Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation

Part of the mitochondrial 12S ribosomal RNA gene was amplified and sequenced for 26 marsupials. Multiple alignments for these sequences as well as seven additional sequences taken from GenBank were obtained using CLUSTAL. PAUP was used for phylogenetic analysis and to obtain random tree-length distributions. Analyses were performed with and without phylogenetic constraints. Our results clearly show that 12S rDNA contains phylogenetic signal at and above the ordinal level and is thus appropriate for addressing phylogenetic questions deep in the mammalian tree. Standard parsimony analyses provide some support for a clade containing diprotodontians, dasyurids,Dromiciops, andNotoryctes; transversion parsimony analysis suggests the possible inclusion of peramelids as well. Within the Diprotodontia, vombatids and phascolarctids cluster together on transversion parsimony and phalangerids may be associated with this clade. The enigmatic tarsipedids are apparently part of a clade that also contains pseudocheirids, petaurids, and acrobatids. The 12S sequences suggest that the origination of extant marsupial orders peaked 15 million years later than the equivalent taxonomic diversification of extant placental orders and may be entirely post-Cretaceous. Families of diprotodontian marsupials originated during the Eocene and early Oligocene, which is consistent with previous single-copy DNA hybridization results.     

Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences

Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.     

The Constitutional Amine of Antibiotic YA-56

In addition to the previously reported six amino acids and two carbohydrates (one disaccharide), 3-aminopropionamidine was isolated as a constituent from the acid hydrolyzate of the antibiotic YA–56X, one of the major component of antibiotic YA–56 complex. Based on the hitherto found informations, structural comparison of the antibiotic YA–56 X and Y was made with phleomycins, bleomycins, zorbamycin and zorbonomycin B to which antibiotic YA–56 closely related. Among those, zorbamycin was identical with antibiotic YA–56 X.     

Planktic foraminiferal molecular evolution and their polyphyletic origins from benthic taxa

Phylogenetic analyses based on partial sequences of the small subunit (SSU) ribosomal (r) RNA gene have shown that the planktic and benthic foraminifera form a distinct monophyletic group within the eukaryotes. In order to determine the evolutionary relationships between benthic and planktic foraminifers, representatives of spinose and non-spinose planktic genera have been placed within a molecular SSU rDNA phylogeny containing sequences of the benthic suborders available to date. Our phylogenetic analysis shows that the planktic foraminifers are polyphyletic in origin, not evolving solely from a single ‘globigerinid-like’ lineage in the Mid-Jurassic, but derived from at least two ancestral benthic lines. The benthic ancestor of Neogloboquadrina dutertrei may have entered the plankton later than the Mid-Jurassic, and further investigation of related extant species should provide an indication of the timing of this event. The evolutionary origin of the non-spinose species Globorotalia menardii remains unclear. The divergences of the planktic spinose species generally support recent phylogenies based on the fossil record, which infer a radiation from a globigerinid common ancestor in the Mid- to Late Oligocene. The branching pattern indicates that there are possibly four distinct groups within the main spinose clade, with large evolutionary distances being observed between them. Globigerinoides conglobatus clusters strongly with Globigerinoides ruber and are divergent from Globigerinella siphonifera, Orbulina universa and Globigerinoides sacculifer.Conserved regions of the SSU rRNA gene show sufficient variation to discriminate foraminifers at the species level. Large genetic differences have been observed between the pink and white forms of Gs. ruber and between Ge. siphonifera Type I and II. The two types of Ge. siphonifera cannot be discriminated by traditional palaeontological methods, which has considerable implications for tracing fossil lineages and for the estimation of molecular evolutionary rates based upon the fossil record. The conserved regions show a high degree of sequence identity within a species, providing signature sequences for species identification. The variable regions of the gene may prove informative for population level studies in some species although complete sequence identity was observed in G. sacculifer and O. universa between specimens collected from the Caribbean and Western Pacific.     

STUDIES ON ULTRASTRUCTURE AND THREE‐GENE PHYLOGENY OF THE GENUS MALLOMONAS (SYNUROPHYCEAE)1

The genus Mallomonas, a common and often abundant member of the planktic community in many freshwater habitats worldwide, consists of 180 species divided into 19 sections and 23 series. Classification of species is based largely on ultrastructural characteristics of the siliceous scales and bristles that collectively form a highly organized covering over the cell. However, the relative importance of the different siliceous features of the scales, such as the dome, V rib, and secondary structures, as well as the different types of scales, in understanding the evolution and phylogeny of the genus is little known. In this study, we investigated the scale and bristle ultrastructure, along with sequences of three genes, for 19 isolates (18 species) of Mallomonas (18 isolates were from Korean habitats). The isolates represented nine of the 19 sections. Sequences for both the nuclear SSU and LSU rDNA and plastid LSU of RUBISCO (rbcL) genes for each of the 19 Mallomonas isolates and four outgroups were determined. Bayesian and maximum‐likelihood (ML) analyses of the data revealed that Mallomonas consists of two strongly supported clades. Mallomonas bangladeshica (E. Takah. et T. Hayak.) Siver et A. P. Wolfe was at the base of the first clade that included taxa from the sections Planae and Heterospinae, both of which lack a V rib on the shield of the scales. Our results indicated that the sections Planae and Heterospinae should be combined. The second clade, with Mallomonas insignis Penard and Mallomonas punctifera Korshikov at the base, contained taxa from the sections Mallomonas, Striatae, Akrokomae, Annulatae, Torquatae, Punctiferae, and Insignes, all of which have V ribs or well‐developed marginal ribs on the scales. Sister relationships between Mallomonas and Striatae were strongly supported, but interrelations among the remaining sections were not resolved, probably due to inclusion of too few species. Our results suggest that the current classification of the genus Mallomonas at the section level will require some revision. Additional species will need to be added in future analyses.     

Phylogenetic Relationships of the Marine Nematode Family Comesomatidae

The phylogenetic relationships of the Comesomatidae have remained unresolved at the family level because they have diagnostic morphological features of both the Monhysterida and the Chromadorida. A comparison of the partial sequence of 18S rDNA from representative taxa of Comesomatidae and of morphological data, analyzed in conjunction with molecular and morphological data from monhysterids and chromadorids, suggests a closer relationship of the Comesomatidae with Monhysterida than with Chromadorida.     

PHYLOGENY OF GRACILARIA LEMANEIFORMIS (RHODOPHYTA) BASED ON SEQUENCE ANALYSIS OF ITS SMALL SUBUNIT RIBOSOMAL RNA CODING REGION1

The small subunit ribosomal RNA (rRNA) sequence of Gracilaria lemaneiformis Bory Weber-van Bosse was inferred from analysis of rRNA coding regions that were amplified by the polymerase chain reaction method. Comparison of the G. lemaneiformis small subunit rRNA to homologous genes of diverse eukaryotes demonstrated that the red algal divergence was nearly simultaneous with the separation of plants, fungi, animals and many other protist lineages. This result conflicts with those of 5S rRNA sequence and plastid based phytogenies which suggest that red algae represent an early divergence in the eukaryotic line of descent. Further, algae appear to be of polyphyletic origin and red algae are unrelated to higher fungi.     

Phylogeny of Agavaceae based on ITS rDNA sequence variation

Several systems of classification have been proposed for the family Agavaceae. A distinctive bimodal karyotype and similarities of fruits and seeds strongly support close relationships among Yucca, Hesperaloë, Beschorneria, Furcraea, Agave, Manfreda, Polianthes, Prochnyanthes, and perhaps Hosta. However, Dasylirion, Beaucamea, Nolina, Calibanus, Dracaena, and Sansevieria differ in so many cytological and morphological features that many have concluded they should be excluded from Agavaceae and separated into two families, Nolinaceae and Dracaenaceae. Chloroplast DNA restriction site data support these separations and indicate that Nolinaceae and Dracaenaceae are very close to Convallariaceae (Maianthemum, Convallaria, Aspidistra, Liriope, etc.). In this paper we report the results of an ITS rDNA sequencing study of 40 taxa in Agavaceae sensu lato and related groups in the order Asparagales. Sequence alignments were optimized using the Consistency Index, Retention Index, and Rescaled Consistency Index to find the alignment that exhibited the least amount of homoplasy. The results of our study are congruent with the conclusions drawn from cytological, immunological, cpDNA, and rbcL studies, which support a narrow interpretation of Agavaceae and a close relationship among Convallariaceae, Dracaenaceae, and Nolinaceae. In addition, the ITS sequence data provide evidence for some interesting relationships within these families.     

General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.