A molecular phylogenetic study of southern African Apiaceae

It has been suggested that southern Africa is the origin of the predominantly herbaceous Apiaceae subfamily Apioideae and that the woody habit is plesiomorphic. We expand previous molecular phylogenetic analyses of the family by considering all but three of the approximately 38 genera native to southern Africa, including all genera whose members, save one, have a woody habit. Representatives of five other genera are included because they may be closely related to these southern African taxa. Chloroplast DNA rps16 intron and/or nuclear rDNA ITS sequences for 154 accessions are analyzed using maximum parsimony, Bayesian, and maximum likelihood methods. Within Apioideae, two major clades hitherto unrecognized in the subfamily are inferred. The monogeneric Lichtensteinia clade is sister group to all other members of the subfamily, whereas the Annesorhiza clade (Annesorhiza, Chamarea, and Itasina) plus Molopospermum (and Astydamia in the ITS trees) are the successive sister group to all Apioideae except Lichtensteinia. Tribe Heteromorpheae is expanded to include Pseudocarum, "Oreofraga" ined., and five genera endemic to Madagascar. The southern African origin of subfamily Apioideae is corroborated (with subsequent migration northward into Eurasia along two dispersal routes), and the positions of the herbaceous Lichtensteinia and Annesorhiza clades within the subfamily suggest, surprisingly, that its ancestor was herbaceous, not woody.     

A molecular phylogenetic study of ecological diversification in the Australian lizard genus Ctenophorus.

We present phylogenetic analyses of the lizard genus Ctenophorus using 1,639 aligned positions of mitochondrial DNA sequences containing 799 parsimony-informative characters for samples of 22 species of Ctenophorus and 12 additional Australian agamid genera. Sequences from three protein-coding genes (ND1, ND2, and COI) and eight intervening tRNA genes are examined using both parsimony and maximum-likelihood analyses. Species of Ctenophorus form a monophyletic group with Rankinia adelaidensis, which we suggest placing in Ctenophorus. Ecological differentiation among species of Ctenophorus is most evident in the kinds of habitats used for shelter. Phylogenetic analyses suggest that the ancestral condition is to use burrows for shelter, and that habits of sheltering in rocks and shrubs/hummock grasses represent separately derived conditions. Ctenophorus appears to have undergone extensive cladogenesis approximately 10-12 million years ago, with all three major ecological modes being established at that time.     

Species specificity of thromboplastin. A phylogenetic study.

Having studied the influence of thromboplastin preparations derived from cold and warm-blooded species on the plasma of 12 vertebrates (carp, frog, turtle, hen, rabbit, rat, mouse, guinea-pig, ground squirrel, dog, sheep and man) we have established that among the species far from each other phylogenetically, the phenomenon of species specificity could be demonstrated in general. It was found that the extrinsic coagulation system measured by Quick times can well be activated in every examined species. Simultaneously, in plasmas of turtle and hen the intrinsic clotting system proved to be deficient.     

Analysis of phylogenetic relationship among five mulberry (Morus) species using molecular markers.

Species identification in mulberry (Morus) continues to be a point of great debate among scientists despite the number of criteria such as floral characters, wood, and leaf anatomical and biochemical characters used to identify the species within this genus. However, no consensus system of classification has emerged. Hence, an investigation was undertaken with inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers to find out the possibility of using these DNA markers to confirm the identity of genotypes in a particular species. Fifteen ISSR and 15 RAPD primers generated 86% and 78% polymorphism, respectively, among 19 mulberry genotypes. The polymorphism among the species varied from 50% to 57% in ISSR markers and 31% to 53% in RAPD markers. Similarity coefficients were higher among the genotypes of M. latifolia, M. bombycis and M. alba. Cluster analyses separated genotypes of M. laevigata and M. indica from those of the other species. Population structure analysis of these species further showed high genetic differentiation coefficients (GST), high heterozygosity between two species (DST), and total heterozygosity among populations (Ht) coupled with considerably low gene flow (Nm) when M. laevigata was paired with other species. Based on these parameters and the result of cluster analysis it is concluded that M. laevigata can be considered as a separate species of mulberry, whereas the other four species may be grouped together and treated as subspecies.     

Aspergillus niger contains the cryptic phylogenetic species A. awamori

Aspergillus section Nigri is an important group of species for food and medical mycology, and biotechnology. The Aspergillus niger 'aggregate' represents its most complicated taxonomic subgroup containing eight morphologically indistinguishable taxa: A. niger, Aspergillus tubingensis, Aspergillus acidus, Aspergillus brasiliensis, Aspergillus costaricaensis, Aspergillus lacticoffeatus, Aspergillus piperis, and Aspergillus vadensis. Aspergillus awamori, first described by Nakazawa, has been compared taxonomically with other black aspergilli and recently it has been treated as a synonym of A. niger. Phylogenetic analyses of sequences generated from portions of three genes coding for the proteins β-tubulin (benA), calmodulin (CaM), and the translation elongation factor-1 alpha (TEF-1α) of a population of A. niger strains isolated from grapes in Europe revealed the presence of a cryptic phylogenetic species within this population, A. awamori. Morphological, physiological, ecological and chemical data overlap occurred between A. niger and the cryptic A. awamori, however the splitting of these two species was also supported by AFLP analysis of the full genome. Isolates in both phylospecies can produce the mycotoxins ochratoxin A and fumonisin B?, and they also share the production of pyranonigrin A, tensidol B, funalenone, malformins, and naphtho-γ-pyrones. In addition, sequence analysis of four putative A. awamori strains from Japan, used in the koji industrial fermentation, revealed that none of these strains belong to the A. awamori phylospecies.     

A molecular assessment of the iron stress response in the two phylogenetic clades of Trichodesmium

Trichodesmium spp. play key roles in global carbon and nitrogen budgets and thus defining what controls their productivity is important for understanding climate change. While iron availability has been shown to be an important chemical factor for controlling both growth and nitrogen fixation rates in Trichodesmium , all culture experiments to date have focused solely on representatives from one clade of Trichodesmium . Genomic sequence analysis determined that the Trichodesmium erythraeum (IMS101) genome contains many of the archetypical genes involved in the prokaryotic iron stress response. Focusing on three of these genes, isiB , idiA and feoB , we found that all three showed an iron stress response in axenic T. erythraeum (IMS101), and their sequences were well conserved across four species in our Trichodesmium culture collection [consisting of two T. erythraeum strains (IMS101 and GBRTRLI101), two Trichodesmium tenue strains (Z-1 and H9-4), Trichodesmium thiebautii and Trichodesmium spiralis ]. With clade-specific quantitative PCR (qPCR) primers for one of these genes, isiB , we found that high isiB expression at low Fe levels corresponded to specific reductions in N₂ fixation rates in both major phylogenetic clades of Trichodesmium (the T. erythraeum clade and T. tenue clade). With regard to the two clades, the most significant difference determined was temperature optima, while more subtle differences in growth, N₂ fixation rate and gene expression responses to Fe stress were also observed. However the apparent conservation of the Fe stress response in the Trichodesmium genus suggests that it is an important adaptation for their niche in the oligotrophic ocean.     

A new species of Lactarius (subgenus Gerardii) from two relict Fagus grandifolia var. mexicana populations in Mexican montane cloud forests

A new milkcap species, Lactarius fuscomarginatus, was found in the subtropical region of central Veracruz (eastern Mexico) associated with two relict populations of Fagus grandifolia var. mexicana. The species is characterized macroscopically by its dark pileus and stipe and by its distant and whitish lamellae with blackish to blackish brown edges. A molecular phylogenetic analyses based on ITS and LSU nucDNA sequences confirms the delimitation of this new taxon and places L. fuscomarginatus in subgenus Gerardii. A detailed morphological comparison is given with similar species.     

基于叶绿体基因rbcL和psbA-trnH间区探讨石杉科植物系统关系

关于石杉科Huperziaceae植物的分类,一直存在一些争议。在旧的分类体系中石杉科植物被包含在一个混合的石松科Lycopodiaceae和多谱系的石松属Lycopodium中。本文利用叶绿体rbcL基因和psbA-trnH基因间区序列探讨石杉科植物的系统位置及石杉科内部的分类关系,用最大简约法和邻接法对自测序列结合由GenBank下载的rbcL及psbA-trnH基因间区序列进行系统发育分析。结果显示,石杉科与Phylloglossum属关系较近,与石松科关系较疏远。在石杉科中热带石杉属Huperzia植物和马尾杉属Phlegmariurus植物的关系要比它们与其他石杉属植物更近。所以,我们的rbcL基因数据不支持秦仁昌关于石杉科分为石杉属和马尾杉属的分类处理。但是,因为我们的psbA-trnH序列没有包括热带种类,对石杉属植物和马尾杉属植物的关系无验证。因此需要更多的样品和序列数据进一步探讨石杉科的演化关系。     

New case of long-term persistence of Paranosema locustae (Microsporidia) in melanopline grasshoppers (Orthoptera: Acrididae: Melanoplinae) of Argentina

We report an additional case of long-term persistence of Paranosema locustae in grasshoppers of Argentina. The pathogen was introduced from North America on rangeland at Loncopué, Neuquén province. Microsporidia were not detected in pre-introduction samples whereas infected grasshoppers were found 11 years after introduction. Affected grasshoppers were the melanoplines Dichroplus elongatus, Dichroplus maculipennis, and Scotussa lemniscata, some of them with high spore loads. The case highlights the ability of P. locustae to recycle in local grasshopper communities by parasitizing susceptible species other than the natural hosts.     

Taxonomy and phylogenetic relationships of two species of Hypocrea with Trichoderma anamorphs

Hypocrea patella is reevaluated. Its Trichoderma anamorph is described and the phylogenetic position of the species is determined through sequences of the ITS regions of rDNA. It is sister to a clade that includes Trichoderma longibrachiatum/H. schweinitzii. Hypocrea patella f. tropica is accepted for a Costa Rican collection. Hypocrea neorufa and its Trichoderma anamorph are described. Its phylogenetic position is determined by sequences of the ITS region of rDNA and the protein-coding translation-elongation factor (EF-1α). It is derived from within a clade that includes T. viride/H. rufa, T. atroviride/H. atroviridis, T. koningii/H. koningii and T. asperellum. Deceased August 2002.     

Morphological and ITS rDNA-based phylogenetic identification of two new species in Tinctoporellus

Two new poroid wood-inhabiting basidiomycetes, Tinctoporellus bubalinus and T. hinnuleus, are described and illustrated based on morphological characteristics and phylogenetic analysis of rDNA ITS sequences. Tinctoporellus bubalinus is characterized by annual, resupinate basidiocarps, white to buff coloured pore surface and thin- to slightly thick-walled, richly branched and contorted dendrohyphidia. Tinctoporellus hinnuleus is characterized by annual, resupinate basidiocarps, cinnamon, clay-buff to fawn pore surface, thin-walled, richly branched and contorted brown dendrohyphidia. Discriminating characters between the new species and the closely related species are discussed. A key to accepted species in Tinctoporellus is provided.     

A molecular phylogenetic study of the freshwater talitrid amphipod Orchestia cavimana (Crustacea).

In this paper we performed a molecular phylogenetic study of Orchestia cavimana, the sole talitrid amphipod inhabiting beaches of European freshwater lakes and rivers. For that purpose, we have PCR amplified and sequenced regions of the mitochondrial cytochrome oxidase subunit I (COI) gene, basing our analysis on both nucleotide and amino acid sequences and considering also structural classes of the COI enzyme. Phylogenetic analyses were conducted by neighbour-joining (NJ) and maximum-parsimony (MP) methods comparing homologous sequences of talitrids and other Crustacea. In both NJ and MP trees, O. cavimana shows a basal placement with respect to other talitrid amphipods.     

A standardized reanalysis of molecular phylogenetic hypotheses of Gobioidei

Gobioidei is a suborder of perciform fishes with about 2000 species distributed worldwide. Despite the evolutionary and ecological importance of gobioids, their phylogenetic inter- and intrarelationships are still poorly understood. Only a few studies (either morphological or molecular) have tackled the phylogeny of Gobioidei as a whole. Of these, only six studies thus far have addressed gobioid intrarelationships based on molecular data (each using different taxon sampling, genes, outgroups and method of phylogenetic inference), yielding contrasting results regarding the phylogenetic relationships among major lineages. In this study, we have reanalysed data from four of these molecular phylogenetic studies of Gobioidei under standardization criteria (same outgroup and methods of phylogenetic inference) in order to assess the robustness of their results, as well as to identify which parts of the gobioid tree are least resolved. Results from all datasets reanalysed in this study are generally similar to those of the respective original studies, and suggest broad patterns of phylogenetic relationships among gobioid lineages. However, there are numerous topological discrepancies among the four studies, support is low for many phylogenetic relationships and topology tests are unable to reject the vast majority of alternative topologies tested. The concatenation of datasets yields a relatively robust phylogeny of major lineages of Gobioidei, but there are some issues of overlap and missing data, which are ameliorated with the inclusion of additional homologous sequences from GenBank that increase dataset completeness. Because both monophyly of major gobioid groups and phylogenetic relationships among them cannot be fully resolved, it is clear that further phylogenetic research is needed, and this should be accompanied by a major taxonomic revision of the Gobioidei. Nevertheless, even with the relatively unstable nature of the available molecular phylogenies, there are some monophyletic units that can be identified, and a basic structure of the gobioid tree appears evident.     

Comparative FISH analysis in five species of Eyprepocnemidine grasshoppers

The chromosomal localization of ribosomal DNA, and a 180 bp satellite DNA isolated from Spanish Eyprepocnemis plorans specimens, has been analysed in five Eyprepocnemidinae species collected in Russia and Central Asia. Caucasian E. plorans individuals carried each of the two DNAs, but the rDNA was limited to only two chromosomes (S(9) and S(11)) in sharp contrast to Spanish specimens that show 4-8 rDNA clusters and to Moroccan specimens which carry rDNA in almost all chromosomes. The four remaining species, however, lacked the 180 bp tandem repeat, and showed rDNA clusters in one (S(9) in Thisoicetrinus pterostichus), two (S(9) and S(10) in Eyprepocnemis unicolor; M(8) and S(11) in Heteracris adspersa), or three (S(9), S(10), and S(11) in Shirakiacris shirakii) chromosome pairs. The implications of these findings for the evolution of these two chromosome markers in this group of species are discussed.     

A phylogenetic study of Lepidapedoides Yamaguti, 1970 (Digenea) with a key and descriptions of two new species from Western Australia

Two new species of the genus Lepidapedoides are described from the aulopodid teleost Aulopus purpurissatus from south-western Australia. Both are distinguished from other Lepidapedoides spp. by their pedunculate ventral sucker. Lepidapedoides pistoris n. sp. and L. elongatrium n. sp. are distinguished by the possession of a narrow, elongate form, a long ventral sucker to ovary distance, the vitellarium reaching only to the posterior level of the cirrus-sac, the cirrus-sac length and the deep genital atrium with the metraterm entering distally to its base in L. elongatrium. A key to species of the genus is given. A character matrix is included for the genus. Poorly resolved phylogenetic trees indicate two main lineages in the genus. The two new species described here are resolved as sister taxa. The new combination Lepidapedoides freitasi (Kohn &; Fernandes, 1970) is formed for Acanthocolpoides freitasi.     

A phylogenetic study on vertebrate mitochondrial DNA polymerase.

We have started a phylogenetic survey for the mitochondrial DNA polymerase and present in this study the results obtained for all the different classes for the vertebrates. The operating conditions include the purification of mitochondria, the analysis of the DNA polymerase activity in the extract and the determination of the sedimentation coefficient on sucrose gradients. The utilization of digitonin for removing the external membrane of the organelle and contaminating proteins has been generalized since this detergent shows no effect on the activities of either DNA polymerases alpha or gamma. The results obtained for the mitochondria of different classes of vertebrates show that the activity responding to the specific assay of DNA polymerase gamma tended invariably to increase during purification while that of DNA polymerase alpha tended to decrease. Furthermore in almost all the cases the gamma-polymerase represented the only DNA polymerase activity found in the mitochondria after digitonin treatment. The analysis of the sedimentation patterns of the mitochondrial DNA polymerase strongly suggests the presence of a single type of DNA polymerase showing the typical properties of the gamma-polymerase. It is concluded that the vertebrate mitochondria contain a well-defined and unique form of DNA polymerase which corresponds to the DNA polymerase gamma.     

The primary structure of two molecular species of porcine organ-common type acylphosphatase.

Electrophoretically homogeneous preparations of organ-common type acylphosphatase from porcine testis and brain were separated into two molecular species by reversed-phase liquid chromatography. From tryptic peptide map analysis, it was inferred that each of the two testis proteins is the same as the corresponding one of the two brain proteins. The complete primary structures of the two acylphosphatases from testis were then determined. The one molecular species consists of 100 amino acid residues: [sequence; see text] The other consists of 98 amino acid residues identical to the 3rd-100th residues of the above sequence and is also acetylated at the amino-terminal alanine. The 98-residue sequence has only 59% homology with porcine muscle acylphosphatase, but has 92% homology with human erythrocyte acylphosphatase. It was thus confirmed that the major acylphosphatases in testis, brain, and erythrocyte belong to the same organ-common type isoenzyme, distinct from the muscle type isoenzyme.