Population size and genome size in fishes: a closer look.

The several thousand-fold range in genome size among animals has remained a subject of active research and debate for more than half a century, but no satisfactory explanation has yet been provided. Many one-dimensional models have been postulated, but so far none has been successful in accounting for observed patterns in genome size diversity. The recent model based on differences in effective population size appeared to gain empirical support with a study of genome size and inferred effective population size in fishes, but there were several questionable aspects of the analysis. First, it was based on an assumption that microsatellite heterozygosity indicates long-term effective population size, whereas in actuality these markers evolve quickly and are sensitive to demographic events. Second, it included both ancient polyploids and non-polyploids, the former of which did not gain their current genome sizes through the accumulation of slightly deleterious mutations as required in the model. Third, the analysis neglected the tremendous influence that Pleistocene glaciation bottlenecks had on heterozygosities in freshwater (and far less so, marine) fishes. In sum, it is apparent that genomes reached their current sizes in most fishes long before contemporary microsatellite heterozygosities were shaped, and that ancient polyploidy rather than the accumulation of mildly deleterious transposon insertions in small populations is the dominant factor that has influenced the large end of the range of genome sizes among fishes.     

Sample size for a phylogenetic inference.

The objective of this work is to describe sample-size calculations for the inference of a nonzero central branch length in an unrooted four-species phylogeny. Attention is restricted to independent binary characters, such as might be obtained from an alignment of the purine-pyrimidine sequences of a nucleic acid molecule. A statistical test based on a multinomial model for character-state configurations is described. The importance of including invariable sites in models for sequence change is demonstrated, and their effect on sample size is quantified. The methods are applied to a four-species alignment of small-subunit rRNA sequences derived from two archaebacteria, a eubacteria and a eukaryote. We conclude that the information in these sequences is not sufficient to resolve the branching order of this tree. Estimates of the number of aligned nucleotide positions required to provide a reasonably powerful test are given.     

R-loop stability as a function of RNA structure and size.

The sequence-specific formation of R-loops can be assayed using RNAs which overlap a HindIII cleavage site in a 3.5 kb plasmid. Chemical modification of the displaced DNA strand has permitted stabilization of these R-loops and allowed a systematic investigation of the dependence of these triple-stranded structures on the chain length and structure of the input RNA. RNAs as short as 50 nt form stable R-loops if 5-allylamine uridines (Uaa-RNA) are used in place of normal uridines; normal RNAs must be 100 nt long to form R-loops quantitatively. Since acetic anhydride decreases the hybridization efficiency of Uaa-RNAs, the positive charge of the RNAs must diminish the electrostatic repulsion of the three negatively charged phosphodiester backbones. The dependence of R-loop stability on the length of RNA can be stimulated with a random walk model, which also applies to strand migration within Holiday junctions. R-loop hybridization provides a versatile method to generate single-stranded DNA in a sequence-selective manner.     

Correlation of tooth size and body size in living hominoid primates, with a note on relative brain size in Aegyptopithecus and Proconsul.

Second molar length and body weight are used to test the correlation between tooth size and body size in living Hominoidea. These variates are highly correlated (r= 0.942, p less than 0.001), indicating that tooth size can be used in dentally unspecialized fossil hominoids as one method of predicting the average body weight of species. Based on tooth size, the average body weight of Aegyptopithecus zeuxis is estimated to have been beteen 4.5 and 7.5 kg, which is corroborated by known cranial and postcranial elements. Using Radinsky's estimates of brain size, the encephalization quotient (EQ) for Aegyptopithecus was between 0.65 and 1.04. A similar analysis for Proconsul africanus yields a body weight between 16 and 34 kg, and an EQ between 1.19 and 1.96.     

Overdominant alleles in a population of variable size.

An approximate method is developed to predict the number of strongly overdominant alleles in a population of which the size varies with time. The approximation relies on the strong-selection weak-mutation (SSWM) method introduced by J. H. Gillespie and leads to a Markov chain model that describes the number of common alleles in the population. The parameters of the transition matrix of the Markov chain depend in a simple way on the population size. For a population of constant size, the Markov chain leads to results that are nearly the same as those of N. Takahata. The Markov chain allows the prediction of the numbers of common alleles during and after a population bottleneck and the numbers of alleles surviving from before a bottleneck. This method is also adapted to modeling the case in which there are two classes of alleles, with one class causing a reduction in fitness relative to the other class. Very slight selection against one class can strongly affect the relative frequencies of the two classes and the relative ages of alleles in each class.     

Brain size,head size and behaviour of a passerine bird

A recent increase in comparative studies of the ecological and evolutionary consequences of brain size in birds and primates in particular have suggested that cognitive abilities constitute a central link. Surprisingly, there are hardly any intraspecific studies investigating how individuals differing in brain size behave, how such individuals are distributed and how brain size is related to life history and fitness components. Brain mass of the barn swallow Hirundo rustica was strongly predicted by external head volume, explaining 99.5% of the variance, allowing for repeatable estimates of head volume as a reflection of brain size. Repeatability of head volume within and between years was high, suggesting that measurement errors were small. In a 2 years study of 501 individual adult barn swallows, I showed that head volume differed between sexes and age classes, with yearlings having smaller and more variable heads than older individuals, and females having smaller and more variable heads than males. Large head volume was not a consequence of large body size, which was a poor predictor of head volume. Birds with large heads arrived early from spring migration, independent of sex and age, indicating that migratory performance may have an important cognitive component. Head volume significantly predicted capture date and recapture probability, suggesting that head volume is related to learning ability, although morphological traits such as wing length, aspect ratio and wing area were unimportant predictors. Intensity of defence of offspring increased with head volume in females, but not in males. Barn swallows with large heads aggregated in large colonies, suggesting that individuals with large heads were more common in socially complex environments. These results suggest that brain size is currently under natural and sexual selection, and that micro‐evolutionary processes affecting brain size can be studied under field conditions.     

Change of pupil size as a function of exercise.

Exercise was found to dilate the pupil area while the exercise took place, while the area showed constriction following the exercise period. Exercise-induced change in the size of the pupil was minimal. Pupillary dilation was greatest under conditions of maximal exercise. In exercise under a consistent load, pupillary dilation increased as the exercise time was prolonged. With lower lighting, there was virtually no dilation with exercise.     

Particle size of airborn Cryptococcus neoformans in a tower.

Nearly 10(6) cells of Cryptococcus neoformans were cultured per g of pigeon droppings in a vacant tower. The air in the tower contained an average of 45 viable cells of C. neoformans per 100 liters: 60% of the cells were less than 4.7 micron in diameter. It is estimated that a human exposed to this atmosphere for 1 h would have 41 cells of c. neoformans deposited in the lungs. Sweeping resulted in the aerosolization of large numbers of cells of C. neoformans from 4.7 to 11 micron in diameter, the number of cells less than 4.7 micron remained relatively constant. One minute after sweeping, 4.4% of viable airborne cells of C. neoformans were less than 1.1 micron in diameter. We believe that this is the first report of isolating such small cells of C. neoformans from a natural site.     

The effective size of a natural drosophila subobscura population.

The effective size of a natural Drosophila subobscura population has been computed by drawing together various pieces of ecological information. The value, for both variance and inbreeding effective numbers, is approximately 400. This is largely due to reductions caused by a winter bottleneck and non-random distributions of family sizes. Areas where such estimates might be refined further are pointed out, and the implications of the results are discussed.     

Extrahypophysial distribution of thyrotropin as a function of brain size.

Determination by radioimmunoassay of thyrotropin in the brains of rats and humans reveals that the dimensions within which the hormone is found is the same for rodents and primates but that the anatomical regions in which the hormone is found depends on brain size. Thyrotropin is widely distributed in the brain of rats but is found only in the hypothalamic regions of the human brain. These findings suggest that the pituitary is the sole site of synthesis of this hormone.     

Optical monitoring of bubble size and shape in a pulsating bubble surfactometer.

The pulsating bubble surfactometer (PBS) is often used for in vitro characterization of exogenous lung surfactant replacements and lung surfactant components. However, the commercially available PBS is not able to dynamically track bubble size and shape. The PBS therefore does not account for bubble growth or elliptical bubble shape that frequently occur during device use. More importantly, the oscillatory volume changes of the pulsating bubble are different than those assumed by the software of the commercial unit. This leads to errors in both surface area and surface tension measurements. We have modified a commercial PBS through the addition of an image-acquisition system, allowing real-time determination of bubble size and shape and hence the accurate tracking of surface area and surface tension. Compression-expansion loops obtained with the commercially available PBS software were compared with those provided by the image-analysis system for dipalmitoylphosphatidylcholine, Infasurf, and Tanaka lipids (dipalmitoylphosphatidylcholine-palmitoyloleoylphosphatidyl-glycerol-palmitic acid, 68:22:9) at concentrations of 0.1 and 1.0 mg/ml and at frequencies of 1 and 20 cycles/min. Whereas minimum surface tension as determined by the image-analysis system is similar to that measured by the commercially available software, the maximum surface tension and the shapes of the interfacial area-surface tension loops are quite different. Differences are attributable to bubble drift, nonsinusoidal volume changes, and variable volume excursions seen with the modified system but neglected by the original system. Image analysis reveals that the extent of loop hysteresis is greatly overestimated by the commercial device and that an apparent, rapid increase in surface tension upon film expansion seen in PBS loops is not observed with the image-analysis system. The modified PBS system reveals new dynamic characteristics of lung surfactant preparations that have not previously been reported.     

Spatiotemporal relationship between adult census size and genetic population size across a wide population size gradient

Adult census population size (N) and effective number of breeders (N_b) are highly relevant for designing effective conservation strategies. Both parameters are often challenging to quantify, however, making it of interest to determine whether one parameter can be generalized from the other. Yet, the spatiotemporal relationship between N and N_b has not been well characterized empirically in many taxa. We analysed this relationship for 5–7 consecutive years in twelve brook trout populations varying greatly in N (49‐10032) and N_b (3‐567) and identified major environmental variables affecting the two parameters. N or habitat size alone explained 47–57% of the variance in N_b, and N_b was strongly correlated with effective population size. The ratio N_b/N ranged from 0.01 to 0.45 and increased at small N or following an annual decrease in N, suggesting density‐dependent constraints on N_b. We found no evidence for a consistent, directional difference between variability in N_b and/or N_b/N among small and large populations; however, small populations had more varying temporal variability in N_b/N ratios than large populations. Finally, N_b and N_b/N were 2.5‐ and 2.3‐fold more variable among populations than temporally within populations. Our results demonstrate a clear linkage between demographic and evolutionary parameters, suggesting that N_b could be used to approximate N (or vice versa) in natural populations. Nevertheless, using one variable to infer the other to monitor trends within populations is less recommended, perhaps even less so in small populations given their less predictable N_b vs. N dynamics.     

Genome size in Arachis duranensis: a critical study.

Arachis duranensis is a diploid wild relative of the tetraploid cultivated peanut Arachis hypogaea. The literature indicates two 2C genomic DNA mean values (genome size) for A. duranensis, 4.92 and 5.64 pg, and intraspecific variation of up to 11% negatively correlated with altitude above sea level of the collection sites has been reported. Our recent investigations of Arachis species have shown that unrecognized technical problems with peanut material may have influenced previous genome-size data and rendered them open to critical comments. In the present study, 20 accessions of A. duranensis were investigated by means of DNA flow cytometry (propidium iodide staining) and several of these also by Feulgen DNA image analysis. Pisum sativum was used as the internal standard (2C = 8.84 pg). 2C values in A. duranensis were about half those described previously and varied between 2.49 and 2.87 pg (flow cytometry). This variation was statistically significant and reproducible. There was a negative correlation of genome size with latitude and altitude above sea level of the collection sites. Such a correlation had been already found in one of the previous studies. However, the incongruences between the absolute DNA content values obtained in the present investigation and those in the literature point to the importance of carrying out methodological studies on best practice in DNA-content determinations in plants.     

Geographic variation in body size and sexual size dimorphism of a seed-feeding beetle

Body size of many animals varies with latitude: body size is either larger at higher latitudes (Bergmann's rule) or smaller at higher latitudes (converse Bergmann's rule). However, the causes underlying these patterns are poorly understood. Also, studies rarely explore how sexual size dimorphism varies with latitude. Here we investigate geographic variation in body size and sexual size dimorphism of the seed-feeding beetle Stator limbatus, collected from 95 locations along a 38 degrees range in latitude. We examine 14 variables to test whether clines in environmental factors are adequate to explain geographic patterns of body size. We found that body size and sexual size dimorphism of S. limbatus varied considerably with latitude; beetles were smaller but more dimorphic at lower latitudes. Body size was not correlated with a gradient in mean temperature, contrary to the commonly accepted hypothesis that clines are produced by latitudinal gradients in temperature. Instead, we found that three factors were adequate to explain the cline in body size: clinal variation in host plant seed size, moisture (humidity), and seasonality (variance in humidity, precipitation, and temperature). We also found that the cline in sexual size dimorphism was partially explainable by a gradient in moisture, though moisture alone was not sufficient to explain the cline. Other ecological or environmental variables must necessarily contribute to differences in selection on male versus female body size. The main implications of our study are that the sexes differ in the magnitude of clinal variation in body size, creating latitudinal variation in sexual size dimorphism, and that clines in body size of seed beetles are likely influenced by variation in host seed size, water availability, and seasonality.     

Effective population size of a population with stochastically varying size

For a Wright–Fisher model with mutation whose population size fluctuates stochastically from generation to generation, a heterozygosity effective population size is defined by means of the equilibrium average heterozygosity of the population. It is shown that this effective population size is equal to the harmonic mean of population size if and only if the stochastic changes of population size are uncorrelated. The effective population size is larger (resp. smaller) than the harmonic mean when the stochastic changes of population size are positively (resp. negatively) autocorrelated. These results and those obtained so far for other stochastic models with fluctuating population size suggest that the property that effective population sizes are always larger than the harmonic mean under the fluctuation of population size holds only for continuous time models such as diffusion and coalescent models, whereas effective population sizes can be equal to or smaller than the harmonic mean for discrete time models.     

Cellular and enzymatic activities of a synthetic heteropolymer double-stranded RNA of defined size.

We have synthesized a novel heteropolymer double-stranded RNA (dsRNA) molecule of defined length and strandedness (dsRNA309) and evaluated its ability to induce cytokine gene expression, activate dsRNA-dependent enzymes, and inhibit both tumor cell growth and virus replication. Unlike the conventionally studied synthetic homopolymer dsRNAs, polyinosinic acid:polycytidylic acid (poly(I-C)) and its mismatched analogue polyinosinic:polycytidylic, uridylic acid (poly(I-C12,U), dsRNA309 possessed restricted biological activity. dsRNA309 was unable to inhibit tumor cell growth or efficiently induce cytokine (i.e. interferon-beta and interleukin-1 alpha) gene expression. However, dsRNA309 was able to inhibit virus replication and activate dsRNA-dependent intracellular enzymes, 2'-5' oligoadenylate synthetase (2'-5' A synthetase) and the dsRNA-activated inhibitor kinase in in vitro assay systems. Overall, dsRNA309 provided a means for examining the mechanisms governing the dsRNA-regulated antiviral and antiproliferative responses, and studies with dsRNA309 demonstrated that the ability of a synthetic dsRNA to activate dsRNA-dependent intracellular enzymes does not necessarily predict the same gene inducing capacity.