Evolution of ancient lake bivalves: the Lymnocardiinae (Cardiidae) of the Caspian Sea

The Caspian Sea as the largest continental water body in the world is known for its comparably high levels of biodiversity and endemism, also in mollusks. The evolution of a euryhaline taxon of cardiid bivalves, the Lymnocardiinae of the Ponto-Caspian region, remains unclear today. We studied material from the whole recent range of Lymnocardiinae (i.e., the Caspian, the Azov, and the Black Seas) using a LSU rDNA phylogeny aiming at (a) testing the monophyly of Lymnocardiinae and (b) determining the phylogenetic relationships within Cardiidae. Lymnocardiinae s.str. were monophyletic, i.e., a distinct group that included species of Hypanis, Didacna, and Monodacna. Lymnocardiinae as often understood, i.e., including Cerastoderma, are not monophyletic in our analysis and Cerastoderma should thus be transferred to Cardiinae. The Lymnocardiinae s.str. had a shallow tree topology and were poorly resolved. No clearcut biogeographical pattern could be derived from the phylogeny, i.e., species stemming from respective Ponto-Caspian regions, do not necessarily cluster together. We discuss a scenario of the evolutionary history and biogeographical (as well as taxonomic) implications. Given the complex history of the Ponto-Caspian region and the Caspian Sea in particular, the Lymnocardiinae would represent an interesting study object for addressing the consequences of environmental changes on biotic evolution at various spatial and temporal scales.     

Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the crustacean order isopoda

The expansion segments within the eukaryote nuclear 23S-like ribosomal RNA molecule are now well characterized in many diverse organisms. A different base compositional bias, a higher propensity for size variability, and an increased evolutionary rate distinguish these regions from the universally conserved core regions of the molecule. In addition, some expansion segments of higher eukaryotes exhibit significant sequence simplicity which is hypothesized to occur by slippage-mediated mutational processes. We describe the discovery of extreme size variation of the D3 expansion segment in the crustacean order Isopoda. Among 11 species D3 varies in size from 180 to 518 nucleotides but maintains a homologous secondary structure. The D3 size is significantly positively correlated to relative simplicity factor (RSF), indicating that growth is most likely by insertion of simple sequences. D3 size and RSF correlate approximately with a morphology-based phylogeny, and within oniscideans RSF increases as more recent divergences occur. The D3 ofArmadillidium vulgare, with an RSF of 1.87, is the highest value recorded for any known expansion segment. Regions of high sequence simplicity in nuclear ribosomal RNA were previously only known from the higher vertebrate lineage. Here we demonstrate that this phenomenon occurs in a more extreme condition within a monophyletic invertebrate lineage. The extreme size changes identified could indicate that expansion segments are an extraneous element in the functioning ribosome.     

Mosaic evolution of rodent B1 elements

We have determined sequences of PCR-amplified B 1 elements from hamster and rat (Myomorpha), chipmunk (Sciuromorpha), and guinea pig (Caviomorpha). Between three and six B 1 subfamilies were found in these species. In the phylogenetic analysis Bl sequences of hamster, mouse, and rat clustered separately from those of chipmunk and those of guinea pig. This is consistent with an independent evolution of B1 elements in separate rodent lineages. We exclude the possibility of convergent mutations to explain certain diagnostic characters within the modern B1 quasi-dimers and view these elements as mosaic structures assembling preexisting mutations. Furthermore, the presence of Alu-like structural motifs supports the hypothesis of the monophyletic origin of Alu and B1 repeats, i.e., from a common 7SL RNA-derived retroposing monomeric element. Correspondence to: E. Zitkiewicz     

Comparison of the stepwise and convergent approaches in the solid-phase synthesis of rat Tyr0-atriopeptin II

Tyr⁰-Atriopeptin II was synthesized on a 2-chlorotrityl resin by both the stepwise and the convergent approach. For both methods an Fmoc/tBu(Trt)-based protection scheme was used. The convergent methodology utilizes the sequential condensation of four protected peptide fragments. These were chosen so that after every condensation reaction, the amino-terminal region of the newly formed resin-bound peptide did not contain a -turn. This designed convergent synthesis gave the target peptide in much higher yield and purity than the conventional step-by-step synthesis.     

Phylogenetic analysis of pelecaniformes (aves) based on osteological data: implications for waterbird phylogeny and fossil calibration studies

Background

Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group''s fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving) and temporal diversification (e.g., the origins of modern families). Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis) were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification.

Methodology/Principal Findings

Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae), Prophaethon and Lithoptila (successive sister taxa to Phaethontidae), and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae). These relationships are invariant when ‘backbone’ constraints based on recent avian phylogenies are imposed.

Conclusions/Significance

Relationships of extant pelecaniforms inferred from morphology are more congruent with molecular phylogenies than previously assumed, though notable conflicts remain. The phylogenetic position of the Plotopteridae implies that wing-propelled diving evolved independently in plotopterids and penguins, representing a remarkable case of convergent evolution. Despite robust support for the placement of fossil taxa representing key calibration points, the successive outgroup relationships of several “stem fossil + crown family” clades are variable and poorly supported across recent studies of avian phylogeny. Thus, the impact these fossils have on inferred patterns of temporal diversification depends heavily on the resolution of deep nodes in avian phylogeny.     

Patenting the products of genetic engineering

Until the most recent times, products of nature were unpatentable, not as failing to qualify as a manufacture for which patent protection may be sought under 35 U.S.C. §101, but because they were mere isolates of natural products. Genetically engineered microorganisms (e.g., Chakrabarty's plasmid-injected oil eatingPseudomonas) and biologically pure cultures of wild strains (e.g., Bergy'sStreptomyces which produces the antibiotic lincomycin) open uncharted waters in patent law.     

Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences

Phylogenetic relationships among embryophytes (tracheophytes, mosses, liverworts, and hornworts) were examined using 21 newly generated mitochondrial small-subunit (19S) rDNA sequences. The "core" 19S rDNA contained more phylogenetically informative sites and lower homoplasy than either nuclear 18S or plastid 16S rDNA. Results of phylogenetic analyses using parsimony (MP) and likelihood (ML) were generally congruent. Using MP, two trees were obtained that resolved either liverworts or hornworts as the basal land plant clade. The optimal ML tree showed hornworts as basal. That topology was not statistically different from the two MP trees, thus both appear to be equally viable evolutionary hypotheses. High bootstrap support was obtained for the majority of higher level embryophyte clades named in a recent morphologically based classification, e.g., Tracheophyta, Euphyllophytina, Lycophytina, and Spermatophytata. Strong support was also obtained for the following monophyletic groups: hornworts, liverworts, mosses, lycopsids, leptosporangiate and eusporangiate ferns, gymnosperms and angiosperms. This molecular analysis supported a sister relationship between Equisetum and leptosporangiate ferns and a monophyletic gymnosperms sister to angiosperms. The topologies of deeper clades were affected by taxon inclusion (particularly hornworts) as demonstrated by jackknife analyses. This study represents the first use of mitochondrial 19S rDNA for phylogenetic purposes and it appears well-suited for examining intermediate to deep evolutionary relationships among embryophytes.     

Vegetation changes in forests of the Krkonoše Mts. over a period of air pollution stress (1980–1995)

Species composition of the understory of spruce (Picea abies (L.) Karsten) and beech (Fagus sylvatica L.) forests subjected to intense air pollution stress in the Krkonoe Mts., Czech Republic, showed directional changes over the last 15 years. The changes were documented with repeated observations of 29 permanent plots, initiated in 1980 and analysed with constrained ordination methods (Canonical Correspondence Analysis). Ground layer changes were mainly associated with the loss of canopy foliage from air pollution stress. The increased amount of the light at ground level resulted in increased herb cover. The initially dominant species (e.g., Calamagrostis villosa (Chaix) J. F. Gmelin, Deschampsia flexuosa (L.) P. B., Vaccinium myrtillus L., Athyrium distentifolium Tausch) were those that increased in cover. Moss cover, and moss and herb richness, declined over the course of the study. Thus, the changes in tree canopy are accompanied with changes in the forest understory, which in turn can affect the dynamics of these forests.     

The importance of PS I chlorophyll red forms in light-harvesting by leaves

We have investigated the importance of the long wavelength absorbing spectral forms (red forms) of Photosystem I in photosynthetic light harvesting by leaves. To this end leaf spectra were simulated by using a linear combination of absorption (OD) spectra of purified Photosystem I, Photosystem II and LHC II, multiplied by an empirical multiple scattering chloroplast/leaf conversion function. In this way it is demonstrated that while the PS I red forms account for only about 4–5% of light absorption in a normal daylight environment, in different shadelight environments these long wavelength pigments may be responsible for up to 40% of total photon capture. In the context of maximising the photosynthetic quantum efficiency under the low light conditions of shadelight, this relative increase in the absorption cross section of PS I can be understood by considering the increased synthesis of the major PS II antenna complex, LHC II, known to occur in plants growing under these light conditions. It is demonstrated that for plants in a moderate to deep shadelight regime the PS II cross section needs to increase by 50% to 100% via LHC II synthesis to balance the increased PS I absorption by the red forms. The possibility that under shade light conditions the increased PS I cross section may serve in cyclic phosphorylation is also discussed.     

Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences

Aciculosporium and Heteroepichloë (Clavicipitaceae) are characteristic bambusicolous fungi in east Asia. In this study, we examined their intergeneric relationships based on the ALDH1-1 gene, which encodes a member of the aldehyde dehydrogenase family. In the clavicipitaceous fungi examined in this study, the nucleotide sequence of the third exon of ALDH1-1 (Exon-3) is 889 bp in length and has no insertion/deletion. A phylogenetic tree based on Exon-3 indicated that the clavicipitaceous fungi could be divided into two large groups: Cordyceps, Nomuraea, and Ustilaginoidea species formed a paraphyletic group, and the other grass biotrophic species formed a monophyletic group. This monophyletic group was further divided into three groups with high bootstrap support: i.e., species with Neotyphodium anamorphs (e.g., Epichloë), species with Ephelis anamorphs (e.g., Heteroepichloë), and Aciculosporium-Claviceps species. We discuss the relationships among Aciculosporium, Heteroepichloë, and other clavicipitaceous fungi.     

A simple classification of the volvocine algae by formal languages

There are several explanations of why certain primitive multicellular organisms aggregate in particular forms and why their constituent cells cooperate with one another to a particular degree. Utilizing the framework of formal language theory, we have derived one possible simple classification of the volvocine algae—one of the primitive multicells—for some forms of aggregation and some degrees of cooperation among cells. The volvocine algae range from the unicellular Chlamydomonas to themulticellular Volvox globator, which has thousands of cells. The classification we use in this paper is based on the complexity of Parikh sets of families on Chomsky hierarchy in formal language theory. We show that an alga with almost no space closed to the environment, e.g., Gonium pectorale, can be characterized by , one with a closed space and no cooperation, e.g., Eudorina elegans, by , and one with a closed space and cooperation, e.g., Volvox globator, by . This classification should provide new insights into the necessity for specific forms and degrees of cooperation in the volvocine algae.     

Behavior,body types and the irreversibility of evolution

A functional approach to evolutionary morphology is emphasized in this paper. This perspective differs from the current structuralist trend, which emphasizes the constraining role of developmental paths. In addition, the present approach agrees with the adaptationist paradigm. It is further argued that three types of phenomena are better understood in this light: i.- the existence of evolutionary trends, ii.- the maintenance of certain structural features within a given taxon, and iii.- the irreversibility of evolution.     

Aspects of Reproductive Biology of the Scalloped Hammerhead Shark, Sphyrna Lewini, off Northeastern Brazil

Ninety four scalloped hammerhead sharks, Sphyrna lewini (53 females and 41 males) ranging in size from 121 to 321cm total length (TL), were collected from surface gillnetters operating off northeastern Brazil and throughout the southwestern equatorial Atlantic Ocean between January and December 1996. A common regression for TL and eviscerated weight (EW) was calculated as, logEW = –11.786 + 2.889 logTL. Females and males were categorised into reproductive stages (4 and 2, respectively) according to morphological changes in their gonads. Size at sexual maturity for females was estimated to be 240cm, while males appeared to mature at between 180 and 200cm. Gravid females had between 2 and 21 embryos or pups, varying in TL from 3 to 38cm. There was no relationship between maternal length and size of litter. Copulation and parturition appear to occur outside the sampled area and possibly closer to the coast. With the exception of slightly lower uterine and ovarian fecundities, the results support the few existing data on the reproductive cycle of S. lewini in other areas.     

Spin probe clustering in human erythrocyte ghosts

Summary A model has been developed for 5-nitroxide stearate, I(12,3), distribution in human erythrocyte ghosts which accurately predicts ESR spectral alterations observed with increased probe/total lipid (P/L) at 37°C. This spin probe occupies a class of high-affinity, noninteracting sites at low loading. Saturation occurs with increasing probe concentration, and, at higher loading, the probe inserts itself at initially dilute sites to form membranebound clusters of variable size. No low probe remains at high P/L where all I(12,3) clusters in a concentrated phase. This model allows determination of the dilute/clustered probe ratio, and shows that I(12,3) segregates in erythrocytes at what might otherwise be considered low P/L (e.g., 1/359). These findings validate the earlier use of empirical parameters to estimate probe sequestration in biological membranes.     

An Analytical Model of Gene Evolution with 9 Mutation Parameters: An Application to the Amino Acids Coded by the Common Circular Code

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64× 64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4× 4 and the trinucleotide mutation matrix 64× 64 with three and six parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. An application of this model allows an evolutionary study of the common circular code of eukaryotes and prokaryotes and its 12 coded amino acids. The main property of this code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. However, since its identification in 1996, amino acid information coded by has never been studied. Very unexpectedly, this evolutionary model demonstrates that random substitutions in this code and with particular values for the nine substitutions parameters retrieve after a certain time of evolution a frequency distribution of these 12 amino acids very close to the one coded by the actual genes.     

Studies on the sites expressing evolutionary changes in the structure of eukaryotic 5S ribosomal RNA

Summary We have determined the complete sequences of 5S rRNAs from a lamprey (Lampetra reissneri), a lancelet (Branchiostoma belcheri), silkworms (Philosamia cynthia ricini, Bombyx mori, Antheraea pernyi), and a silkworm hybrid (artificially fertilized hybrid species ofPhilosamia cynthia ricini x Bombyx mori ), as well as those of cotton seeds (Gossypium hirsutum L.). Having compared more than 170 eukaryotic 5S rRNAs of which seven sequences have been determined by our group as mentioned above, we have found that the evolutionary sites that exist at special locations in these structures are closely related to the evolution of eukaryotes. The changes proceed step by step in an orderly way, i.e., the change in nucleotide residues of the evolutionary sites depends on the order of the evolution of the species and shows group-specific patterns.     

Preparative centrifugation — a new method for preparing pollen concentrates suitable for radiocarbon dating by AMS

Methods of preparative centrifugation eliminate many of the difficulties involved in preparing pollen concentrates from deposits rich in resistant organic material. Density centrifugation for the separation of pollen from a gyttja sample rich in resistant organic matter was tested. Combining centrifugations in two CsCl solutions, one of higher density and one of lower density than pollen, a pure pollen fraction was successfully prepared. Data on the isodensity and sedimentation rate of fossilized recent pollen from twelve tree taxa are also presented, and the potential for separating a single taxon from pollen assemblages is demonstrated.