Deriving dispersal distances from genetic data.

Dispersal is one of the most important factors determining the genetic structure of a population, but good data on dispersal distances are rare because it is difficult to observe a large sample of dispersal events. However, genetic data contain unbiased information about the average dispersal distances in species with a strong sex bias in their dispersal rates. By plotting the genetic similarity between members of the philopatric sex against some measure of the distance between them, the resulting regression line can be used for estimating how far dispersing individuals of the opposite sex have moved before settling. Dispersers showing low genetic similarity to members of the opposite sex will on average have originated from further away. Applying this method to a microsatellite dataset from lions (Panthera leo) shows that their average dispersal distance is 1.3 home ranges with a 95% confidence interval of 0.4-3.0 home ranges. These results are consistent with direct observations of dispersal from our study population and others. In this case, direct observations of dispersal distance were not detectably biased by a failure to detect long-range dispersal, which is thought to be a common problem in the estimation of dispersal distance.     

Estimation of evolutionary distances from protein spatial structures

New equations are derived to estimate the number of amino acid substitutions per site between two homologous proteins from the root mean square (RMS) deviation between two spatial structures and from the fraction of identical residues between two sequences. The equations are based on evolutionary models, analyzing predominantly structural changes and not sequence changes. Evolution of spatial structure is treated as a diffusion in an elastic force field. Diffusion accounts for structural changes caused by amino acid substitutions, and elastic force reflects selection, which preserves protein fold. Obtained equations are supported by analysis of protein spatial structures. Received: 21 September 1995 / Accepted: 19 May 1997     

Perfectly complementary nucleic acid enzymes

The ability to maximize the use of available nucleic acid sequence space would have been crucial during the presumed RNA world and confers selective advantage in many contemporary organisms. One way to access sequence space at a higher density would be to make use of both strands of a duplex nucleic acid for the production of functional molecules. As a demonstration of this possibility, two pairs of nucleic acid enzymes were engineered to be perfect complements, each with the capacity to adopt a distinct structure and catalyze a particular chemical transformation. Both members of each pair of enzymes exhibited nearly the same level of activity as the canonical form of the corresponding catalytic motif. The ability to generate functional nucleic acids encoded by both strands of a duplex has implications for the evolution of catalytic nucleic acids and the prospects for realizing maximum functionality from a given genetic sequence. Present address (Scott T. Kuhns): CancerVax Corp., 9393 Towne Center Drive, San Diego, CA 92121, USA     

Improved error bounds for genetic distances from DNA sequences

The genetic distance between two DNA sequences may be measured by the average number of nucleotide substitutions per position that has occurred since the two sequences diverged from a common ancestor. Estimates of this quantity can be derived from Markov models for the substitution process, while the variances are estimated using the delta method and confidence intervals calculated assuming normality. However, when the sampling distribution of the estimator deviates from normality, such intervals will not be accurate. For simple one-parameter models of nucleotide substitution, we propose a transformation of normal confidence intervals, which yields an almost exact approximation to the true confidence intervals of the distance estimators. To calculate confidence intervals for more complicated models, we propose the saddlepoint approximation. A simulation study shows that the saddlepoint-derived confidence intervals are a real improvement over existing methods.     

Physiological responses at short distances from a parametric speaker

In recent years, parametric speakers have been used in various circumstances. In our previous studies, we verified that the physiological burden of the sound of parametric speaker set at 2.6 m from the subjects was lower than that of the general speaker. However, nothing has yet been demonstrated about the effects of the sound of a parametric speaker at the shorter distance between parametric speakers the human body. Therefore, we studied this effect on physiological functions and task performance. Nine male subjects participated in this study. They completed three consecutive sessions: a 20-minute quiet period as a baseline, a 30-minute mental task period with general speakers or parametric speakers, and a 20-minute recovery period. We measured electrocardiogram (ECG) photoplethysmogram (PTG), electroencephalogram (EEG), systolic and diastolic blood pressure. Four experiments, one with a speaker condition (general speaker and parametric speaker), the other with a distance condition (0.3 m and 1.0 m), were conducted respectively at the same time of day on separate days. To examine the effects of the speaker and distance, three-way repeated measures ANOVA (speaker factor x distance factor x time factor) were conducted. In conclusion, we found that the physiological responses were not significantly different between the speaker condition and the distance condition. Meanwhile, it was shown that the physiological burdens increased with progress in time independently of speaker condition and distance condition. In summary, the effects of the parametric speaker at the 2.6 m distance were not obtained at the distance of 1 m or less.     

Estimation of genetic distances from human and mouse introns

Background  

Using genetic distances measured from exons, it has been observed that the mutation rate is not constant along mammalian chromosomes. Exons constitute only 1% of the human genome, however, and thus they cannot provide a complete picture of the mutational variation in the genome.     

Why ontogenetic homology criteria can be misleading: lessons from digit identity transformations

As the basis for comparative biology, correctly assigning character homology is critical. Yet, identifying homologous characters in practice is often challenging. Among the major roadblocks is that the mechanistic bases of character homology remain in question. Thus, investigators must rely on several independent lines of evidence (e.g., character anatomy, phylogenetic distribution, or embryological position); however, these distinct sources of evidence often lead to conflicting diagnoses of character homology. What is more, there is no consensus regarding the relative importance of distinct lines of evidence for determining character homology. Here, we review the difficulties that have hindered the search for the mechanistic bases of character identity, and relate these issues to a recently proposed mechanistic hypothesis of character identity--the Character Identity Network Hypothesis. Next, using two well-studied cases of homology conflict (i.e., avian and skink digit identity), we assess the utility of different lines of evidence in diagnosing homology. We conclude that, when comparing adult structures, because anatomical characters more closely reflect the actions of the developmental genetic mechanisms of character individuation they are more reliable than embryological homology criteria.     

Analysis of the Scattering of Surface Plasmon Polariton Waves from a Perfectly Conducting Circular Cylinder

Surface plasmon polariton (SPP) waves are the most extensively studied waves among various types of surface waves because they are easy to excite and have been used in many optical applications particularly for plasmonic communication, sensing, and harvesting solar energy. In all these applications, especially on-chip plasmonic communication, scattering can be an important issue to deal with. Therefore, this paper aimed to theoretically inspect the scattering pattern of SPP waves from a perfect electric conductor (PEC) cylindrical scatterer. The cylindrical wave approach is used to solve the scattering problem by a cylindrical object placed below a metallic layer. The scattering is investigated thoroughly by changing the size of the scatterer and its distance from the interface along which the SPP wave is excited. As the size of the scatterer increases, the scattering increases significantly. On the other hand, when the distance of the scatterer from the interface is increased, the scattered field becomes small. Two-dimensional field maps are produced for the incident angle at which SPP is excited. Numerical results are also presented for other incident angles to make a comparison. Furthermore, the forward and backward far-fields are significantly enhanced if the SPP wave is scattered in comparison with when the SPP wave is not present.

     

Constrained global optimization for estimating molecular structure from atomic distances.

Finding optimal three-dimensional molecular configurations based on a limited amount of experimental and/or theoretical data requires efficient nonlinear optimization algorithms. Optimization methods must be able to find atomic configurations that are close to the absolute, or global, minimum error and also satisfy known physical constraints such as minimum separation distances between atoms (based on van der Waals interactions). The most difficult obstacles in these types of problems are that 1) using a limited amount of input data leads to many possible local optima and 2) introducing physical constraints, such as minimum separation distances, helps to limit the search space but often makes convergence to a global minimum more difficult. We introduce a constrained global optimization algorithm that is robust and efficient in yielding near-optimal three-dimensional configurations that are guaranteed to satisfy known separation constraints. The algorithm uses an atom-based approach that reduces the dimensionality and allows for tractable enforcement of constraints while maintaining good global convergence properties. We evaluate the new optimization algorithm using synthetic data from the yeast phenylalanine tRNA and several proteins, all with known crystal structure taken from the Protein Data Bank. We compare the results to commonly applied optimization methods, such as distance geometry, simulated annealing, continuation, and smoothing. We show that compared to other optimization approaches, our algorithm is able combine sparse input data with physical constraints in an efficient manner to yield structures with lower root mean squared deviation.     

Root distribution at various distances from clove trees growing in Indonesia

Efficient fertilizer application requires an understanding of the distribution of roots and soil nutrients in the soil profile. Cultural practices for clove trees in Indonesia has resulted in phosphorus (P) fertilizer being applied at the canopy edge; however, in these high P fixing soils efficient P fertilizer application should occur with the highest root densities. The objective of this study, therefore, was to determine the rooting distribution at various distances from the tree and soil depths for clove (Eugenia aromatica OK; variety Zanzibar) trees growing on an Andosol soil at Modoinding, Indonesia. Root distributions were determined to a 100-cm soil depth using soil cores at 0.5, 1.0 and 1.5 times the canopy radius for five 10-year-old clove trees grown on either level terrain or 23% slopes. Clove root length and weight densities decreased with soil depth and distance from the tree base. Fine clove roots (1 mm dia) comprised 72% of the total root length and was three to five times higher underneath the canopy than that outside the canopy. Roots were concentrated in the upper soil horizons; however, up to 36% of the total root length was found at a depth of 50–100 cm. Clove roots for trees growing at the level landscape position had the highest root length densities. Intercropped species root length densities were higher than clove root length densities at 1.5 times the canopy radius whereas intercropped root weight densities were higher than that for clove roots at both 1.5 and 1 times the canopy radius. Results suggest that fertilizer applications should be placed closer to the tree trunk rather than at the canopy edge to maximize P uptake by clove roots.     

Dispersal distances of Tree Swallows estimated from continent-wide and limited-area data

ABSTRACT.   Dispersal is a critical link between organismal and population biology, yet, because of their mobility, our understanding of the causes and consequences of long-distance dispersal by birds remains poorly known. Methods used to study dispersal include (1) marking and recapturing individuals in a limited study area to estimate survival and dispersal rates, and (2) relying on volunteers to mark and recapture individuals over larger areas. We compared these two methods for measuring dispersal distances of Tree Swallows ( Tachycineta bicolor ) using recapture data from a limited-area study in New York State (the Swallow Dispersal Study, SDS) and the recapture dataset from the U.S. Bird Banding Laboratory (BBL). Analysis of BBL records revealed a difference in the dispersal distance distributions (DDD) for data reported before and after 1967. In the earlier data, 84% of the 238 records were for birds within 13.6 km of their first banding location, whereas only 22% of the 799 records in the more recent data were reported in this closest distance belt. These differences are almost certainly due to changes in reporting protocols instituted by the BBL in the mid-1960s. We corrected for recapture effort in the SDS, and, using this corrected SDS data for the proportion of birds returning in the closest distance belt and the recent BBL for the proportions of more distant movements, we created what we think is the best composite DDD for Tree Swallows. Even though dispersal distances up to 2367 km have been reported, the composite DDD indicates that fewer than 3% of birds disperse more than 100 km and that 85% disperse less than 15 km between years. Thus, our results suggest that the dispersal behavior of most individuals can be examined effectively at more local spatial scales. Studies of dispersal and mortality would be facilitated if all recaptures of banded birds were reported with accurate spatial coordinates to the Bird Banding Laboratory.