Modelling plant species richness using functional groups

Conservation biologists increasingly rely on spatial predictive models of biodiversity to support decision-making. Therefore, highly accurate and ecologically meaningful models are required at relatively broad spatial scales. While statistical techniques have been optimized to improve model accuracy, less focus has been given to the question: How does the autecology of a single species affect model quality? We compare a direct modelling approach versus a cumulative modelling approach for predicting plant species richness, where the latter gives more weight to the ecology of functional species groups. In the direct modelling approach, species richness is predicted by a single model calibrated for all species. In the cumulative modelling approach, the species were partitioned into functional groups, with each group calibrated separately and species richness of each group was cumulated to predict total species richness. We hypothesized that model accuracy depends on the ecology of individual species and that the cumulative modelling approach would predict species richness more accurately. The predictors explained plant species richness by ca. 25%. However, depending on the functional group the deviance explained varied from 3 to 67%. While both modelling approaches performed equally well, the models of the different functional groups highly varied in their quality and their spatial richness pattern. This variability helps to improve our understanding on how plant functional groups respond to ecological gradients.     

Species, functional groups, and thresholds in ecological resilience

The cross-scale resilience model states that ecological resilience is generated in part from the distribution of functions within and across scales in a system. Resilience is a measure of a system's ability to remain organized around a particular set of mutually reinforcing processes and structures, known as a regime. We define scale as the geographic extent over which a process operates and the frequency with which a process occurs. Species can be categorized into functional groups that are a link between ecosystem processes and structures and ecological resilience. We applied the cross-scale resilience model to avian species in a grassland ecosystem. A species' morphology is shaped in part by its interaction with ecological structure and pattern, so animal body mass reflects the spatial and temporal distribution of resources. We used the log-transformed rank-ordered body masses of breeding birds associated with grasslands to identify aggregations and discontinuities in the distribution of those body masses. We assessed cross-scale resilience on the basis of 3 metrics: overall number of functional groups, number of functional groups within an aggregation, and the redundancy of functional groups across aggregations. We assessed how the loss of threatened species would affect cross-scale resilience by removing threatened species from the data set and recalculating values of the 3 metrics. We also determined whether more function was retained than expected after the loss of threatened species by comparing observed loss with simulated random loss in a Monte Carlo process. The observed distribution of function compared with the random simulated loss of function indicated that more functionality in the observed data set was retained than expected. On the basis of our results, we believe an ecosystem with a full complement of species can sustain considerable species losses without affecting the distribution of functions within and across aggregations, although ecological resilience is reduced. We propose that the mechanisms responsible for shaping discontinuous distributions of body mass and the nonrandom distribution of functions may also shape species losses such that local extinctions will be nonrandom with respect to the retention and distribution of functions and that the distribution of function within and across aggregations will be conserved despite extinctions.     

Running to stand still: temperature effects on species richness, species turnover, and functional community dynamics

The information on temperature-mediated changes in biodiversity in local assemblages is scarce and mainly addresses the change in species richness. However, warming may have more consistent effects on species turnover than on the number of species. Moreover, very few studies extended the analysis of changes in biodiversity and species composition to questions of associated ecosystem functions such as primary production. Here, we synthesize 4 case studies employing microalgal microcosms within the Aquashift priority program to ask (1) do warming-related shifts in species richness correspond to changes in the rate of biomass production, (2) do similar relationships prevail for evenness, and (3) do warming-related shifts in species turnover stabilize or destabilize biomass production? Two of the four cases are previously unpublished, and for a third case, the link between diversity and functional consequences of temperature was not analyzed before. We found accelerated loss of species with warming in all cases. Biomass production was lower with lower species richness in most cases but increased with lower evenness. Most importantly, the relation between functional and compositional stability was different between cases: More rapid extinction resulted in more variable biomass in 2 cases conducted with a limited species pool, indicating that compositional destabilization relates to functional variability. By contrast, the only experiment with a large species pool (30 species) allowed previously rare species to become dominant in the community and showed more stable biomass at high turnover, indicating that compensatory dynamics (turnover) can promote functional stability. These 4 independent experiments highlight the need to consider both compositional and functional consequences of altered temperature regimes.     

Prediction of germination rates of weed species: Relationships between germination speed parameters and species traits

In fields, the timing of weed emergence flushes is mostly related to the timing and rate of seed germination, which depend on seed dormancy level, soil temperature and water potential conditions as well as soil tillage and crop sowing date. Seed germination parameters are essential in weed dynamics models to account for the effects of soil conditions on weed demography. Since these parameters are difficult to measure, our objective was to test the possibility of estimating them from easily accessible information. Seed germination parameters (germination lag-time, time to mid-germination and mid-germination rate) were measured or collected from the literature for 25 weed species with contrasted seed characteristics. Correlations were then searched for between these parameters and morphological, chemical and physiological seed traits as well as seed dormancy level. The dormancy level was positively correlated with speed of germination parameters. Earliness of germination was positively correlated with seed lipid content and the seed area to mass ratio. Germination was also earlier and faster in species with a high base temperature for germination. These relationships explained about half the observed variability in germination speed parameters but should be further tested before being used to predict the germination behaviour of weed species in the field in different seasons.     

Importance of species traits for species distribution in fragmented landscapes

Knowledge of the relationship between species traits and species distribution in fragmented landscapes is important for understanding current distribution patterns and as background information for predictive models of the effect of future landscape changes. The existing studies on the topic suffer from several drawbacks. First, they usually consider only traits related to dispersal ability and not growth. Furthermore, they do not apply phylogenetic corrections, and we thus do not know how considerations of phylogenetic relationships can alter the conclusions. Finally, they usually apply only one technique to calculate habitat isolation, and we do not know how other isolation measures would change the results. We studied the issues using 30 species forming congeneric pairs occurring in fragmented dry grasslands. We measured traits related to dispersal, survival, and growth in the species and recorded distribution of the species in 215 grassland fragments. We show many strong relationships between species traits related to both dispersal and growth and species distribution in the landscape, such as the positive relationship between habitat occupancy and anemochory and negative relationships between habitat occupancy and seed dormancy. The directions of these relationships, however, often change after application of phylogenetic correction. For example, more isolated habitats host species with smaller seeds. After phylogenetic correction, however, they turn out to host species with larger seeds. The conclusions also partly change depending on how we calculate habitat isolation. Specifically, habitat isolation calculated from occupied habitats only has the highest predictive power. This indicates slow dynamics of the species. All the results support the expectation that species traits have a high potential to explain patterns of species distribution in the landscape and that they can be used to build predictive models of species distribution. The specific conclusions are, however, dependent on the technique used, and we should carefully consider this when comparing among different studies. Since different techniques answer slightly different questions, we should attempt to use analyses both with and without phylogenetic correction and explore different isolation measures whenever possible and compare the results.     

Epiphyte metapopulation dynamics are explained by species traits, connectivity, and patch dynamics

The colonization-extinction dynamics of many species are affected by the dynamics of their patches. For increasing our understanding of the metapopulation dynamics of sessile species confined to dynamic patches, we fitted a Bayesian incidence function model extended for dynamic landscapes to snapshot data on five epiphytic lichens among 2083 mapped oaks (dynamic patches). We estimate the age at which trees become suitable patches for different species, which defines their niche breadth (number of suitable trees). We show that the colonization rates were generally low, but increased with increasing connectivity in accordance with metapopulation theory. The rates were related to species traits, and we show, for the first time, that they are higher for species with wide niches and small dispersal propagules than for species with narrow niches or large propagules. We also show frequent long-distance dispersal in epiphytes by quantifying the relative importance of local dispersal and background deposition of dispersal propagules. Local stochastic extinctions from intact trees were negligible in all study species, and thus, the extinction rate is set by the rate of patch destruction (tree fall). These findings mean that epiphyte metapopulations may have slow colonization-extinction dynamics that are explained by connectivity, species traits, and patch dynamics.     

Interactions between environment, species traits, and human uses describe patterns of plant invasions

Although invasive alien species (IAS) are a major threat to biodiversity, human health, and economy, our understanding of the factors controlling their distribution and abundance is limited. Here, we determine how environmental factors, land use, life-history traits of the invaders, residence time, origin, and human usage interact to shape the spatial pattern of invasive alien plant species in South Africa. Relationships between the environmental factors and the extrinsic and intrinsic attributes of species were investigated using RLQ analysis, a multivariate method for relating a species-attribute table to an environmental table by way of a species presence/absence table. We then clustered species according to their position on the RLQ axes, and tested these groups for phylogenetic independence. The first three axes of the RLQ explained 99% of the variation and were strongly related to the species attributes. The clustering showed that, after accounting for environmental factors, the spatial pattern of IAS in South Africa was driven by human uses, life forms, and reproductive traits. The seven clusters of species strongly reflected geographical distribution, but also intrinsic species attributes and patterns of human use. Two of the clusters, centered on the genera Acacia and Opuntia, were phylogenetically non-independent. The remaining clusters comprised species of diverse taxonomic affinities, but sharing traits facilitating invasion in particular habitats. This information is useful for assessing the extent to which the potential spread of recent introductions can be predicted by considering the interaction of their biological attributes, region of origin, and human use.     

Multidimensional trade-offs in species responses to disturbance: implications for diversity in a subtropical forest

Species employ diverse strategies to cope with natural disturbance, but the importance of these strategies for maintaining tree species diversity in forests has been debated. Mechanisms that have the potential to promote tree species coexistence in the context of repeated disturbance include life history trade-offs in colonization and competitive ability or in species' ability to survive at low resource conditions and exploit the temporary resource-rich conditions often generated in the wake of disturbance (successional niche). Quantifying these trade-offs requires long-term forest monitoring and modeling. We developed a hierarchical Bayes model to investigate the strategies tree species employ to withstand and recover from hurricane disturbance and the life history trade-offs that may facilitate species coexistence in forests subject to repeated hurricane disturbance. Unlike previous approaches, our model accommodates temporal variation in process error and observations from multiple sources. We parameterized the model using growth and mortality data from four censuses of a 16-ha plot taken every five years (1990-2005), together with damage data collected after two hurricanes and annual seed production data (1992-2005). Species' susceptibilities to hurricane damage as reflected by changes in diameter growth and fecundity immediately following a storm were weak, highly variable, and unpredictable using traditional life history groupings. The lower crowding conditions (e.g., high light) generated in the wake of storms, however, led to greater gains in growth and fecundity for pioneer and secondary-forest species than for shade-tolerant species, in accordance with expectation of life history. We found moderate trade-offs between survival in high crowding conditions, a metric of competitive ability, and long-distance colonization. We also uncovered a strong trade-off between mean species fecundity in low crowding conditions, a metric of recovery potential, and competitive ability. Trade-offs in competitive and colonization ability, in addition to successional niche processes, are likely to contribute to species persistence in these hurricane-impacted forests. The strategies species employ to cope with hurricane damage depend on the degree to which species rely on sprouting, repair of adult damage, changes in demographic rates in response to enhanced resource availability after storms, or long-distance dispersal as recovery mechanisms.     

Ecological problems of tree species in protected ecosystems of Orissa, India

The tree layer vegetation of two protected ecosystems i.e. Similipal Biosphere Reserve (SBR) and Bhitarkanika National Park (BNP) of eastern ghat was analysed for structure, composition and diversity. With respect to the tree species composition the two protected ecosystems were differed from each other at the family, genera and species level. About 117 tree species representing 85 genera and 42 families were recorded in SBR. The average number of species per hectare was 32.5. However, a total of 29 tree species representing 22 genera and 16 families were recorded in BNP with an average number of species per hectare of 24.17. Species dominancy of the two protected areas was also different due to their difference in habitat condition. In SBR Shorea robusta was the most dominant species while in BNP Excoecaria agallocha was the most dominant species. Shannon-Wiener species diversity was 3.15 for Similipal and 2.314 for Bhitarkanika indicating that Similipal was highly diverse than Bhitarkanika. In general both the protected ecosystems of Orissa are highly rich in biodiversity and are characteristics of good ecological wealth of eastern ghat. Thus conservation and management practices are essential for the sustainability of their biodiversity.     

Pre-migratory life history stages of juvenile Arctic birds: costs, constraints, and trade-offs

Many young birds on the Arctic tundra are confronted by a challenging task: they must molt their feathers and accumulate fat stores for the autumn migration before climatic conditions deteriorate. Our understanding of the costs and constraints associated with these stages is extremely limited. We investigated post-juvenal molt and premigratory fattening in free-ranging juvenile White-crowned Sparrows (Zonotrichia leucophrys gambelii) on the Arctic tundra. We found evidence for trade-offs between premigratory fat accumulation and molt: heavily molting birds had significantly less fat. Birds increased the rate of fat accumulation as the season progressed, but we found no evidence of a similar increase in rate of molt. Using a controlled captive study to isolate the energetic costs of body feather replacement, we found no difference in fat or size-corrected mass of birds actively growing body feathers as compared to controls. Molting birds, however, consumed 17% more food than controls, suggesting a significant cost of body feather growth. Our results provide evidence of significant costs, constraints, and trade-offs associated with post-juvenal molt and premigratory fat accumulation in young Arctic birds.     

Environmental variability and allocation trade-offs maintain species diversity in a process-based model of succulent plant communities

Ecological theory suggests that environmental variability can promote coexistence, provided that species occupy differential niches. In this study, we focus on two questions: (1) Do allocation trade-offs provide a sufficient basis for niche differentiation in succulent plant communities? (2) What is the relative importance of different forms of environmental variability on species diversity and community composition? We approach these questions with a generic, individual-based simulation model. In our model, plants compete for water in a spatially explicit environment. Species differ in their size at maturity and in the allocation of carbon to roots, leaves and storage tissue. The model was fully specified with independent literature data. Model output was compared to characteristics of a species-rich community in the semi-arid Richtersveld (South Africa). The model reproduced the coexistence of plants with different sizes at maturity, the dominance of succulent shrubs, and the level of vegetation cover. We analyzed the effects of three forms of environmental variability: (a) temporal fluctuations in precipitation (rain and fog), (b) spatial heterogeneity of water supply due to run-on and run-off processes and (c) ‘rock pockets’ that limit root competition in space. The three types of variability had differential effects on diversity: diversity exhibited a strong hump-shaped response to temporal variation. Spatial variability increased diversity, with the strongest increase occurring at intermediate levels of temporal variability. Finally, rock pockets had the weakest effect, but contributed to diversity by providing refuges for small species, particularly at low temporal variability. The model thus shows that spatio-temporal variation of resource supply can maintain diversity over long time scales even in small systems, as is the case in the Richtersveld succulent communities. Trade-offs in allocation provide the basis for necessary niche differentiation. By describing resource competition between individual plants, our model provides a mechanistic basis for the link from species traits to community composition at given environmental conditions. It thereby contributes to an understanding of the forces shaping plant communities. Such an understanding is critical to reduce the threats environmental change poses to biodiversity and ecosystem services.     

Fourth-corner generation of plant functional response groups

Plant functional response groups (PFGs) are now widely established as a tool to investigate plant—environment relationships. Different statistical methods to form PFGs are used in the literature. One way is to derive emergent groups by classifying species based on correlation of biological attributes and subjecting these groups to tests of response to environmental variables. Another way is to search for associations of occurrence data, environmental variables and trait data simultaneously. The fourth-corner method is one way to assess the relationships between single traits and habitat factors. We extended this statistical method to a generally applicable procedure for the generation of plant functional response groups by developing new randomization procedures for presence/absence data of plant communities. Previous PFG groupings used either predefined groups or emergent groups i.e. classifications based on correlations of biological attributes (Lavorel et al Trends Ecol Evol 12:474–478, 1997), of the global species pool and assessed their functional response. However, since not all PFGs might form emergent groups or may be known by experts, we used a permutation procedure to optimise functional grouping. We tested the method using an artificial test data set of virtual plants occurring in different disturbance treatments. Direct trait-treatment relationships as well as more complex associations are incorporated in the test data. Trait combinations responding to environmental variables could be clearly distinguished from non-responding combinations. The results are compared with the method suggested by Pillar (J Veg Sci 10:631–640) for the identification of plant functional groups. After exploring the statistical properties using an artificial data set, the method is applied to experimental data of a greenhouse experiment on the assemblage of plant communities. Four plant functional response groups are formed with regard to differences in soil fertility on the basis of the traits canopy height and spacer length.     

Matching species traits to environmental variables: a new three-table ordination method

This paper addresses the question of studying the joint structure of three data tablesR,L andQ. In our motivating ecological example, the central tableL is a sites-by-species table that contains the number of organisms of a set of species that occurs at a set of sites. At the margins ofL are the sites-by-environment data tableR and the species-by-trait data table Q. For relating the biological traits of organisms to the characteristics of the environment in which they live, we propose a statistical technique calledRLQ analysis (R-mode linked toQ-mode), which consists in the general singular value decomposition of the triplet (R ^t D _I LD _J Q,D _q ,D _p ) whereD _I ,D _J ,D _q ,D _p are diagonal weight matrices, which are chosen in relation to the type of data that is being analyzed (quantitative, qualitative, etc.). In the special case where the central table is analysed by correspondence analysis,RLQ maximizes the covariance between linear combinations of columns ofR andQ. An example in bird ecology illustrates the potential of this method for community ecologists.     

Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity

The degree to which turnover in biological communities is structured by deterministic or stochastic factors and the identities of influential deterministic factors are fundamental, yet unresolved, questions in ecology. Answers to these questions are particularly important for projecting the fate of forests with diverse disturbance histories worldwide. To uncover the processes governing turnover we use species-level molecular phylogenies and functional trait data sets for two long-term tropical forest plots with contrasting disturbance histories: one forest is older-growth, and one was recently disturbed. Having both phylogenetic and functional information further allows us to parse out the deterministic influences of different ecological filters. With the use of null models we find that compositional turnover was random with respect to phylogeny on average, but highly nonrandom with respect to measured functional traits. Furthermore, as predicted by a deterministic assembly process, the older-growth and disturbed forests were characterized by less than and greater than expected functional turnover, respectively. These results suggest that the abiotic environment, which changes due to succession in the disturbed forest, strongly governs the temporal dynamics of disturbed and undisturbed tropical forests. Predicting future changes in the composition of disturbed and undisturbed forests may therefore be tractable when using a functional-trait-based approach.     

北京西山地区不同林分健康状况比较研究

以不同树种林分健康状况比较研究为切入点,以北京西山地区同一时期的油松×侧柏混交林、油松（Pinus tabulaeformis）林、侧柏（Platycladus orientalis）林和栓皮栎（Quercus variabis）林为研究对象。通过构建林分健康评价指标体系,计算林分综合健康指数,分别对不同林分的健康状况进行了分析和比较,探讨不同林分开展森林健康经营的关键环节,同时也从森林健康的角度说明造林树种选择的重要性。研究结果表明：各林分综合健康指数都为正值但数值都不高,这表明目前各林分都处于健康状态,但对外界扰动反应较为敏感,按健康状况排序：油松×侧柏林0．234〉栓皮栎林0．186〉油松林0．145〉侧柏林0．128;从单个指标看,各林分中都有负值指标出现,由此揭示,对负值指标的调整和增加正向指标的指标值是森林健康经营的关键。     

Spatial and covariate-varying relationships among dominant tree species in Utah

Environmental and Ecological Statistics - The presence and establishment of a tree species at a particular spatial location is influenced by multiple physiological and environmental filters such as...     

Scenarios of global bioenergy production: The trade-offs between agricultural expansion, intensification and trade

Increased future demands for food, fibre and fuels from biomass can only be met if the available land and water resources on a global scale are used and managed as efficiently as possible. The main routes for making the global agricultural system more productive are through intensification and technological change on currently used agricultural land, land expansion into currently non-agricultural areas, and international trade in agricultural commodities and processed goods. In order to analyse the trade-offs and synergies between these options, we present a global bio-economic modelling approach with a special focus on spatially explicit land and water constraints as well as technological change in agricultural production. For a global bioenergy demand scenario reaching 100 ExaJoule (EJ) until 2055 we derive a required rate of productivity increase on agricultural land between 1.2 and 1.4 percent per year under different land allocation options. A very high pressure for yield increase occurs in Sub-Saharan Africa and the Middle East, even without additional bioenergy demand. Moreover, we analyse the implicit values (shadow prices) of limited water resources. The shadow prices for bioenergy are provided as a metric for assessing the trade-offs between different land allocation options and as a link between the agricultural and energy sector.     

外来红树植物无瓣海桑的入侵生态特征

无瓣海桑因其具有速生性的特点而被广泛的用于滩涂海岸造林和控制外来杂草互花米草。但是同样作为外来种,无瓣海桑其自身的入侵性及生态风险已经成为近年来研究的一大热点。依据外来种风险评估的侧重点,分别从定居特性、传播特性及其影响等方面总结了国内外无瓣海桑的入侵生态特征的相关研究,表明无瓣海桑具有速生、高生产力、对低温和土壤具有一定的适应性、已在澳门等地出现扩散入侵现象等利于入侵的特点;但是同时它生态位宽度中等,繁殖率较低,并且它的种植会改善红树林生态系统土壤养分,有利于乡土红树植物的生长。现有对无瓣海桑入侵生态特征的定性研究并不能完全确定其入侵性和生态风险。因此今后需采用风险评估模型等手段对无瓣海桑入侵性进行更为深入地评估。     

Predicting tree species presence and basal area in Utah: A comparison of stochastic gradient boosting,generalized additive models,and tree-based methods

Many efforts are underway to produce broad-scale forest attribute maps by modelling forest class and structure variables collected in forest inventories as functions of satellite-based and biophysical information. Typically, variants of classification and regression trees implemented in Rulequest's^© See5 and Cubist (for binary and continuous responses, respectively) are the tools of choice in many of these applications. These tools are widely used in large remote sensing applications, but are not easily interpretable, do not have ties with survey estimation methods, and use proprietary unpublished algorithms. Consequently, three alternative modelling techniques were compared for mapping presence and basal area of 13 species located in the mountain ranges of Utah, USA. The modelling techniques compared included the widely used See5/Cubist, generalized additive models (GAMs), and stochastic gradient boosting (SGB). Model performance was evaluated using independent test data sets. Evaluation criteria for mapping species presence included specificity, sensitivity, Kappa, and area under the curve (AUC). Evaluation criteria for the continuous basal area variables included correlation and relative mean squared error. For predicting species presence (setting thresholds to maximize Kappa), SGB had higher values for the majority of the species for specificity and Kappa, while GAMs had higher values for the majority of the species for sensitivity. In evaluating resultant AUC values, GAM and/or SGB models had significantly better results than the See5 models where significant differences could be detected between models. For nine out of 13 species, basal area prediction results for all modelling techniques were poor (correlations less than 0.5 and relative mean squared errors greater than 0.8), but SGB provided the most stable predictions in these instances. SGB and Cubist performed equally well for modelling basal area for three species with moderate prediction success, while all three modelling tools produced comparably good predictions (correlation of 0.68 and relative mean squared error of 0.56) for one species.     

Sperm allocation in relation to male traits, female size, and copulation behaviour in freshwater crayfish species

Sperm competition is a well-recognised agent in the evolution of sperm and ejaculate structure, as well as variation in female quality. Models of the evolution of ejaculate expenditure predict that male body condition, female fecundity and the risk and intensity of sperm competition may be the ultimate factors shaping optimal ejaculate size. We investigated sperm allocation in Austropotamobius italicus, a freshwater crayfish exhibiting a coercive mating system and external fertilisation, in relation to male and female traits and copulation behaviour under laboratory conditions. We found that mating males were sensitive to female size and produced larger ejaculates when mating with larger females, which were more fecund in terms of number of eggs produced. We found no evidence for female egg production being sperm-limited, as the number of eggs was not dependent on male sperm expenditure. Copulation duration and number of ejaculations reliably predicted the amount of sperm transferred, and both these behavioural measures positively covaried with female body size. These results indicate that male freshwater crayfish can modulate their sperm expenditure in accordance with cues that indicate female fecundity. In addition, a novel finding that emerged from this study is the decrease in sperm expenditure with male body size, which may either suggest that large, old male crayfish are better able than small males to economise sperm at a given mating to perform multiple matings during a reproductive season, or that they experience senescence of their reproductive performance.