Investigation on the causes of stoichiometric error in genome size estimation using heat experiments: consequences on data interpretation

BACKGROUND AND AIMS: In microdensitometry and flow cytometry, estimation of nuclear DNA content in a sample requires a standard with a known nuclear DNA content. It is assumed that dye accessibility to DNA is the same in the sample and standard nuclei. Stoichiometric error arises when dye accessibility is not proportional between the sample and standard. The aim of the present study was to compare the effects of standardization (external-internal) on nuclear fluorescence of two Coffea species and petunia when temperature increases, and the consequences on genome size estimation. METHODS: Two coffee tree taxa, C. liberica subsp dewevrei (DEW) and C. pseudozanguebarieae (PSE), and Petunia hybrida were grown in a glasshouse in Montpellier, France. Nuclei were extracted by leaf chopping and at least 2 h after nuclei extraction they were stained with propidium iodide for approx. 3 min just before cytometer processing. In the first experiment, effects of heat treatment were observed in mixed (DEW + petunia) and unmixed extracts (petunia and DEW in separate extracts). Nine temperature treatments were carried out (21, 45, 55, 60, 65, 70, 75, 80 and 85 degrees C). In a second experiment, effects of heating on within-species genome size variations were investigated in DEW and PSE. Two temperatures (21 and 70 degrees C) were selected as representative of the maximal range of chromatin decondensation. KEY RESULTS AND CONCLUSIONS: In coffee trees, sample and standard nuclei reacted differently to temperature according to the type of standardization (pseudo-internal vs. external). Cytosolic compounds released in the filtrate would modify chromatin sensitivity to decondensation. Consequently, the 'genome size' estimate depended on the temperature. Similarly, intraspecific variations in genome size changed between estimations at 21 degrees C and 70 degrees C. Consequences are discussed and stoichiometric error detection methods are proposed, along with proposals for minimizing them.     

Analysis of the tomato fruit growth response to temperature and plant fruit load in relation to cell division, cell expansion and DNA endoreduplication

BACKGROUND AND AIMS: To better understand the regulation of fruit growth in response to environmental factors, the effects of temperature and plant fruit load on cell number, cell size and DNA endoreduplication were analysed. METHODS: Plants were grown at 20/20 degrees C, 25/25 degrees C and 25/20 degrees C day/night temperatures, and inflorescences were pruned to two ('2F') or five ('5F') flowers. KEY RESULTS AND CONCLUSIONS: Despite a lower fruit growth rate at 20/20 degrees C, temperature did not affect final fruit size because of the compensation between cell number and size. The higher cell number at 20/20 degrees C (9.0 x 10(6) against 7.9 x 10(6) at 25/25 degrees C and 7.7 x 10(6) at 25/20 degrees C) resulted from an extended period of cell division, and the smaller cell size was due to a shorter period of expansion rather than a lower expansion rate. By contrast, the lower fruit growth rate and size of 5F fruits compared with 2F fruits resulted from the slow down of cell expansion, whereas the number of cells was hardly affected in the proximal fruit. However, within the inflorescence the decreasing gradient of fruit size from proximal to distal fruits was due to a decrease in cell number with similar cell size. Fruit size variations within each treatment were always positively correlated to variations in cell number, but not in cell size. Negative correlations between cell size and cell number suggested that cells of tomato pericarp can be seen as a population of competing sinks. Mean ploidy was slightly delayed and reduced in 5F fruits compared with 2F fruits. It was highest at 25/25 degrees C and lowest at 25/20 degrees C. Treatments did not affect ploidy and cell size in similar ways, but within each treatment, positive correlations existed between mean ploidy and cell size, though significant only in the 2F-25/20 treatment.     

The C-value enigma in plants and animals: a review of parallels and an appeal for partnership

• Aims Plants and animals represent the first two kingdomsrecognized, and remain the two best-studied groups in termsof nuclear DNA content variation. Unfortunately, the traditionalchasm between botanists and zoologists has done much to preventan integrated approach to resolving the C-value enigma, thelong-standing puzzle surrounding the evolution of genome size.This grand division is both unnecessary and counterproductive,and the present review aims to illustrate the numerous linksbetween the patterns and processes found in plants and animalsso that a stronger unity can be developed in the future. • Scope This review discusses the numerous parallels thatexist in genome size evolution between plants and animals, including(i) the construction of large databases, (ii) the patterns ofDNA content variation among taxa, (iii) the cytological, morphological,physiological and evolutionary impacts of genome size, (iv)the mechanisms by which genomes change in size, and (v) thedevelopment of new methodologies for estimating DNA contents. • Conclusions The fundamental questions of the C-valueenigma clearly transcend taxonomic boundaries, and increasedcommunication is therefore urged among those who study genomesize evolution, whether in plants, animals or other organisms.     

The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints

BACKGROUND AND AIMS: Nuclear DNA content (C-value) varies approximately 1000-fold across the angiosperms, and this variation has been reported to have an effect on the quality of AFLP fingerprints. Various methods have been proposed for circumventing the problems associated with small and large genomes. Here we investigate the range of nuclear DNA contents across which the standard AFLP protocol can be used. METHODS: AFLP fingerprinting was conducted on an automated platform using the standard protocol (with 3 + 3 selective bases) in which DNA fragments are visualized as bands. Species with nuclear DNA contents ranging from 1C = 0.2 to 32.35 pg were included, and the total number of bands and the number of polymorphic bands were counted. For the species with the smallest C-value (Bixa orellana) and for one of the species with a large C-value (Damasonium alisma), alternative protocols using 2 + 3 and 3 + 4 selective bases, respectively, were also used. KEY RESULTS: Acceptable AFLP traces were obtained using the standard protocol with 1C-values of 0.30-8.43 pg. Below this range, the quality was improved by using 2 + 3 selective bases. Above this range, the traces were generally characterized by a few strongly amplifying bands and noisy baselines. Damasonium alisma, however, gave more even traces, probably due to it being a tetraploid. CONCLUSIONS: We propose that for known polyploids, genome size is a more useful indicator than the 1C-value in deciding which AFLP protocol to use. Thus, knowledge of ploidy (allowing estimation of genome size) and C-value are both important. For small genomes, the number of interpretable bands can be increased by decreasing the number of selective bases. For larger genomes, increasing the number of bases does not necessarily decrease the number of bands as predicted. The presence of a small number of strongly amplifying bands is likely to be linked to the presence of repetitive DNA sequences in high copy number in taxa with large genomes.     

Effective size of populations under partial inbreeding and selection on a set of linked additive genes

The prediction theory of effective population size (Ne) is extended to cover selection on a set of linked additive genes and partial inbreeding (partial selfing or partial full-sib mating). Ne under selection is generally expressed as a function of the cumulative change in frequency of a neutral gene due to the random association between the neutral and selected genes generated by finite sampling. In this study, the association under partial selfing was classified into two types, the association between the neutral and selected genes on the same gamete, and the association between the neutral and selected genes each on the different gametes in the same parent. For partial full-sib mating, an additional association, i.e., the association between the neutral and selected genes each in the different parents in the same family, was included in the model. According to this classification of the association, the coefficient accounting for the cumulative change in frequency of the neutral gene was partitioned into two or three components. A method for computing the partitioned coefficients was obtained from the transition matrix approach, in which the joint effect of linkage, selection and partial inbreeding was taken into account. To assess the joint effects of linkage, selection and partial inbreeding on Ne, numerical computations with the obtained expressions were carried out. The effect of linkage on Ne was generally small, except for an extremely small genome size, while the partial inbreeding resulted in a drastic reduction in Ne. For a given genome size, Ne was essentially independent of the length and number of chromosomes. Some of these results were verified by stochastic simulations.     

The relationship between nuclear DNA content and leaf strategy in seed plants

BACKGROUND AND AIMS: Species' 2C-values (mass of DNA in G(1) phase 2n nuclei) vary by at least four orders of magnitude among seed plants. The 2C-value has been shown to be co-ordinated with a number of other species traits, and with environmental variables. A prediction that species 2C-values are negatively related to leaf life span (LL) and leaf mass per area (LMA) is tested. These leaf traits are components of a major dimension of ecological variation among plant species. METHODS: Flow cytometry was used to measure the 2C-values for 41 Australian seed plant species, 40 of which were new to the literature. Where possible, LL and LMA data from the global literature were combined with 2C-values from our data set and online C-value databases. KEY RESULTS: Across all species, weak positive relationships were found between 2C-values and both LL and LMA; however, these did not reflect the relationships within either angiosperms or gymnosperms. Across 59 angiosperm species, there were weak negative relationships between 2C-values and both LL (r2 = 0.13, P = 0.005) and LMA (r2 = 0.15, P = 0.002). These relationships were the result of shifts to longer LL and greater LMA in woody compared with herbaceous growth forms, with no relationships present within growth forms. It was not possible to explain a positive relationship between 2C-values and LMA (r2 = 0.30, P = 0.024) across 17 gymnosperm species. The 2C-value was not related to LL or LMA either across species within orders (except for LMA among Pinales), or as radiation divergences in a model phylogeny. CONCLUSIONS: Gymnosperms appear to vary along a spectrum different from angiosperms. Among angiosperms, weak negative cross-species relationships were associated with growth form differences, and traced to a few divergences deep in the model phylogeny. These results suggest that among angiosperms, nuclear DNA content and leaf strategy are unrelated.     

Tutorial: using confidence curves in medical research

Confidence intervals represent a routinely used standard method to document the uncertainty of estimated effects. In most cases, for the calculation of confidence intervals the conventional fixed 95% confidence level is used. Confidence curves represent a graphical illustration of confidence intervals for confidence levels varying between 0 and 100%. Although such graphs have been repeatedly proposed under different names during the last 40 years, confidence curves are rarely used in medical research. In this paper, we introduce confidence curves and present a short historical review. We draw attention to the different interpretation of one- and two-sided statistical inference. It is shown that these two options also have influence on the plotting of appropriate confidence curves. We illustrate the use of one- and two-sided confidence curves and explain their correct interpretation. In medical research more emphasis on the choice between the one- and two-sided approaches should be given. One- and two-sided confidence curves are useful complements to the conventional methods of presenting study results.     

Torpor and thermal energetics in a tiny Australian vespertilionid,the little forest bat (<Emphasis Type="Italic">Vespadelus vulturnus</Emphasis>)

Data on thermal energetics for vespertilionid bats are under-represented in the literature relative to their abundance, as are data for bats of very small body mass. Therefore, we studied torpor use and thermal energetics in one of the smallest (4 g) Australian vespertilionids, Vespadelus vulturnus. We used open-flow respirometry to quantify temporal patterns of torpor use, upper and lower critical temperatures (T _uc and T _lc) of the thermoneutral zone (TNZ), basal metabolic rate (BMR), resting metabolic rate (RMR), torpid metabolic rate (TMR), and wet thermal conductance (C _wet) over a range of ambient temperatures (T _a). We also measured body temperature (T _b) during torpor and normothermia. Bats showed a high proclivity for torpor and typically aroused only for brief periods. The TNZ ranged from 27.6°C to 33.3°C. Within the TNZ T _b was 33.3±0.4°C and BMR was 1.02±0.29 mlO₂ g⁻¹ h⁻¹ (5.60±1.65 mW g⁻¹) at a mean body mass of 4.0±0.69 g, which is 55 % of that predicted for a 4 g bat. Minimum TMR of torpid bats was 0.014±0.006 mlO₂ g⁻¹ h⁻¹ (0.079±0.032 mW g⁻¹) at T _a=4.6±0.4°C and T _b=7.5±1.9. T _lc and C _wet of normothermic bats were both lower than that predicted for a 4 g bat, which indicates that V. vulturnus is adapted to minimising heat loss at low T _a. Our findings support the hypothesis that vespertilionid bats have evolved energy-conserving physiological traits, such as low BMR and proclivity for torpor.     

Fertilization competence and sperm size variation in sperm-heteromorphic insects

Between species, variation in sperm size has been related to male–female coevolution and male–male competition. In contrast, variation within species is poorly understood. A particular case of intraspecific sperm-size variation occurs in sperm-heteromorphic species, where males produce distinct sperm morphotypes, usually only one of which is fertile. This allows to investigate sperm size variation under different selection regimes. Nonfertile morphotypes, whose role is aside from fertilization, may have other functions, and this may be reflected by changes in developmental processes and a different phenotype compared to fertile sperm. We show that the intraspecific coefficient of variation in sperm length is up to four times lower for fertile than nonfertile morphotypes across 150 sperm-heteromorphic species (70 butterfly, 71 moth, 9 diopsid fly species). This is in agreement with a previous study on 11 species in the Drosophila obscura group. Significantly lower variation in fertile than nonfertile sperm morphometry may result from fertilization-related selection for optimal sperm size, novel functions of nonfertile sperm, or from tighter control of fertile sperm development. More data are needed to clarify the consequences and adaptive significance of within-morph variation, and its consistent pattern across sperm-heteromorphic insects.Co-ordinating editor: Hurst     

The Combined Effects of Pre- and Post-Insemination Sexual Selection on Extreme Variation in Male Body Size

Orb-weaving spiders of the genus Nephila are notable for their sexual size dimorphism, with dwarf males and giant females. However, less well known is the extreme size polymorphism of males that is characteristic of some species. For example, adult male body size in N. edulis varies by an order of magnitude. Previous experiments reveal that male mating behaviour covaries with body size, suggesting the size variation is maintained by opposing pre- and post-insemination sexual selection pressures. Here, we test this idea by allowing males of different sizes to compete directly and simultaneously for access to females. Using the sterile-male technique for paternity assessment, we show that two competing males drawn from the extremes of size variations, split paternity the same way as two males of the same size drawn from the intermediate sizes. The paternity of a large male dropped from 50% to 30% on average if he competed against two instead of one small male. The large male increased his mating frequency when there were more rivals but required a much lower total duration of copulation to achieve the same paternity share. These data are consistent with the idea that opposing pre- and post-insemination selection pressures at least partly explain the variation in male body size. Co-ordinating editor: L.D. Hurst