Evolution of the 28S ribosomal RNA gene in anurans: regions of variability and their phylogenetic implications

Fifteen restriction sites were mapped to the 28S ribosomal RNA gene of individuals representing 54 species of frogs, two species of salamanders, a caecilian, and a lungfish. Eight of these sites were present in all species examined, and two were found in all but one species. Alignment of these conserved restriction sites revealed, among anuran 28S rRNA genes, five regions of major length variation that correspond to four of 12 previously identified divergent domains of this gene. One of the divergent domains (DD8) consists of two regions of length variation separated by a short segment that is conserved at least throughout tetrapods. Most of the insertions, deletions, and restriction-site variations identified in the 28S gene will require sequence-level analysis for a detailed reconstruction of their history. However, an insertion in DD9 that is coextensive with frogs in the suborder Neobatrachia, a BstEII site that is limited to representatives of two leptodactylid subfamilies, and a deletion in DD10 that is found only in three ranoid genera are probably synapomorphies.      

Structural and evolutionary comparisons of four alleles of the mouse immunoglobulin kappa chain gene,Igk-VSer

The mouseIgK-VSer gene encodes an immunoglobulin light chain variable region which gives rise to two phenotypic polymorphisms of mouse chains. The nucleotide sequences of coding and flanking regions of theIgk-VSer ^c andIgk-VSer ^d alleles found in recently inbred strains of wild mice are compared with those of theIgk-VSer ^a andIgk-VSer ^b alleles described previously. Results suggest that the gene is evolving randomly and that framework 2 and complentarity determining region 2 are preserved, presumably for overall light chain structure. Results indicate that all four allels have an octamer motif upstream of the gene which should be functional and allow prediction of whether or not the product of the germ line gene will be detectable as either the I_B-peptide or Ef1^a phenotypic polymorphism. Southern hybridization of genomic DNA using as probe a 1-kbXba I-Xba I fragment located approximately 4 kb upstream of the BALB/cIgk-VSer ^b coding region demonstrated the presence of homologous DNA in mice bearing theIgk-VSer ^a allele and absence from mice bearing theIgk-VSer ^c andIgk-VSer ^d alleles. Nucleotide sequence comparison of BALB/c and SK/CamRk (Igk-VSer ^d ) DNA in this region demonstrated that BALB/c contained an insertion 2.4 kb in length which was absent from SK/CamRk. Both strains contain DNA homologous to the reverse complement of the mouse Bam5 repetitive element at the point of the insertion, with BALB/c containing approximately 70 nucleotides more of the element than SK/CamRk. Surprisingly, the strains containing DNA related to theXba I-Xba I probe are not those determined to be the most similar by nucleotide sequence comparisons and by the Phylogenetic Analysis Using Parsimony program. The evolutionary relationship of the alleles and a possible basis for the inconsistency presented by theXba I-Xba I fragment-related DNA are discussed.     

Mobilization of ferritin iron in erythroblasts by chelating agents

Intracellular ferritin in newt (Triturus cristatus) erythroblasts was accessible to the chelating effects of EDTA and pyridoxal phosphate. EDTA (0.5-1 mM) promoted release of radioactive iron from ferritin of pulse-labelled erythroblasts during chase incubation, but its continuous presence was not necessary for ferritin iron mobilization. Brief exposure to EDTA was sufficient to release 60-70% of ferritin 59Fe content during ensuing chase in EDTA-free medium. EDTA also suppressed cellular iron uptake and utilization for heme synthesis, but these activities were restored upon its removal. Pyridoxal-5'-phosphate (0.5-5 mM) also stimulated loss of radioactive iron from ferritin; however, ferritin iron release by pyridoxal phosphate required its continued presence. Unlike EDTA, pyridoxal phosphate did not interfere with iron uptake or its utilization for heme synthesis. Chelator-mobilized ferritin iron accumulated initially in the hemolysate as a low-molecular-weight component and appeared to be eventually released into the medium. No radioactive ferritin was found in the medium of chelator-treated cells, indicating that secretion or loss of ferritin was not responsible for decreasing cellular ferritin 59Fe content. Moreover, there was no transfer of radioactive iron between the low-molecular-weight component released into the medium and plasma transferrin. These results indicate that chelator-released ferritin iron is not available for cellular utilization in heme synthesis and that ferritin iron released by this process is not an alternative or complementary iron source for heme synthesis. Correlation of these data with effects of succinylacetone inhibition of heme synthesis and with previous studies indicates that the main role of erythroid cell ferritin is absorption and storage of excess iron not used for heme synthesis.     

ARAGONITE IN HALIMED A AND TYDEMANIA (ORDER SIPHON ALES)12

The mineral component of the marine green algal genus Halimeda is the orthorhombic calcium carbonate (aragonite); its presence appears to be a generic characteristic. Tydemania expeditionis also precipitates aragonite in contradistinction to species of the red alga Corallina wliich precipitate calcium carbonate of the hexagonal form (calcite). The analyses are based on x-ray diffraction methods. Although other inorganic substances arc present, the amounts are minor and probably represent contaminants. Specimens that are to be studied for mineral components should not be stored in formalin.     

Leeward bank margin Halimeda meadows and draperies and their sedimentary importance on the western Great Bahama Bank slope

Bryopsidalean algal meadows in water depths of 20–40 m on the leeward side of western Great Bahama Bank (WGBB) lie between non-skeletal-dominated sand flats on the bank top to the east and a cemented steep escarpment to the west. The meadows contain dense populations of rhipsalian Halimeda species, as well as Udotea and Rhipocephalus. Extensive populations of other Halimeda species (opuntioids) occur at greater depths on the cemented rocky escarpment, growing as drapes or vines rather than as upright thalli. These meadows and draperies are important sources of coarse-grained carbonate sediments. This is shown by (1) deeper bank-edge sediments (30–60 m) containing considerably more Halimeda fragments than do the bank top, non-skeletal sands, and (2) the coarser fraction of slope sediments (down to 200 m) dominated by Halimeda plates, partly or extensively altered and internally cemented by magnesian calcite and aragonite. A transect across the bank margin from bank top (<10 m) to lower slope (300 m) provides a useful comparison for the locus of sediment production and accumulation. The production of Halimeda in these bank-edge habitats approximates that in the Great Barrier Reef or off Indonesia and Nicaragua in similar water depths. The apparent lack of thick sediment accumulation in WGBB compared to that seen elsewhere may reflect the high rates of downslope transport off Great Bahama Bank.     

Signal, noise, and reliability in molecular phylogenetic analyses.

DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.     

NUCLEAR RIBOSOMAL DNA PHYLOGENY OF HALIMEDALES REVEALS SEVERAL POLYPHYLETIC GENERA

Halimedales (Chlorophyta) are widely distributed in reefs and lagoons throughout the tropics and subtropics. One genus, Chlorodesmis, consists of simple, branching siphons that persist into the mature sexual phase. In most other genera, only the juvenile stages exhibit such simple anatomy. Their mature, often‐calcified thalli possess complex siphonal anatomy and differentiation depending on the location in the thallus. We obtained a nuclear ribosomal DNA phylogeny encompassing many genera in order to unravel the evolution of this complexity. Results pinpoint Caulerpa as outgroup to a clade with all other genera included in this study. The first dichotomy separates Halimeda from the remaining genera. Distinct gametangial anatomy defines these two principal clades. Within the remainder, Tydemania and its sister Flabellia are nearest neighbors to a clade containing Rhipocephalus, Udotea, Penicillus and Chlorodesmis. The latter three genera are polyphyletic. Therefore, character states of thallus superstructure defining these genera appear to be homoplasies. Chlorodesmis represents a case of neoteny where the juvenile stage persists into reproductive maturity. We will evaluate which morphological characters do change state in agreement with the molecular phylogeny and can, therefore, serve as diagnostic characters for a more natural classification.     

Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference

We investigated the usefulness of a parallel genetic algorithm for phylogenetic inference under the maximum-likelihood (ML) optimality criterion. Parallelization was accomplished by assigning each "individual" in the genetic algorithm "population" to a separate processor so that the number of processors used was equal to the size of the evolving population (plus one additional processor for the control of operations). The genetic algorithm incorporated branch-length and topological mutation, recombination, selection on the ML score, and (in some cases) migration and recombination among subpopulations. We tested this parallel genetic algorithm with large (228 taxa) data sets of both empirically observed DNA sequence data (for angiosperms) as well as simulated DNA sequence data. For both observed and simulated data, search-time improvement was nearly linear with respect to the number of processors, so the parallelization strategy appears to be highly effective at improving computation time for large phylogenetic problems using the genetic algorithm. We also explored various ways of optimizing and tuning the parameters of the genetic algorithm. Under the conditions of our analyses, we did not find the best-known solution using the genetic algorithm approach before terminating each run. We discuss some possible limitations of the current implementation of this genetic algorithm as well as of avenues for its future improvement.