DISCONTINUOUS MITOCHONDRIAL AND CHLOROPLAST LARGE SUBUNIT RIBOSOMAL RNAs AMONG GREEN ALGAE: PHYLOGENETIC IMPLICATIONS1

To provide insights into the occurrence, evolution, and phylogenetic distribution of discontinuous mitochondrial and chloroplast large subunit ribosomal RNAs (LSU rRNAs) among green algae, we surveyed 12 taxa representing three classes of green algae: the Chlorophyceae, Pleurastrophyceae, and Micromonadophyceae (sensu Mattox and Stewart 1984). We present evidence that discontinuous mitochondrial and chloroplast LSU rRNAs are quite widespread among green algae. Mitochondrial LSU rRNAs appear discontinuous in zoosporic chlorophycean lineages displaying a clockwise or directly opposed configuration in their flagellar apparatus, as well as in chlorococcalean autosporic taxa phylogenetically related to them, but are continuous among zoosporic green algal lineages with a counterclockwise flagellar apparatus configuration, as well as among chlorococcalean autosporic taxa phylogenetically related to them. Chloroplast LSU rRNAs appear discontinuous in all of the lineages investigated. Discontinuous mitochondrial LSU rRNA represents a molecular trait that might have originated at or near the base of Chlorophyceae, whereas discontinuous chloroplast LSU rRNA might have developed very early in the evolutionary history of the green algal group itself. We suggest, therefore, that the presence of discontinuous mitochondrial but not chloroplast LSU rRNA can be used as an additional character in assessing phylogenetic affiliations among green algae.     

A synthetic theory of molecular evolution

According to the neo-Darwinian view of evolution evolution rate nu depends solely on the environment variation rate gamma, whereas in the non-Darwinian view evolution rate is determined mainly by the mutation rate mu. We have studied two kinds of population genetics models which exhibit both types of evolution in different parametric regions: one is a dynamical model representing infinite population, and the other is a Markov process model representing a nearly monomorphic finite population. In the infinite population model, after proving general time-derivative and mu-derivative formulas for the population average of quantitative traits, we show that if the mutation rate is adaptively determined, mu must be larger than nu in the stationary state. Loads of evolution are obtained in both regions. A high evolution rate such as nu = 1 per genome per generation is consistent with Haldane's value of tolerable load if and only if the functional constraint is not large and selection is weak, independent of whether the evolution is neo-Darwinian or non-Darwinian. As the selection intensity increases, nu is shown to change discontinuously from nearly mu to gamma at the transition point. In the finite population model, the transition of v is not discontinuous, but is very steep. On the other hand, no steep change of polymorphism takes place at the transition point. The steepness of the transition in our model suggests that real molecular evolution can be divided into either neo-Darwinian or non-Darwinian,and that the intermediate type of evolution is rather rare.     

Models for cultural inheritance. I. Group mean and within group variation

Evolution of a cultural trait has been considered at a theoretical level. Cultural evolution is to be kept distinct from biological evolution, but the discrimination of the two may be difficult in actual cases. In cultural evolution, not only the parents of an individual but also other members of the group, contribute directly to determining the value of a trait in the individual. The cumulative effect of members of the group other than the parents has been called the group effect g. The expected value of the trait of an individual in the next generation has been assumed in the model to be the weighted mean of the individual value (as determined by the trait values in the parent or parents plus a random contribution $\text{E}$ the new variation per generation), and the group mean value, the individual and the group contributions being weighted as (1 ? g) to g. Effects of age and peers and of generations earlier than parental have also been analyzed.It has been demonstrated that, if g is different from zero and positive, however small, in spite of new variation arising at every generation the variation of the trait within the group will stabilize at a finite level. The stable amount of the variation depends on the mode of transmission, which has been considered here to be either uniparental or biparental, on the value of g, on the size of the group if the progeny size is not constant, and on the amount of new variation produced per generation. Independent groups will differentiate one from the other randomly, at a rate which is a function of the mode of transmission (uni or biparental), the g value, and the size of the group. Ways to study discontinuous traits have been given. If discontinuity arises from imposition of a perceptive threshold on the existing variation, and therefore the variate is not truly discontinuous, its behavior is still predictable by the same rules, and a transformation for study of the frequencies of observations above or below threshold has been given, which permits the prediction of the trend of changes with time. A truly discontinuous character will undergo fixation of one or other character state, as for alleles in random genetic drift, but the rate of fixation will be decreased by group action.     

陕南张家沟剖面寒武纪早期微体化石Hexaconularia sichuanensis的新材料*

陕南西乡张家沟剖面的寒武系下部岩层中发现了大量原始锥石类,根据整体形态特征和原始锥石类化石分类方案将其归属到六方锥石属Hexaconularia。前人对于六方锥石分类方案众多,本文对其进行重新厘定。本文报道的六方锥石新材料在中央锥面上具有两条不连续的角沟,这不仅丰富了种内特征,而且为六方锥石的壳体演化趋势提供了依据。前人发现的该类化石与本文描记的化石类型相同,产地不同,因而具有地层对比意义。     

DNA synthesis on discontinuous templates by human DNA polymerases: implications for non-homologous DNA recombination.

DNA polymerases catalyze the synthesis of DNA using a continuous uninterrupted template strand. However, it has been shown that a 3'-->5' exonuclease-deficient form of the Klenow fragment of Escherichia coli DNA polymerase I as well as DNA polymerase of Thermus aquaticus can synthesize DNA across two unlinked DNA templates. In this study, we used an oligonucleotide-based assay to show that discontinuous DNA synthesis was present in HeLa cell extracts. DNA synthesis inhibitor studies as well as fractionation of the extracts revealed that most of the discontinuous DNA synthesis was attributable to DNA polymerase alpha. Additionally, discontinuous DNA synthesis could be eliminated by incubation with an antibody that specifically neutralized DNA polymerase alpha activity. To test the relative efficiency of each nuclear DNA polymerase for discontinuous synthesis, equal amounts (as measured by DNA polymerase activity) of DNA polymerases alpha, beta, delta (+/- PCNA) and straightepsilon (+/- PCNA) were used in the discontinuous DNA synthesis assay. DNA polymerase alpha showed the most discontinuous DNA synthesis activity, although small but detectable levels were seen for DNA polymerases delta (+PCNA) and straightepsilon (- PCNA). Klenow fragment and DNA polymerase beta showed no discontinuous DNA synthesis, although at much higher amounts of each enzyme, discontinuous synthesis was seen for both. Discontinuous DNA synthesis by DNA polymerase alpha was seen with substrates containing 3 and 4 bp single-strand stretches of complementarity; however, little synthesis was seen with blunt substrates or with 1 bp stretches. The products formed from these experiments are structurally similar to that seen in vivo for non-homologous end joining in eukaryotic cells. These data suggest that DNA polymerase alpha may be able to rejoin double-strand breaks in vivo during replication.     

Rejoining kinetics of DNA single- and double-strand breaks in normal and DNA ligase-deficient cells after exposure to ultraviolet C and gamma radiation: an evaluation of ligating activities involved in different DNA repair processes

The repair kinetics for rejoining of DNA single- and double-strand breaks after exposure to UVC or gamma radiation was measured in cells with deficiencies in DNA ligase activities and in their normal counterparts. Human 46BR cells were deficient in DNA ligase I. Hamster EM9 and EM-C11 cells were deficient in DNA ligase III activity as a consequence of mutations in the XRCC1 gene. Hamster XR-1 cells had mutation in the XRCC4 gene, whose product stimulates DNA ligase IV activity. DNA single- and double-strand breaks were assessed by the comet assay in alkaline conditions and by the technique of graded-field gel electrophoresis in neutral conditions, respectively. 46BR cells, which are known to re-ligate at a reduced rate the DNA single-strand breaks incurred during processing of damage induced by UVC but not gamma radiation, were shown to have a normal repair of radiation-induced DNA double-strand breaks. EM9 cells exhibited a reduced rate of rejoining of DNA single-strand breaks after exposure to ionizing radiation, as reported previously, as well as UVC radiation. EM-C11 cells were deficient in the repair of radiation-induced-DNA single-strand breaks but, in contrast to EM9 cells, demonstrated the same kinetics as the parental cell line in the resealing of DNA breaks resulting from exposure to UVC radiation. Both EM9 and EM-C11 cells displayed a significant defect in rejoining of radiation-induced-DNA double-strand breaks. XR-1 cells were confirmed to be highly deficient in the repair of radiation-induced DNA double-strand breaks but appeared to rejoin DNA single-strand breaks after UVC and gamma irradiation at rates close to normal. Taken together these results indicate that: (1) DNA ligase I is involved only in nucleotide excision repair; (2) DNA ligase IV plays an important role only in repair of DNA double-strand breaks; and (3) DNA ligase III is implicated in base excision repair and in repair of DNA double-strand breaks, but probably not in nucleotide excision repair.     

The mechanism of vertebrate nonhomologous DNA end joining and its role in V(D)J recombination

The vertebrate immune system generates double-strand DNA (dsDNA) breaks to generate the antigen receptor repertoire of lymphocytes. After those double-strand breaks have been created, the DNA joinings required to complete the process are carried out by the nonhomologous DNA end joining pathway, or NHEJ. The NHEJ pathway is present not only in lymphocytes, but in all eukaryotic cells ranging from yeast to humans. The NHEJ pathway is needed to repair these physiologic breaks, as well as challenging pathologic breaks that arise from ionizing radiation and oxidative damage to DNA.     

What are the genomic drivers of the rapid evolution of PRDM9?

Mammalian Prdm9 has been proposed to be a key determinant of the positioning of chromosome double-strand breaks during meiosis, a contributor to speciation processes, and the most rapidly evolving gene in human, and other animal, genomes. Prdm9 genes often exhibit substantial variation in their numbers of encoded zinc fingers (ZFs), not only between closely related species but also among individuals of a species. The near-identity of these ZF sequences appears to render them very unstable in copy number. The rare sequence differences, however, cluster within ZF sites that determine the DNA-binding specificity of PRDM9, and these substitutions are frequently positively selected. Here, possible drivers of the rapid evolution of Prdm9 are discussed, including selection for efficient pairing of homologous chromosomes or for recombination of deleterious linked alleles, and selection against depletion of recombination hotspots or against disease-associated genome rearrangement.     

A superoxide anion induced DNA strand-break metabolic pathway in human leukocytes: effects of vanadate

Superoxide anion (O2-) is an active oxygen species found in virtually all cells grown in the presence of oxygen. In vivo, the highest concentration of this oxygen radical is found after granulocytes have been exposed to particles or the tumor promoter, phorbol myristate acetate. O2- is released from the cell as a "respiratory burst," which is followed shortly by the appearance of strand breaks in the DNA of the producing cell. In the present report, we have continued our investigation into the mechanism by which extracellular O2- causes breakage of intracellular DNA. Although hydrogen peroxide is present and could also cause strand breaks, its effects are eliminated by the addition of catalase. When the amount of O2- is increased threefold by adding glucose to the medium, the number of breaks increases only slightly, suggesting that the number of breaks that could be induced is limited. The strand-break process is abruptly interrupted by the addition of metabolic poisons such as ionophore A23187, fluoride, or 2-deoxyglucose, but ATP does not appear to be involved. The number of O2(-)-induced strand breaks is increased in the presence of sodium orthovanadate and decreased by A23187. Orthovanadate prevents the inhibition caused by A23187. Reaction of O2- with orthovanadate itself appears not to be responsible for the enhancement of breaks by orthovanadate. We propose that orthovanadate exerts its effect by acting as an inhibitor of a phosphoprotein phosphatase and that A23187 acts to deplete intracellular Ca2+. These data support our hypothesis that the O2- radical causes strand breaks not by attacking the DNA but rather by activating a specific metabolic DNA strand-break pathway.     

Complement system of bony and cartilaginous fish

Accumulating evidence indicates that the complement system experienced a discontinuous development at an early stage of vertebrate evolution. Invertebrates such as echinoderms and ascidians, and the most primitive extant vertebrates, the cyclostomes, seem to have a primitive complement system equipped only with the alternative and lectin pathways. In contrast, cartilaginous fish and higher vertebrates seem to have a modern complement system which has two additional pathways, namely the classical and lytic pathways. Recent molecular analyses of the complement system of bony and cartilaginous fish have not only confirmed the above conclusion, but also revealed a unique characteristic of the complement system of fish, where certain key component genes are duplicated. The complement system seems to play a more pivotal role in body defence in fish, whose adaptive immunity is considered to be at a relatively undeveloped state.     

Phylogeographic analyses of the southern leopard frog: the impact of geography and climate on the distribution of genetic lineages vs. subspecies

The southeastern United States is a major phylogeographic break hotspot for amphibians, but the processes underlying this hotspot remain to be explicitly tested. We test the correlation of genetic lineages with subspecies breaks in the southeastern United States and the association of such breaks with climate, using Rana sphenocephala as a case study, and place our results in the broader context of the Alabama‐Appalachian suture zone (AL‐Appalachian SZ). We use genetic and ecological methods to (i) determine whether genetic lineages are coincident with the AL‐Appalachian SZ or the subspecies and (ii) test the correlation of major climatic breaks with genetic structure and morphological variation in R. sphenocephala. Bayesian phylogenetic analyses of the ND1 mtDNA gene and microsatellite cluster analyses revealed two distinct lineages with over 4% sequence divergence. The geographic distributions of the two lineages are concordant with the AL‐Appalachian SZ but do not correspond to the ranges of the subspecies based on morphology. Mantel tests revealed that isolation by distance and historical barriers to gene flow, rather than climate, are the major drivers of genetic divergence at neutral loci. Examination of climate breaks across the Southeast revealed a pattern incongruent with suture zone hotspots, suggesting that phylogenetic structure has been driven primarily by historical factors, such as isolation, the Appalachian Mountains and the Apalachicola/Chattahoochee/Flint River Basin. However, climate breaks are consistent with the geographic distribution of the subspecies of R. sphenocephala, suggesting that environmental pressures may be driving divergence in morphological traits that outpaces molecular evolution.     

Comparative development of aseptate and septate anthers of Annonaceae

We compared anther development in 13 genera and 15 species of Annonaceae to document the nature and development of anther septa. In aseptate anthers, all sporogenous initials proceed to sporogenesis and meiosis. In septate anthers, a small number of sporogenous initials, in a discontinuous distribution pattern, differentiate into sporogenous cells; the remaining initials become sterile and form cellular septa that partition each anther lobe into multiple sporangial chambers. In species where the septum is 1-2 cell layers thick, the entire septum becomes tapetal (T-type septa) and breaks down before anther dehiscence. In species in which the septum is three or more cell layers thick, only the layer in direct contact with the sporogenous cells becomes tapetal, and the remaining cells become parenchymatous (P-type septa). These thicker P-type septa are sometimes visible in dehisced anthers. Both types are homologous in ontogeny and are highly associated with the production of compound pollen. We propose that the evolution of anther septation in Annonaceae was mainly driven by the requirement for highly efficient nutrient and physical support to the development of large, compound pollen units.     

Chromosome aberrations induced by aphidicolin

The expression of aphidicolin (apc)-produced common fragile sites and chromosome aberrations observed 24 h after apc treatment was studied in a normal individual. The chromosome lesions (gaps and breaks) induced by apc are expressed as full chromosomal aberrations in later cell divisions. We compared chromosome rearrangements or anomalies induced by apc (detected in 45.4% of metaphases analyzed) with those present in human neoplasia or involved in primate evolution. We found that 55.7% of deletions observed in our study coincided with deletions implicated in several types of neoplasia. However, none of 49 translocations observed in our study coincided with those described as recurrently associated with human neoplasia, probably due to their unbalanced nature. When chromosome aberrations detected in our study (only deletions and inversions were taken into account) were compared to those involved in primate evolution, we found a low rate of coincidence. The low coincidence between chromosome alterations in neoplasia and evolution and those observed in our study could be explained because we analyzed chromosome alterations that had not been selected, whereas those present in chromosome evolution and in neoplasia had been subjected to a selection process.     

Concordant genetic breaks, identified by combining clustering and tessellation methods, in two co-distributed alpine plant species

Natural genetic breaks may indicate limitations to gene flow or the presence of contact zones of previously isolated populations. Molecular evidence suggests that genetic breaks have aggregated in distinct geographical areas. We propose a new application of well-established statistical methods for analysing multilocus genetic data to identify intraspecific genetic breaks. The methodological approach combines Bayesian clustering with a spatially explicit maximum-difference algorithm to visualize and quantify breaks between clusters. We used amplified fragment length polymorphism data of two co-distributed, silicicolous alpine plant species, Geum montanum and Geum reptans , exhaustively sampled on a consistent, regular grid over their entire range of the European Alps and the Carpathians. We found a distinct and highly similar allocation of genetic breaks in both species. The pattern of breaks did not conform to scenarios of glacial refugial survival, alternatively in peripheral refugia or on nunataks, as expected because of the species' ecologies (late-successional low alpine vs. early-successional high alpine). Our findings rather substantiated the postulate of a general pattern of genetic breaks in alpine plants and corresponded well with biogeographical regions formerly described. Our approach could serve as a tool not only for landscape genetics and comparative phylogeography, but also for floristics or faunistics to compare biogeographic with phylogeographic breaks.     

Genome-wide amplifications caused by chromosomal rearrangements play a major role in the adaptive evolution of natural yeast

The relative importance of gross chromosomal rearrangements to adaptive evolution has not been precisely defined. The Saccharomyces cerevisiae flor yeast strains offer significant advantages for the study of molecular evolution since they have recently evolved to a high degree of specialization in a very restrictive environment. Using DNA microarray technology, we have compared the genomes of two prominent variants of S. cerevisiae flor yeast strains. The strains differ from one another in the DNA copy number of 116 genomic regions that comprise 38% of the genome. In most cases, these regions are amplicons flanked by repeated sequences or other recombination hotspots previously described as regions where double-strand breaks occur. The presence of genes that confer specific characteristics to the flor yeast within the amplicons supports the role of chromosomal rearrangements as a major mechanism of adaptive evolution in S. cerevisiae. We propose that nonallelic interactions are enhanced by ethanol- and acetaldehyde-induced double-strand breaks in the chromosomal DNA, which are repaired by pathways that yield gross chromosomal rearrangements. This mechanism of chromosomal evolution could also account for the sexual isolation shown among the flor yeast.     

XRCC3 controls the fidelity of homologous recombination: roles for XRCC3 in late stages of recombination

XRCC3 is a RAD51 paralog that functions in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). XRCC3 mutation causes severe chromosome instability. We find that XRCC3 mutant cells display radically altered HR product spectra, with increased gene conversion tract lengths, increased frequencies of discontinuous tracts, and frequent local rearrangements associated with HR. These results indicate that XRCC3 function is not limited to HR initiation, but extends to later stages in formation and resolution of HR intermediates, possibly by stabilizing heteroduplex DNA. The results further demonstrate that HR defects can promote genomic instability not only through failure to initiate HR (leading to nonhomologous repair) but also through aberrant processing of HR intermediates. Both mechanisms may contribute to carcinogenesis in HR-deficient cells.     

Synergistic induction of hydroxyl radical-induced DNA single-strand breaks by chromium(VI) compound and cigarette smoke solution

Chromium(VI) compounds and cigarette smoke are known human carcinogens. We found that K2Cr2O7 and cigarette smoke solution synergistically induced DNA single-strand breaks (0.23+/-0.04 breaks per DNA molecule) in pUC118 plasmid DNA. K2Cr2O7 alone or cigarette smoke solution alone induced much less strand breaks (0.03+/-0.01 or 0.07+/-0.02 breaks per DNA molecule, respectively). The synergistic effect was prevented by catalase and by hydroxyl radical scavengers such as deferoxamine, dimethylsulfoxide, d-mannitol, and Tris, but not by superoxide dismutase. Ascorbic acid enhanced the synergism. Glutathione inhibited strand breakage only at high concentrations. Electron spin resonance (ESR) studies using a hydroxyl radical trap demonstrated that hydroxyl radicals were generated when DNA was incubated with K2Cr2O7 and cigarette smoke solution. Hydroxyl radical adduct decreased dose-dependently when strand breakage was prevented by catalase, deferoxamine, dimethylsulfoxide, d-mannitol or Tris, but not significantly by superoxide dismutase. We also used ESR spectroscopy to study the effects of different concentration of ascorbic acid and glutathione. The results showed that hydroxyl radical, which is proposed as a main carcinogenic mechanism for both chromium(VI) compounds and cigarette smoke solution was mainly responsible for the DNA breaks they induced.     

Diskontinuierlich aktive Gene und Evolution Eine Diskussion am Beispiel der Archaeognatha (Insecta)

Discontinuous activity of genes and evolution - a discussion based on examples of the Archaeognatha (Insecta) On the basis of examples, mainly from the group of Archaeognatha (Insecta) it seems probable that, in multicellular organisms, there is not only a discontinuous activity of genes and groups of genes during the individual development, but also during the phylogenesis. The possibility that silent genes can be reactivated is probably an essential reason for the existence of parallelisms and homologous tendencies. Both conceptions have a complementary importance for an establishment of taxa ana the reconstruction of phylogenesis and are defined according to evolutionary genetics. The examples are discussed and the necessity of similar comparative studies in other supraspecific taxa is emphasized.     

Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America

A recent test for the existence of suture zones in North America, based on hybrid zones studied since 1970, found support for only two of the 13 suture zones identified by Remington in 1968 (Swenson and Howard 2004). One limitation of that recent study was the relatively small number of hybrid zones available for mapping. In this study, we search for evidence of clustering of contact zones between closely related taxa using data not only from hybrid zones but from species range maps of trees, birds, and mammals and from the position of phylogeographic breaks within species. Digital geographic range maps and a geographic information system approach allowed for accurate and rapid mapping of distributional data. Areas of contact between closely related species and phylogeographic breaks within species clustered into areas characterized by common physiographic features or predicted by previously hypothesized glacial refugia. The results underscore the general importance of geographic barriers to dispersal (mountain chains) and climate change (periods of cooling alternating with periods of warming, which lead to the contraction and expansion of species ranges) in species evolution.