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     

Genetic diversity and phylogeny analysis of Anabaena azollae based on RFLPs detected in Azolla-Anabaena azollae DNA complexes using nif gene probes

The cyanobacterium Anabaena has both symbiotic and free-living forms. The genetic diversity of Anabaena strains symbiotically associated with the aquatic fern Azolla and the evolutionary relationships among these symbionts were evaluated by means of RFLP (restriction fragment length polymorphism) experiments. Three DNA fragments corresponding to nif genes were cloned from the free-living cyanobacterium Anabaena PCC 7120 and used as probes. A mixture of Azolla, Anabaena and bacterial DNA was extracted from Azolla fronds and digested with two restriction enzymes. Single-copy RFLP signals were detected with two of the probes in all Azolla Anabaena examined. Multiple-copy RFLP signals were obtained from the third probe which corresponded to a part of the nif N gene. A total of 46 probe/enzyme combinations were scored as present or absent and used to calculate pairwise Nei's genetic distances among symbiotic Anaebaena strains. Phylogenetic trees summarizing phenetic and cladistic relationships among strains were generated according to three different evolutionary scenarios: parsimony, UPGMA and neighbour joining. All trees revealed identical phylogenetic relationships. Principal component analysis was also used to evaluate genetic similarities and revealed three groups: group one contains the cyanobacteria associated with plants from the Azolla section, group two contains those associated with plants from the pinnata species and group three contains those associated with plants from the nilotica species. The same groups had already been identified earlier in a random amplified polymorphic DNA (RAPD) analysis of Azolla-Anbaena DNA complexes, suggesting that the present Azolla taxonomy should be revised. We now suggest a taxonomy of Anabaena azollae that is parallel to such a revised Azolla taxonomy. An Azolla chloroplast DNA sequence derived from Oryza sativa was also used as an RFLP probe on Azolla DNA to confirm the presence of plant DNA in the total genomic DNA extracted from ferns with or without the symbiont. Our results also suggest that total DNA extracted from the Azolla-Anabaena complexes includes both plant and symbiont DNA and can be used equally well for RFLP analysis of host plant or symbiotic cyanobacteria.     

The size and diversity of the soil seed banks and the light requirements of the species in sunny and shady natural communities of the Białowieża Primeval Forest

The research was conducted in two natural forest communities: Potentillo albae-Quercetum (oak forest) which allows much light to reach the forest floor and Tilio-Carpinetum typicum (hornbeam forest) which shades the herb layer heavily. The seed banks were estimated from numbers of seedlings emerging from soil samples over one growing season.(1) Our results confirm the hypothesis that persistent seed banks are mainly formed by species with high light requirements. Of the species found predominantly in the seed bank and absent from the herb layer or occurring there very rarely in both communities 83% of species and 70% of seedlings were strongly light-demanding (Ellenberg's light index 6–9). However, the results do not support the hypothesis that seed banks in natural deciduous forest communities are small, poor in species and do not reflect the species composition of herb layer.(2) The seed banks of both communities were rich in species and relatively large. Species richness in the oak forest turned out to be higher than in the hornbeam forest (51 vs 45 species/2.4 m₂), but size was smaller (2659 vs 5789 seedlings/2.4 m₂). In the oak forest the most abundant species in the seed bank was Galium boreale, but it constituted only 19% of the total number of seedlings, whereas in the hornbearn forest the dominant species, Urtica dioica, constituted 57% of the total.(3) In each community the species composition of the seed bank and the herb layer was very similar (>70%).(4) The seed bank was more diverse in the oak forest than in the hornbeam forest (H 2.34 vs 1.68).(5) The seed banks of both communities differed in the contribution of species with varied light requirements; in the sunny oak forest species with high light requirements dominated, whereas in the shady hornbeam forest both strongly and moderately light-demanding species had similar contributions.Nomenclature: Follows Ehrendorfer (1973) and Matuszkiewicz (1981).     

Problems with Parsimony in Sequences of Biased Base Composition

Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis demonstrates that parsimony can be misleading even when levels of sequence divergence are as low as 10%; parsimony incorrectly infers an excess of common to rare changes. Caution must therefore be excercised in the use of parsimony. Received: 13 November 1997 / Accepted: 18 June 1998     

Low Divergence in rDNA ITS Sequences Among Five Species of Fucus (Phaeophyceae) Suggests a Very Recent Radiation

Sequences from the two ribosomal DNA internal transcribed spacers (ITS1 and ITS2) were compared among five species of Fucus. Based on the present taxon sampling, parsimony analysis showed that Fucus serratus is the sister-group of the remaining Fucus species when Ascophyllum nodosum was used as an outgroup. The topology of the tree was (Fucus serratus (F. lutarius (F. vesiculosus (F. spiralis+F. ceranoides)))). The extremely low variation observed suggests a very recent radiation of the genus which supports the view widely accepted that the Fucales are among the most evolutionarily advanced of the brown algae. We further note that sequence differences between Fucus and Ascophyllum were 28%: this does not rule out the utility of ITS sequences within the Fucaceae. The very low number of informative positions allows to demonstrate empirically that distance matrix methods group on the basis of symplesiomorphies. Received: 17 February 1997 / Accepted: 17 April 1997     

Determination of digestive enzyme kinetics: a new method to define trophic niches in freshwater snails

 Fluorogenic substrate analogues (MUF substrates) are very sensitive in detecting hydrolytic enzymes. This method was adapted for the quantitative analysis of extracellular enzymes in snails and other animals. It was then used to determine cellobiase, chitobiase, protease, esterase, phosphatase and lipase in the digestive tract of Radix peregra and Bithynia tentaculata. The method was sensitive enough to determine the complete enzyme kinetics (K _m, V _max values) in the esophagus, stomach, digestive gland and intestine of single animals adapted to various natural foods. With the exception of lipase and phosphatase, K _m values were between 15 and 30 mmol l^–1, independent of prefeeding. Enzyme activities, in contrast, changed with food conditions: cellobiase-activities ranged from 80 to 8000 picokatal, esterase from 500 to 3000 pKat, chitobiase from 150 to 750 pKat and protease from 100 to 1100 pKat per animal. R. peregra had cellobiase activities 10 times higher than B. tentaculata. For chitobiase, esterase and protease the enzyme activities were in the same order of magnitude in both species. All enzymes differed significantly in activity between prefeeding regimes. This variability with prefeeding was much higher in Bithynia than in Radix. These results help to better define the trophic niches and feeding specializations of the two species studied. Received: 12 April 1996 / Accepted: 26 June 1996     

华夏鱼科(Huashiidae)的系统关系及分类学意义

本文用 Hennig 86 软件对华夏鱼类的系统关系进行了重新探讨,认为目前将华夏鱼类归入骨舌鱼超目是由于简约性的缘故.同时,本文对简约原则的适用性进行了讨论.     

Phase locking of biological clocks

Radial isochron clocks (RICs) and their response to external signals and coupling with other RICs are studied. RICs are derived as phase approximations to self-sustained oscillators. Their response to single impulses (phase resetting) and to repetitive impulses is determined. This response may be harmonic or chaotic. Finally, the effect of coupling between clocks is studied. Simple coupling is shown to exhibit rhythm splitting like that observed in fish and small mammals. New phase locking results for general weakly coupled RIC systems are also derived.Supported in part by the National Science Foundation under grants MCS-80-15359 (FCH) and MCS-79-02505 (JPK)     

A note on the estimation of selective values from recaptures of marked animals when selection pressures remain constant over time

An equation is given for the estimation of selective values from data obtained by mark-recapture experiments, assuming that selective pressures remain constant while the experiments are carried out. The equation does not have an explicit solution but can readily be solved using a trial-and-error method. The use of the equation is illustrated on some data reported byKettlewell et al. (1969) from an experiment involving typica and edda morphs of the moth Amathes glareosa. It is found that the edda morph apparently had a selective advantage of about 12% per day compared to the typica morph and that this is significantly different from zero. Using another methodKettlewell concluded that the selective advantage of the edda morph was only 7% and that this was not statistically significant.     

An analysis of foundress group size inRopalidia fasciata (Hymenoptera: Vespidae), with zero-truncated distributions

Summary Distribution patterns of foundress group size ofRopalidia fasciata did not fit to 0-truncated Poisson series due to overdispersion. Six of seven distributions fitted to 0-truncated negative binomial series, but, for most cases, neither Brass' moment method nor the maximum liklihood method could be used due to disproportionately high frequency of nests with single foundress. Existence of two kinds of foundresses was suggested. This work was supported in part by a Grant-in-Aid (No. 62304002) from the Ministry of Education, Science and Culture, Japan.