A new method for characterizing point patterns in plant ecology

Abstract. This paper describes new methods for the detection of the characteristics of spatial point patterns, based on counting plants in the circumcircles of triangles defined by triplets of the points themselves. In addition to counting points in the circumcircle, a further refinement is to count also the points in a ring around the circumcircle of the same area. This approach can be applied in a univariate form, with one species or one kind of plant, to detect and evaluate the best‐defined patches of plants and gaps. In the bivariate form, the method can be used to investigate the spatial characteristics of the relationship between different kinds of plants. These methods are illustrated by application to several data sets. In particular, the method is shown to be useful in describing the spatial relationship between seedlings and trees, both when the seedlings are on the forest floor beneath the canopy trees and when the seedlings represent post‐fire regeneration.     

A practical approach to the study of spatial structure in simple cases of heterogeneous vegetation

Abstract. Spatial heterogeneity is a characteristic of most natural ecosystems which is difficult to handle analytically, particularly in the absence of knowledge about the exogenous factors responsible for this heterogeneity. While classical methods for analysis of spatial point patterns usually require the hypothesis of homogeneity, we present a practical approach for partitioning heterogeneous vegetation plots into homogeneous subplots in simple cases of heterogeneity without drastically reducing the data. It is based on the detection of endogenous variations of the pattern using local density and second‐order local neighbour density functions that allow delineation of irregularly shaped subplots that could be considered as internally homogeneous. Spatial statistics, such as Ripley's K‐function adapted to analyse plots of irregular shape, can then be computed for each of the homogeneous subplots. Two applications to forest ecological field data demonstrate that the method, addressed to ecologists, can avoid misinterpretations of the spatial structure of heterogeneous vegetation stands.     

Spatial pattern and process in forest stands within the Virginia piedmont

Abstract. Question: Underlying ecological processes have often been inferred from the analysis of spatial patterns in ecosystems. Using an individual‐based model, we evaluate whether basic assumptions of species’life‐history, drought‐susceptibility, and shade tolerance generate dynamics that replicate patterns between and within forest stands. Location: Virginia piedmont, USA. Method: Model verification examines the transition in forest composition and stand structure between mesic, intermediate and xeric sites. At each site, tree location, diameter, and status were recorded in square plots ranging from 0.25 to 1.0 ha. Model validation examines the simulated spatial pattern of individual trees at scales of 1–25 m within each forest site using a univariate Ripley's K function. Results: 7512 live and dead trees were surveyed across all sites. All sites exhibit a consistent, significant shift in pattern for live trees by size, progressing from a clumped understorey (trees ± 0.1 m in diameter) to a uniform overstorey (trees > 0.25 m). Simulation results reflect not only the general shift in pattern of trees at appropriate scales within sites, but also the general transition in species composition and stand structure between sites. Conclusions: This shift has been observed in other forest ecosystems and interpreted as a result of competition; however, this hypothesis has seldom been evaluated using simulation models. These results support the hypothesis that forest pattern in the Virginia piedmont results from competition involving species’life‐history attributes driven by soil moisture availability between sites and light availability within sites.     

The effect of conspecific density,herbivory, and bamboo on seedling dynamics of a dominant oak in a Neotropical highland forest

Conspecific negative density dependence (CNDD) is one of the main mechanisms influencing diversity maintenance in tropical forests. Tropical highland forests, in contrast to most lowland forests, are commonly dominated by a few tree species, and testing the importance of density dependence effects on seedling establishment of dominant trees may provide insights on the mechanisms regulating population dynamics and forest composition of tropical highlands. We tested the effect of CNDD regulation on seedling survival and recruitment of Quercus costaricensis, a monodominant oak in the Talamanca highland forests of Costa Rica. We used Ripley's K and generalized linear mixed models to test the effects of conspecific density, distance to the nearest adult, density of Chusquea bamboo shoots, and herbivory on the annual survival probability of 3579 seedlings between 2014 and 2017. We did not find a significant effect of CNDD on seedling survival. However, bamboo density and herbivory both significantly decreased oak seedling survival. All seedlings had signs of herbivory and predator satiation may explain the lack of density dependent regulation in seedlings of this species. We argue that the lack of intraspecific density regulation at the seedling stage may contribute to explain the dominance of Q. costaricensis in the highland forests of Costa Rica. Local seedling dynamics of this endemic oak are instead regulated by herbivory and the density of Chusquea. Abstract in Spanish is available with online material.     

Can isotropy vs. anisotropy in the spatial association of plant species reveal physical vs. biotic facilitation?

In dryland ecosystems and other harsh environments, a large part of the vegetation is often clustered, appearing as ‘islands’. If ‘independent’ species, usually colonizers, can be distinguished from species which are ‘dependent’ on the presence of the colonizing species for successful establishment and/or persistence, the type of spatial pattern of the association ‐ isotropic (spatially symmetric) or anisotropic (spatially asymmetric) ‐ can give information on the underlying environmental factors driving the process of association. Modified spatial pattern analysis based on Ripley's K‐function can be applied to bivariate clustered patterns by cardinal direction in order to detect possible anisotropy in the pattern of association. The method was applied to mapped distribution patterns of two types of semi‐arid shrubland in southeastern Spain. In shrubland of Retama sphaerocarpa, low shrubs of Artemisia barrelieri were significantly clustered under the canopy of the Retama shrubs in all four cardinal directions, suggesting an isotropic facilitation effect. In low shrubland dominated by Anthyllis cytisoides and Artemisia barrelieri, Anthyllis shrubs occurred more frequently than expected on the eastern side (and downslope) of an Artemisia shrub. The possible environmental factors driving the two association patterns are discussed and recommendations for further applications of the analytical method are given.     

Spatial patterns and associations in a Quercus‐Betula forest in northern China

Question: Are species‐specific regeneration strategies and competition the dominant processes facilitating species coexistence in a Quercus liaotungensis dominated temperate deciduous forest? Location: Dongling Mountains, North China, 1300 m a.s.l. Methods: Ripley's K‐function was used to characterize the spatial patterns and spatial associations of two dominant tree species, Quercus liaotungensis and Betula dahurica, and a common subcanopy species, Acer mono, at different growth stages (adult, sapling, seedling). Results: Seedlings, saplings and adults of all three species exhibited clumped distributions at most spatial scales. Quercus seedlings and saplings were positively associated with conspecific adult trees and spatially independent of dead trees suggesting that seed dispersal and vegetative regeneration influenced the spatial patterning of Quercus trees. Betula seedlings and saplings were positively associated with both live and dead trees of conspecific adults at small scales (<5 m) but negatively associated with live and dead trees of other species indicating sprouting as an important mechanism of reproduction. Saplings of Acer had a strong spatial dependence on the distribution of conspecific adult trees indicating its limited seed dispersal range. Negative associations between adult trees of Betula and Quercus demonstrated interspecific competition at local scales (<5 m). Conclusions: Different regeneration strategies among the three species play an important role in regulating their spatial distribution patterns, while competition between individuals of Betula and Quercus at the adult stage also contributes to spatial patterning of these communities. The recruitment limitations of Betula and Quercus may affect the persistence of these species and the long‐term dynamics of the forest.     

Composition,structure and diversity of cove forest stands in the Great Smoky Mountains: a patch dynamics perspective

Abstract. Cove forests of the Great Smoky Mountains are North American examples of old-growth temperate forest. Ecological attributes of seven stands were studied using one 0.6 - 1.0 ha plot per stand. Stand basal area (39 - 55 m²/ha) and biomass (326 - 471 Mg/ha) were high for temperate deciduous forest. Density ranged from 577 to 1075 stems/ha. All stands had a mixture of deciduous canopy species. Only rarely did a single species comprise more than half of the stand by density, basal area or biomass. Shade-intolerant species were present at low levels (1 - 5 % of total stand density). A wide range of stem diameters was characteristic of most species. However, some species lacked small stems, indicating discontinuous regeneration. Stands tended to have 10 - 20 tree species per ha and at least five species had biomass levels > 10 Mg/ha, indicating high evenness. Canopy gaps covered 10 % of the total area (2 - 21 % by stand). Gaps and conspecific patches of canopy trees > 0.05 ha in size were infrequent. Spatial analyses revealed a variety of patterns among species at inter-tree distances of 1 to 25 m. When all species were combined, juveniles showed aggregation, and adults were often hyperdispersed. Analyses for individual species confirmed that the mosaic of canopy species is influenced by non-random spatial processes. Adults of several species were aggregated at distances > 10 m. Juveniles of all major species exhibited aggregation. Several species exhibited regeneration near conspecific adults. This pattern suggested limited mobility for such species within the shifting mosaic. A diverse patchwork resulted despite the fact that many species did not exhibit segregation of adults and juveniles. Further understanding of patch dynamics and the potential for compositional steady state in cove forests requires long-term study with spatial data.     

108 years of change in spatial pattern following selective harvest of a Pinus ponderosa stand in northern Arizona,USA

Questions: How did an initial tree harvest in 1894 influence the spatial and temporal patterns of Pinus ponderosa recruitment? How do these patterns compare to our understanding of P. ponderosa stand dynamics prior to Euro‐American settlement? How might spatial pattern information, particularly with respect to patch characteristics, inform current restoration and management practices? Location: A 2.59‐ha permanent sample plot in the Fort Valley Experimental Forest, Flagstaff, Arizona. The plot was selectively harvested in 1894 and measured in 1909 and 2002. Methods: We used historical stem‐map and ledger data, contemporary data, and dendrochronological techniques to reconstruct stand structure (tree size, age, location) in three scenarios: (1) unharvested (1909), (2) harvested (1909), and (3) contemporary (2002). We used Clark and Evans' R, Ripley's K(t) univariate analysis, and correlogram analysis to assess the spatial pattern in each scenario. We also used Ripley's K₁₂(t) bivariate analysis and tree age data to examine spatial and temporal recruitment patterns as observed in the contemporary scenario. Results and Conclusions: The unharvested stand was aggregated at scales up to 28 m. The selective harvest accentuated the spatial patchiness of the stand in 1909 and changed spatial patterns by homogenizing tree size within patches. By 2002, the stand was a single patch dominated by small trees. Post‐harvest recruitment patterns were not spatially random; Pinus seedlings initially established in natural grass openings and then proceeded to fill‐in stump patches created by harvesting. Knowledge of spatial pattern should be explicitly incorporated into restoration activities in these forests.     

Beyond the tropics: forest structure in a temperate forest mapped plot

Question: How do the diversity, size structure, and spatial pattern of woody species in a temperate (Mediterranean climate) forest compare to temperate and tropical forests? Location: Mixed evergreen coastal forest in the Santa Cruz Mountains, California, USA. Methods: We mapped, tagged, identified, and measured all woody stems (≥1 cm diameter) in a 6‐ha forest plot, following Center for Tropical Forest Science protocols. We compared patterns to those found in 14 tropical and 12 temperate forest plots. Results: The forest is dominated by Douglas‐fir (Pseudotsuga menziesii) and three species of Fagaceae (Quercus agrifolia, Q. parvula var. shrevei, and Lithocarpus densiflorus), and includes 31 woody species and 8180 individuals. Much of the diversity was in small‐diameter shrubs, treelets, and vines that have not been included in most other temperate forest plots because stems <5‐cm diameter had been excluded from study. The density of woody stems (1363 stems ha^?1) was lower than that in all but one tropical plot. The density of large trees (diameter ≥30 cm) and basal area were higher than in any tropical plot. Stem density and basal area were similar to most other temperate plots, but were less than in low‐diversity conifer forests. Rare species were strongly aggregated, with the degree of aggregation decreasing with abundance so that the most common species were significantly more regular than random. Conclusions: The patterns raise questions about differences in structure and dynamics between tropical and temperate forests; these need to be confirmed with additional temperate zone mapped plots that include small‐diameter individuals.     

Molecular insights into Aβ42 protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study

The aggregation of amyloid β‐peptide (Aβ₄₂) into toxic oligomers, fibrils, has been identified as a key process in Alzheimer's disease (AD) progression. The role of halogen‐substituted compounds have been highlighted in the disassembly of Aβ protofibril. However, the underlying inhibitory mechanism of Aβ₄₂ protofibril destabilization remains elusive. In this regard, a combined molecular docking and molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a fluorinated compound, D744 , which has been reported previously for potential in vitro and in vivo inhibitory activity against Aβ₄₂ aggregation and reduction in the Aβ‐induced cytotoxicity. The molecular docking analysis highlights that D744 binds and interacts with chain A of the protofibril structure with hydrophobic contacts and orthogonal multipolar interaction. MD simulations reveal destabilization of the protofibril structure in the presence of D744 due to the decrease in β‐sheet content and a concomitant increase of coil and bend structures, increase in the interchain D23‐K28 salt bridge distance, decrease in the number of backbone hydrogen bonds, increase in the average distance between Cα atoms, and decrease in the binding affinity between chains A and B of the protofibril structure. The binding free‐energy analysis between D744 and the protofibril structure with Molecular Mechanics Poisson‐Boltzmann Surface Area (MM‐PBSA) reveal that residues Leu17, Val18, Phe19, Phe20, Ala21, Glu22, Asp23, Leu34, Val36, Gly37, and Gly38 of chain A of the protofibril structure contribute maximum towards binding free energy (ΔG _binding  = −44.87 kcal/mol). The insights into the underlying inhibitory mechanism of small molecules that show potential in vitro anti‐aggregation activity against Aβ₄₂ will be beneficial for the current and future AD therapeutic studies.