Molekulare und., adaptive Evolution, Kladistik und Stammesgeschichte1: Ergänzungen zu einer Arbeitshypothese

Molecular and “adaptive” evolution, cladistic and phylogeny. Supplementations to a working hypothesis The methods of molecular biology and morpholo for the taxonomical assessment have given in several cases very different results. The following examples are discussed: Ailuropoda melanoleuca as an ursoid member of the Carnivora (Ursidae or Ailuropodidae?), Homo saiens and his position to the African apes (Pan and Gorilla) (Pongidae or Hominidae?), Theroipithecus gelada and its affinities to the baboons (Papionini or Theropithecini ?) and Oreopithecus bambolii from the late Miocene of Italy and its taxonomical position within the catarrhine primates. For the three extant species not only the “two level evolution” (molecular and morphological-adaptative evolution) is evident, but also the working hypothesis, that the “adaptative” evolution is more rapidly as the molecular evolution, as the author is suggesting since 1969. The results of molecular methods (immunoloy, amino acid sequences, electrophoresis, DNA-DNA hybridization) are more important for the phylogeny than for the taxonomy. For the cladistic method it is clear, that a cladogram is not a phylogenetic tree, as suggested Peter Ax (1984).     

Functional mode of NtHSP17.6, a cytosolic small heat-shock protein fromNicotiana tabacum

Small heat-shock proteins (sHsps) are ubiquitous stress proteins with molecular chaperone activity. They share characteristic homology with the α-crystallin protein of the mammalian eye lens as well as being ATP-independent in their chaperone activity. We isolated a clone for a cytosolic class I sHsp,NtHSP17.6, fromNicotiana tabacum, and analyzed its functional mode for such activity. Following its transformation intoEscherichia coli and its over-expression, NtHSPI 7.6 was purified and examinedin vitro. This purified NtHSPI 7.6 exhibited typical chaperone activity in a light-scattering test. It was enable to protect a model substrate, firefly luciferase, from heat-induced aggregation. Non-denaturing PAGE showed that NtHSP17.6 formed a dodecamer in its native conformation, and was bound to its substrate under heat stress. A labeling test with bis-ANS indicated that this binding might be linked to newly exposed hydrophobic sites of the NtHSPI 7.6 complexes during heat shock. Based on these data, we suggest that NtHSP17.6 is a molecular chaperone that functions as a dodecamer in a heat-induced manner.     

Molecular phylogeny and evolution of the AsianAconitum subgenusAconitum (Ranunculaceae)

Classification of the genusAconitum (Ranunculaceae) has long been considered quite difficult because its species show high levels of morphological and ecological variability. The molecular phylogeny of Asian aconites,Aconitum subgenusAconitum was, therefore, studied based on RFLP and sequences of the intergenic spacer between thetrnL (UAA) 3′ exon andtrnF (GAA), and of thetrnL intron, of the chloroplast DNA. UsingAconitum subgenusLycoctonum as an outgroup, we obtained a statistically reliable molecular tree composed of six clades branched radiatively at the very base. There are three clades of Japanese aconites, a single clade of the species of Yunnan and Himalayas, and two clades of Siberian plants. All the tetraploid taxa of Japan we studied did not show any difference based on the molecular characters analyzed, though they have been classified into many taxa. Evolution and phytogeography of the Asian aconites as well as the phylogeny are discussed.     

Embryology of <Emphasis Type="Italic">Petrosavia</Emphasis> (Petrosaviaceae,Petrosaviales): evidence for the distinctness of the family from other monocots

The affinities of Petrosavia, a rare, leafless, mycoheterotrophic genus composed of two species indigenous to East to Southeast Asia, have long been uncertain. However, recent molecular analyses show that the genus is sister to Japonolirion osense. Japonolirion and Petrosavia comprise the Petrosaviaceae, which are now placed in its own order, Petrosaviales, distinct from other monocots based on molecular analyses. We conducted an embryological study of Petrosavia, comparing it to Japonolirion, as well as to basal monocots (Acorus and Araceae) and more derived monocots (Nartheciaceae, Velloziaceae, and Triuridaceae). Our results showed that Petrosavia is very similar in embryology to Japonolirion, with both genera sharing a glandular anther tapetum, simultaneous cytokinesis in microspore mother cells, anatropous and crassinucellate ovules, T-shaped tetrads of megaspores, ab initio Cellular-type endosperm, and a mature seed coat composed of the exotesta, endotesta, and endotegmen. The two genera of Petrosaviaceae are clearly distinct from Acorus, and all Araceae, Nartheciaceae, Velloziaceae, and Triuridaceae genera in various combinations of characters. Thus, both molecular and embryological evidence support the distinctness of the Petrosaviaceae from other monocots and its placement in its own order, Petrosaviales.     

Treponema pallidum and the quest for outer membrane proteins

Treponema pallidum, the syphilis spirochaete, has a remarkable ability to evade the humoral and cellular responses it elicits in infected hosts. Although formerly attributed to the presence of an outer coat comprised of serum proteins and/or mucopolysaccharides, current evidence indicates that the immuno-evasiveness of this bacterium is largely the result of its unusual molecular architecture. Based upon a combination of molecular, biochemical, and ultrastructural data, it is now believed that the T. pallidum outer membrane (OM) contains a paucity of poorly immunogenic transmembrane proteins (‘rare outer membrane proteins’) and that its highly immunogentc proteins are lipoproteins anchored predominantly to the periplasmic leaflet of the cytoplasmic membrane. The presence in the T. pallidum OM of a limited number of transmembrane proteins has profound implications for understanding syphilis pathogenesis as well as treponemal physiology. Two major strategies for molecular characterization of rare outer membrane proteins have evolved. The first involves the identification of candidate OM proteins as fusions with Escherichia coli alkaline phosphatase. The second involves the characterization of candidate OM proteins identified in outer membranes isolated from virulent T. pallidum. Criteria to define candidate OM proteins and for definitive identification of rare OM proteins are proposed as a guide for future studies.     

728. SALVIA OXYPHORA

The Bolivian endemic Salvia oxyphora Briq. is described and illustrated; the circumstances of its discovery, possible reasons for its reduced population in the wild and suggestions for its cultivation are given. The molecular status of Salvia and the probable break‐up of the genus as traditionally circumscribed are discussed.     

High level production of supra molecular weight poly (3-hydroxybutyrate) by metabolically engineered<Emphasis Type="Italic">Escherichia coli</Emphasis>

The supra molecular weight poly ([R]-3-hydroxybutyrate) (PHB), having a molecular weight greater than 2 million Da, has recently been found to possess improved mechanical properties compared with the normal molecular weight PHB, which has a molecular weight of less than 1 million Da. However, applications for this PHB have been hampered due to the difficulty of its production. Reported here, is the development of a new metabolically engineeredEscherichia coli strain and its fermentation for high level production of supra molecular weight PHB. RecombinantE. coli strains, harboring plasmids of different copy numbers containing theAlcaligenes latus PHB biosynthesis genes, were cultured and the molecular weights of the accumulated PHB were compared. When the recombinantE. coli XL 1-Blue, harboring a medium-copy-number pJC2 containing theA. latus PHB biosynthesis genes, was cultivated by fed-batch culture at pH 6.0, supra molecular weight PHB could be produced at up to 89.8 g/L with a productivity of 2.07 g PHB/L-h. The molecular weight of PHB obtained under these conditions was as high as 22 MDa, exceeding by an order of magnitude the molecular weight of PHB typically produced inRalstonia eutropha or recombinantE. coli     

Evolution of blindness in scolopendromorph centipedes (Chilopoda: Scolopendromorpha): insight from an expanded sampling of molecular data

Relative to its diversity (34 genera, 700 species), Scolopendromorpha has been undersampled in molecular phylogenetic analyses compared with the other chilopod orders. Previous analyses based on morphology have not resolved several key controversies in systematics and evolutionary morphology unambiguously. Here we apply new molecular and morphological data to scolopendromorph phylogenetics, with a focus on the evolution of blindness. The taxonomic sample includes 19 genera, many lacking previous molecular data, and diverse, cosmopolitan genera of Scolopendridae are sampled by multiple species. Phylogenetic analysis with Direct Optimization used 94 morphological characters and ca. 4.5 kb of sequence data from two nuclear (18S and 28S rRNA) and two mitochondrial (16S rRNA and COI) loci. A single most‐parsimonious cladogram selected after sensitivity analyses resolves Scolopendromorpha as monophyletic, and divides it into a blind clade of three families (Plutoniumidae, Cryptopidae, Scolopocryptopidae) and its ocellate sister group, Scolopendridae. Some species‐rich, cosmopolitan genera (Cormocephalus, Otostigmus, Scolopendra) in Scolopendridae are non‐monophyletic, and in several instances (e.g. New and Old World Scolopendra) relationships are more congruent with geographical distributions than with traditional classifications. The tribe Asanadini is particularly subject to parameter‐sensitivity, nesting in the combined analysis within Scolopendrini but as sister to all other Scolopendrinae for molecular data alone. The total‐evidence tree unambiguously optimizes trunk segmentation: a 23‐segmented trunk has a single origin in the blind clade. © The Willi Hennig Society 2011.     

Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations, we investigate the preferential binding of metal ion such as Na⁺ and molecular ions such as tetramethyl ammonium (TMA⁺) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO⁺) to double-stranded DNA. The thermodynamic driving force for a particular molecular ion-DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO⁺. The ion binding processes are found to be entropically favourable. In addition, the contribution of hydrophobic effects towards the entropic stabilisation (in case of TMA⁺) and the effect of hydrogen bonding contributing to enthalpic stabilisation (in case of CHO⁺) have also been investigated.     

Integrated analyses of chromosome, molecular and morphological variability in the Andean mice Eligmodontia puerulus and E. moreni (Rodentia, Cricetidae, Sigmodontinae)

Patterns of evolution and systematics of sigmodontine rodents are matters of continuous revision and debate. The silky mouse, Eligmodontia, is a phyllotine rodent adapted to arid environments. Chromosomal and molecular data have identified six species in this genus. Among these E. puerulus and E. moreni are sister taxa from the high Andean and lowland deserts, respectively, with large chromosomal differences and intermediate levels of molecular divergence. The purpose of our study was to quantify the degree of variability (morphological, cytogenetic, and molecular) and to analyze its evolutionary implications within, and between, these sister species in the Monte and Puna biomes of Argentina. Our results show a high variability at the chromosomal and molecular level, but low morphological differentiation among populations of E. puerulus. Diploid numbers vary from 31 to 37 due to a complex Robertsonian system, whereas cytochrome-b distances range from 0.15% to 5.75%. On the other hand, E. moreni shows high morphological differentiation between populations, but low intraspecific differentiation at the molecular (from 0.73% to 1.4%) and chromosomal level (2n = 52). Comparison of E. puerulus with E. moreni reveals high morphological and chromosomal distinction between them, but absence of molecular differentiation. Our results suggest that: (1) the high genetic variability of E. puerulus could be associated to its geographic distribution in the complex topography of the high Andean Puna; (2) the high morphological differentiation between E. moreni and E. puerulus could be the result of natural selection; and (3) molecular polyphyly between E. puerulus and E. moreni could be due to introgression or a recent split of these taxa. Finally, our results emphasize the need to integrate different datasets in the analysis of species variability and diversification, as tools for understanding their evolutionary histories.     

How does the annelid Alvinella pompejana deal with an extreme hydrothermal environment?

Alvinella pompejana, the so-called Pompeii worm (Desbruyères and Laubier, 1980), is found exclusively in association to high temperature venting, at the surface of hydrothermal chimneys of the East Pacific Rise. The main characteristics of this emblematic species is its tolerance to high temperature but its ability to colonize extremely hot substrates has been the subject of much controversy. In the last decade, new tools allowing in situ and in vivo investigation have been determinant in the understanding of the strategies and adaptations required to colonize such an extremely hot environment. New data relative to the characterization of the animal habitat conditions, on one hand, to the molecular adaptations of this organism and the colonization processes by this species, on the other hand, are now available. Advanced methods and tools, that have fostered the physico-chemical characterization of vent habitats in recent years, are first reviewed. Factors controlling the physico-chemical variability of vent habitats and the threats A. pompejana might effectively face are discussed. The exceptional thermotolerance of this species and the maximum temperature it could sustain are then considered in the light of molecular data relative to its collagen stability. Life history traits as well as biological controls on tube micro-habitat conditions are discussed on the basis of new in situ and in vivo experiments and characterization. Finally, the current knowledge and opened questions related to the molecular adaptations to chemical stresses are briefly stated. The ability of Alvinella pompejana to colonize these substrates is far from being fully understood, but the exceptional properties of its extracellular biopolymers and the behavior of the worm can be now considered as major clues in the colonization process. Alvinella pompejana could thus stand at the limits authorized for its biological machinery in a highly dynamic environment where temperature can readily reach lethal values, but where temperature regulation by the animal itself would prevent exposure to deleterious thermal spikes. The dynamic system associating this pioneer species and its associated microflora might be viewed as a key to the subsequent colonization of these environments by less tolerant species, highlighting A. pompejana as a new type of ecosystem bioengineer.     

A phylogeny of Pacific fiddler crabs of the subgenus Minuca (Crustacea,Brachyura, Ocypodidae: Uca) with the description of a new species from a tropical gulf in Pacific Costa Rica

The phylogeny of all Pacific fiddler crab representatives of the subgenus Minuca Bott, 1954 (sensu Beinlich and von Hagen, 2006) is reconstructed. For the molecular analysis, Cox1 mitochondrial and 28S ribosomal nuclear DNA sequences were used. According to these data, same transisthmian sister species relationships are confirmed and a new species of the genus Uca Leach, 1814, Uca osa sp. n., is described from Golfo Dulce, a tropical gulf in Pacific Costa Rica. Morphological as well as molecular data confirm distinctness of this species compared with all other members of the subgenus Minuca, to which it belongs. Distinctive morphological traits are presented to distinguish Uca osa sp. n. from its congeners in the Eastern Pacific.     

Stable nuclear transformation of Gonium pectorale

Background  

Green algae of the family Volvocaceae are a model lineage for studying the molecular evolution of multicellularity and cellular differentiation. The volvocine alga Gonium is intermediate in organizational complexity between its unicellular relative, Chlamydomonas, and its multicellular relatives with differentiated cell types, such as Volvox. Gonium pectorale consists of ~16 biflagellate cells arranged in a flat plate. The detailed molecular analysis of any species necessitates its accessibility to genetic manipulation, but, in volvocine algae, transformation procedures have so far only been established for Chlamydomonas reinhardtii and Volvox carteri.     

富油微藻布朗葡萄藻分子生态学研究进展

分子生态学是研究生命系统与环境系统相互作用机理及其分子机制的科学,可以从宏观和微观结合的角度真实反映生态现象的本质。简述产烃布朗葡萄藻形态与化学种等生理生态特征的基础上,综述了近年来国内外布朗葡萄藻分子生态学研究的新进展,主要包括分子系统发育学及其与化学种、基因组、地理来源等之间的关系。经典分类学上,关于布朗葡萄藻属于绿藻门(Chlorophyta)还是黄藻门(Xanthophyta)存在争议,而基于18S核糖体核糖核酸(18S ribosomal ribonucleic acid,18S rRNA)序列的分子系统发育学研究结果将布朗葡萄藻界定为绿藻门、共球藻纲(Trebouxiophyceae)。依据藻株的产烃种类和化学结构特征,可将布朗葡萄藻划分为A、B和L 3个化学种,而布朗葡萄藻的分子系统学进化关系与化学种间高度统一。在基因组大小上,位于同一大亚聚群中的化学种B与L间却存在明显差异,而进化关系较远的化学种B与A间则更相近。不同地理来源布朗葡萄藻的18S rRNA序列和内部转录间隔区(internal transcribed spacer,ITS)多态性较高,提示不同地缘藻株间存有较高的遗传多样性。探讨了布朗葡萄藻分子生态学研究尚待解决的问题,并对今后相关研究做了展望。     

Conformation of amylose in water. I. Light-scattering and sedimentation-equilibrium measurements

The conformation of amylose in aqueous solution has been found to be dependent on its molecular weight. When the molecular weight of amylose is outside of the so-called “dissolving gap” described by Burchard (6500<M_r<160,000) it behaves as a random coil, whereas when its molecular weight is within the “dissolving gap,” it easily aggregates forming a rigid coil which is the B-type (retrograded) amylose. The conformation of this rigid coil is suggested to be a double helix.     

Enzymatic synthesis of (+)- and (-)-bisdechlorogeodin with sulochrin oxidase from Penicillium frequentans and Oospora sulphurea-ochracea

Sulochrin oxidase is a blue copper-containing glycoenzyme that catalyzes a stereospecific formation of bisdechlorogeodin from sulochrin. The enzyme has been isolated from Penicillium frequentans and Oospora sulphureaochracea which catalyzes the formation of (+)-form and (-)-form of bisdechlorogeodin respectively. The Penicillium enzyme has a molecular weight of 157,000 and contains 19.5% of carbohydrates. Amino acid and carbohydrate compositions are given. The enzyme has probably a dimeric structure containing 6 Cu-atoms. Apparent K _m-values of various substrates are presented. The Oospora enzyme has a molecular weight of 128,000 and except for its stereospecificity its properties are very similar to those of the Penicillium enzyme.     

Bryoerythrophyllum duellii Blockeel (Bryophyta: Pottiaceae), a new moss species from Greece and Cyprus,and its molecular affinities

A moss first collected on Crete by Prof. Ruprecht Düll in 1976 but never satisfactorily identified is described as a new species, Bryoerythrophyllum duellii. It is known from five localities in Greece and Cyprus. It belongs to the B. recurvirostrum group, and its status as a distinct taxon is supported by molecular data. The molecular relationships of the genus Bryoerythrophyllum are discussed, and they suggest that the genus is monophyletic only if Erythrophyllopsis, Mironia and Saitobryum are included. The B. recurvirostrum and B. wallichii groups apparently form a young complex of taxa that are not very diverse molecularly, but sometimes have a distinctive morphology. Bryoerythrophyllum duellii is one of several lineages within this complex that may have experienced a longer period of reproductive isolation leading to the fixation of distinctive morphological and molecular features.     

Taxonomic notes on Cimicifuga nanchuanensis (Ranunculaceae), a hitherto imperfectly known species from China

Cimicifuga nanchuanensis P. K. Hsiao (Ranunculaceae) has been regarded as an imperfectly known species. Based on critical examination of herbarium specimens and living plants we have determined that it is a morphologically distinctive species and that its geographical range is much wider than believed before, far from locally endemic to its type locality. Our cytological examination reveals the species to be a diploid (2n = 16). Our molecular phylogenetic analyses using nrDNA and cpDNA datasets confirm our morphological observations. As the generic concept and delimitation of Actaea L., in which Cimicifuga Wernisch. and Souliea Franch. are included, have also been strongly corroborated by our molecular phylogenetic analyses, here we adopt a broad Actaea and make a new combination for the species in question, i.e. Actaea nanchuanensis (P. K. Hsiao) J. P. Luo, Q. Yuan & Q. E. Yang.     

Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups

Background  

Alpha proteobacteria are one of the largest and most extensively studied groups within bacteria. However, for these bacteria as a whole and for all of its major subgroups (viz.Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, SphingomonadalesandCaulobacterales), very few or no distinctive molecular or biochemical characteristics are known.