Evolution of the Mitochondrial Cytochrome Oxidase II Gene in Collembola

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data. Received: 12 January 1996 / Accepted: 10 August 1996     

Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria

We show that in animal mitochondria homologous genes that differ in guanine plus cytosine (G + C) content code for proteins differing in amino acid content in a manner that relates to the G + C content of the codons. DNA sequences were analyzed using square plots, a new method that combines graphical visualization and statistical analysis of compositional differences in both DNA and protein. Square plots divide codons into four groups based on first and second position A + T (adenine plus thymine) and G + C content and indicate differences in amino acid content when comparing sequences that differ in G + C content. When sequences are compared using these plots, the amino acid content is shown to correlate with the nucleotide bias of the genes. This amino acid effect is shown in all protein-coding genes in the mitochondrial genome, including cox I, cox II, and cyt b, mitochondrial genes which are commonly used for phylogenetic studies. Furthermore, nucleotide content differences are shown to affect the content of all amino acids with A + T- and G + C-rich codons. We speculate that phylogenetic analysis of genes so affected may tend erroneously to indicate relatedness (or lack thereof) based only on amino acid content. Received: 3 July 1996 / Accepted: 6 November 1996     

II. Phospholipid exchange and size enlargement in sonicated vesicles induced by a ‘critical’ fatty acid concentration

Size enlargement of dipalmitoyl phosphatidylcholine vesicles was greatly accelerated in the range of the phase-transition temperatures, when fatty acid concentration was above a threshold level (‘critical’ concentration). This ‘critical’ concentration varied with the length of the fatty acid chain. The size enlargement process had second-order kinetics dependent on the vesicle concentration. Alkaline pH and low ionic strength inhibited the rate of size enlargement.Phospholipid exchange between dimyristoyl and dipalmitoyl phosphatidylcholine vesicles increased abruptly above a ‘critical’ fatty acid concentration. The donor vesicles were those vesicles in which fatty acids reached the ‘critical’ concentration. The phospholipid exchange occurred both in fluid- and in solid-state vesicles. The ‘critical’ fatty acid concentration accelerating the phospholipid exchange process was lower than that accelerating the size enlargement process.The phospholipid exchange process explained in terms of a diminished hydrophobic attraction among the phospholipid molecules of the bilayer occurs via a free phospholipid molecule transfer through the aqueous phase. The size enlargement process is interpreted in terms of high fatty acid concentration in the membrane fluid domains. The membrane structure is locally perturbed inducing vesicle sticking after collision.     

Selection studies in sugarcane (Saccharum sp. hybrids)

Summary An approximate method to determine sample size for the estimation of population variance, ², is given. The estimate of ² is denoted as s² . Based on the assumption of a normal distribution for (s²/²–1), the sample size is approximately equal to 20,000 z² _p,/k²; where z is a standard normal deviate, p is the probability that s² ( 100¦s² – ²¦/²) is less than, or equal to, a critical value k, and k (measured as gDs²) is the desired precision of s² .The expected value of s², with respect to sample size, and the expected cumulative frequencies of s² over sample size for various k values are given. Their goodness of fit to the observed results was satisfactory except for populations that were different from normal. The observed values were taken from a study on four yield components in five sugarcane polycross progenies, grown in two contrasting environments over 2 years in three selection stages.The expected s² was found to be independent of the population coefficient of variance.Research suppoted in part by USDA, ARS, grant #12-14-5001-34. Published with the approval of the Director as Paper No. 412 in the Journal Series of the Experiment Station, Hawaiian Sugar Planters' Association.     

Molecular considerations in the evolution of bacterial genes

Summary Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationships, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of thegap andompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of theompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzyme in these lineages.     

Strand symmetry of mutation rates in theβ-globin region

Summary It has been suggested that there may be inequalities in the types of substitution on the two DNA strands (in particular, in the frequencies of transversions from R to Y and from Y to R) due to a higher error rate on the lagging than the leading strand during replication. Reexamination of 11 kb of the -globin region sequenced in six primates fails to confirm this suggestion. Examination of the 73-kb -globin region sequenced in humans shows that the frequency of pyrimidines in different parts of this region is more variable than expected in a random sequence, but the pattern is more consistent with nonrandomness generated by DNA turnover mechanisms than with strand asymmetry due to a higher error rate on the lagging strand.     

Factors affecting the reproductive success of the crab spider Misumenoides formosipes: the covariance between juvenile and adult traits

Summary To examine the importance of covariance between stages in traits related to foraging, we quantified the relationships between reproductive success and sizerelated variability in weight gain in juvenile and adult instars of the crab spider Misumenoides formosipes (Araneae: Thomisidae). Prereproductive weight and fecundity are both highly correlated with carapace width, a linear measure of size which does not change within an instar. In field populations, adult females with larger carapaces gain more weight and are more likely to reproduce than females with smaller carapaces. The growth rate of spiders fed ad libitum in the laboratory is unrelated to size, suggesting that size-related differences in the field are due to variation in prey-capture success. Adult females with a carapace width less than 3.4 mm comprised 22% of the population, but were never found to reproduce. Of the individuals that did reproduce, a 17% increase in carapace width resulted in a 100% increase in fecundity. Juvenile stages must be examined to understand adult foraging and reproductive success, because the net weight gained by juvenile instars determines adult size. The final weight gained by spiders in the antepenultimate and penultimate instars explained nearly all the variation in carapace width in the penultimate and adult instars, respectively. We found that constraints on foraging in late juvenile stages are different from the adult stage. Penultimate foraging behavior differs from that of adults, because of constraints on foraging in the period preceding ecdysis. Additionally, in both late juvenile instars, carapace width had little or no effect on the final weight gained within the instar suggesting that factors that affect foraging are different between the juvenile and adult stages. These analyses stress the fact that to fully understand the effects of foraging on reproductive success, we must examine stage-specific constraints throughout an organism's life history.     

Growth and reproduction of asexual konjak plants (Amorphophalus konjac K. koch)

To examine the differences of the growth and reproduction of different-aged plants, 0-, 1-, and 2-year plants ofAmorphophalus konjac were investigated. RGR and daily net production per unit productive part, relative net-production rate (α′), of the 0-year plant were largest, although NAR was highest in the 2-year plant. This was due to the large LAR of the 0-year plant, owing to its large SLA. With increase in age, LAR decreased and NAR increased. Thus, it appeared that the age of plant exerts two opposite effects on dry-matter production. Since these effects cancel each other out, differences in RGR and α′ between the two older plants were not significant. We estimated that plant size appears to be primarily responsible for these effects. The 0-year plant showed the least distribution ratio of net production into reproductive (storage) organs, and the highest productivity of the reproductive part. The ratio of the production of corm to total reproductive-part production, the D-reproduction index, was independent of age, and critical size in vegetative propagation could not be detected.     

Postmetamorphic growth,survival, and age at first reproduction of the salamander,hynobius nebulosus tokyoensis Tago in relation to a consideration on the optimal timing of first reproduction

The postmetamorphic growth and survival of the salamander Hynobius nebulosus tokyoentisTago were surveyed in the study site located in Habu village of Hinodemachi, a suburb of Tokyo City, during 1975–1981. A laboratory experiment on the growth rate of juveniles was conducted in parallel with the field survey. The result indicated that this salamander grew at the rate of 8,mm in s.v.l. per year during the juvenile stage, but its growth rate decreased markedly as low as 1.8 mm for males and 1.1 mm for females, once it had attained sexual maturity. According to the “capture-recapture” procedure the annual survival rate after metamorphosis was found to be quite high; that is, approximately 0.7. By using the growth rate of juveniles and the difference between the sizes at metamorphosis and sexual maturity, the age at first reproduction was estimated to be 4 year for males and 5 year for females. From the data obtained in this study, the intrinsic rates of increase (r) were calculated for various values of age at first reproduction under different survival schedules, and the relationship between the age at first reproduction and fitness as measured by r was examined. The result indicated that an optimal age maximizing fitness always existed under respective survival schedules, and the observed age at first reproduction of this salamandei was found to coincide well with the predicted optimal age.