Simply the best: the transition of savanna saplings to trees

Tree cover in savannas is determined as much by disturbances from fire and herbivory as by rainfall and soil resources. Fire especially acts to limit tree cover via a demographic bottleneck, limiting the recruitment of tree saplings to adults. Because sapling growth rates determine rates of sapling to tree recruitment, predicting changes in tree cover requires data on sapling growth rates, commonly expressed as population means. Here, we discuss the variability in sapling growth rates in Acacia populations in a savanna in Hluhluwe iMfolozi Park in South Africa. Saplings growing at mean rates under typical fire regimes in African savannas would likely never escape the fire‐trap to become adults. Only the fastest growing saplings could grow above the flame zone between fires. We suggest that maximum growth rates are more ecologically relevant than mean growth rates in natural populations and experiments. Maximum growth rates are better than mean growth rates as predictors of sapling release within species, as shown here, and probably of which species are likely ‘winners’ in savanna tree communities.     

The Relationship of the Nutritive State of the Prey Organism Paramecium aurelia to the Growth and Encystment of Didinium nasutum

SYNOPSIS. Only well fed Paramecium aurelia , grown either monoflorally or on a mixture of 2 species of bacteria, are adequate to maintain optimal fission rates and encystment rates for Didinium nasutum. Progressive starvation of paramecia prior to their being fed to didinia leads to decreased fission rates, the appearance of abnormal cells and a loss of ability to encyst by the didinia. This depression can be fully overcome by allowing the didinia to feed again upon well nourished paramecia. A minimum of 45 well-fed paramecia is required daily for each Didinium if maximal fission rates are to be maintained. Encystment and fission appear to be mutually exclusive processes, but encystment rates are related to fission rates and seem to be exclusive of the density of the didinial culture.     

Nest defence in the American goldfinch

In the American goldfinch (Carduelis tristis), vocalizations during nest defence consist largely of two different types of calls: either ‘sweeet’ (SWT) or ‘bearbee’ (BB). By recording call rates and behaviour during controlled experiments, it was demonstrated that: (1) SWT calls have a rallying function and attract more goldfinches than BB calls; (2) goldfinches attempt to distract potential predators away from their nests; (3) BB calls cause a decrease in nestling conspicuousness, both audibly and visually; (4) call rates show a positive relationship with increasing conspicuousness of nestlings; (5) call rates of BB and SWT calls vary inversely with danger to the nest; (6) high call rates are given by parents with successful nests whereas low call rates are associated with failures caused by nest predation; (7) call rates show a positive relationship with clutch and brood size; (8) call rates and types did not vary with different potential predators; and (9) call rates and types used by males and females are related to their respective roles in the nesting cycle. Several hypotheses are discussed that might explain changes in call rates through the nesting cycle.     

Partitioning the variation in mammalian substitution rates

We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymous substitution rates and that lineage effects are stronger for synonymous substitution rates than for amino acid substitution rates. Gene-by-lineage interactions, equivalent to overdispersion corrected for lineage effects, are found in amino acid substitutions but not in synonymous substitutions. The variance in the ratio of amino acid and synonymous substitution rates is dominated by gene effects, but there is also a significant gene-by-lineage interaction.     

Integration and recovery processes contribute to the temporal selectivity of neurons in the midbrain of the northern leopard frog, Rana pipiens

This study examined the mechanisms underlying amplitude modulation selectivity in the anuran auditory midbrain. Single units were recorded extracellularly in the torus semicircularis of the northern leopard frog, Rana pipiens. Two physiologically distinct classes of neurons were identified, based on their response latencies and their selectivities to pulse repetition rates. Cells in one group had short response latencies (median = 31 ms) and responded best to pulse repetition rates below 40 Hz. Tuning to low amplitude modulation rates was largely determined by recovery processes and phasic response properties. Cells in the second group had much longer latencies (median=81 ms) and were generally selective for pulse repetition rates greater than 40-50 Hz. Sensitivity to higher amplitude modulation rates resulted from integration processes; these units only responded when a threshold number of pulses were presented at a minimum pulse density (amplitude modulation rate). At amplitude modulation rates above their best rate, their responses decreased, apparently due to inadequate recovery time between pulses.     

Modeling the evolution of the human mitochondrial genome.

Mitochondrial DNA data have been used extensively to study evolution and early human origins. These applications require estimates of the rate at which nucleotide substitutions occur in the DNA sequence. We consider the problem of estimating substitution rates in the presence of site-to-site rate variation. A coalescent model is presented that allows for different substitution rates for purines and pyrimidines, as well as more detailed models that allow fast and slow rates within each of the purine and pyrimidine classes. A method for estimating such rates is presented. Even for these simple models of site heterogeneity, there are, typically, insufficient data to obtain reliable estimates of site-specific substitution rates. However, estimates of the average rate across all sites appear to be relatively stable even in the presence of site heterogeneity. Simulations of models with site-to-site variation in mutation rate show that hypervariable sites can produce peaks in the pairwise difference curves that have previously been attributed to population dynamics.     

Modernization and childlessness among the governorates of the Arab Republic of Egypt, 1976

This paper examines the degree to which childlessness is influenced by levels of modernization among the governorates of the Arab Republic of Egypt. The data have been derived mainly from the 1976 Population and Housing Census of the Arab Republic of Egypt. The childlessness rates used are based on census data on number of children born to married women. In 1976, the higher the levels of modernization, the lower the rates of childlessness among women aged 30 and over, and the higher the rates of childlessness among women aged 20-30. The lower rates are found in and around Cairo, and some of the governorates with higher rates are in Upper Egypt. Of the 25 governorates, Suez has the lowest childlessness rate. To some degree, the patterns of childlessness may be affected by changing patterns in age-specific 1st marriage rates. The childlessness rates for the younger women in the Egyptian governorates are associated with some of the modernization variables. The findings suggest that childlessness among women aged 30 and older is mostly involuntary, but that for younger women it is partly voluntary. Increases in modernization among the Egyptian governorates should, therfore, result in net increases in rates of childlessness and net decreases in fertility. There are at least 3 statistically independent sources of variation in modernization which characterize the governorates of Egypt: factors that reflect structural development, female status, and health personnel.     

Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates

Measurements provide the basis for process monitoring and control as well as for model development and validation. Systematic approaches to increase the accuracy and credibility of the empirical data set are therefore of great value. In (bio)chemical conversions, linear conservation relations such as the balance equations for charge, enthalpy, and/or chemical elements, can be employed to relate conversion rates. In a pactical situation, some of these rates will be measured (in effect, be calculated directly from primary measurements of, e.g., concentrations and flow rates), as others can or cannot be calculated from the measured ones. When certain measured rates can also be calculated from other measured rates, the set of equations, the accuracy and credibility of the measured rates can indeed be improved by, respectively, balancing and gross error diagnosis. The balanced conversion rates are more accurate, and form a consistent set of data, which is more suitable for further application (e.g., to calculate nonmeasured rates) than the raw measurements. Such an approach has drawn attention in previous studies. The current study deals mainly with the problem of mathematically classifying the conversion rates into balanceable and calculable rates, given the subset of measured rates. The significance of this problem is illustrated with some examples. It is shown that a simple matrix equation can be derived that contains the vector of measured conversion rates and the redundancy matrix R. Matrix R plays a predominant role in the classification problem. In supplementary articles, significance of the redundancy matrix R for an improved gross error diagnosis approach will be shown. In addition, efficient equations have been derived to calculate the balanceable and/or calculable rates. The method is completely based on matrix algebra (principally different from the graph-theoretical approach), and it is easily implemented into a computer program. (c) 1994 John Wiley & Sons, Inc.     

Faster Speciation and Reduced Extinction in the Tropics Contribute to the Mammalian Latitudinal Diversity Gradient

The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals) peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas) reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha), high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha), or both (Chiroptera and Rodentia). Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the “out of the tropics” hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern.     

Effect of the ascidian Styela clava on the growth of small holothurians of the species Apostichopus japonicus

We studied the effect of the common ascidian Styela clava on the growth of small holothurians of the species Apostichopus japonicus (Selenka, 1867). In a traditional aquaculture system, the oxygen consumption rates, ammonia excretion rates, and ingestion rates of small A. japonicus were reduced significantly, which suggested that this group was stressed by the presence of large A. japonicus, and that this stress grew stronger with time. Oxygen consumption rates, ammonia excretion rates, and ingestion rates of small A. japonicus in an integrated aquaculture (IA) system with S. clava, microalgae, and A. japonicus were higher than those observed in the traditional culture system. Metabolic and digestive enzymes were more active in small A. japonicus in the IA system than in those in the traditional aquaculture system. These results suggest that the IA model did not affect the growth of large A. japonicas, but produced a marked positive impact on the growth of small individuals.     

Submillisecond folding of the peripheral subunit-binding domain.

Folding and unfolding rates have been measured for the peripheral subunit-binding domain, a small three-helix protein. The protein folds very fast, with rates too rapid to be measured using traditional stopped-flow techniques. Folding and unfolding rates were measured as a function of temperature using dynamic NMR lineshape analysis. At the lowest temperature at which there is sufficient broadening to measure rates, 41 degrees C, the folding rate is 16,050 s(-1). Thus, the halftime required for folding is 43 micros. At the same temperature, the unfolding rate is 2800 s(-1). Identical rates were measured using resolved resonances from Val16 in the loop and Val21 at the end of the 310-helix. Folding rates have been correlated with protein topology, and this correlation is consistent with the rapid folding of the peripheral subunit-binding domain. The results presented here show that the peripheral subunit-binding domain is the third fastest folding protein for which rates have been estimated. The folding rate is the fastest that has been directly measured and provides further support for the importance of chain topology as a major determinant of folding rates.     

Associations between the rates of maturation and growth in the short bones of the hand

Serial radiographs of the hand-wrist were used to analyze the associations within bones between the rates of change in skeletal maturity, diaphyseal and epiphyseal lengths and diaphyseal width. In previous studies of these children, it has been shown that these rates are linear in relation to chronological age. The associations between the rates of change in these parameters were analyzed using the slopes (b values) for regression lines flitted to the data in each child. In individual bones, most of the correlation coefficients were moderate to low; some were negative. For most associations in each sex they were relatively high for metacarpal II. The rates of skeletal maturation and diaphyseal elongation were correlated more highly in the girls than in the boys but the rates of skeletal maturation and epiphyseal elongation were correlated more highly in the boys. When bones were considered in groups, relatively high correlations were noted for the metacarpals and ray II, lower correlations were common for the middle and distal phalanges. There was no evidence of real neighborhood effects but marginal effects were present.     

The effects of parasitism by the plerocercoid of Schistocephalus solidus Muller 1776 (Pseudophyllidea) on the respiration of the three-spined stickleback Gasterosteus aculeatus L.

Rates of oxygen consumption by parasitized and unparasitized sticklebacks were recorded at three levels of activity in February and August. Negative correlations were demonstrated between specific respiratory rates and fish body weights. At routine and maximum activity, infected fish consumed more oxygen than uninfected fish. At minimum activity levels no significant differences in respiration rates were detected. Seasonal variation in respiration rates was attributed to acclimation. Difficulties of determining specific respiration rates for parasitized organisms are discussed and attempts are made to assess the physiological basis of the respiratory and behavioural characteristics of infected fish.     

Molecular clocks and the incompleteness of the fossil record

Molecular clocks can be evaluated by comparing absolute rates of evolution and by performing relative-rate tests. Typically, calculations of absolute rates are based on earliest observed occurrences in the fossil record. Relative-rate tests, on the other hand, merely require an unambiguous outgroup. A major disadvantage of relative-rate tests is their insensitivity to concomitant and equal rate changes in all lineages. Apparent differences in absolute rates, in turn, may be artifacts that are attributable to an incomplete fossil record.Recently developed methods in quantitative biostratigraphy recognize the incompleteness of the fossil record and allow us to place confidence intervals on the endpoints of taxon ranges. These methods are applicable to taxa whose fossil records are of markedly different quality. When we extend these methods and integrate molecular and paleontologic data, we can test the null hypothesis that seemingly disparate rates of molecular evolution are in fact equal under the simplifying assumption that fossils are randomly and independently distributed over their temporal ranges and that fossils can be accurately placed in a phylogenetic context. We can also estimate the range of ticking rates, if any, that are compatible with known fossil data. Ultimately, more accurate rate estimates for widely divergent taxa should allow for more meaningful comparisons of evolutionary rates.DNA hybridization data for monotremes and marsupials suggest a 17-fold difference for 14 different rate calculations with a mean value of approximately 1% divergence per million years. Variation among marsupials is sevenfold. However, when we apply appropriate statistical tests and make additional allowances for fossils of uncertain taxonomic assignment, etc., all 14 rates are compatible with a molecular clock ticking at approximately 0.4% divergence per million years. In addition, this analysis brings relative- and absolute-rate tests into accord.     

Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae

Although mutation rates are a key determinant of the rate of evolution they are difficult to measure precisely and global mutations rates (mutations per genome per generation) are often extrapolated from the per-base-pair mutation rate assuming that mutation rate is uniform across the genome. Using budding yeast, we describe an improved method for the accurate calculation of mutation rates based on the fluctuation assay. Our analysis suggests that the per-base-pair mutation rates at two genes differ significantly (3.80x10(-10) at URA3 and 6.44x10(-10) at CAN1) and we propose a definition for the effective target size of genes (the probability that a mutation inactivates the gene) that acknowledges that the mutation rate is nonuniform across the genome.     

Testing the link between the latitudinal gradient in species richness and rates of molecular evolution

Numerous hypotheses have been proposed to explain latitudinal gradients in species richness, but all are subject to ongoing debate. Here we examine Rohde's (1978, 1992) hypothesis, which proposes that climatic conditions at low latitudes lead to elevated rates of speciation. This hypothesis predicts that rates of molecular evolution should increase towards lower latitudes, but this prediction has never been tested. We discuss potential links between rates of molecular evolution and latitudinal diversity gradients, and present the first test of latitudinal variation in rates of molecular evolution. Using 45 phylogenetically independent, latitudinally separated pairs of bird species and higher taxa, we compare rates of evolution of two mitochondrial genes and DNA-DNA hybridization distances. We find no support for an effect of latitude on rate of molecular evolution. This result casts doubt on the generality of a key component of Rohde's hypothesis linking climate and speciation.     

A Proposed Method for Specifying the Temperature History of Cells During the Rapid Cool-down of Plant Specimens

Existing methods for defining cool-down rates of plant specimensquenched in cryogenic liquids are considered unsatisfactory. An analytical method is proposed for specifying the temperaturehistory and cool-down rates at particular cell locations withina plant specimen. This method should provide realistic peakcool-down rates when examining cell structures and the survivalrate of cell systems.     

Naupliar growth versus egg production in the calanoid copepod Centropages typicus

Growth rates of the copepod Centropages typicus were assessedduring May 1998 in the Alboran Sea. The goal of the work wasto compare field growth rates of juvenile (artificial cohortmethod) and adult copepods (female egg production rates) underan extensive range of natural conditions. The results showedthat adult and juvenile growth rates were similar in some stations,while in others no such relationship was apparent. In contrastto the common belief that juvenile growth may be saturated undernatural conditions whereas adults may be food-limited, in mostof our study, adult growth rates were greater than juveniles.We discuss these results in the light of food availability atthe surveyed stations. In summary, the assumption that copepodgrowth rates estimated through egg production rates of adultsare equivalent to juvenile growth is not always valid.     

Development, growth and egg production of the two copepod species Centropages hamatus and Centropages typicus in the laboratory

Laboratory experiments were set up in order to determine andcompare developmental rates, growth rates, generation timesand egg production rates for the two calanoid copepod speciesCentropages typicus and Centropages hamatus. The nauplii showeda higher developmental rate than the copepodites for both specieswith quite different individual stage durations, which gaveno indication of isochronal development. For C typicus equiproportionaldevelopment was found. The growth rates were exponential andhighest for the largest species C typicus, and for both speciesthe juvenile growth rates were very similar to the egg productionrates of the adults.     

Heterogeneity of the gradients performed by the freeze-thaw method

Gradients produced by the freeze-thaw method were analyzed at various rates of freezing. The shape of the gradient depended on the rate of freezing. At high rates the pattern did not change but at low rates the steepness of the gradient increased with time. Solutes concentrated at the bottom in a fashion which depended on the density of the solvent and on the rate of freezing. It should also be noted that the gradient was not uniform over the entire surface as the concentration of solute increased near the wall of the test tube.