Weak Competition Among Tropical Tree Seedlings: Implications for Species Coexistence

The intensity of competition among forest tree seedlings is poorly understood, but has important ramifications for their recruitment and for the maintenance of species diversity. Intense competition among seedlings could allow competitively dominant species to exclude subordinate species. Alternatively, the low density and small stature of forest tree seedlings could preclude intense interseedling competition. In this case, other processes, such as size-asymmetric competition with adults, interactions with consumers, or neutral dynamics would prevail as those structuring the forest understory. We tested the intensity of, and potential for, intraspecific competition among tree seedlings of three species ( Brosimum alicastrum , Matisia cordata , and Pouteria reticulata ) in two Neotropical rain forests. We reduced stem densities by up to 90 percent and monitored individual growth and survival rates for up to 24 mo. Individual growth and survival rates were generally unrelated to stem density. Contrary to the predicted behavior of intensely competing plant populations, the distribution of individual heights did not become more left-skewed with time for any species, regardless of plot density; i.e. , excesses of short, suppressed individuals did not accumulate in high-density plots. We further measured the overlap of zones of influence (ZOIs) to assess the potential for resource competition. Seedling ZOIs overlapped only slightly in extremely dense monodominant plots, and even less in ambient-density plots of mixed composition. Our results thus suggest that interseedling competition was weak. Given the low density of tree seedlings in Neotropical forests, we infer that resource competition among seedlings may be irrelevant to their recruitment.     

Tree Competition and Species Coexistence in a Sub-boreal Forest, Northern Japan

The growth and mortality patterns and the mode of competitionof six tree species forming a sub-boreal climax forest in Hokkaido,northern Japan, were investigated based on the diffusion modelat the level of the individual tree 2 m height in a 2·3-hastudy site. Picea jezoensis, Picea glehnii, Betula ermanii andAbies sachalinensis were dominant species, occupying approx.94% of the total basal area. Sorbus commixta and Acer ukurunduensewere subordinate species occupying approx. 6% of the total basalarea. A model for individual growth was developed, consideringboth intra- and inter-specific competition and the degree ofcompetitive asymmetry. Asymmetry was found in intraspecificcompetition of Sorbus commixta and Acer ukurunduense. Piceajezoensis, Betula ermanii and Abies sachalinensis showed symmetricintraspecific competition. There was little interspecific competitionamongst Picea jezoensis, Picea glehnii and Betula ermanii. Abiessachalinensis competed symmetrically with Picea jezoensis (onlyvery weakly, P < 0·1) and Betula ermanii (P < 0·01).Picea glehnii gave no indication of inter- or intra-specificcompetition. The growth of the four dominant species was neveraffected by the two subordinate species; the growth of the twosubordinate species was governed by the abundances of the fourdominant species, the sum of which almost amounted to standcrowdedness (i.e. symmetric competitive effect and one-sidedcompetitive direction). On the scale of 2·3 ha of thesub-boreal forest, symmetric competition prevailed over one-sidedor asymmetric competition although statistical evidence forany competitive effects was rather weak. This was probably dueto the relatively low tree density and stand crowdedness ofthis climax forest. Little competition between the dominantspecies suggested by relatively low proportions of r²-valuesattributable to competitive effects indicates weak organizationamongst the component species (i.e. species were more or lessindependent of each other) at the level of the individual tree 2 m height on the 2·3-ha scale.Copyright 1995, 1999Academic Press Climax forest, diffusion model, individual growth, one-sided competition, size structure, symmetric competition     

Effects of Species Diversity on Establishment and Coexistence: A Phylloplane Fungal Community Model System

A model system was devised, evaluating the influence that species diversity (species richness) has on fungal establishment and coexistence. Seven members of the fungal phylloplane community of Vaccinium macrocarpon (American cranberry) were selected to assess how species diversity affected development and coexistence of another community member, Pestalotia vaccinii. Pestalotia was engaged in competitive interactions on 1% Malt Extract Agar (MEA) petri dishes with each of the seven individual saprotrophs (two-way interaction), in random combinations with three of the seven saprotrophs (four-way interaction), and in random combinations with five of the seven saprotrophs (six-way interaction). The saprotrophic fungi used in this study were Aspergillus sp., Alternaria alternata, Cladosporium cladosporoides, Curvularia lunata, Epicoccum purpuracens, Penicillium sp., and Pithomyces chartarum. We hypothesized that species diversity would have a significant impact on the establishment and coexistence of Pestalotia vaccinii in culture. In an effort to minimize density-dependent effects, the number of viable spores employed in the three types of interactions was kept constant. Target spore concentrations of 50 viable spores of P. vaccinii and 50 saprotroph spores were used, regardless of the number of species involved in the interaction. This proved to be a very important factor in the experiment. As our results show, species diversity had little or no effect on the establishment and coexistence of Pestalotia vaccinii; however, spore density played an extremely important role in the establishment and development of fungal propagules in our model.     

Disturbance Level Determines the Regeneration of Commercial Tree Species in the Eastern Amazon

The effects of reduced‐impact logging (RIL) on the regeneration of commercial tree species were investigated, as long‐term timber yields depend partly on the availability of seedlings in a managed forest. On four occasions during a 20‐month period in the Tapajós National Forest (Eastern Amazon, Brazil), seven commercial tree species were assessed as follows: the long‐lived pioneers Bagassa guianensis and Jacaranda copaia; the partially shade‐tolerant Hymenaea courbaril, Dipteryx odorata, and Carapa guianensis; and the totally shade‐tolerant Symphonia globulifera and Manilkara huberi. In 2439 10 × 10 m plots, all individuals < 20 cm diameter at breast height (dbh) were assessed over three intervals, before, during, and after the forest being logged. Before logging, the density of seedlings and saplings of the seven species did not change. Logged trees were spatially aggregated, with 9.2 percent of the plots being heavily impacted by logging. After logging, the recruitment rate increased more than the mortality rate, so that post‐harvesting densities of seedlings and saplings increased. The increase in density was concentrated in logged plots with more disturbances. It is concluded that post‐harvesting heterogeneity of micro‐environments created by RIL may be an important component to be taken into account for sustainable forest management and conservation of commercial species.     

The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space

When organisms need to perform multiple tasks they face a fundamental tradeoff: no phenotype can be optimal at all tasks. This situation was recently analyzed using Pareto optimality, showing that tradeoffs between tasks lead to phenotypes distributed on low dimensional polygons in trait space. The vertices of these polygons are archetypes—phenotypes optimal at a single task. This theory was applied to examples from animal morphology and gene expression. Here we ask whether Pareto optimality theory can apply to life history traits, which include longevity, fecundity and mass. To comprehensively explore the geometry of life history trait space, we analyze a dataset of life history traits of 2105 endothermic species. We find that, to a first approximation, life history traits fall on a triangle in log-mass log-longevity space. The vertices of the triangle suggest three archetypal strategies, exemplified by bats, shrews and whales, with specialists near the vertices and generalists in the middle of the triangle. To a second approximation, the data lies in a tetrahedron, whose extra vertex above the mass-longevity triangle suggests a fourth strategy related to carnivory. Each animal species can thus be placed in a coordinate system according to its distance from the archetypes, which may be useful for genome-scale comparative studies of mammalian aging and other biological aspects. We further demonstrate that Pareto optimality can explain a range of previous studies which found animal and plant phenotypes which lie in triangles in trait space. This study demonstrates the applicability of multi-objective optimization principles to understand life history traits and to infer archetypal strategies that suggest why some mammalian species live much longer than others of similar mass.     

Lessons Learned While Integrating Habitat,Dispersal, Disturbance,and Life-History Traits into Species Habitat Models Under Climate Change

We present an approach to modeling potential climate-driven changes in habitat for tree and bird species in the eastern United States. First, we took an empirical-statistical modeling approach, using randomForest, with species abundance data from national inventories combined with soil, climate, and landscape variables, to build abundance-based habitat models for 134 tree and 147 bird species. We produced lists of species for which suitable habitat tends to increase, decrease, or stay the same for any region. Independent assessments of trends of large trees versus seedlings across the eastern U.S. show that 37 of 40 species in common under both studies are currently trending as modeled. We developed a framework, ModFacs, in which we used the literature to assign default modification factor scores for species characteristics that cannot be readily assessed in such models, including 12 disturbance factors (for example, drought, fire, insect pests), nine biological factors (for example, dispersal, shade tolerance), and assessment scores of novel climates, long-distance extrapolations, and output variability by climate model and emission scenario. We also used a spatially explicit cellular model, SHIFT, to calculate colonization potentials for some species, based on their abundance, historic dispersal distances, and the fragmented nature of the landscape. By combining results from the three efforts, we can create projections of potential climate change impacts over the next 100 years or so. Here we emphasize some of the lessons we have learned over 16 years in hopes that they may help guide future experiments, modeling efforts, and management.     

TRADER: A package for Tree Ring Analysis of Disturbance Events in R

Studies using tree-rings to reconstruct forest disturbance dynamics are common and their number has been increasing in the recent years. Despite the evident need for a common set of tools for verification, replication and comparison across studies, only a few DOS programmes for disturbance detection exist and they are for limited purposes only. Currently, the ideal statistical environment for the task is R, which is becoming the primary tool for various types of tree-ring analyses. This has led to the development of TRADER (Tree Ring Analysis of Disturbance Events in R), an open-source software package for R that provides an analysis of tree growth history for disturbance reconstructions. We have implemented four methods, which are commonly used for the detection of disturbance events: radial-growth averaging criteria developed by Nowacki and Abrams, 1997, the boundary-line method (Black and Abrams, 2003), the absolute-increase method (Fraver and White, 2005), and the combination of radial-growth averaging and boundary-line techniques (Splechtna et al., 2005). TRADER, however, enables the analysis of disturbance history by a total of 24 published methods. Furthermore, functions for the detection of tree recruitment and growth trends were also included. The main features of the presented package are described and their application is shown on a real tree-ring datasets. The package requires little knowledge of the R environment giving straightforward analyses with suitable parameters, but at the same time it is easily modifiable by the more experienced user. The package improves research efficiency and facilitates replication of previous studies. One of its major advantages is that it offers the possibility for comparison between different methods of disturbance history reconstruction.     

Split Probabilities and Species Tree Inference Under the Multispecies Coalescent Model

Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the probabilities of splits on gene trees under the multispecies coalescent model, and how their features might inform species tree inference. After investigating the behavior of split consensus methods, we investigate split invariants—that is, polynomial relationships between split probabilities. These invariants are then used to show that, even though a split is an unrooted notion, split probabilities retain enough information to identify the rooted species tree topology for trees of 5 or more taxa, with one possible 6-taxon exception.     

Spatial Complementarity and the Coexistence of Species

Coexistence of apparently similar species remains an enduring paradox in ecology. Spatial structure has been predicted to enable coexistence even when population-level models predict competitive exclusion if it causes each species to limit its own population more than that of its competitor. Nevertheless, existing hypotheses conflict with regard to whether clustering favours or precludes coexistence. The spatial segregation hypothesis predicts that in clustered populations the frequency of intra-specific interactions will be increased, causing each species to be self-limiting. Alternatively, individuals of the same species might compete over greater distances, known as heteromyopia, breaking down clusters and opening space for a second species to invade. In this study we create an individual-based model in homogeneous two-dimensional space for two putative sessile species differing only in their demographic rates and the range and strength of their competitive interactions. We fully characterise the parameter space within which coexistence occurs beyond population-level predictions, thereby revealing a region of coexistence generated by a previously-unrecognised process which we term the triadic mechanism. Here coexistence occurs due to the ability of a second generation of offspring of the rarer species to escape competition from their ancestors. We diagnose the conditions under which each of three spatial coexistence mechanisms operates and their characteristic spatial signatures. Deriving insights from a novel metric — ecological pressure — we demonstrate that coexistence is not solely determined by features of the numerically-dominant species. This results in a common framework for predicting, given any pair of species and knowledge of the relevant parameters, whether they will coexist, the mechanism by which they will do so, and the resultant spatial pattern of the community. Spatial coexistence arises from complementary combinations of traits in each species rather than solely through self-limitation.     

Soil Nematode Diversity: Species Coexistence and Ecosystem Function

Soil nematode species diversity is often high, both at ecosystem and single soil-core scales. First, how can so many species coexist? There is evidence of niche partitioning, notably of physical space, but vast interspecific overlaps and trait plasticity seem equally common. It appears that coexistence of species with similar resource needs is made possible by small-scale disturbance and predation, which likely reduce local population sizes and interspecific competition. Regional processes such as dispersal, large-scale disturbance, and aggregation, which govern ecosystem level diversity, may also affect local species interactions and soil-core scale diversity. Second, what is the significance of having so many species, with so few trophic functions, for ecosystem processes? Focusing on bacterivore diversity, it is clear that species contributions to decomposition, likely to differ as a function of individual biologies, are concealed by the trophic group approach. However, considerable functional redundancy probably exists, which may explain why decomposition processes are maintained in highly disturbed soils despite the extinction of many species. Thus, soil nematode diversity is important for the long-term stability of soil functioning, and merits protection and further study.     

Aggregation and the Coexistence of Competing Parasitoid Species

In nature, many insect species are attacked by more than one specialized species of parasitoid. We examine whether parasitoid aggregation among patches containing hosts can promote the coexistence of specialized parasitoids on the same host species. We construct models to analyze the effects of three types of parasitoid aggregation: direct density-dependent, inverse density-dependent, and density-independent aggregation. All three types of aggregation may facilitate coexistence, provided the parasitoid species show behavioral differences that produce different patterns of aggregation. By deriving general conditions of coexistence of parasitoids, we show that all three types of aggregation act to facilitate coexistence in the same way—by increasing the covariance between the distributions of susceptible hosts and the least common parasitoid. Although they act in the same way, in general the effect of density-independent aggregation in facilitating coexistence is greater than either direct or inverse density-dependent aggregation. This suggests that density-independent aggregation may have the greatest potential to facilitate the coexistence of specialize parasitoids using the same host.     

Differing Life History Characteristics Support Coexistence of Tree Soil Generalist and Specialist Species in Tropical Rain Forests

Niche differentiation is a prominent mechanism for explaining tree species coexistence in tropical rain forests. Theory predicts that species that are specialized on a set of environmental conditions should competitively exclude generalists in those conditions, and that environmental heterogeneity allows the coexistence of many different species based on niche specialization. Yet, many tropical tree species of the family Dipterocarpaceae have broadly similar habitat preferences, with some occurring widely across several soil types. These soil generalists clearly persist despite the presence of other dipterocarp species that show clear soil specialization. We evaluate comparative seedling performance (growth and survival) of six Shorea species (Dipterocarpaceae) which differ in their adult tree habitat associations within the Sepilok Forest Reserve (Borneo, Malaysia). We tested the hypothesis that seedlings of species associated with a particular soil type perform better on that soil type than seedlings of soil generalist species, with generalists in turn performing better than specialists on a different soil type. We conducted a reciprocal transplant experiment including two soil types (alluvial and mudstone) and two light treatments (gap and understory). The soils differed in soil acidity, Al and P concentration. Observed species‐specific differences in seedling responses to soil, light, and occasional flooding events could partially explain observed adult distribution, although not all species could be fully differentiated along these axes. Other trade‐offs, such as investment in defense against herbivores and tolerance to soil waterlogging, may play additional roles in explaining coexistence of these species.     

Tree Species Composition and Diversity at Different Levels of Disturbance in Popa Mountain Park,Myanmar

Tropical forests are highly threatened by human activities, even within the protected areas that have been established to conserve biodiversity. Human activities may have different degrees of impact on vegetation structure, composition and diversity. Some studies have measured direct evidence of human activities in forming disturbance gradients, while others have quantified canopy cover as a proxy for disturbance. When measurement is confined to human activities, disturbance may be underestimated in areas of poor canopy cover where forest degrading activities have ceased. Where measurements are restricted to canopy cover, disturbance may be underestimated in areas of extensive canopy cover that may have been subject to past disturbances, and overestimated for areas where canopy cover is naturally sparse. Combining indicators of past and present disturbances is therefore necessary to examine the full spectrum of human disturbances. Forest vegetation in Popa Mountain Park, Myanmar was surveyed and classified into three levels of disturbance—undisturbed, medium disturbed and highly disturbed—derived from evidence of cutting and canopy cover. The forests are second or third growth after clearing for agriculture in the early 20th century. All trees with ≥10 cm diameter at breast height in 168 sample plots (10 m × 10 m) were identified and measured. Density, basal area and diversity decreased and dominance rose when disturbance increased. Canonical correspondence analysis (CCA) clearly discriminated three forest stands and CCA axes were significantly correlated to soil moisture, soil nitrogen, elevation, slope, aspect, distance from park boundary and distance from villages. Abstract in Myanmar is available at http://www.blackwell‐synergy.com/loi/btp .     

Host Specificity of Pathogenic Pythium Species: Implications for Tree Species Diversity

In the Janzen–Connell hypothesis, host-specific natural enemies enhance species diversity and influence the structure of plant communities. This study tests the explicit assumption of host specificity for soil pathogens of the genus Pythium that cause damping-off disease of germinating seeds and seedlings. We isolated Pythium spp. from soil of a tropical forest in Panama. Then, in an inoculation experiment, we determined the pathogenicity of 75 tropical isolates of unknown pathogenicity and seven pathogenic temperate isolates of Pythium on seeds and/or seedlings of eight tropical tree species. Only three tropical isolates, one identified as P. ultimum and two as P. aphanidermatum , were pathogenic. Tropical pathogenic isolates were pathogenic on 4–6 of eight tree species. Temperate isolates were pathogenic on 0–4 of eight species, indicating that some tropical tree species are susceptible to novel isolates of Pythium . No tree species was susceptible to all isolates and two species were not susceptible to any isolate. Collectively, these results indicate that these Pythium isolates vary widely in their pathogenicity, causing differential mortality of potential host species; likewise, the tree species vary in their susceptibility to a given Pythium isolate. These differences in pathogenicity and susceptibility indicate some support for the Janzen–Connell assumption of host specificity. While they are not restricted to a single species, their intermediate level of specificity suggests that Pythium spp. have the potential to have some effect on forest community structure and diversity.     

Robinia pseudoacacia L.: A Lesser Known Tree Species for Biomass Production

Experiments with fast-growing tree species for biomass production in Germany have been mainly focused on the growth performance of Populus and Salix spp. Among the lesser-known species for energy plantations is Robinia pseudoacacia L. Special features of this species are its drought tolerance and its ability to fix nitrogen. Given the large share of marginal arable land in NE-Germany and the predicted climate change, R. pseudoacacia is expected to grow in importance. In order to evaluate the growth performance of this species under extreme conditions, four experiments were established in the post-mining landscape of the Lusatian lignite-mining district (NE-Germany). Biomass production was estimated for 3- to 14-year-old shoots on 4- to 14-year-old roots. Results for the annual production of oven-dried biomass of R. pseudoacacia ranged between 3 and 10 t ha^?1, which was substantially greater than the biomass of poplar and willow clones established on the same site. Economic analysis results show that the rotation period, the duration of the plantation, and the harvesting costs are important parameters for the economic return and cash flow in short-rotation coppice cultivation. The results show that the cultivation of R. pseudoacacia is an economically competitive land-use strategy for the post-mining landscapes considered in our study.     

Species, clusters and the ‘Tree of life’: A graph-theoretic perspective

A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a ‘Tree of Life’. In this paper we use an approach based on discrete mathematics to address a basic question: could one delineate this hierarchical structure in nature purely by reference to the ‘genealogy’ of present-day individuals, which describes how they are related with one another by ancestry through a continuous line of descent? We describe several mathematically precise ways by which one can naturally define collections of subsets of present day individuals so that these subsets are nested (and so form a tree) based purely on the directed graph that describes the ancestry of these individuals. We also explore the relationship between these and related clustering constructions.     

tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.     

A New Model for Size-Dependent Tree Growth in Forests

Tree growth, especially diameter growth of tree stems, is an important issue for understanding the productivity and dynamics of forest stands. Metabolic scaling theory predicted that the 2/3 power of stem diameter at a certain time is a linear function of the 2/3 power of the initial diameter and that the diameter growth rate scales to the 1/3 power of the initial diameter. We tested these predictions of the metabolic scaling theory for 11 Japanese secondary forests at various growth stages. The predictions were not supported by the data, especially in younger stands. Alternatively, we proposed a new theoretical model for stem diameter growth on the basis of six assumptions. All these assumptions were supported by the data. The model produced a nearly linear to curvilinear relationship between the 2/3 power of stem diameters at two different times. It also fitted well to the curvilinear relationship between diameter growth rate and the initial diameter. Our model fitted better than the metabolic scaling theory, suggesting the importance of asymmetric competition among trees, which has not been incorporated in the metabolic scaling theory.