Transitions and transversions in evolutionary descent: An approach to understanding

Summary In this paper I lay a quantitative theoretical groundwork for understanding the proportions of the possible types of base substitutions observed between 12 genes sharing a common ancestor and isolated from extant species. The experimentally observed types of base substitution between two sequenced genes do not give a direct measure of the types of base substitutions that occur during evolutionary descent. However, by use of a statistical assemblage of these observations, we can recover, without the assumption of parsimony, the conditional base substitution probabilities that determine this descent. Three methods—direct count, regression, and informational entropy maximization—are described by which these probabilities can be estimated from experimental data. The methods are complementary in that each is most useful for somewhat different types of experimental data. These methods are used to study the ratio of transversions to transitions during gene divergence. Though this ratio is not constant during divergence, it does approach a stable limiting value that in principle can vary from zero, corresponding to 100% transition differences, to infinity, corresponding to 0% transition differences. In practice the limiting ratio tends to hover around a value of two, which is expected on a random basis. However, base substitution pathways that are very nonrandom also may lead to a limiting ratio of exactly two, so that such a value is not diagnostic for random pathways. The limiting ratio can be directly calculated from a knowledge of the twelve conditional probabilities for each type of base substitution, or from a knowledge of the equilibrium base composition of the DNAs compared. An expression is given for this calculation. Fifteen years ago Jean Derancourt, Andrew Lebor and Emile Zuckerkandl (1967), analyzing the amino acid sequence of globin chains coded by nuclear genes, made the original observation that the proportion of transition differences decreases with increasing evolutionary time. Recently Brown et al. (1982) and Brown and Simpson (1982) have reported a decrease in the observed proportion of transition differences in mitochondrial DNA with increasing evolutionary divergence. The conditions that must be satisfied for this type of behavior to occur at stable base composition and with stable base substitution probabilities are defined. Multiple substitutionsper se do not lead to a decrease in transition differences with increasing evolutionary divergence.     

cDNA and amino acid sequences of rainbow trout (Oncorhynchus mykiss) lysozymes and their implications for the evolution of lysozyme and lactalbumin

Summary The complete 129-amino-acid sequences of two rainbow trout lysozymes (I and II) isolated from kidney were established using protein chemistry microtechniques. The two sequences differ only at position 86, I having aspartic acid and II having alanine. A cDNA clone coding for rainbow trout lysozyme was isolated from a cDNA library made from liver mRNA. Sequencing of the cloned cDNA insert, which was 1 kb in length, revealed a 432-bp open reading frame encoding an amino-terminal peptide of 15 amino acids and a mature enzyme of 129 amino acids identical in sequence to II. Forms I and II from kidney and liver were also analyzed using enzymatic amplification via PCR and direct sequencing; both organs contain mRNA encoding the two lysozymes. Evolutionary trees relating DNA sequences coding for lysozymesc and α-lactalbumins provide evidence that the gene duplication giving rise to conventional vertebrate lysozymesc and to lactalbumin preceded the divergence of fishes and tetrapods about 400 Myr ago. Evolutionary analysis also suggests that amino acid replacements may have accumulated more slowly on the lineage leading to fish lysozyme than on those leading to mammal and bird lysozymes.     

Evolution of glutamate dehydrogenase genes: Evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life

Summary The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family 1) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family 11) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotesin distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree. Offprint requests to: B. Labedan     

Ancient origin of lactalbumin from lysozyme: Analysis of DNA and amino acid sequences

Summary Parsimony trees relating DNA sequences coding for lysozymesc and -lactalbumins suggest that the gene duplication that allowed lactalbumin to evolve from lysozyme preceded the divergence of mammals and birds. Comparisons of the amino acid sequences of additional lysozymes and lactalbumins are consistent with this view. When all base positions are considered, the probability that the duplication leading to the lactalbumin gene occurred after the start to mammalian evolution is estimated to be 0.05–0.10. Elimination of the phylogenetic noise generated by fast evolution and compositional bias at third positions of codons reduced this probability to 0.002–0.03. Thus the gene duplication may have long preceded the acquisition of lactalbumin function.     

Monte Carlo simulation in phylogenies: An application to test the constancy of evolutionary rates

Monte Carlo simulation has commonly been used in phylogenetic studies to test different tree-reconstruction methods, and consequently, its application for testing evolutionary models can be considered as a natural extension of this usage. Repetitive simulation of a given evolutionary process, under the restrictions imposed by the model to be tested, along a determinate tree topology allow the estimate of probability distributions for the desired parameters. Next, the phylogenetic tree can be reconstructed again without the constraints of the model, and the parameter of interest, derived from this tree, can be compared to the corresponding probability distribution derived from the restricted, simulated trees. As an example we have used Monte Carlo simulation to test the constancy of evolutionary rates in a set of cytochrome-c protein sequences. Correspondence to: J. Dopazo     

Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals

The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs.     

A small basic ribosomal protein in Sulfolobus solfataricus equivalent to L46 in yeast: structure of the protein and its gene

The structure of the gene for a small, very basic ribosomal protein in Sulfolobus solfataricus has been determined and the structure of the protein coded by this gene (L46e) has been confirmed by partial amino acid sequencing. The protein shows substantial sequence homology to the eukaryotic ribosomal proteins L39 in rat and L46 in yeast. There is no sequence homology to any of the eubacterial ribosomal proteins suggesting that this protein is absent in the eubacterial ribosome.     

Evolution and instability in ring species complexes: An in silico approach to the study of speciation

Ring species are a biological complex that theoretically forms when an ancestral population extends its range around a geographic barrier and, despite low-level gene flow, differentiates until reproductive isolation exists when terminal populations come into secondary contact. Due to their rarity in nature, little is known about the biological factors that promote the formation of ring species. We use evolutionary algorithms operating on two simple computational problems (SAW and K-max) to study the process of speciation under the conditions which may yield ring species. We vary evolutionary parameters to measure their influence on ring species’ development and stability over evolutionary time. Using the SAW problem, ring species consistently form, i.e. fertility is negatively correlated with distance (R-values between −0.097 and −0.821, p<0.001), and terminal populations show substantial infertility. However, all SAW simulations demonstrate instability in the complex after sympatric zones are established between terminal populations. Higher mutation rates and larger dispersal/breeding radii promote ring species’ formation and stability. Using a problem with a simple fitness landscape, the K-max problem, ring species do not form. Instead, speciation around the ring occurs before ring closure as good genotypes become locally dominant.     

Hydrogen-isotope composition of leaf water in C3 and C4 plants: its relationship to the hydrogen-isotope composition of dry matter

The natural abundance hydrogen-isotope composition of leaf water ( ) and leaf organic matter ( _D ^org ) was measured in leaves of C₃ and C₄ dicotyledons and monocotyledons. The value of leaf water showed a marked diurnal variation, greatest enrichment being observed about midday. However, this variation was greater in the more slowly transpiring C₄ plants than in C₃ plants under comparable environmental conditions. A model based on analogies with a constant feed pan of evaporating water was developed and the difference between C₃ and C₄ plants expressed in terms of either differences in kinetic enrichment or different leaf morphology. Microclimatic and morphological features of the leaves which may be associated with this factor are discussed. There was no daily excursion in the _D ^org value in leaves of either C₃ or C₄ plants. When _D ^org values were referenced to the mean values during the period of active photosynthesis, the discrimination against deuterium during photosynthetic metabolism (D) was greater in C₃ plants (-117 to -121) than in C₄ plants (-86 to -109).These results show that the different water use strategies of C₃ and C₄ plants are responsible for the measured difference in deuterium-isotope composition of leaf water. However, it is unlikely that these physical processes account fully for the differences in hydrogen-isotope composition of the products of C₃ and C₄ photosynthetic metabolism.Symbols Hydrogen-isotope composition of leaf water - _D ^org hydrogen-isotope composition of leaf organic matter     

An equilibrium thermodynamic model of the sequestration of calcium phosphate by casein micelles and its application to the calculation of the partition of salts in milk

An equilibrium thermodynamic model of the interaction of calcium, phosphate and casein in milk is described in which the micellar calcium phosphate is assumed to be in the form of calcium phosphate nanoclusters. A generalized empirical formula for the nanocluster is used to define the molar ratios of small ions (Ca, Mg, P_i and citrate) to a casein phosphorylated sequence (phosphate centre, PC). From this model, a method of calculating the partition of milk salts into diffusible and non-diffusible fractions is obtained. No arbitrary assumptions are made, no fitting of adjustable parameters is done and the PCs in the caseins are defined by inspection of their primary structures. In addition to the salt partition, the mole fractions of the individual caseins not complexed to the calcium phosphate through one or more of their PCs are computed and a generic stability rule for milks is derived. The use of the model is illustrated by calculations of the partition of salts in a standard milk and by comparison with experimental data on the partition of salts in the milk of individual cows. The generic stability rule is applied to the individual milks to determine whether the micellar calcium phosphate is thermodynamically stable. According to the calculations, compositions that might lead to pathological calcification in the lumen of the mammary gland were seldom found in primiparous healthy cows in early or mid lactation but occurred more often in multiparous animals, in late lactation and during mastitic infection.Abbreviations ACP amorphous calcium phosphate - Cit citrate - CN casein - CPN calcium phosphate nanocluster - DCPD dicalcium phosphate dihydrate - HA hydroxyapatite - IAP ion activity product - MCP micellar calcium phosphate - MWCO molecular weight cut-off - OCP octacalcium phosphate - PC phosphate centre - TCC tricalcium citrate     

Estimating index of population trend by re-sampling techniques (jackknife and bootstrap) and its application to the life table study of rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae)

Taking a published natural population life table of rice leaf roller, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), as an example, we estimated the population trend index, I, via re‐sampling methods (jackknife and bootstrap), determined its statistical properties and illustrated the application of these methods in determining the control effectiveness of bio‐agents and chemical insecticides. Depending on the simulation outputs, the smoothed distribution pattern of the estimates of I by delete‐1 jackknife is visually distinguishable from the normal density, but the smoothed pattern produced by delete‐d jackknife, and logarithm‐transformed smoothed patterns produced by both empirical and parametric bootstraps, matched well the corresponding normal density. Thus, the estimates of I produced by delete‐1 jackknife were not used to determine the suppressive effect of wasps and insecticides. The 95% percent confidence intervals or the narrowest 95 percentiles and Z‐test criterion were employed to compare the effectiveness of Trichogramma japonicum Ashmead and insecticides (powder, 1.5% mevinphos + 3% alpha‐hexachloro cyclohexane) against the rice leaf roller based on the estimates of I produced by delete‐d jackknife and bootstrap techniques. At α= 0.05 level, there were statistical differences between wasp treatment and control, and between wasp and insecticide treatments, if the normality is ensured, or by the narrowest 95 percentiles. However, there is still no difference between insecticide treatment and control. By Z‐test criterion, wasp treatment is better than control and insecticide treatment with P‐value < 0.01. Insecticide treatment is similar to control with P‐value > 0.2 indicating that 95% confidence intervals procedure is more conservative. Although similar conclusions may be drawn by re‐sampling techniques, such as the delta method, about the suppressive effect of trichogramma and insecticides, the normality of the estimates can be checked and guaranteed, and the correlation among sequential life stages of rice leaf roller is also considered in the estimation. Judged by the P‐values from Z‐test, the delta method is more conservative.     

An immunological method to combine the measurement of active and total myeloperoxidase on the same biological fluid,and its application in finding inhibitors which interact directly with the enzyme

Abstract

Myeloperoxidase (MPO) is a pro-oxidant enzyme involved in inflammation, and the measurement of its activity in biological samples has emerged essential for laboratory and clinical investigations. We will describe a new method which combines the SIEFED (specific immunological extraction followed by enzymatic detection) and ELISA (ELISAcb) techniques to measure the active and total amounts of MPO on the same human sample and with the same calibration curve, as well as to define an accurate ratio between both the active and total forms of the enzyme.

The SIEFED/ELISAcb method consists of the MPO extraction from aqueous or biological samples by immobilized anti-MPO antibodies coated onto microplate wells. After a washing step to eliminate unbound material, the activity of MPO is measured in situ by adding a reaction solution (SIEFED). Following aspiration of the reaction solution, a secondary anti-MPO antibody is added into the wells and the ELISAcb test is carried out in order to measure the total MPO content.

To validate the combined method, a comparison was made with SIEFED and ELISA experiments performed separately on plasma samples isolated from human whole blood, after a neutrophil stimulation.

The SIEFED/ELISAcb provides a suitable tool for the measurement of specific MPO activity in biological fluids and for the estimation of the inhibitory potential of a fluid. The method can also be used as a pharmacological tool to make the distinction between a catalytic inhibitor, which binds to MPO and inhibits its activity, and a steric inhibitor, which hinders the enzyme and prevents its immunodetection.     

Use of life table statistics and degree-day values to predict the invasion success of Gonatocerus ashmeadi (Hymenoptera: Mymaridae), an egg parasitoid of Homalodisca coagulata (Hemiptera: Cicadellidae), in California

Life table statistics and degree-day requirements for Gonatocerus ashmeadi Girault, a parasitoid of the glassy-winged sharpshooter Homalodisca coagulata (Say), were used to estimate the number of expected parasitoid generations in California (USA). Between two to 51 and one to 37 generations per year were estimated across different climatic regions in California, using life table and degree-day models, respectively. Temperature-based values for net reproductive rate, R_o, were estimated in California using a laboratory-derived equation and ranged from zero to approximately 48 and analyses indicate that a minimum of eight generations are required each year to sustain a population increase of G. ashmeadi. Long-term weather data from 381 weather stations across California were used with an Inverse-Distance Weighting algorithm to map temperature-based estimations for the entire state of California. This Geographic Information Systems model was used to determine number of G. ashmeadi generations based on day-degree accumulation, T_c, and R_o. GIS mapping indicated that Californian counties in the north, central west coast, central west and Sierra Nevada regions may be climatic conditions unfavorable for supporting the permanent establishment of invading populations of G. ashmeadi should H. coagulata successfully establish year-round populations in these areas. Southern counties in California that experience warmer year round temperatures and support year round populations of H. coagulata, appear to be conducive to the establishment of permanent populations of G. ashmeadi. The mechanisms facilitating G. ashmeadi invasion and the implications of these temperature-based estimates for biological control of H. coagulata are discussed.     

An image analysis method for the precise selection and quantitation of fluorescently labeled cellular constituents: application to the measurement of human muscle cells in culture

The accurate measurement of the morphological characteristics of cells with nonuniform conformations presents difficulties. We report here a straightforward method using immunofluorescent staining and the commercially available imaging program Adobe Photoshop, which allows objective and precise information to be gathered on irregularly shaped cells. We have applied this measurement technique to the analysis of human muscle cells and their immunologically marked intracellular constituents, as these cells are prone to adopting a highly branched phenotype in culture. Use of this method can be used to overcome many of the long-standing limitations of conventional approaches for quantifying muscle cell size in vitro. In addition, wider applications of Photoshop as a quantitative and semiquantitative tool in immunocytochemistry are explored.     

Amino acid composition of the protein in preemergence nests of Polistes (Polistes) riparius, and its similarity to the consubgeneric wasp, P. (P.) chinensis (Hymenoptera: Vespidae)

Amino acid composition of the protein in the oral secretion, which is widely used for construction and maintenance of social wasp nests, was analyzed in preemergence nests of Polistes (Polistes) riparius. The kinds and proportion (%) of amino acids of the protein detected from nests of P. riparius were very similar to those of a consubgeneric species, P. (P.) chinensis, but were conspicuously different from those of other social wasp genera. Further, it was estimated that protein contents in oral secretion of P. riparius were nearly the same as those of P. chinensis; namely, foundresses of P. riparius, which build much larger nests than those of P. chinensis, did not reduce relative protein contents to produce more oral secretion at a smaller cost. Amino acid composition may reflect phylogenetic relationships among wasp taxa. Received: March 10, 2000 / Accepted: May 29, 2000     

Dynamics of the fungal symbionts in the gallery system and the mycangia of the ambrosia beetle,Xylosandrus mutilatus (Blandford) (Coleoptera: Scolytidae) in relation to its life history

The dynamics of the fungal symbionts in the gallery system and the mycangia of the ambrosia beetle,Xylosandrus mutilatus, were studied in relation to its life history using both isolation experiments and scanning electron microscopy (SEM). In the galleries,Ambrosiella sp. was predominant during the larval stages but its relative dominance gradually decreased during the development of the larvae. In contrast, yeasts (mainlyCandida sp.) andPaecilomyces sp. dominated continuously in the galleries after eclosion.Ambrosiella sp. was consistently stored in the mycangia in all adult stages, except in the teneral and overwintering adults when the other fungi were dominant. No fungal spores occurred in the mycangia of the adult beetles reared under aseptic conditions from the pupal stage, while onlyAmbrosiella sp. was stored in those reared from the teneral-adult stage. These results suggest that: (i) Xmutilatus is associated with at least three fungal species, among whichAmbrosiella sp. is the most essential food resource for development of the broods; (ii) immediately after eclosion, new female adults may take at least four associated fungal species, with no or incomplete selection, into their mycangia from the walls of the cradles; and (iii) conditions may well be produced in the mycangia of both matured and dispersing beetles whereby only the spores ofAmbrosiella sp. can proliferate.     

Determination of the investigational anti-cancer drug 5,6-dimethylxanthenone-4-acetic acid and its acyl glucuronide in Caco-2 monolayers by liquid chromatography with fluorescence detection: application to transport studies

5,6-Dimethylxanthenone-4-acetic acid (DMXAA) is a potent cytokine inducer, with a bioavailability of >70% in the mouse. The aim of this study was to develop and validate HPLC methods for the determination of DMXAA and DMXAA acyl glucuronide (DMXAA-G) in the human intestinal cell line Caco-2 monolayers. The developed HPLC methods were sensitive and reliable, with acceptable accuracy (85-115% of true values) and precision (intra- and inter-assay CV < 15%). The total running time was within 6.8 min, with acceptable separation of the compounds of interest. The limit of quantitation (LOQ) values for DMXAA and DMXAA-G were 14.2 and 24 ng/ml, respectively. The validated HPLC methods were applied to examine the epithelial transport of DMXAA and DMXAA-G by Caco-2 monolayers. The permeability coefficient (Papp) values (overall mean +/- S.D., n = 3-9) of DMXAA over 10-500 microM were independent of concentration for both apical (AP) to basolateral (BL) (4.0 +/- 0.4 x 10(-5)cm/s) and BL-AP (4.3 +/- 0.5 x 10(-5)cm/s) transport, and of similar magnitude in either direction, with net efflux ratio (Rnet) values of 1-1.3. However, the Papp values for the BL to AP transport of DMXAA-G were significantly greater than those for the AP to BL transport, with Rnet values of 17.6, 6.7 and 4.5 at 50, 100 and 200 microM, respectively. Further studies showed that the transport of DMXAA-G was Na+- and energy-dependent, and inhibited by MK-571 [a multidrug resistance associated protein (MRP) 1/2 inhibitor], but not by verapamil and probenecid. These data indicate that the HPLC methods for the determination of DMXAA and DMXAA-G in the transport buffer were simple and reliable, and the methods have been applied to the transport study of both compounds by Caco-2 monolayers. DMXAA across Caco-2 monolayers was through a passive transcellular process, whereas the transport of DMXAA-G was mediated by MRP1/2.