Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements

Phylogenetic relationships among the metazoan phyla are the subject of an ongoing controversy. Analysis of mitochondrial gene arrangements is a powerful tool to investigate these relationships; however, its previous application outside of individual animal phyla has been hampered by the lack of informative out-group data. To address this shortcoming, we determined complete mitochondrial DNA sequences for the demosponges Geodia neptuni and Tethya actinia, two representatives of the most basal animal phylum, the Porifera. With sponges as an outgroup, we investigated phylogenetic relationships of nine bilaterian phyla using both breakpoint analysis of global mitochondrial gene arrangements and maximum parsimony analysis of mitochondrial gene adjacencies. Our results provide strong support for a group that includes protostome (but not deuterostome) coelomate, pseudocoelomate, and acoelomate animals, thus clearly rejecting the Coelomata hypothesis. Two other groups of bilaterian animals, Lophotrochozoa and Ambulacraria, are also supported by our analyses. However, due to the remarkable stability of mitochondrial gene arrangements in Deuterostomia and the Ecdysozoa, conclusions on their evolutionary history cannot be drawn.     

Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom

The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.     

The "new" chemosystematics: phylogeny and phytochemistry

For almost a decade it has been acknowledged that the flowering plant dichotomy of monocotyledons and dicotyledons does not reflect the evolution of angiosperms. Despite this, conclusions in the field of chemosystematics are still drawn from, and rely on, non-phylogenetic botanical classifications such as those of Cronquist, Dahlgren and Takhtajan. In this paper the two alkaloids colchicine and camptothecin are used as examples of how phylogenetic systematics may be applied to alkaloid chemosystematics.     

"Tissue" transglutaminase in animal development

The "tissue" transglutaminase is a multifunctional enzyme that in its cross-linking configuration catalyzes Ca2+ -dependent reactions resulting in post-translational modification of proteins by establishing epsilon(gamma-glutamyl) lysine cross-links and/or covalent incorporation of biogenic amines (di- and poly-amines and histamine) into proteins. Several laboratories have shown that in Vertebrates, "tissue" transglutaminase (tTG) gene expression specifically characterizes cells undergoing apoptosis or programmed cell death (PCD). The Ca2+ -dependent activation of this enzyme leads to the formation of detergent-insoluble cross-linked protein polymers in cells undergoing PCD. This insoluble protein scaffold could stabilize the integrity of the dying cells before their clearance by phagocytosis, preventing the non-specific release of harmful intracellular components (e.g. lysosomal enzymes, nucleic acids, etc.) and consequently inflammatory responses and scar formation in bystander tissues. In this review we attempt to present an overview of the current knowledge on tTG expression and regulation in animal reproduction and development. The data available so far further strengthen the relationship existing between tTG expression and the induction of PCD.     

An optimal algorithm for perfect phylogeny haplotyping.

Inferring haplotype data from genotype data is a crucial step in linking SNPs to human diseases. Given n genotypes over m SNP sites, the haplotype inference (HI) problem deals with finding a set of haplotypes so that each given genotype can be formed by a combining a pair of haplotypes from the set. The perfect phylogeny haplotyping (PPH) problem is one of the many computational approaches to the HI problem. Though it was conjectured that the complexity of the PPH problem was O(nm), the complexity of all the solutions presented until recently was O(nm (2)). In this paper, we make complete use of the column-ordering that was presented earlier and show that there must be some interdependencies among the pairwise relationships between SNP sites in order for the given genotypes to allow a perfect phylogeny. Based on these interdependencies, we introduce the FlexTree (flexible tree) data structure that represents all the pairwise relationships in O(m) space. The FlexTree data structure provides a compact representation of all the perfect phylogenies for the given set of genotypes. We also introduce an ordering of the genotypes that allows the genotypes to be added to the FlexTree sequentially. The column ordering, the FlexTree data structure, and the row ordering we introduce make the O(nm) OPPH algorithm possible. We present some results on simulated data which demonstrate that the OPPH algorithm performs quiet impressively when compared to the previous algorithms. The OPPH algorithm is one of the first O(nm) algorithms presented for the PPH problem.     

The phylogeny of gutierrezia: An eclectic approach

One approach to the problem of deducing the genealogy of a set of organisms is to propose several hypotheses using different procedures, based on different evolutionary inferences. Such an approach was followed here, and four different phylogenies were constructed, three of them computer built. Consistency with independently obtained phenetic, cytological, and phytogeographical data was used to select the most probable phylogenetic tree among the four. It is shown that the most probable tree is one constructed under the assumption that character states found close to the mean and/or modal values for the genus are primitive. It is also shown that certain phylogenetic conclusions obtain in all four phylogenies.     

Motor polarization dominance and "animal hypnosis"

Two kinds of dominanta were simultaneously formed under conditions of chronic experiments in rabbits. The motor polarization dominanta was formed under exposure of the right sensorimotor cortex of an animal to direct anodic current, and the state of "animal hypnosis" (the second dominanta) was induced. Animal behavior and electrophysiological characteristics were recorded. It was shown that the "animal hypnosis" induced at the optimum of the right motor polarization dominanta inhibited the motor reaction of the "dominant" extremity to testing stimuli. After the "animal hypnosis session, exposure of the right sensorimotor cortex to anodic current produced the latent excitation focus, which did not reach the level of summation. Two days later, exposure to testing stimuli developed the latent foci at first in the right cortex and then in subcortical structures. In the course of recovery of the motor polarization dominanta and its further change for the state characteristic of the "animal hypnosis", the patterns of cortical EEG coherence in the delta range typical of each kind of dominanta alternated in parallel with the time course of state changes.     

The newer vaccines

Vaccination is a powerful weapon in the control of animal diseases and many highly successful vaccines have been developed, particularly for virus diseases such as rinderpest, foot-and-mouth disease and Newcastle disease. Despite their extraordinary success, however, there are sufficient problems associated with their production and quality control to warrant a re-examination of the methods in current use. Dissection of virus particles into biologically active fragments has shown that their immunizing activity is usually carried on a single protein. With the identification of the genes coding for these individual proteins it is now possible to express these immunogens in both prokaryotic and eukaryotic cells. Moreover, the immunogenic sites of some of these proteins have been identified, synthesized in E. coli cells or by chemical methods and shown to possess immunizing activity. It is too early to put a time-scale on the commercial availability of the new vaccines. However, the potential advantages of such products over conventional vaccines has led to considerable effort in this field of research and progress has been so rapid that new vaccines could be available within the next few years.     

A twist in time--the evolution of spiral cleavage in the light of animal phylogeny

Recent progress in reconstructing animal relationships enables us to draw a better picture of the evolution of important characters such as organ systems and developmental processes. By mapping these characters onto the phylogenetic framework, we can detect changes that have occurred in them during evolution. The spiral mode of development is a complex of characters that is present in many lineages, such as nemerteans, annelids, mollusks, and polyclad platyhelminthes. However, some of these lineages show variations of this general program in which sub-characters are modified without changing the overlying pattern. Recent molecular phylogenies suggest that spiral cleavage was lost, or at least has deviated from its original pattern, in more lineages than was previously thought (e.g., in rotifers, gastrotrichs, bryozoans, brachiopods, and phoronids). Here, I summarize recent progress in reconstructing the spiralian tree of life and discuss its significance for our understanding of the spiral-cleavage character complex. I conclude that more detailed knowledge of the development of spiralian taxa is necessary to understand the mechanisms behind these changes, and to understand the evolutionary changes and adaptations of spiralian embryos.     

How our view of animal phylogeny was reshaped by molecular approaches: lessons learned

In the late 1980s, researchers began applying molecular sequencing tools to questions of deep animal phylogeny. These advances in sequencing were accompanied with improvements in computation and phylogenetic methods, and served to significantly reshape our understanding of metazoan evolution. Prior to this time, researchers asserted phylogenetic hypotheses based on their experience with taxa and to some degree, their authority. Molecular phylogenetic tools provided discrete methods and objective characters for reconstructing phylogeny. Nonetheless, major changes to widely accepted views, such as animal phylogeny, take time to be accepted. Development and acceptance of our current understanding of animal evolution occurred in three main phases: initial hypotheses based on 18S data, confirmation with additional molecular markers, and continued refinement with phylogenomics. With the advent of ideas such as Lophotrochozoa and Ecdysozoa, flaws in the traditional view became apparent. We now understand that complex morphological and embryological features (e.g., segmentation, coelom formation, development of body cavities) are much more evolutionarily plastic than previously recognized. Here, I explore how the transition from the traditional to the modern phylogenetic understanding of animal phylogeny occurred and examine some implications of this change in understanding. As the field moves forward, the utility of morphological and embryological characters for reconstruction of deep animal phylogeny should be discouraged. Instead, these characters should be interpreted in the light of independent phylogeny.     

真核生物系统发育和多样性概观

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.     

A "holistic" kinesin phylogeny reveals new kinesin families and predicts protein functions

Kinesin superfamily proteins are ubiquitous to all eukaryotes and essential for several key cellular processes. With the establishment of genome sequence data for a substantial number of eukaryotes, it is now possible for the first time to analyze the complete kinesin repertoires of a diversity of organisms from most eukaryotic kingdoms. Such a "holistic" approach using 486 kinesin-like sequences from 19 eukaryotes and analyzed by Bayesian techniques, identifies three new kinesin families, two new phylum-specific groups, and unites two previously identified families. The paralogue distribution suggests that the eukaryotic cenancestor possessed nearly all kinesin families. However, multiple losses in individual lineages mean that no family is ubiquitous to all organisms and that the present day distribution reflects common biology more than it does common ancestry. In particular, the distribution of four families--Kinesin-2, -9, and the proposed new families Kinesin-16 and -17--correlates with the possession of cilia/flagella, and this can be used to predict a flagellar function for two new kinesin families. Finally, we present a set of hidden Markov models that can reliably place most new kinesin sequences into families, even when from an organism at a great evolutionary distance from those in the analysis.     

"Lipotyphlan" phylogeny based on the growth hormone receptor gene: a reanalysis

From an evolutionary perspective, "insectivores" have been one of the most important mammalian groups for over a century. Morphologists have successively pruned flying lemurs, elephant shrews, and tree shrews from Insectivora, but have retained chrysochlorids, tenrecs, erinaceids, soricids, talpids, and solenodontids in crown-group Lipotyphla. With the appearance of large molecular data sets, the monophyly of Lipotyphla has proved untenable. Rather, an emerging consensus is that Lipotyphla is a diphyletic taxon comprised of two monophyletic groups, Afrosoricida and Eulipotyphla. A recent paper by Malia et al. [Mol. Phylogenet. Evol. 24 (2002) 91-101] challenged this view and argued that "While the data [Growth Hormone Receptor] were unable to support the orders Lipotyphla, Eulipotyphla, and Tenrecoidea [= Afrosoricida] this was most likely due to the polyphyly of these groups and not to problems associated with the gene itself such as saturation or highly divergent sequences em leader " (p. 100). We analyzed Malia et al.'s original GHR data set (at both nuclear and protein level), an expanded GHR data set that included 49 additional sequences, and a concatenated data set that included GHR, BRCA1, vWF, and A2AB for a diverse selection of lipotyphlan taxa. Although protein analyses proved inconclusive, all analyses at the DNA level clearly show that the statement of Malia et al. is erroneous. Indeed, likelihood analyses with GHR and with the concatenated data set provide more support for Eulipotyphla and Afrosoricida than for competing hypotheses. These results also highlight the potential pitfalls of single-gene and parsimony-only analyses.