The need for speed

DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation.     

The need for speed: informed land acquisitions for conservation in a dynamic property market

Land acquisition is a common approach to biodiversity conservation but is typically subject to property availability on the public market. Consequently, conservation plans are often unable to be implemented as intended. When properties come on the market, conservation agencies must make a choice: purchase immediately, often without a detailed knowledge of its biodiversity value; survey the parcel and accept the risk that it may be removed from the market during this process; or not purchase and hope a better parcel comes on the market at a later date. We describe both an optimal method, using stochastic dynamic programming, and a simple rule of thumb for making such decisions. The solutions to this problem illustrate how optimal conservation is necessarily dynamic and requires explicit consideration of both the time period allowed for implementation and the availability of properties.     

The need for speed. II. Myelin in calanoid copepods

Speed of nerve impulse conduction is greatly increased by myelin, a multi-layered membranous sheath surrounding axons. Myelinated axons are ubiquitous among the vertebrates, but relatively rare among invertebrates. Electron microscopy of calanoid copepods using rapid cryofixation techniques revealed the widespread presence of myelinated axons. Myelin sheaths of up to 60 layers were found around both sensory and motor axons of the first antenna and interneurons of the ventral nerve cord. Except at nodes, individual lamellae appeared to be continuous and circular, without seams, as opposed to the spiral structure of vertebrate and annelid myelin. The highly organized myelin was characterized by the complete exclusion of cytoplasm from the intracellular spaces of the cell generating it. In regions of compaction, extracytoplasmic space was also eliminated. Focal or fenestration nodes, rather than circumferential ones, were locally common. Myelin lamellae terminated in stepwise fashion at these nodes, appearing to fuse with the axolemma or adjacent myelin lamellae. As with vertebrate myelin, copepod sheaths are designed to minimize both resistive and capacitive current flow through the internodal membrane, greatly speeding nerve impulse conduction. Copepod myelin differs from that of any other group described, while sharing features of every group. Accepted: 8 January 2000     

A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times

MOTIVATION: The high pace of viral sequence change means that variation in the times at which sequences are sampled can have a profound effect both on the ability to detect trends over time in evolutionary rates and on the power to reject the Molecular Clock Hypothesis (MCH). Trends in viral evolutionary rates are of particular interest because their detection may allow connections to be established between a patient's treatment or condition and the process of evolution. Variation in sequence isolation times also impacts the uncertainty associated with estimates of divergence times and evolutionary rates. Variation in isolation times can be intentionally adjusted to increase the power of hypothesis tests and to reduce the uncertainty of evolutionary parameter estimates, but this fact has received little previous attention. RESULTS: We provide approximations for the power to reject the MCH when the alternative is that rates change in a linear fashion over time and when the alternative is that rates differ randomly among branches. In addition, we approximate the standard deviation of estimated evolutionary rates and divergence times. We illustrate how these approximations can be exploited to determine which viral sample to sequence when samples representing different dates are available.     

The need for anonymous genetic counseling and testing.

Concerns are mounting about the risks of genetic discrimination resulting from the release of predictive and presymptomatic genetic test results to employers, insurers, and others. The ability to keep this information confidential is questionable, particularly in view of the expansion of electronic medical databases. One solution is to afford individuals access to anonymous genetic counseling and testing. Probands would be identified only by a code that would not reveal personal information, and test results would be stored, retrieved, and released solely on the basis of this code. The experience with anonymous HIV testing, while not completely analogous, suggests that such an approach would be both practical and effective.     

Marine reserves: the need for systems

Highly protected marine reserves are areas of the sea in which human disturbances are minimised so that the full natural biological diversity is maintained or, more often, allowed to recover to a more natural state. Europe has very few marine reserves; they are very small and almost all are in the Mediterranean. There are at present no official plans to create effective systems of marine reserves. Europe has many so-called Marine Protected Areas (MPAs). These are marine areas with some extra regulations or planning procedures. MPAs aim to make human activities more efficient and more sustainable. MPAs are user-orientated, knowledge-based, locality-dependent, problem-solving extensions of standard marine planning and management. Marine reserves are quite different. All extractive and potentially disturbing human activities are prohibited. The burden of proof is reversed; no evidence of damage or danger to particular species or habitats is required; all marine life is protected on principle. The concept of marine reserves is simple and practical, but because it is new, different and additional to existing marine management, the idea is seen by many as revolutionary. Basic biological principles and practical experience in many countries make it clear that marine reserves are important to science and education, essential for conservation and useful in resource management. These features apply in all regions and ecosystems. They are independent of climate, biogeography, current human activities and the present management. Representative and viable systems of marine reserves are needed in all regions. Fishing and other human disturbances have been widespread and intensive for so long that it is very difficult to predict the stages of recovery that occur in marine reserves. Furthermore, while some features change rapidly (e.g. numbers of previously targeted species), recovery continues for a long time (e.g. fourth- and fifth-order trophic and structural changes after >25 years). None of this alters the fact that, in scientific terms, marine reserves are controls not manipulations. Such controls are required if scientists are to understand the intrinsic processes and obtain data that are not confounded by human activities (e.g. separating natural variation from fishing effects). No significant progress will be made to establish marine reserves in Europe until scientists speak out strongly and clearly on the issue. We consider it is part of our professional duty as marine biologists to state publicly and frequently the need for a representative, replicated, networked and sustainable system of highly protected marine reserves. We doubt if our grandchildren will accept any excuses if we fail. Guest editors: J. Davenport, G. Burnell, T. Cross, M. Emmerson, R. McAllen, R. Ramsay & E. Rogan Challenges to Marine Ecosystems     

No need for speed: slow development of fungi in extreme environments

Microbial growth under extreme conditions is often slow. This is partly because large amounts of energy are diverted into cellular mechanisms that allow survival under hostile conditions. Because this challenge is universal and diversity in extreme environments is low compared to non-extreme environments, slow-growing microorganisms are not overgrown by other species. In some cases, especially when nutrients are scarce, slow growth was even shown to increase stress tolerance. And in at least some species of extremotolerant and extremophilic fungi, growth rate appears to be coupled with their very unusual morphologies, which in turn may be an adaptation to extreme conditions. However, there is more than one strategy of survival in extreme environments. Fungi that thrive in extremes can be divided into (i) ubiquitous and polyextremotolerant generalists and (ii) rarely isolated specialists with narrow ecological amplitudes. While generalists can compete with mesophilic species, specialists cannot. When adapting to extreme conditions, the risk of an evolutionary trade-off in the form of reduced fitness under mesophilic conditions may limit the maximum stress tolerance achievable by polyextremotolerant generalists. At the same time, specialists are rarely found in mesophilic environments, which allows them to evolve to ever greater extremotolerance, since a reduction of mesophilic fitness is likely to have little impact on their evolutionary success.     

The need for a formal invalidation process for animal and non-animal tests

A plethora of regulations require that many chemicals and chemical products are tested for efficacy and/or toxicity. When permitted to operate effectively and without bias, the ECVAM/ICCVAM/OECD validation process can be used to independently establish that new animal and non-animal test procedures are sufficiently relevant and reliable for their stated purposes and should be considered for regulatory use. However, the validation process is under threat because of vested interests of various kinds, and it is clear that many currently-accepted animal tests and candidate animal and non-animal tests do not, and could never, meet the agreed criteria for necessity, test development, prevalidation, validation and acceptance. We therefore need an invalidation process to parallel and protect the validation process, so that such methods could be independently reviewed and declared irrelevant and/or unreliable for their claimed purposes. An additional advantage of such a process would be that valuable resources would no longer be wasted in attempts to secure the acceptance of inherently inadequate tests.     

The relation between maximal running speed and body mass in terrestrial mammals

The available data on maximal running speeds of mammals are presented, and the relationship between speed and body mass is considered. For all mammals ( n = 106), maximal running speed scales as (body mass)^0–17; however, the largest mammals are not the fastest, and an optimal size with regards to running ability is suggested ( 119 kg). Maximal running speeds are, on the average, somewhat more than twice maximal aerobic speeds.
Within the Artiodactyla, Carnivora or Rodentia, maximal running speed is mass independent, in agreement with theoretical expectations for geometrically similar animals (Thompson, 1917; Hill, 1950). McMahon's (1975 b ) model for elastic similarity is therefore not supported by the available data on maximal running speeds, and there appears to be no necessary correspondence between scaling of limb bone proportions and running ability.     

The importance of ingestion rates for estimating food quality and energy intake

Testing ecological or socioecological models in primatology often requires estimates of individual energy intake. It is a well established fact that the nutrient content (and hence the energy content) of primate food items is highly variable. The second variable in determining primate energy intake, i.e., the ingestion rate, has often been ignored, and few studies have attempted to estimate the relative importance of the two predictors. In the present study individual ingestion rates were measured in two ecologically very different populations of Hanuman langurs (Semnopithecus entellus) at Jodhpur, India, and Ramnagar, Nepal. Protein and soluble sugar concentrations in 50 and 100 food items. respectively, were measured using standardized methods. Variation in ingestion rates (gram of dry matter per minute) was markedly greater among food items than among langur individuals in both populations, but did not differ systematically among food item categories defined according to plant part and age. General linear models (GLMs) with ingestion rate, protein, and soluble sugar content explained 40-80% of the variation in energy intake rates (kJ/min). The relative importance of ingestion rates was either similar (Ramnagar) or much greater (Jodhpur) than the role of sugar and/or protein content in determining the energy intake rates of different items. These results may impact socioecological studies of variation in individual energy budgets, investigations of food choice in relation to chemical composition or sensory characteristics, and research into habitat preferences that measures habitat quality in terms of abundance of important food sources. We suggest a definition of food quality that includes not only the amount of valuable food contents (energy, vitamins, and minerals) and the digestibility of different foods, but also the rate at which the food can be harvested and processed. Such an extended definition seems necessary because time may constrain primates when feeding competition is intense and foraging is risk-prone.     

Codon equilibrium II: Its use in estimating silent-substitution rates

Summary We study the equilibrium in the use of synonymous codons by eukaryotic organisms and find five equations involving substitution rates that we believe embody the important implications of equilibrium for the process of silent substitution. We then combine these five equations with additional criteria to determine sets of substitution rates applicable to eukaryotic organisms. One method employs the equilibrium equations and a principle of maximum entropy to find the most uniform set of rates consistent with equilibrium. In a second method we combine the equilibrium equations with data on the man-mouse divergence to determine that set of rates that is most neutral yet consistent with both types of data (i.e., equilibrium and divergence data). Simulations show this second method to be quite reliable in spite of significant saturation in the substitution process. We find that when divergence data are included in the calculation of rates, even though these rates are chosen to be as neutral as possible, the strength of selection inferred from the nonuniformity of the rates is approximately doubled. Both sets of rates are applied to estimate the human-mouse divergence time based on several independent subsets of the divergence data consisting of the quartet, C- or T-ending duet, and A- or G-ending duet codon sets. Both rate sets produce patterns of divergence times that are shortest for the quartet data, intermediate for the CT-ending duets, and longest for the AG-ending duets. This indicates that rates of transitions in the duet-codon sets are significantly higher than those in the quartet-codon sets; this effect is especially marked for AG, the rate of which in duets must be about double that in quartets.     

Codon equilibrium II: Its use in estimating silent-substitution rates

We study the equilibrium in the use of synonymous codons by eukaryotic organisms and find five equations involving substitution rates that we believe embody the important implications of equilibrium for the process of silent substitution. We then combine these five equations with additional criteria to determine sets of substitution rates applicable to eukaryotic organisms. One method employs the equilibrium equations and a principle of maximum entropy to find the most uniform set of rates consistent with equilibrium. In a second method we combine the equilibrium equations with data on the man-mouse divergence to determine that set of rates that is most neutral yet consistent with both types of data (i.e., equilibrium and divergence data). Simulations show this second method to be quite reliable in spite of significant saturation in the substitution process. We find that when divergence data are included in the calculation of rates, even though these rates are chosen to be as neutral as possible, the strength of selection inferred from the nonuniformity of the rates is approximately doubled. Both sets of rates are applied to estimate the human-mouse divergence time based on several independent subsets of the divergence data consisting of the quartet, C- or T-ending duet, and A- or G-ending duet codon sets. Both rate sets produce patterns of divergence times that are shortest for the quartet data, intermediate for the CT-ending duets, and longest for the AG-ending duets. This indicates that rates of transitions in the duet-codon sets are significantly higher than those in the quartet-codon sets; this effect is especially marked for A----G, the rate of which in duets must be about double that in quartets.