Cluster analysis of spatial patterns in Malaysian tree species

Tree species in tropical rain forests exhibit a rich panoply of spatial patterns that beg ecological explanation. The analysis of tropical census data typically relies on spatial statistics, which quantify the average aggregation tendency of a species. In this article we develop a cluster-based approach that complements traditional spatial statistics in the exploration and analysis of ecological hypotheses for spatial pattern. We apply this technique to six study species within a fully mapped 50-ha forest census in peninsular Malaysia. For each species we identify the scale(s) of spatial aggregation and the corresponding tree clusters. We study the correlation between cluster locations and abiotic variables such as topography. We find that the distribution of cluster sizes exhibits equilibrium and nonequilibrium behavior depending on species life history. The distribution of tree diameters within clusters also varies according to species life history. At different spatial scales, we find evidence for both niche-based and dispersal-limited processes producing spatial pattern. Our methodology for identifying scales of aggregation and clusters is general; we discuss the method's applicability to spatial problems outside of tropical plant ecology.     

Towards patterns tree of gene coexpression in eukaryotic species

MOTIVATION: Cellular pathways behave coordinated regulation activity, and some reported works also have affirmed that genes in the same pathway have similar expression pattern. However, the complexity of biological systems regulation actually causes expression relationships between genes to display multiple patterns, such as linear, non-linear, local, global, linear with time-delayed, non-linear with time-delayed, monotonic and non-monotonic, which should be the explicit representation of cellular inner regulation mechanism in mRNA level. To investigate the relationship between different patterns, our work aims to systematically reveal gene-expression relationship patterns in cellular pathways and to check for the existence of dominating gene-expression pattern. By a large scale analysis of genes expression in three eukaryotic species, Saccharomyces cerevisiae, Caenorhabditis elegans and Human, we constructed gene coexpression patterns tree to systematically and hierarchically illustrate the different patterns and their interrelations. RESULTS: The results show that the linear is the dominating expression pattern in the same pathway. The time-shifted pattern is another important relationship pattern. Many genes from the different pathway also present coexpression patterns. The non-linear, non-monotonic and time-delayed relationship patterns reflect the remote interactions between the genes in cellular processes. Gene coexpression phenomena in the same pathways are diverse in different species. Genes in S.cerevisiae and C.elegans present strong coexpression relationships, especially in C.elegans, coexpression is more universal and stronger due to its special array of genes. However in Human, gene coexpression is not apparent and the human genome involves more complicated functional relationships. In conclusion, different patterns corresponding to different coordinating behaviors coexist. The patterns trees of different species give us comprehensive insight and understanding of genes expression activity in the cellular society.     

The reaction of hyaluronic acid and its monomers, glucuronic acid and N-acetylglucosamine, with reactive oxygen species

Synovial fluid is a approximately 0.15% (w/v) aqueous solution of hyaluronic acid (HA), a polysaccharide consisting of alternating units of GlcA and GlcNAc. In synovial fluid of patients suffering from rheumatoid arthritis, HA is thought to be degraded either by radicals generated by Fenton chemistry (Fe2+/H2O2) or by NaOCl generated by myeloperoxidase. We investigated the course of model reactions of these two reactants in physiological buffer with HA, and with the corresponding monomers GlcA and GlcNAc. meso-Tartaric acid, arabinuronic acid, arabinaric acid and glucaric acid were identified by GC-MS as oxidation products of glucuronic acid. When GlcNAc was oxidised, erythronic acid, arabinonic acid, 2-acetamido-2-deoxy-gluconic acid, glyceric acid, erythrose and arabinose were formed. NaOCl oxidation of HA yielded meso-tartaric acid; in addition, arabinaric acid and glucaric acid were obtained by oxidation with Fe2+/H2O2. These results indicate that oxidative degradation of HA proceeds primarily at glucuronic acid residues. meso-Tartaric acid may be a useful biomarker of hyaluronate oxidation since it is produced by both NaOCl and Fenton chemistry.     

Accounting for spatial autocorrelation in null models of tree species association

A commonly used null model for species association among forest trees is a well‐mixed community (WMC). A WMC represents a non‐spatial, or spatially implicit, model, in which species form nearest‐neighbor pairs at a rate equal to the product of their community proportions. WMC models assume that the outcome of random dispersal and demographic processes is complete spatial randomness (CSR) in the species’ spatial distributions. Yet, stochastic dispersal processes often lead to spatial autocorrelation (SAC) in tree species densities, giving rise to clustering, segregation, and other nonrandom patterns. Although methods exist to account for SAC in spatially‐explicit models, its impact on non‐spatial models often remains unaccounted for. To investigate the potential for SAC to bias tests based upon non‐spatial models, we developed a spatially‐heterogeneous (SH) modelling approach that incorporates measured levels of SAC. Using the mapped locations of individuals in a tropical tree community, we tested the hypothesis that the identity of nearest‐neighbors represents a random draw from neighborhood species pools. Correlograms of Moran's I confirmed that, for 50 of 51 dominant species, stem density was significantly autocorrelated over distances ranging from 50 to 200 m. The observed patterns of SAC were consistent with dispersal limitation, with most species occurring in distinct patches. For nearly all of the 106 species in the community, the frequency of pairwise association was statistically indistinguishable from that projected by the null models. However, model comparisons revealed that non‐spatial models more strongly underestimated observed species‐pair frequencies, particularly for conspecific pairs. Overall, the CSR models projected more significant facilitative interactions than did SH models, yielding a more liberal test of niche differences. Our results underscore the importance of accounting for stochastic spatial processes in tests of association, regardless of whether spatial or non‐spatial models are employed.     

Ages and long-term growth patterns of four threatened Vietnamese tree species

Conservation of threatened tree species requires basic information on growth rates and ages. This information is lacking for many species, but can be obtained relatively easily from tree ring analysis. We studied four threatened Vietnamese species: three conifers from high-elevation forests (Calocedrus macrolepis, Dacrydium elatum and Pinus kwangtungensis) and one broad-leaved species from lowland forest (Annamocarya sinensis). We collected increment cores from remnant populations in protected areas and measured ring width. We built chronologies and found significant correlations with rainfall (all species) and temperature (two species), indicating that rings were formed annually. Diameter-age trajectories showed that species reached reproductive size at 60–80 years. Maximum observed ages were 128–229 years. Some species showed large variation in long-term growth rates among individuals, which was partially explained by strong persistence of growth differences. We also assessed whether growth rates changed over time. For certain size categories in some species, we found higher recent growth rates of juvenile trees compared to those in the distant past. This shift requires a cautious interpretation, but is consistent with a CO₂ fertilization effect. For other size categories, we found contrasting results: extant large trees had higher growth rates as small juveniles compared to extant small trees. Such correlations, which we found for all species, suggest a ‘juvenile selection effect’: the preferential survival of fast-growing juveniles to the canopy. Information on ages, historical growth rates and juvenile selection effect is relevant for the planning of conservation actions.     

Immunogold EM reveals a close association of plectin and the desmin cytoskeleton in human skeletal muscle.

Plectin is a multifunctional cytoskeletal linker protein with an intermediate filament-binding site and sequence elements with high homology to actin-binding domains. Mutations of the human plectin gene as well as the targeted inactivation of its murine analog cause a generalized blistering skin disorder and muscular dystrophy, thus implying its essential role in cells that are exposed to mechanical stress. In the present study we report the characterization of two new domain-specific plectin antibodies as well as ultrastructural localization of plectin in normal human skeletal muscle. Using immunogold electron microscopy, we localized plectin at three prominent sites: 1) Plectin is found at regularly spaced intervals along the cytoplasmic face of the plasma membrane. 2) It is distinctly localized at filamentous bridges between Z-lines of peripheral myofibrils and the sarcolemma and 3) at structures forming the intermyofibrillar scaffold. At the latter two locations, plectin and desmin were found to colocalize. Our ultrastructural analysis suggests that plectin may have a central role in the structural and functional organization of the intermediate filament cytoskeleton in mature human skeletal muscle.     

Diurnal patterns of respiration in the leaves of four forest tree species

Respiration along the cyanide-sensitive, cytochrome pathway and the cyanide-in-sensitive, alternative pathway was monitored over a 24-h period in the leaves of Acerrubrum, Betula papyrifera, Populus tremuloides and Quercus rubra excised in the field. Populus displayed the greatest rate of total respiration, followed by Betula, Quercus and Acer . All species displayed the capacity for the alternative pathway as well as some engagement of the pathway, although the level of engagement in Acer was very low. In all species investigated there were no marked diurnal trends in any respiration variable measured. Leaf soluble sugar levels remained at a relatively constant level throughout the sampling period. It is concluded that respiration did not show diurnal fluctuations because substrate supply in the leaf was maintained at a constant level.     

Comparative recruitment patterns of two non-pioneer canopy tree species in French Guiana

Summary A comparative study was conducted on the recruitment patterns of two non-pioneer tree species, one dispersed by arboreal mammals and birds (Virola michelii, Myristicaceae) and the other by rodents (Moronobea coccinea, Clusiaceae). These species differ in fruiting phenology, seed size, dispersal distance, germination time and seed nutrient exhaustion. In both species, establishment patterns were consistent with the escape hypothesis and the Janzen-Connell model. Virola seeds need not be buried to survive and germinate, and may produce a seedling carpet beneath the parent. Moronobea seedlings only establish from seeds buried by scatterhoarding rodents in the surrounding understory. One-year survival of Virola seedlings was 47.8% and was greater >10 m than < 10 m from the largest parent tree. In contrast, survival of Moronobea seedlings was 56% 3 years after seed dispersal. Survival of juveniles was greater in gaps than in the understory for Virola but not for Moronobea. Moronobea survival was greater than Virola survival in both microhabitats. Both species establish in the understory, yet both grew faster in gaps. Virola appeared to be more gap-dependent than Moronobea which may persist several years in the understory until a gap occurs. Virola and Moronobea illustrate two intermediate recruitment patterns along an hypothetical continuum of nonpioneer species replacement (Bazzaz and Pickett 1980; Swaine and Whitmore 1988).     

Distribution patterns of tree species in an evergreen broadleaved forest in eastern China

Ecological assembly rules in evergreen broad-leaved forest are far from clear understanding. Spatial dispersion of individuals in a species is central in ecological theory. We analyzed the spatial patterns as well as associations between adult and juvenile of each tree species in a 5-ha subtropical evergreen broad-leaved forest plot in eastern China. Out of the 74 species occurring with more than 10 individuals, 88.4% of these species are aggregated. Most of them are aggregated from small to large scales. Spatial distributions of some species corre-spond with topography. Many bad dispersed species in the Baishanzu exhibit a highly aggregated distribution at small scales. These suggest that environmental heterogeneity and/or dispersal limitation may be the most important mechanisms that control the distribution patterns of these species. Our observations of the aggregations of abundant species basically support the hypothesis that dispersal limitation decreases as the number of reproductive trees increases. The rest species are randomly distributed, with less than 10 individuals. For most common species, spatial aggregation is weaker in larger diameter classes, and the distance between adults is larger than that between juveniles and adults, suggesting that density-dependence works on loosing aggregation and excluding conspecific juveniles away from adult trees. However, the density-dependent effect is not strong enough to eliminate all seedlings near adult trees and to result in a regular distribution of trees; thus the density dependence is usually masked by the refuge effect.     

长白山次生林乔木树种空间分布格局

应用RipleyK函数,分析了长白山一个5．2hm^2次生林样地内乔木树种的空间分布以及主要乔木树种的幼树、小树、大树的空间分布和空间关系。结果表明：共调查到34种乔木,其中常见种27种,少见种7种,共计15688株;在27个常见种中,有23个种在空间上主要呈聚集分布,另外4个种主要表现为随机分布;在7个少见种中,均主要表现为随机分布;簇毛槭、假色槭、水曲柳、臭松和红松随着种群发育（幼树→小树→大树）聚集强度逐渐减弱,直至趋向于随机分布,其他树种的空间分布随种群发育未表现出明显的变化规律;在10个主要树种组成的45个种对中,有11个种对表现出显著正相关,1个种对为显著负相关。     

Distribution patterns of tree species in an evergreen broadleaved forest in eastern China

Ecological assembly rules in evergreen broad-leaved forest are far from clear understanding. Spatial dispersion of individuals in a species is central in ecological theory. We analyzed the spatial patterns as well as associations between adult and juvenile of each tree species in a 5-ha subtropical evergreen broad-leaved forest plot in eastern China. Out of the 74 species occurring with more than 10 individuals, 88.4% of these species are aggregated. Most of them are aggregated from small to large scales. Spatial distributions of some species correspond with topography. Many bad dispersed species in the Baishanzu exhibit a highly aggregated distribution at small scales. These suggest that environmental heterogeneity and/or dispersal limitation may be the most important mechanisms that control the distribution patterns of these species. Our observations of the aggregations of abundant species basically support the hypothesis that dispersal limitation decreases as the number of reproductive trees increases. The rest species are randomly distributed, with less than 10 individuals. For most common species, spatial aggregation is weaker in larger diameter classes, and the distance between adults is larger than that between juveniles and adults, suggesting that density-dependence works on loosing aggregation and excluding conspecific juveniles away from adult trees. However, the density-dependent effect is not strong enough to eliminate all seedlings near adult trees and to result in a regular distribution of trees; thus the density dependence is usually masked by the refuge effect.     

Spatial patterns and competition of tree species in a Douglas-fir chronosequence on Vancouver Island

While the successional dynamics and large-scale structure of Douglas-fir forest in the Pacific Northwest region is well studied, the fine-scale spatial characteristics at the stand level are still poorly understood. Here we investigated the fine-scale spatial structure of forest on Vancouver Island, in order to understand how the three dominant species, Douglas-fir, western hemlock, and western redcedar, coexist and partition space along a chronosequence comprised of immature, mature, and old-growth stands. We quantified the changes in spatial distribution and association of the species along the chronosequence using the scale-dependent point pattern analyses pair-correlation function g(r) and Ripley's L-function. Evidence on intra- and inter-specific competition was also inferred from correlations between nearest-neighbor distances and tree size. Our results show that 1) the aggregation of Douglas-fir in old-growth was primarily caused by variation in local site characteristics, 2) only surviving hemlock were more regular than their pre-mortality patterns, a result consistent with strong intra-specific competition, 3) inter-specific competition declined rapidly with stand age due to spatial resource partitioning, and (4) tree death was spatially randomly distributed among larger overstory trees. The study highlights the importance of spatial heterogeneity for the long-term coexistence of shade-intolerant pioneer Douglas-fir and shade-tolerant western hemlock and western redcedar.     

Radial patterns of xylem sap flow in non-, diffuse- and ring-porous tree species

We investigated radial patterns of sap flux density and wood properties in the sapwood of young loblolly pine (Finns taeda L.), mature white oak (Quercus alba L.) and sweetgum (Liquidambar styraciflua L.), which represent three major classes of wood anatomy: non-porous (coniferous), ring-porous and diffuse-porous. Radial measurements of xylem sap flux density were made in sections of xylem extending to 20 mm and 20–40 mm from the cambium. These measurements were compared with measurements of the relative water content (R_s) and sapwood specific gravity (ρ_r) of corresponding radial sections. In both hardwood species, sap flow differences were rarely significant between the two depth intervals. In pine, a 59% reduction in daily sap flux density from outer to inner sapwood was found. This could not be accounted for by a 3% drop in R_s; rather, an accompanying 9% reduction in ρ_r indicated a transition between the depth intervals from mature to juvenile sapwood, and is the probable cause of the lower flux rate in the inner xylem of pine.     

Spatial and temporal patterns of seed attack and germination in a large-seeded neotropical tree species

It has long been argued that seed dispersal enhances recruitment in tropical trees by allowing offspring to `escape' strong density/distance-dependent attack by insects, pathogens and rodents. Here we examined the effects of canopy openness and parent-offspring distance upon the frequency and timing of Chlorocardium rodiei seed attack and germination within a 15-ha plot of Guyanan tropical rain forest. Seeds were artificially dispersed beneath parent trees, in the understorey away from trees and in gaps. Analysing our data from an 85-week period of regular monitoring, we found that the main spatial gradients, canopy openness and distance to nearest adult conspecific, do not lead to differences in the final number of seeds attacked by infesting scolytid beetles or rodents. The timing of beetle attack, however, varied along the distance gradient and this difference affords seeds at further distances a `window' in which to germinate and produce a seedling before attack. Canopy openness was not a good predictor of rooting success, but distance was strongly associated with root and shoot formation success and the mean time to shoot formation. There was a strong negative effect of distance on the likelihood of a seed being colonised by scolytid beetles prior to removal by rodents and shoot failure was strongly associated with prior infestation. We believe these results bring a key point to bear on the well-established notion of distance-dependent attack on seeds in tropical rainforests, viz. that seed characteristics (size, germination syndrome) and the timing of attack may be more important in explaining patterns of early seedling recruitment than distance. Our studies suggest that advantages accrued through dispersal in species like Chlorocardium will depend heavily on the `race' between seed germination and attack. In the case of Chlorocardium, the `race' can be lost at considerable distances due to its prolonged dormancy and the temporal fluctuations in fruitfall and rainfall which influence attack and germination. The results presented here suggest that the lag between seed attack and germination in tropical trees can regulate the influence of parent-offspring distance on cohort recruitment at this life history stage. Received: 5 March 1998 / Accepted: 6 December 1998