Tropical forest diversity,environmental change and species augmentation: After the intermediate disturbance hypothesis

Abstract. It is not simple to predict how environmental changes may impact tropical forest species diversity. Published hypotheses are almost invariably too incomplete, too poorly specified and too dependent upon unrealistic assumptions to be useful. Ecologists have sought theoretical simplicity, and while this has provided many elegant abstract concepts, it has hindered the attainment of more practical goals. The problem is not how to judge the individual hypotheses and arguments, but rather how to build upon and combine the many hard-won facts and principles into an integrated science. Controversy is inevitable when the assumptions, definitions and applications of a given hypothesis are unclear. Elegance, as an end in itself, has too often been used to justify abstract simplification and a lack of operational definition. Clarifying and combining hypotheses while avoiding assumptions provides a potentially more useful, if less elegant, standpoint. An appraisal of Connell's intermediate disturbance hypothesis, and its application to long-term observations from a Ugandan forest illustrates these concerns. Current emphases encourage ecologists to exclude consideration of environmental instability and non-pristine ecosystems. In reality, many environmental changes and ecological processes contribute to both the accumulation and erosion of diversity, at all spatial and temporal scales. Site histories, contexts, long-term processes, species-pool dynamics, and the role of people require greater emphasis. These considerations reveal that many environmental changes, even those associated with degradation, can lead to a transient rise in species densities. Drawing on related studies, such as forest yield prediction, suggests that the formulation and calibration of simulation models provides the most tractable means to address the complexity of real vegetation. Simulation-based approaches will become increasingly useful both in unifying the study of vegetation dynamics and in providing improved predictive capacity. Quantification of the processes, scales and sensitivities of the dynamics of tropical forest communities remains a major challenge.     

Wald Tests of Location for Symmetric Nonnormal Data

For nonnormal data we suggest a test of location based on a broader family of distributions than normality. Such a test will in a sense fall between the standard parametric and non parametric tests. We see that the Wald tests based on this family of distributions have some advantages over the score tests and that they perform well in comparison to standard parametric and nonparametric tests in a variety of situations. We also consider when and how to apply such tests in practice.     

Nucleotide sequence and molecular characterization of a gene encoding GTP-binding protein from Streptococcus gordonii

A 1286-bp fragment of chromosomal DNA from Streptococcus gordonii strain Challis was cloned and sequenced. The gene sgg consisted of 897-bp nucleotides encoding a 299-amino acid polypeptide (33 200 Da). The deduced amino acid sequence exhibited significant similarity to Era, G protein of Escherichia coli. The nucleotide binding assay demonstrated that recombinant Sgg bound [³²P]GTP but not [³²P]ATP, [³²P]CTP, or [³²P]UTP. These findings indicate that Sgg is a member of the G protein superfamily in the genus Streptococcus.     

Structural and functional studies of the nicotinic acetylcholine receptor by solid-state NMR

Over the last seven years, solid-state NMR has been widely employed to study structural and functional aspects of the nicotinic acetylcholine receptor. These studies have provided detailed structural information relating to both the ligand binding site and the transmembrane domain of the receptor. Studies of the ligand binding domain have elucidated the nature and the orientation of the pharmacophores responsible for the binding of the agonist acetylcholine within the agonist binding site. Analyses of small transmembrane fragments derived from the nicotinic acetylcholine receptor have also revealed the secondary structure and the orientation of these transmembrane domains. These experiments have expanded our understanding of the channels structural properties and are providing an insight into how they might be modulated by the surrounding lipid environment. In this article we review the advances in solid-state NMR applied to the nicotinic acetylcholine receptor and compare the results with recent electron diffraction and X-ray crystallographic studies.Presented at the Biophysical Society Meeting on Ion channels – from structure to disease held in May 2003, Rennes, France     

Carry‐over Effects of Size at Metamorphosis in Red‐eyed Treefrogs: Higher Survival but Slower Growth of Larger Metamorphs

Most animals have complex life histories, composed of a series of ecologically distinct stages, and the transitions between stages are often plastic. Anurans are models for research on complex life cycles. Many species exhibit plastic timing of and size at metamorphosis, due to both environmental constraints on larval growth and development and adaptive plastic responses to environmental variation. Models predicting optimal timing of metamorphosis balance cost/benefit ratios across stages, assuming that size affects growth and mortality rates in each stage. Much research has documented such effects in the larval period, but we lack an equal understanding of juvenile growth and mortality. Here, we examine how variation in size at metamorphosis in the Neotropical red‐eyed treefrog, Agalychnis callidryas, affects post‐metamorphic growth, foraging, and behavior in the lab as well as growth and survival in the field. Surprisingly, many individuals lost mass for weeks after metamorphosis. In the lab, larger metamorphs lost more mass following metamorphosis, ate similar amounts, had lower food conversion efficiencies, and grew more slowly after mass loss ceased than did smaller ones. In field cages larger metamorphs were more likely to survive than smaller ones; just one froglet died in the lab. Our data suggest that size‐specific differences in physiology and behavior influence these trends. Comparing across species and studies, large size at metamorphosis generally confers higher survival; size effects on growth rates vary substantially among species, in both magnitude and direction, but may be stronger in the tropics.     

Measurement of Scaled Residual Dipolar Couplings in Proteins Using Variable-angle Sample Spinning

NMR spectra of ubiquitin in the presence of bicelles at a concentration of 25% w/v have been recorded under sample spinning conditions for different angles of rotation. For an axis of rotation equal to the magic angle, the (1)H/(15)N HSQC recorded without any (1)H decoupling in the indirect dimension corresponds to the classical spectrum obtained on a protein in an isotropic solution and allows the measurement of scalar J-couplings (1) J (NH). For an angle of rotation smaller than the magic angle, the bicelles orient with their normal perpendicular to the spinning axis, whereas for an angle of rotation greater than the magic angle the bicelles orient with their normal along the spinning axis. This bicelle alignment creates anisotropic conditions that give rise to the observation of residual dipolar couplings in ubiquitin. The magnitude of these dipolar couplings depends directly on the angle that the rotor makes with the main magnetic field. By changing this angle in a controlled manner, residual dipolar couplings can be either scaled up or down thus offering the possibility to study simultaneously a wide range of dipolar couplings in the same sample.     

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13–158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.