岛屿生物地理学理论：模型与应用

前言岛屿有许多显著特征,如地理隔离,生物类群简单。这些特点为重复性研究和统计学分析奠定了基础,从而有利于许多深入而细致的生物学研究。因此,岛屿为发展和检验自然选择、物种形成及演化,以及生物地理学和生态学诸领域的理论和假设,提供了重要的自然实验室。岛屿生物地理学理论(MacArthurwilson学说)即为岛屿生物学研究中所产生的著名理论之一。该理论发展之     

Evaluation of terrestrial plants extracts for uranium sorption and characterization of potent phytoconstituents

Sorption capacity of four plants (Funaria hygrometrica, Musa acuminata, Brassica juncea and Helianthus annuus) extracts/fractions for uranium, a radionuclide was investigated by EDXRF and tracer studies. The maximum sorption capacity, i.e., 100% (complete sorption) was observed in case of Musa acuminata extract and fractions. Carbohydrate, proteins, phenolics and flavonoids contents in the active fraction (having maximum sorption capacity) were also determined. Further purification of the most active fraction provided three pure molecules, mannitol, sorbitol and oxo-linked potassium oxalate. The characterization of isolated molecules was achieved by using FTIR, NMR, GC-MS, MS-MS, and by single crystal-XRD analysis. Of three molecules, oxo-linked potassium oxalate was observed to have 100% sorption activity. Possible binding mechanism of active molecule with the uranyl cation has been purposed.     

Diversity of non-native terrestrial arthropods on woody plants in Canada

A list of non-native phytophagous insects and mites on woody plants (trees, shrubs, vines) in Canada was compiled using information from literature and input from taxonomists. The 419 recorded species include Hemiptera (53% of species), Lepidoptera (22%), Coleoptera (13%) and Hymenoptera (9%). Almost all species originate from the Palearctic, especially Europe, reflecting historical trade patterns. About 41% of species were directly introduced to Canada from countries of origin, and the remainder spread from the United States of America (USA) after initial establishment there. Major ports on the east and west coasts, on Lake Erie and Lake Ontario are the main points of entry for exotic species directly introduced, and southern British Columbia (BC), Ontario (ON) and Quebec (QC) are the major points of entry for species spreading from the USA. Consequently, BC, ON, QC and Nova Scotia have the highest diversity of non-native species, and the prairie provinces and northern territories have the lowest. The extent of the distribution of individual species is related to length of time in Canada, number of introductions and dispersal abilities. Almost all native woody plant genera in Canada have been invaded by exotic phytophages. The large majority of phytophages occur on angiosperms. Woody plant genera with the largest distribution, highest species diversity and highest local abundances tend to host the greatest number of non-native species, including Picea, Pinus, Malus, Prunus, Salix, Betula, Quercus, Pyrus and Populus. The arrival rate of species in Canada increased from the late nineteenth century until about 1960, and declined rapidly thereafter. Quarantine legislation enacted in the USA in 1912 and in Canada in 1976 seems to have reduced the rate of insect invasion. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Allometric scaling of maximum population density: a common rule for marine phytoplankton and terrestrial plants

A primary goal of macroecology is to identify principles that apply across varied ecosystems and taxonomic groups. Here we show that the allometric relationship observed between maximum abundance and body size for terrestrial plants can be extended to predict maximum population densities of marine phytoplankton. These results imply that the abundance of primary producers is similarly constrained in terrestrial and marine systems by rates of energy supply as dictated by a common allometric scaling law. They also highlight the existence of general mechanisms linking rates of individual metabolism to emergent properties of ecosystems.     

Nestedness and migratory status of avian assemblages in North America and Europe

We examine patterns of nestedness and species incidence for the resident and migrant components of avifaunas in North America and Europe. While all assemblages were significantly nested, there were no significant differences between North American and European avifaunas overall in nestedness or incidence. Residents did not differ from migrants in their adherence to a nested distribution, but did exhibit significantly higher incidences when continental affiliation was ignored.¶We develop a new nestedness index that examines each species' relative contribution to an assemblage's overall pattern of nestedness. The relative nestedness index exhibits a quadratic relationship with incidence such that species with low incidences and species with high incidences generally increase the overall level of nestedness, while species with intermediate incidence tend to decrease nestedness.     

Persistence, extinction and different species pools within the flora of lake islands in western Ireland

The vascular flora on twenty-nine lake islands in Lough Corrib, western Ireland was surveyed in 1992–93. Thirteen of these islands had been surveyed by the author in 1974 (Roden, 1979). Data on species–area curves and species turnover between 1974 and 1992 are presented. Species numbers on each island did not change greatly in the 18-year interval and extinctions were most common on smaller islands. It is known that six of the islands surveyed are less than 150 years old and their flora must have immigrated over open water during that period. It is shown that this group of species has a different log species/log area regression than the remaining flora, with a much shallower slope (low Z value). The proportion of less widespread species was greatest on islands nearest to the mainland. The implication of different slopes in different species groups and the restriction of turnover to rare species is discussed with reference to the island Theory of Biogeography.     

A probabilistic framework for microarray data analysis: Fundamental probability models and statistical inference

Gene expression studies generate large quantities of data with the defining characteristic that the number of genes (whose expression profiles are to be determined) exceed the number of available replicates by several orders of magnitude. Standard spot-by-spot analysis still seeks to extract useful information for each gene on the basis of the number of available replicates, and thus plays to the weakness of microarrays. On the other hand, because of the data volume, treating the entire data set as an ensemble, and developing theoretical distributions for these ensembles provides a framework that plays instead to the strength of microarrays. We present theoretical results that under reasonable assumptions, the distribution of microarray intensities follows the Gamma model, with the biological interpretations of the model parameters emerging naturally. We subsequently establish that for each microarray data set, the fractional intensities can be represented as a mixture of Beta densities, and develop a procedure for using these results to draw statistical inference regarding differential gene expression. We illustrate the results with experimental data from gene expression studies on Deinococcus radiodurans following DNA damage using cDNA microarrays.     

A parameterization of leaf phenology for the terrestrial ecosystem component of climate models

Leaf phenology remains one of the most difficult processes to parameterize in terrestrial ecosystem models because our understanding of the physical processes that initiate leaf onset and senescence is incomplete. While progress has been made at the molecular level, for example by identifying genes that are associated with senescence and flowering for selected plant species, a picture of the processes controlling leaf phenology is only beginning to emerge. A variety of empirical formulations have been used with varying degrees of success in terrestrial ecosystem models for both extratropical and tropical biomes. For instance, the use of growing degree‐days (GDDs) to initiate leaf onset has received considerable recognition and this approach is used in a number of models. There are, however, limitations when using GDDs and other empirically based formulations in global transient climate change simulations. The phenology scheme developed for the Canadian Terrestrial Ecosystem Model (CTEM), designed for inclusion in the Canadian Centre for Climate Modelling and Analysis coupled general circulation model, is described. The representation of leaf phenology is general enough to be applied over the globe and sufficiently robust for use in transient climate change simulations. Leaf phenology is functionally related to the (possibly changing) climate state and to atmospheric composition rather than to geographical boundaries or controls implicitly based on current climate. In this approach, phenology is controlled by environmental conditions as they affect the carbon balance. A carbon‐gain‐based scheme initiates leaf onset when it is beneficial for the plant, in carbon terms, to produce new leaves. Leaf offset is initiated by unfavourable environmental conditions that incur carbon losses and these include shorter day length, cooler temperatures, and dry soil moisture conditions. The comparison of simulated leaf onset and offset times with observation‐based estimates for temperate and boreal deciduous, tropical evergreen, and tropical deciduous plant functional types at selected locations indicates that the phenology scheme performs satisfactorily. Model simulated leaf area index and stem and root biomass are also compared with observational estimates to illustrate the performance of CTEM.     

Divergence and biogeography of the recently evolved Macaronesian red Festuca (Gramineae) species inferred from coalescence-based analyses

Studying the biogeography and the phylogeography of the endemic Macaronesian red Festuca species (Loliinae, Poaceae) is of prime interest in understanding the speciation and colonization patterns of recently evolved groups in oceanic archipelagos. Coalescence‐based analyses of plastid trnLF sequences were employed to estimate evolutionary parameters and to test different species‐history scenarios that model the pattern of species divergence. Bayesian IM estimates of species divergence times suggested that ancestral lineages of diploid Macaronesian and Iberian red fescues could have diverged between 1.2 and 1.57 Ma. When empirical data were compared to coalescence‐based simulated distributions of discordance and p‐distance statistics, two species‐history models were chosen in which the first branching lineage derived in Canarian Festuca agustinii. Its sister lineage could have involved a recent polytomy leading to the Madeiran Festuca jubata, the Azorean Festuca francoi + Festuca petraea and the continental Festuca rivularis lineages (Canarian model) or the sequential branching of lineages leading to F. jubata and finally to the sister clades of F. rivularis and F. francoi + F. petraea (Sequential model). Nested clade phylogeographic analysis (NCPA) and a first adapted host–parasite co‐evolutionary ParaFit method were used to detect the phylogeographic signal. NCPA inferred long‐distance colonizations for the entire diploid red Festuca complex, but allopatric‐fragmentation and isolation‐by‐distance (IBD) patterns were inferred within archipelagos. In addition, the ParaFit method suggested a generalized pattern of a stepping‐stone model at all hierarchical levels. Maximum‐likelihood‐based dispersal‐extinction‐cladogenesis (DEC) models were superimposed on the Sequential model species tree. The three‐independent‐colonization (3IC) model was the best supported biogeographic scenario, concurring with previous analysis based on multilocus AFLP data.     

The ability of climate envelope models to predict the effect of climate change on species distributions

Climate envelope models (CEMs) have been used to predict the distribution of species under current, past, and future climatic conditions by inferring a species' environmental requirements from localities where it is currently known to occur. CEMs can be evaluated for their ability to predict current species distributions but it is unclear whether models that are successful in predicting current distributions are equally successful in predicting distributions under different climates (i.e. different regions or time periods). We evaluated the ability of CEMs to predict species distributions under different climates by comparing their predictions with those obtained with a mechanistic model (MM). In an MM the distribution of a species is modeled based on knowledge of a species' physiology. The potential distributions of 100 plant species were modeled with an MM for current conditions, a past climate reconstruction (21 000 years before present) and a future climate projection (double preindustrial CO₂ conditions). Point localities extracted from the currently suitable area according to the MM were used to predict current, future, and past distributions with four CEMs covering a broad range of statistical approaches: Bioclim (percentile distributions), Domain (distance metric), GAM (general additive modeling), and Maxent (maximum entropy). Domain performed very poorly, strongly underestimating range sizes for past or future conditions. Maxent and GAM performed as well under current climates as under past and future climates. Bioclim slightly underestimated range sizes but the predicted ranges overlapped more with the ranges predicted with the MM than those predicted with GAM did. Ranges predicted with Maxent overlapped most with those produced with the MMs, but compared with the ranges predicted with GAM they were more variable and sometimes much too large. Our results suggest that some CEMs can indeed be used to predict species distributions under climate change, but individual modeling approaches should be validated for this purpose, and model choice could be made dependent on the purpose of a particular study.     

The variation of REE (rare earth elements) patterns in soil-grown plants: a new proxy for the source of rare earth elements and silicon in plants

Rare earth elements (REEs) in five species of soil-grown plants (Taxodium japonicum, Populus sieboldii, Sasa nipponica, Thea sinensis and Vicia villosa) and in the soil on which each plant grew were determined with an inductively coupled plasma mass spectrometer (ICP-MS) in order to observe the variation in the distribution of REEs and to elucidate their source in soil-grown plants. The plant samples were divided into root (secondary root and main root), trunk (stem) and leaf; the soils into water soluble (soil_{soluble fraction}), HCl and HNO₃ soluble (soil_{non-silicate fraction}) and HF soluble (soil_{silicate fraction}). The REE abundances of samples were compared using REE patterns where the abundances were normalized to those of a chondrite and plotted on a logarithmic scale against the atomic number. All the plants showed similar REE patterns independent of species and location, and a W-shape variation (W-type tetrad effect) and abundance depletion of cerium (negative Ce anomaly) were found in each REE patterns of plants, more conspicuous tetrad effect being observed in HREE (heavier rare earth elements) region than in LREE (lighter rare earth elements) region. The overall variation of REE patterns of each secondary root was not similar to that of soil_{soluble fraction}, but similar to that of soil_{silicate fraction} except for the tetrad effect and Ce anomaly. The REE patterns can be interpreted by the idea that plants of different species take in REEs and Si from different parts in the soil. The results of this study seem to imply that Sasa nipponica and Vicia villosa take in free REEs and Si rather directly from silicate in the soil, and that a majority of REEs and Si in Taxodium japonicum and Thea sinensis are originated from the soluble fraction in the soil.     

Comments on specific categories in flowering plants

The paper offers comments arising from the author's experience as a practising taxonomist on two aspects of what is often called the species problem: the reality of species and species as individuals. Three different meanings of reality are distinguished and discussed in this context: mental reality, biological reality and evolutionary reality. The author holds the view that, on all three definitions, species must be judged to be real. On the argument concerning species as individuals, the opinions ofHull, Ghiselin and others are carefully presented but rejected by the author, who retains the belief that species are classes and not individuals.Dedicated to the memory of JohnS. L. Gilmour.     

Putting the plants back into plant ecology: six pragmatic models for understanding and conserving plant diversity

BACKGROUND: There is a compelling need to protect natural plant communities and restore them in degraded landscapes. Activities must be guided by sound scientific principles, practical conservation tools, and clear priorities. With perhaps one-third of the world's flora facing extinction, scientists and conservation managers will need to work rapidly and collaboratively, recognizing each other's strengths and limitations. As a guide to assist managers in maintaining plant diversity, six pragmatic models are introduced that are already available. Although theoretical models continue to receive far more space and headlines in scientific journals, more managers need to understand that pragmatic, rather than theoretical, models have the most promise for yielding results that can be applied immediately to plant communities. SIX PRAGMATIC MODELS: For each model, key citations and an array of examples are provided, with particular emphasis on wetlands, since "wet and wild" was my assigned theme for the Botanical Society of America in 2003. My own work may seem rather prominent, but the application and refinement of these models has been a theme for me and my many students over decades. The following models are reviewed: (1) species-area: larger areas usually contain more species; (2) species-biomass: plant diversity is maximized at intermediate levels of biomass; (3) centrifugal organization: multiple intersecting environmental gradients maintain regional landscape biodiversity; (4) species-frequency: a few species are frequent while most are infrequent; (5) competitive hierarchies: in the absence of constraints, large canopy-forming species dominate patches of landscape, reducing biological diversity; and (6) intermediate disturbance: perturbations such as water level fluctuations, fire and grazing are essential for maintaining plant diversity. CONCLUSIONS: The good news is that managers faced with protecting or restoring landscapes already have this arsenal of tools at their disposal. The bad news is that far too few of these models are appreciated.