Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life

The origin and diversification of RNA secondary structure were traced using cladistic methods. Structural components were coded as polarized and ordered multi-state characters, following a model of character state transformation outlined by considerations in statistical mechanics. Several classes of functional RNA were analyzed, including ribosomal RNA (rRNA). Considerable phylogenetic signal was present in their secondary structure. The intrinsically rooted phylogenies reconstructed from evolved RNA structure depicted those derived from nucleic acid sequence at all taxonomical levels, and grouped organisms in concordance with traditional classification, especially in the archaeal and eukaryal domains. Natural selection appears therefore to operate early in the information flow that originates in sequence and ends in an adapted phenotype. When examining the hierarchical classification of the living world, phylogenetic analysis of secondary structure of the small and large rRNA subunits reconstructed a universal tree of life that branched in three monophyletic groups corresponding to Eucarya, Archaea, and Bacteria, and was rooted in the eukaryotic branch. Ribosomal characters involved in the translational cycle could be easily traced and showed that transfer RNA (tRNA) binding domains in the large rRNA subunit evolved concurrently with the rest of the rRNA molecule. Results suggest it is equally parsimonious to consider that ancestral unicellular eukaryotes or prokaryotes gave rise to all extant life forms and provide a rare insight into the early evolution of nucleic acid and protein biosynthesis. Received: 13 September 2000 / Accepted: 27 August 2001     

The Rooting of the Universal Tree of Life Is Not Reliable

Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides, for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome analysis.     

Around the Tuscan Table: Food, Family and Gender in Twentieth-Century Florence

Around the Tuscan Table: Food, Family and Gender in Twentieth-Century Florence . Carole M. Counihan. New York: Routledge, 2004. 248 pp.     

Influence of Sugars on in vitro Rooting and Acclimatization of Carob Tree

Carob tree (Cerafoma siliqua L.) micropropagated shoots were rooted on half-strength Murashige and Skoog medium, supplemented with different types and concentrations of sugars, in order to determine the effects of sugar composition and concentration on in vitro rooting and in vivo establishment of the plantlets. Among the various sugars tested, the best rooting response was obtained with 145 mM sucrose, both in terms of rooting frequency and index of rooting. The use of filter-sterilized rather that autoclaved fructose increased root number and root length. Sugar treatment during rooting slightly influenced plantlet survival and growth during acclimatization. A reduction in the glucose concentration during rooting was beneficial for plantlet acclimatization.     

Eutherian mammals from the Early Cretaceous of Mongolia

A collection of eutherian mammals consisting of 39 specimens (teeth and jaw fragments) from the ?Aptian or Albian Khoboor Beds in the Gobi Desert, Mongolia, is described. It contains 3 taxa: Prokenna1estes gen.n., assigned to the Otlestidae Nessov, new rank, with 2 shrew size species; P. trofimovi sp.n. and P. minor sp.n.; a heavily worn larger lower molar which will be described elsewhere. It cannot be excluded that P. trofimovi and P. minor are only sexual morphs within the same species. Prokennalestes and Bobolestes Nessov are possibly the oldest known eutherian mammals, but Prokennalestes is morphologically more primitive than Bobolestes. It has a labial mandibular foramen, 5 premolars and 3 molars, 3 cusps in parastylur region, paracone larger than metacone, unwinged conules, no pre- and posteingula, and lower molars with a 3-cusped talonid, which is narrower than the trigonid, Otlestes and Kennalestes may be derived with little modification from Prokennalestes. Prokennalestes gen.n. is congeneric with Prokennalestes Trofimov and Prozalambdalestes Trofimov, which are both nomina nuda.     

Governmentality and the Family: Neoliberal Choices and Emergent Kin Relations in Southern Ethiopia

ABSTRACT  Rather than strictly local expressions of relatedness, kinship in southern Ethiopia has long been entangled with broad political and economic forces as people negotiate relations with each other, past generations, and the state. Accompanying government reforms in the 1990s, idioms of individualism and choice have circulated in transnational and national neoliberal discourses of development, rights, and economics. People in southern Ethiopia who use ideologies of ascribed social statuses to define local social hierarchies have employed these discourses in reshaping relatedness through an expansive trade association, which is referred to as a family and works through kinship principles of descent and generation. Drawing from recent scholarship on kinship and new reproductive technologies, I argue that, through mobile knowledges in neoliberal contexts, people choose this family and its lineage founder, transforming descent relations and land-based ideologies. These choices represent the workings of neoliberal governmentality in altering cultural relations of power and inequality. [Keywords: kinship, neoliberalism, governmentality, hereditary status groups, Ethiopia]     

脊椎动物DMRT基因家族的系统发生及同线性分析

利用本室克隆的DMRT／Dmrt基因以及多个基因数据库中收集的DMRT／Dmrt基因全(或部分)序列,构建了DMRT／Dmrt基因的系统发生树,DMRT／Dmrt基因明显地聚为7类(DMRT／Dmrt1-DMRT／Dmrt7)。以已克隆的斑马鱼Dmrt1基因序列及数据库中人和小鼠的DMRT／Dmrt基因序列,结合基因组数据的比对分析,发现脊椎动物DMRT／Dmrt基因家族成员在基因组中的定位呈现高度保守的同线性,主要集中于两大同线群,即DM-RT／Dmrt1-3和DMRT／Dmrt5∽6。     

A Congruence Study of Molecular and Morphological Data for Eutherian Mammals

The four orders of eutherian mammals which are traditionally placed in the superorder Archonta [Chiroptera (microbats and megabats), Dermoptera (flying lemurs), Primates (primates), and Scandentia (tree shrews)] are among the best-studied taxa of their infraclass from both the molecular and morphological perspectives. Nevertheless, the ordinal relationships of archontans remain unresolved. While morphological studies favor their monophyly, molecular investigations do not. To evaluate these opposing conclusions, parsimony analyses were conducted with three separate sets of DNA sequences from both the nuclear and mitochondrial genomes and one file of morphological data for archontans and other eutherian mammals. Statistical tests of character support and ordinal branching pattern differences documented that the three sets of DNA sequences and their results were homogeneous and congruent, thereby allowing for the combination of these data into one large matrix for further phylogenetic analysis. In contrast, these same tests revealed that the combined sequence and morphological files and their topologies were in strong conflict. Archontan monophyly was supported by the morphological evidence, but this arrangement was strongly rejected by the combined DNA sequences that favored instead a grouping of Dermoptera, Primates, and Scandentia with Lagomorpha (rabbits) and Rodentia (rodents). Resolution of these significant differences will require further evaluations about the homologies and evolutionary properties of the molecular and morphological characters and about the appropriateness of the chosen phylogenetic methods, as well as the incorporation of new comparative data from both sources.     

Rooting of microcuttings: Theory and practice

Summary Poor adventitious root formation is a major obstacle in micropropagation and in conventional propagation. This paper reviews recent progress in the understanding of adventitious root formation as a developmental process focusing on the role of plant hormones and on the effect of rooting conditions on plant performance. Since the discovery of the rhizogenic effect of auxin ca. 70 yr ago, no new broadly applicable rooting treatments have been developed. Recent research, though, may lead to new rooting procedures. Application of wounding-related compounds may be effective in difficult-to-root crops. Furthermore, by adapting conditions during the propagation phase, microcuttings with an enhanced capability to root may be produced. These conditions include elongation of stems (by etiolation or double-layer culture) and repeated subculture (rejuvenation; i.e. transition from adult to juvenile). Data are presented that show that during tissue culture maturation (transition from juvenile to adult) also occurs. The conditions during the in vitro rooting treatment may have a tremendous effect on performance after transfer ex vitro. In particular, accumulation of ethylene during in vitro rooting may have a devastating effect. Addition of stress-protecting compounds during propagation or rooting in vitro may enhance the performance ex vitro. Based on a presentation at the Plant Symposium ‘Rooting of Micropropagated Plants’ at the 2001 Congress of In Vitro Biology held at St. Louis, MO, June 16–20, 2001.     

Rooting the eutherian tree: the power and pitfalls of phylogenomics

Background  

Ongoing genome sequencing projects have led to a phylogenetic approach based on genome-scale data (phylogenomics), which is beginning to shed light on longstanding unresolved phylogenetic issues. The use of large datasets in phylogenomic analysis results in a global increase in resolution due to a decrease in sampling error. However, a fully resolved tree can still be wrong if the phylogenetic inference is biased.     

Rooting molecular trees: problems and strategies

In constructing phylogenies from molecular data both the composition of the ingroup and the choice of outgroup can strongly affect the chances of obtaining the correct topology. This is because tree topology and uneven rates of molecular evolution affect the ability of tree-building algorithms to find the correct tree. Outgroups can be added in one of two ways, either to a single sister clade (preferably the closest) or through addition of single taxa from different clades. On theoretical and empirical grounds the former strategy is shown to be much more beneficial, both in terms of redressing balance and reducing stemminess. For parsimony to perform well some selection of sequence data, through omission or weighting, is also often necessary to reduce levels of homoplasy.