Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene

The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.     

The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments

How to sample alignments from their posterior probability distribution given two strings is shown. This is extended to sampling alignments of more than two strings. The result is first applied to the estimation of the edges of a given evolutionary tree over several strings. Second, when used in conjunction with simulated annealing, it gives a stochastic search method for an optimal multiple alignment.Correspondence to: L. Allison     

Phylogenetic analysis of the stress-70 protein family

The eukaryotic cyto-/nucleoplasmatic 70-kDa heat-shock protein (HSP70) has homologues in the endoplasmic reticulum as well as in bacteria, mitochondria, and plastids. We selected a representative subset from the large number of sequenced stress-70 family members which covers all known branches of the protein family and calculated and manually improved an alignment. Here we present the consensus sequence of the aligned proteins and putative nuclear localization signals (NLS) in the eukaryotic HSP70 homologues. The phylogenetic relationships of the stress-70 group family members were estimated by use of different computation methods. We present a phylogenetic tree containing all known stress-70 subfamilies and demonstrate the usefulness of stress-70 protein sequences for the estimation of intertaxonic phylogeny. Correspondence to: S.A. Reusing     

P-type ATPases of eukaryotes and bacteria: Sequence analyses and construction of phylogenetic trees

The amino acid sequences of 47 P-type ATPases from several eukaryotic and bacterial kingdoms were divided into three structural segments based on individual hydropathy profiles. Each homologous segment was (1) multiply aligned and functionally evaluated, (2) statistically analyzed to determine the degrees of sequence similarity, and (3) used for the construction of parsimonious phylogenetic trees. The results show that all of the P-type ATPases analyzed comprise a single family with four major clusters correlating with their cation specificities and biological sources as follows: cluster 1: Ca²⁺-transporting ATPases; cluster 2: Na⁺- and gastric H⁺-ATPases; cluster 3: plasma membrane H⁺-translocating ATPases of plants, fungi, and lower eukaryotes; and cluster 4: all but one of the bacterial P-type ATPases (specific for K⁺, Cd²⁺, Cu²⁺ and an unknown cation). The one bacterial exception to this general pattern was the Mg²⁺-ATPase of Salmonella typhimurium, which clustered with the eukaryotic sequences. Although exceptions were noted, the similarities of the phylogenetic trees derived from the three segments analyzed led to the probability that the N-terminal segments 1 and the centrally localized segments 2 evolved from a single primordial ATPase which existed prior to the divergence of eukaryotes from prokaryotes. By contrast, the C-terminal segments 3 appear to be eukaryotic specific, are not found in similar form in any of the prokaryotic enzymes, and are not all demonstrably homologous among the eukaryotic enzymes. These C-terminal domains may therefore have either arisen after the divergence of eukaryotes from prokaryotes or exhibited more rapid sequence divergence than either segment 1 or 2, thus masking their common origin. The relative rates of evolutionary divergence for the three segments were determined to be segment 2 < segment 1 < segment 3. Correlative functional analyses of the most conserved regions of these ATPases, based on published site-specific mutagenesis data, provided preliminary evidence for their functional roles in the transport mechanism. Our studies define the structural and evolutionary relationships among the P-type ATPases. They should provide a guide for the design of future studies of structure-function relationships employing molecular genetic, biochemical, and biophysical techniques. Correspondence to: M.H. Saier, Jr.     

Promotion by phloroglucinol of adventitious root formation in micropropagated shoots of adult wild cherry (Prunus avium L.)

Micropropagated shoots of wild cherry (Prunus avium L.) produced roots in auxin-free medium. Phloroglucinol (PG) increased the proportion of shoots that rooted, while phloretic acid reduced this response in medium with or without PG, and cancelled the promotive effect of PG. Concentration of PG also significantly affected rooting in media with and without auxin. The proportion of shoots rooting in media containing auxin, or auxin plus PG, increased with the number of successive subculture, but the proportion that rooted with PG alone was unaffected by the number of subcultures. Before the shoots had become responsive to auxin, 1 mM PG was more effective than auxin in inducing root formation.     

Phenology and anatomy of the reproductive phase of Abies pinsapo Boiss. (Pinaceae)

Phenology and anatomy of the reproductive phase of Abies pinsapo were studied. Male cones and female cones were differentiated in the autumn, and the dormant microsporangia contained pollen mother cells (PMCs) in the premeiotic stage. The male cones broke dormancy at the end of February when the pollen mother cells began meiosis. Pollen grains were shed at the five-celled stage at the end of April-early May. The female cones broke dormancy in mid-April. Anthesis took place at the end of April. No micropylar-pollination droplet was observed. After pollination the female cones developed quickly. The most important loss of cones occurred during the pollination period. The number of archegonia varied from one to three but two was most common. Fertilization took place at the end of June. The embryos developed during the summer, and seeds were dispersed in autumn. The results are discussed in relation to other conifers.     

The effect of electron acceptors on the phytochrome-controlled germination of Paulownia tomentosa seeds

The effect of substances with different redox potentials in the phytochrome-controlled germination of Paulmtnia tomentosa seeds was examined. Up to 25% of water-imbibed seeds germinated upon irradiation with 5 min red light The seeds irradiated with 5 min red light and incubated in substances with redox potentials equal or higher than E'₀= 360 mV [potassium nitrate, potassium hexacyanoferrate (III) or potassium hexachloroiridate (IV)] and sodium nitroprusside germinated up to 80%. The optimal concentration was between 1 and 10 mM. Other electron acceptors such as 2.6-dichlorophenol-indoplhenol, phenazine methosulfate and methylene blue failed to produce and effect. The germination-promoting effect was obtained when the substances were supplied to the incubation medium from the onset of imbibition or at the onset of irradiation. Delay of application of these chemicals until after the red light treatment diminished their effectiveness and the effect was lost after 48 h. The escape from far-red reversibility was evident in the presence of substances which stimulated germination. The results presented support the view that phytochrome-broken dormancy of Paulownia tomentosa seeds is closely connected with redox changes.     

Nutrient distribution in a Swedish tree species experiment

The influence of four tree species on the distribution of nutrients between different compartments of the ecosystem was examined. In a randomized block (n=3) experiment in south-western Sweden, Ca, Mg and K were determined as exchangeable amounts in the mineral soil and as total amounts in the O+A₁ horizons (topsoil) and in the aboveground tree biomass. N contents were determined in all compartments as well as P contents of the aboveground tree biomass and the topsoil. The four tree species planted were: silver fir [Abies alba Mill.] (AA), grand fir [Abies grandis Lindl.] (AG), Norway spruce [Picea abies L. Karst.] (PA) and Japanese larch [Larix leptolepis (Sieb. och Zucc.) Endl.] (LL). At the age of 35–36 years, the total stemwood production of the most productive species, AG, was estimated at 471 m³ ha⁻¹. In relation to AG, LL had produced 80%, PA 73% and AA 37%. The system totals [aboveground tree biomass total + topsoil total + exchangeable (Ca, Mg, K) or total (N) in the mineral soil] of Ca, K and N did not differ significantly at the 5% level between the investigated species. For Mg, the system total in LL was significantly higher than for the other species. There was an indication that LL and AA contained higher amounts of Ca, Mg, K and N in the topsoil but less in the biomass than did AG and PA (partly significant). In the mineral soil, there were no significant differences in the exchangeable pools of Ca and K, nor in the total amounts of N. The biomass nutrient concentrations generally decreased in the order: AA > PA > AG > LL. At stem or whole-tree harvest, the Ca export per biomass unit would more than double in the case of PA compared to LL. LL also contained less N in the biomass than the other species. However, the N content in the biomass did not differ between the most (AG) and the least (AA) productive species, although the production of dry weight biomass (standing + harvested) of AG had been twice that of AA. It is concluded that the nutrient budget of a managed forest may vary considerably depending on the choice of tree species.     

Comparison of phylogenetic relationships based on phospholipid fatty acid profiles and ribosomal RNA sequence similarities among dissimilatory sulfate-reducing bacteria

Abstract Twenty-five isolates of dissimilatory sulfate-reducing bacteria were clustered based on similarity analysis of their phospholipid ester-linked fatty acids (PLFA). Of these, 22 showed that phylogenetic relationships based on the sequence similarity of their 16S rRNA directly paralleled the PLFA relationships. Desulfobacter latus and Desulfobacter curvatus grouped with the other Desulfobacter spp. by 16S rRNA comparison but not with the PLFA analysis as they contained significantly more monoenoic PLFA than the others. Similarly, Desulfovibrio africanus clustered with the Desulfovibrio spp. by 16S rRNA but not with them when analyzed by PLFA patterns because of higher monoenoic PLFA content. Otherwise, clustering obtained with either analysis was essentially congruent. The relationships defined by PLFA patterns appeared robust to shifts in nutrients and terminal electron acceptors. Additional analyses utilizing the lipopolysaccharide-lipid A hydroxy fatty acid patterns appeared not to shift the relationships based on PLFA significantly except when completely absent, as in Gram-positive bacteria. Phylogenetic relationships between isolates defined by 16S rRNA sequence divergence represent a selection clearly different from the multi-enzyme activities responsible for the PLFA patterns. Determination of bacterial relationships based on different selective pressures for various cellular components provides more clues to evolutionary history leading to a more rational nomenclature.     

纵坑切梢小蠹蛀梢期空间分布

在昆明地区,纵坑切梢小蠹(Tomicus piniperda)成虫蛀梢多集中在蛀干木附近。 种群密度以蛀干木为中心向周围呈指数递减,散布半径约30m。在蛀梢过程中,该种群逐渐向新区扩张。在树冠内,纵坑切梢小蠹主要分布在4-10轮枝上。第7轮枝虫口百分率最高。6-7轮枝受害率最大。 树冠上层受害较其下层严重。从树冠水平层次考察,树冠外层虫量相对集中,约为树冠中、内层虫量之和。 树冠内层虫量最少。纵坑切梢小蠹在树冠内的种群分布系由梢径、种群密度、蛀梢行为、降落方式、光照等因素综合影响的结果。