REPLI: A program in BASIC for determination of approximate sample size

REPLI, a program written in elementary BASIC, calculates the approximate sample size, which is required to detect a desired difference between any two group means in an experiment with n groups for a given probability and at three significance levels of the means difference. A prior knowledge of the variability of data in the groups is expected in order to base the estimate on a rational footing. If this knowledge does not exist, an educated guess and/or several trials with different assumptions on the most likely variability can be used. The a priori estimate prevents that sample sizes are completely out of a reasonable range. Since the program is applicable for experimental settings where several groups need be investigated, it is particularly interesting to users of ANOVA and/or comparable non-parametric tests.     

Genetic Variability and Rate of Gene Substitution in a Finite Population under Mutation and Fluctuating Selection

By using a numerical method of solving stochastic difference equations, the level of genetic variability maintained in a finite population and the rate of gene substitution under several models of fluctuating selection intensities were studied. It is shown that mutation and random genetic drift both play an important role in determining genetic variability and the rate of gene substitution. Compared with the case of neutral mutations, the fluctuation of selection intensity caused by temporal and spatial heterogeneity of environments generally increases the rate of gene substitution, but the level of genetic variability may be increased or decreased, depending upon the model and the parameters used. Although such a type of selection per se can not be ruled out, when mutation is taken into account, it is difficult to explain both the observed amount of genetic variability and the rough constancy of evolutionary rate within a framework of fluctuating selection models.     

Beyond R0: demographic models for variability of lifetime reproductive output

The net reproductive rate R0 measures the expected lifetime reproductive output of an individual, and plays an important role in demography, ecology, evolution, and epidemiology. Well-established methods exist to calculate it from age- or stage-classified demographic data. As an expectation, R0 provides no information on variability; empirical measurements of lifetime reproduction universally show high levels of variability, and often positive skewness among individuals. This is often interpreted as evidence of heterogeneity, and thus of an opportunity for natural selection. However, variability provides evidence of heterogeneity only if it exceeds the level of variability to be expected in a cohort of identical individuals all experiencing the same vital rates. Such comparisons require a way to calculate the statistics of lifetime reproduction from demographic data. Here, a new approach is presented, using the theory of Markov chains with rewards, obtaining all the moments of the distribution of lifetime reproduction. The approach applies to age- or stage-classified models, to constant, periodic, or stochastic environments, and to any kind of reproductive schedule. As examples, I analyze data from six empirical studies, of a variety of animal and plant taxa (nematodes, polychaetes, humans, and several species of perennial plants).     

Analysis of allozyme variability in three Plantago species and a comparison to morphological variability

Summary The level of electrophoretic variability in three Plantago species, P. major, P. coronopus, and P. lanceolata, was analyzed in relation to their breeding systems and compared with their morphological variability. From each species several populations were analyzed. The outcrossing P. lanceolata had the highest level of electrophoretic variability and the lowest population differentiation. The inbreeding P. major showed the opposite: a low level of electrophoretic variability and a high population differentiation. P. coronopus, with an intermediate breeding system, had an intermediate level of variability and differentiation. In comparing the species, it appeared that P. coronopus and P. major showed good concordance in the distribution of both kinds of variability, each having only a slightly higher morphological than electrophoretic differentiation between populations. P. lanceolata showed a higher morphological than electrophoretic differentiation between populations. A comparison of populations, within species, revealed good concordance of electrophoretic and morphological variability only within P. coronopus, while some populations of the other two species had relatively lower morphological variability compared with electrophoretic variability.Grassland Species Research Group Publication No. 182     

Differential phenotypic variability among the Apalachee mission populations of La Florida: a diachronic perspective

Phenotypic variability is evaluated in a series of skeletal samples from the Apalachee region of Florida. Based on ethnohistoric evidence, several predictive models for changes in variability are generated. If variability decreases through time, this likely represents the effect of genetic drift in populations experiencing epidemic disease and population loss. If variability increases through time, this suggests that population aggregation or genetic admixture were primary factors shaping the Apalachee population during the mission period. Dental dimensions were collected from a series of precontact (pre-1500), early mission (AD 1633-1650) (San Pedro y San Pablo de Patale), and late mission (post-1657) (San Luis) samples from the Apalachee region and were subjected to univariate and multivariate variability analyses. The results indicate that the late mission San Luis sample was significantly more variable than the Patale or precontact samples; however, the Patale sample exhibited no significant variability change in comparison to the precontact population. This suggests that the missions initially effected limited change in genetic variability in the mission populations. However, San Luis was affected by either admixture or population aggregation to such a degree that the observed variation had increased beyond earlier levels. Given the limited historic evidence for population aggregation at this mission, and the comparatively large resident Spanish population, the increased variability may be indicative of admixture at this mission, and potentially at this mission only. Based on a limited data set, however, it appears that the mission period cannot be typified by a single evolutionary or historic process.     

Phenotypic and genotypic variation of Phragmites australis: Comparison of populations in two human-made lakes of different age and history

Populations of Phragmites australis (CAV.) TRIN. ex STEUD. were studied in the littoral zones of two man-made lakes located in the Třeboň Basin (South Bohemia, the Czech Republic): (1) Opatovický fishpond, a shallow artificial lake constructed in 1510–1514 by damming a shallow valley and used since for carp production, and (2) Halámky sand pit, a new lake formed by sand extraction in 1970–1994. Phenotypic variability was assessed on the basis of shoot morphological and growth characteristics, measured at the time of seasonal maximum aboveground biomass. Genotypic variability was detected using RAPDs, which demonstrated a high clonal diversity in both habitats. The clonal diversity would be strongly underestimated if it were based only on morphological differences. Higher genotypic variability was found in the fishpond reed, not corresponding with low variability in its phenotype performance. Based on analysis of 160 samples, four patterns of genotypic variation were detected: (1) Some stands were genetically uniform and were therefore considered to be monoclonal in both populations studied. (2) Some stands consisted of several clones at the Halámky sand pit. However, these clones showed more similarity within the particular stands than with clones of adjacent stands. (3) In the Opatovický fishpond population, multiclonal stands consisted of clones with a low degree of similarity. (4) Identical clones were detected in several neighbouring stands separated by gaps in the Opatovický fishpond population. The findings support a model of colonization postulating that populations initiated by seeds are initially genetically diverse and over time become dominated by a few clones as a result of competition and selection. These processes then decrease both genetic and morphological variability.     

THE QUANTIFICATION OF SOME PLANT-TAXA CIRCUMSCRIPTIONS

Intrataxon variability is estimated by the technique of numerical taxonomy. Taxa which had been determined by orthodox taxonomic methods are subjected to analyses by numerical phenetics. Comparisons are made of the amounts of cohesion among the members of different taxa in the Bromeliaceae at several taxonomic levels by computing the degrees of similarities between members of the same taxon and of different taxa. Results of these comparisons with several taxa reveal that the variability of a taxon in terms of phenetic distance computed with a large number of characters does not necessarily agree with a subjective appraisal of variability. The method facilitated difficult taxonomic determinations and provided an estimate of the relative evolutionary ages of different taxonomic groups.     

A Strategy to Investigate the Intravarietal Genetic Variability in Vitis vinifera L. for Clones and Biotypes Identification and to Correlate Molecular Profiles with Morphological Traits or Geographic Origins

Grapevine is the most economically important and widely cultivated fruit crop in the world. Molecular markers have been used on Vitis vinifera to distinguish among both varieties and clones. Microsatellites are used to fingerprint varieties and several other techniques, reported in many papers, are used to analyze the differences among clones, but it is not available in the literature as a well defined strategy to screen a large number of Vitis cultivars. In fact, it is often necessary to use different techniques to investigate the genetic variability in different grapevine varieties and a proposed technique is used to study a cultivar, which is often not suitable for either the study of another cultivar or compare the genetic relationship among various cultivars. We describe here a strategy used for the analysis of several grapevine cultivars to describe a universal method to obtain DNA polymorphisms of Vitis vinifera genotypes from the same cultivar by using amplified fragment length polymorphism (AFLP), selective amplification of microsatellite polymorphic loci (SAMPL), microsatellites AFLP (M-AFLP), and ISSR molecular markers. The strategy here adopted permitted both to identify different biotypes (i.e., Primitivo), accessions (i.e., Garnacha tinta), and clones (i.e., Callet, Manto Negro, Moll) among the variability of same variety and to correlate the genetic differences to their geographical origins (i.e., Garnacha tinta; Malvasia nera di Brindisi/Lecce) or morphological traits (i.e., Malvasia of Candia). Here is also described the application of the protocol that allows to highlight the genetic variability accumulated during centuries of cultivations and selections of the same variety in different environments by vine growers.     

Hypocone and metaconule: identification and variability on human molars

Hypocone and metaconule variability was studied in a large sample of upper molars belonging to several human populations. The identification of these cusps does not generally show problems. However, on second and especially on third molars, it is occasionally difficult to decide if a little cup located on the crown distal border is a hypocone or a metaconule. The identification of supernumerary cusps located between the metacone and the hypocone seldom is clarified. We suggest the utility of differentiating if such cusps proceed the hypocone or metacone division and of using metacone variability in dental anthropology studies. An objective classification of the metacone size is proposed to standardize observations. Paper presented at the 4^th congress of the European Anthropology Association (Florence, Sept. 1984).     

Fish mucus metabolome reveals fish life-history traits

Fish mucus has important biological and ecological roles such as defense against fish pathogens and chemical mediation among several species. A non-targeted liquid chromatography–mass spectrometry metabolomic approach was developed to study gill mucus of eight butterflyfish species in Moorea (French Polynesia), and the influence of several fish traits (geographic site and reef habitat, species taxonomy, phylogeny, diet and parasitism levels) on the metabolic variability was investigated. A biphasic extraction yielding two fractions (polar and apolar) was used. Fish diet (obligate corallivorous, facultative corallivorous or omnivorous) arose as the main driver of the metabolic differences in the gill mucus in both fractions, accounting for 23% of the observed metabolic variability in the apolar fraction and 13% in the polar fraction. A partial least squares discriminant analysis allowed us to identify the metabolites (variable important in projection, VIP) driving the differences between fish with different diets (obligate corallivores, facultative corallivores and omnivorous). Using accurate mass data and fragmentation data, we identified some of these VIP as glycerophosphocholines, ceramides and fatty acids. Level of monogenean gill parasites was the second most important factor shaping the gill mucus metabolome, and it explained 10% of the metabolic variability in the polar fraction and 5% in the apolar fraction. A multiple regression tree revealed that the metabolic variability due to parasitism in the polar fraction was mainly due to differences between non-parasitized and parasitized fish. Phylogeny and butterflyfish species were factors contributing significantly to the metabolic variability of the apolar fraction (10 and 3%, respectively) but had a less pronounced effect in the polar fraction. Finally, geographic site and reef habitat of butterflyfish species did not influence the gill mucus metabolome of butterflyfishes.     

Pupil-Linked Arousal Determines Variability in Perceptual Decision Making

Decision making between several alternatives is thought to involve the gradual accumulation of evidence in favor of each available choice. This process is profoundly variable even for nominally identical stimuli, yet the neuro-cognitive substrates that determine the magnitude of this variability are poorly understood. Here, we demonstrate that arousal state is a powerful determinant of variability in perceptual decision making. We measured pupil size, a highly sensitive index of arousal, while human subjects performed a motion-discrimination task, and decomposed task behavior into latent decision making parameters using an established computational model of the decision process. In direct contrast to previous theoretical accounts specifying a role for arousal in several discrete aspects of decision making, we found that pupil diameter was uniquely related to a model parameter representing variability in the rate of decision evidence accumulation: Periods of increased pupil size, reflecting heightened arousal, were characterized by greater variability in accumulation rate. Pupil diameter also correlated trial-by-trial with specific patterns of behavior that collectively are diagnostic of changing accumulation rate variability, and explained substantial individual differences in this computational quantity. These findings provide a uniquely clear account of how arousal state impacts decision making, and may point to a relationship between pupil-linked neuromodulation and behavioral variability. They also pave the way for future studies aimed at augmenting the precision with which people make decisions.     

Assessing uncertainty of nitrate variability in groundwater

Nitrate is the primary form of nitrogen in natural waters and it can easily pass through soil to groundwater. Some levels of nitrate concentration in groundwater can cause some health problems such as methemoglobinemia in infants and several cancers. Since geological structures are not homogeneous, investigation of spatial variability of nitrate concentrations in groundwater is characterized by particularly high uncertainties. In this paper, a novel methodology for measure of uncertainty in groundwater nitrate variability is presented. To appraise the fuzziness, which is a type of uncertainty in spatial models, point cumulative semimadogram (PCSM) measure and a metric distance were employed. Measures of fuzziness have been carried out for each location using the experimental and model PCSMs. Finally an uncertainty map, which defines the regional variation of the uncertainty in different categories, has been composed.     

Sex and recombination in the Hötzel aging model

Why sex evolved and it prevails in nature remain one of thegreat puzzles of evolution. Most biologists would explain that it promotes genetic variability, however this explanation suffers from several difficulties. What advantages might sex confer? The present communication aims at certain investigations related to this question, in this way we introduce sexual recombination on the Hötzel model (with males and females) and wecompare these results with those from asexual reproduction without recombination.     

Retroelements in higher plants.

Representatives of several classes of retroelements have been characterized in a broad range of plant species, where they appear at variable and sometimes very high copy numbers. So far, only a very small number of plant elements have been shown to be active, and this activity seems to be restricted to specific situations of 'genomic shock'. Although it is not yet known whether the presence of retroelements is linked to the high level of variability found in plant genomes, it is now clear that retrotransposons are ancient and ubiquitous components of plant genomes, and could play an important role in plant evolution.     

An approximate likelihood estimator for the prevalence of infections in vectors using pools of varying sizes

There are several arthropods that can transmit disease to humans. To make inferences about the rate of infection of these arthropods, it is common to collect a large sample of vectors, divide them into groups (called pools), and apply a test to detect infection. This paper presents an approximate likelihood point estimator to rate of infection for pools of different sizes, when the variability of these sizes is small and the infection rate is low. The performance of this estimator was evaluated in four simulated scenarios, created from real experiments selected in the literature. The new estimator performed well in three of these scenarios. As expected, the new estimator performed poorly in the scenario with great variability in the size of the pools for some values of the parameter space.     

Proteomic analysis of microvesicles from plasma of healthy donors reveals high individual variability

Healthy blood plasma is required for several therapeutic procedures. To maximize successful therapeutic outcomes it is critical to control the quality of blood plasma. Clearly initiatives to improve the safety of blood transfusions will have a high economical and social impact. A detailed knowledge of the composition of healthy blood plasma is essential to facilitate such improvements. Apart from free proteins, lipids and metabolites, blood plasma also contains cell-derived microvesicles, including exosomes and microparticles from several different cellular origins. In this study, we have purified microvesicles smaller than 220nm from plasma of healthy donors and performed proteomic, ultra-structural, biochemical and functional analyses. We have detected 161 microvesicle-associated proteins, including many associated with the complement and coagulation signal-transduction cascades. Several proteases and protease inhibitors associated with acute phase responses were present, indicating that these microvesicles may be involved in these processes. There was a remarkably high variability in the protein content of plasma from different donors. In addition, we report that this variability could be relevant for their interaction with cellular systems. This work provides valuable information on plasma microvesicles and a foundation to understand microvesicle biology and clinical implications.     

The Hardy-Weinberg principle and its applications in modern population genetics

The discovery of the Hardy-Weinberg principle marked the beginning of the field of population genetics. Over the past hundred years, it has provided a starting point for many population genetic investigations. In this review, the Hardy-Weinberg principle, its statistical testing, and several of its applications in various modern population genetic research areas, including allelic variability and selection in the human leukocyte antigen region, microsatellite genotyping error detection, and accuracy of haplotype estimation, are discussed.     

High infraspecific diversity of wild sunflowers (Helianthus annuus L.) naturally developed in central Argentina

The sunflower's wild relative Helianthus annuus L. is a non-native invader in several regions of the world. It was introduced as an experimental forage plant in central Argentina six decades ago where it probably escaped and developed extended populations coexisting with the sunflower crop. If the invasive taxon was diffused without modifications, it would be expected to have phenotypic similarities with its parental sources. Nine populations representative of different geographic regions of central Argentina were compared with 17 populations from the USA (center of origin) in a common garden study at Bahía Blanca, Argentina using 47 phenotypic traits. The nine invasive wild populations were differentiated among themselves and from the native populations by plant form and life cycle traits, oil composition, inflorescence, and achene morphology. Populations from both continents shared traits related to domesticated sunflower, such as bract width over 0.8 cm, but the frequency of this trait was higher in populations from Argentina. The high variability of wild H. annuus populations from Argentina did not reveal any founder effects. The diversity found in the invasive populations reflected about three-fourths of the phenotypic variability of those from the center of origin, even though the environmental conditions of the Argentine habitats represented only half of the variability present in the North American habitats. The current findings demonstrated that the invasive wild sunflower populations have developed within few decades a high degree of variability, which could be a source of a novel biodiversity useful as a genetic resource for sunflower crop improvement.     

The role of temperature variability on insect performance and population dynamics in a warming world

Despite the amount of research on the consequences of global warming on ecological systems, most studies examine the impact of increases in average temperature. However, there are few studies concerning the role of thermal variability on ecological processes. Based on insect thermal and population ecology, we propose a theoretical framework for organizing the study of the role that thermal mean and variability plays in individual performance, and how it may affect population dynamics. Starting with three predictions of global warming scenarios, we develop null models of the expected changes in individual physiological performance and population dynamics. Ecological consequences in each scenario may range from simple changes in performance to drastic changes in population fluctuations and geographic ranges. In particular, our null models show that potential changes in the intrinsic population growth rate (R_m) will depend on the interaction of mean temperature and thermal variability, and that the net effect of the interaction could be synergistic or antagonistic. To evaluate these null models, we fit performance curves to compiled data from the literature on measurements of R_m at several constant and fluctuating temperatures. The fitted models showed that several of the qualitative characteristics predicted by the null model may be found in the fitted curves. We expect that this framework will be useful as a guide to study the influence of thermal changes on the dynamics of natural populations. Synthesis Despite the common assertion that global warming impacts depend on not only the mean temperatures but also on thermal variability, theoretical approaches to explain how the interaction of thermal mean and variability determines fitness are lacking. Here we propose a framework for studying the role of thermal mean and variability on individual performance and population dynamics. We developed null models that show how changes in the intrinsic population growth rate (R_m) will depend on the interaction of mean temperature and thermal variability, and that the net effect could be synergistic or antagonistic. We expect that this framework will be useful to study the influence of thermal changes on natural populations.