and control areas. Grass cover on plots downwind of vegetation-removal areas decreased over time (2004-2007) despite above average rainfall throughout the period of observation, while grass cover increased downwind of control areas; P. glandulosa cover increased on plots downwind of vegetation-removal areas, while decreasing on plots downwind of control areas. The relationships between vegetation changes and aeolian sediment flux were significant and were best described by a logarithmic function, with decreases in grass cover and increases in shrub cover occurring with small increases in aeolian sediment flux.