Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

Evidence for an episodic model of protein sequence evolution.

The evolution of protein function appears to involve alternating periods of conservative evolution and of relatively rapid change. Evidence for such episodic evolution, consistent with some theoretical expectations, comes from the application of increasingly sophisticated models of evolution to large sequence datasets. We present here some of the recent methods to detect functional shifts, using amino acid or codon models. Both provide evidence for punctual shifts in patterns of amino acid conservation, including the fixation of key changes by positive selection. Although a link to gene duplication, a presumed source of functional changes, has been difficult to establish, this episodic model appears to apply to a wide variety of proteins and organisms.

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

Competing hypotheses seek to explain the evolution of oxygenic and anoxygenic processes of photosynthesis. Since chlorophyll is less reduced and precedes bacteriochlorophyll on the modern biosynthetic pathway, it has been proposed that chlorophyll preceded bacteriochlorophyll in its evolution. However, recent analyses of nucleotide sequences that encode chlorophyll and bacteriochlorophyll biosynthetic enzymes appear to provide support for an alternative hypothesis. This is that the evolution of bacteriochlorophyll occurred earlier than the evolution of chlorophyll. Here we demonstrate that the presence of invariant sites in sequence datasets leads to inconsistency in tree building (including maximum-likelihood methods). Homologous sequences with different biological functions often share invariant sites at the same nucleotide positions. However, different constraints can also result in additional invariant sites unique to the genes, which have specific and different biological functions. Consequently, the distribution of these sites can be uneven between the different types of homologous genes. The presence of invariant sites, shared by related biosynthetic genes as well as those unique to only some of these genes, has misled the recent evolutionary analysis of oxygenic and anoxygenic photosynthetic pigments. We evaluate an alternative scheme for the evolution of chlorophyll and bacteriochlorophyll.

Comparative mitochondrial genomics toward understanding genetics and evolution of arbuscular mycorrhizal fungi

Les champignons mycorhiziens arbusculaires (CMA) sont très répandus dans le sol où ils forment des associations symbiotiques avec la majorité des plantes appelées mycorhizes arbusculaires. Le développement des CMA dépend fortement de la plante hôte, de telle sorte qu'ils ne peuvent vivre à l'état saprotrophique, par conséquent ils sont considérés comme des biotrophes obligatoires. Les CMA forment une lignée évolutive basale des champignons et ils appartiennent au phylum Glomeromycota. Leurs mycélia sont formés d’un réseau d’hyphes cénocytiques dans lesquelles les noyaux et les organites cellulaires peuvent se déplacer librement d’un compartiment à l’autre. Les CMA permettent à la plante hôte de bénéficier d'une meilleure nutrition minérale, grâce au réseau d'hyphes extraradiculaires, qui s'étend au-delà de la zone du sol explorée par les racines. Ces hyphes possèdent une grande capacité d'absorption d’éléments nutritifs qui vont être transportés par ceux-ci jusqu’aux racines. De ce fait, les CMA améliorent la croissance des plantes tout en les protégeant des stresses biotiques et abiotiques. Malgré l’importance des CMA, leurs génétique et évolution demeurent peu connues. Leurs études sont ardues à cause de leur mode de vie qui empêche leur culture en absence des plantes hôtes. En plus leur diversité génétique intra-isolat des génomes nucléaires, complique d’avantage ces études, en particulier le développement des marqueurs moléculaires pour des études biologiques, écologiques ainsi que les fonctions des CMA. C’est pour ces raisons que les génomes mitochondriaux offrent des opportunités et alternatives intéressantes pour étudier les CMA. En effet, les génomes mitochondriaux (mt) publiés à date, ne montrent pas de polymorphismes génétique intra-isolats. Cependant, des exceptions peuvent exister. Pour aller de l’avant avec la génomique mitochondriale, nous avons besoin de générer beaucoup de données de séquençages de l’ADN mitochondrial (ADNmt) afin d’étudier les méchanismes évolutifs, la génétique des population, l’écologie des communautés et la fonction des CMA. Dans ce contexte, l’objectif de mon projet de doctorat consiste à: 1) étudier l’évolution des génomes mt en utilisant l’approche de la génomique comparative au niveau des espèces proches, des isolats ainsi que des espèces phylogénétiquement éloignées chez les CMA; 2) étudier l’hérédité génétique des génomes mt au sein des isolats de l’espèce modèle Rhizophagus irregularis par le biais des anastomoses ; 3) étudier l’organisation des ADNmt et les gènes mt pour le développement des marqueurs moléculaires pour des études phylogénétiques. Nous avons utilisé l’approche dite ‘whole genome shotgun’ en pyroséquençage 454 et Illumina HiSeq pour séquencer plusieurs taxons de CMA sélectionnés selon leur importance et leur disponibilité. Les assemblages de novo, le séquençage conventionnel Sanger, l’annotation et la génomique comparative ont été réalisés pour caractériser des ADNmt complets. Nous avons découvert plusieurs mécanismes évolutifs intéressant chez l’espèce Gigaspora rosea dans laquelle le génome mt est complètement remanié en comparaison avec Rhizophagus irregularis isolat DAOM 197198. En plus nous avons mis en évidence que deux gènes cox1 et rns sont fragmentés en deux morceaux. Nous avons démontré que les ARN transcrits les deux fragments de cox1 se relient entre eux par épissage en trans ‘Trans-splicing’ à l’aide de l’ARN du gene nad5 I3 qui met ensemble les deux ARN cox1.1 et cox1.2 en formant un ARN complet et fonctionnel. Nous avons aussi trouvé une organisation de l’ADNmt très particulière chez l’espèce Rhizophagus sp. Isolat DAOM 213198 dont le génome mt est constitué par deux chromosomes circulaires. En plus nous avons trouvé une quantité considérable des séquences apparentées aux plasmides ‘plasmid-related sequences’ chez les Glomeraceae par rapport aux Gigasporaceae, contribuant ainsi à une évolution rapide des ADNmt chez les Glomeromycota. Nous avons aussi séquencé plusieurs isolats de l’espèces R. irregularis et Rhizophagus sp. pour décortiquer leur position phylogénéque et inférer des relations évolutives entre celles-ci. La comparaison génomique mt nous montré l’existence de plusieurs éléments mobiles comme : des cadres de lecture ‘open reading frames (mORFs)’, des séquences courtes inversées ‘short inverted repeats (SIRs)’, et des séquences apparentées aux plasimdes ‘plasmid-related sequences (dpo)’ qui impactent l’ordre des gènes mt et permettent le remaniement chromosomiques des ADNmt. Tous ces divers mécanismes évolutifs observés au niveau des isolats, nous permettent de développer des marqueurs moléculaires spécifiques à chaque isolat ou espèce de CMA. Les données générées dans mon projet de doctorat ont permis d’avancer les connaissances fondamentales des génomes mitochondriaux non seulement chez les Glomeromycètes, mais aussi de chez le règne des Fungi et les eucaryotes en général. Les trousses moléculaires développées dans ce projet peuvent servir à des études de la génétique des populations, des échanges génétiques et l’écologie des CMA ce qui va contribuer à la compréhension du rôle primorial des CMA en agriculture et environnement.

Phylogenomische Untersuchungen zur Aufklärung des Metazoa-Stammbaums

Zentrales Thema der Arbeit war die Aufklärung von Verwandtschaftsverhältnissen im „Tree of Life“ der vielzelligen Tiere (Metazoa) unter Einsatz großer DNA-Sequenzdatensätze und phylogenomischer Methoden. Zur Untersuchung der internen Phylogenie der Syndermata (= meist freilebende Rädertiere („Rotifera“) + endoparasitische Kratzwürmer (Acanthocephala)) sowie ihrer Position im Metazoen-Stammbaum wurden insgesamt sieben neue mitochondriale (mt) Genome sowie neue Transkriptom-Sequenzdaten von sieben verschiedenen Syndermata-Spezies generiert und/oder analysiert. Die Stammbaumrekonstruktionen auf Grundlage dieser sowie orthologer Sequenzen anderer Spezies in Form von phylogenomischen Datensätzen mit bis zu 82.000 Aminosäurepositionen ergaben folgende Aussagen zur Evolution: (i) Innerhalb der Acanthocephala bilden monophyletische Palaeacanthocephala das Schwestertaxon zu den Eoacanthocephala. Die Archiacanthocephala sind Schwestertaxon zu allen vorgenannten. (ii) Innerhalb der Syndermata bilden die epizoisch lebenden Seisonidea das Schwestertaxon zu den endoparasitischen Acanthocephala (= Pararotatoria), die Bdelloidea sind das Schwestertaxon zu den Pararotatoria (= Hemirotifera) und die Monogononta das Schwestertaxon zu den Hemirotifera. Die klassischen Eurotatoria (= Bdelloidea + Monogononta) sind demnach paraphyletisch. (iii) Innerhalb der Metazoa bilden die Syndermata gemeinsam mit den Gnathostomulida die Gnathifera. Diese sind die Schwestergruppe zu allen anderen Spiralia-Taxa, welche sich in Rouphozoa (= Platyhelminthes + Gastrotricha) sowie die Lophotrochozoa aufspalten. Die Platyzoa (= Gnathifera + Platyhelminthes + Gastrotricha) sind demnach paraphyletisch. Diese phylogenetischen Hypothesen wurden im Hinblick auf ihre Implikationen für die Evolution morphologischer und ökologischer Merkmale interpretiert. Demnach sind während der Evolution dieser Tiergruppen mehrfach sekundäre Verlustereignisse von komplexen morphologischen Merkmalen aufgetreten (laterale sensorische Organe innerhalb der Acanthocephala und das Räderorgan (Corona) innerhalb der Syndermata), was die Verwendung dieser Merkmale im Sinne einer klassisch-morphologischen Phylogenetik kritisch erscheinen lässt. Der Endoparasitismus der Acanthocephala hat sich wahrscheinlich über ein epizoisches Zwischenstadium, wie man es heute noch bei den Seisonidea findet, entwickelt. Der letzte gemeinsame Vorfahre der Spiralia war vermutlich klein und unsegmentiert und besaß keine echte Leibeshöhle (Coelom). Demnach hätten sich Segmentierung und Coelome innerhalb der Metazoa mehrfach unabhängig voneinander (konvergent) entwickelt. Die Arbeit beinhaltete folgende weitere, zum Teil methodische Aspekte: (i) die Analyse der Architektur der mt Genome der Monogononta bestätigte die aberrante Organisation in zwei Subgenomen für die Brachionidae. (ii) Eine Prüfung der Tauglichkeit ribosomaler Proteine für molekular-phylogenetische Arbeiten ergab das Vorhandensein widersprüchlicher phylogenetischer Signale in diesen speziellen Proteinsequenzen. (iii) Es konnte nachgewiesen werden, dass systematische Fehler wie „long-branch attraction“ bei der Positionierung der Syndermata im Stammbaum der Metazoa eine große Rolle spielen und adressiert werden müssen.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Background: High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results: This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion: These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at http://gdm.fmrp.usp.br/s3t/.S3T source code and datasets can also be downloaded from the aforementioned website.

Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae

Background and aims Recent studies have adopted a broad definition of Sapindaceae that includes taxa traditionally placed in Aceraceae and Hippocastanaceae, achieving monophyly but yielding a family difficult to characterize and for which no obvious morphological synapomorphy exists. This expanded circumscription was necessitated by the finding that the monotypic, temperate Asian genus Xanthoceras, historically placed in Sapindaceae tribe Harpullieae, is basal within the group. Here we seek to clarify the relationships of Xanthoceras based on phylogenetic analyses using a dataset encompassing nearly 3/4 of sapindaceous genera, comparing the results with information from morphology and biogeography, in particular with respect to the other taxa placed in Harpullieae. We then re-examine the appropriateness of maintaining the current broad, morphologically heterogeneous definition of Sapindaceae and explore the advantages of an alternative family circumscription. Methods Using 243 samples representing 104 of the 142 currently recognized genera of Sapindaceae s. lat. (including all in Harpullieae), sequence data were analyzed for nuclear (ITS) and plastid (matK, rpoB, trnD-trnT, trnK-matK, trnL-trnF and trnS-trnG) markers, adopting the methodology of a recent family-wide study, performing single-gene and total evidence analyses based on maximum likelihood (ML) and maximum parsimony (MP) criteria, and applying heuristic searches developed for large datasets, viz, a new strategy implemented in RAxML (for ML) and the parsimony ratchet (for MP). Bootstrap analyses were performed for each method to test for congruence between markers. Key results Our findings support earlier suggestions that Harpullieae are polyphyletic: Xanthoceras is confirmed as sister to all other sampled taxa of Sapindaceae s. lat.; the remaining members belong to three other clades within Sapindaceae s. lat., two of which correspond respectively to the groups traditionally treated as Aceraceae and Hippocastanaceae, together forming a clade sister to the largely tropical Sapindaceae s. str., which is monophyletic and morphologically coherent provided Xanthoceras is excluded. Conclusion To overcome the difficulties of a broadly circumscribed Sapindaceae, we resurrect the historically recognized temperate families Aceraceae and Hippocastanaceae, and describe a new family, Xanthoceraceae, thus adopting a monophyletic and easily characterized circumscription of Sapindaceae nearly identical to that used for over a century.

Advances in Sequence Analysis: Theory, Methods, Applications

This book gives a general view of sequence analysis, the statistical study of successions of states or events. It includes innovative contributions on life course studies, transitions into and out of employment, contemporaneous and historical careers, and political trajectories. The approach presented in this book is now central to the life-course perspective and the study of social processes more generally. This volume promotes the dialogue between approaches to sequence analysis that developed separately, within traditions contrasted in space and disciplines. It includes the latest developments in sequential concepts, coding, atypical datasets and time patterns, optimal matching and alternative algorithms, survey optimization, and visualization. Field studies include original sequential material related to parenting in 19th-century Belgium, higher education and work in Finland and Italy, family formation before and after German reunification, French Jews persecuted in occupied France, long-term trends in electoral participation, and regime democratization. Overall the book reassesses the classical uses of sequences and it promotes new ways of collecting, formatting, representing and processing them. The introduction provides basic sequential concepts and tools, as well as a history of the method. Chapters are presented in a way that is both accessible to the beginner and informative to the expert.

Mining for Class-Specific Motifs in Protein Sequence Classification

Background: In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We hypothesize that sequences in lower denominations (n-grams) can be used to explore the sequence landscape and to identify class-specific motifs that discriminate between classes during classification. Discriminative n-grams are short peptide sequences that are highly frequent in one class but are either minimally present or absent in other classes. In this study, we present a new substitution-based scoring function for identifying discriminative n-grams that are highly specific to a class. Results: We present a scoring function based on discriminative n-grams that can effectively discriminate between classes. The scoring function, initially, harvests the entire set of 4- to 8-grams from the protein sequences of different classes in the dataset. Similar n-grams of the same size are combined to form new n-grams, where the similarity is defined by positive amino acid substitution scores in the BLOSUM62 matrix. Substitution has resulted in a large increase in the number of discriminatory n-grams harvested. Due to the unbalanced nature of the dataset, the frequencies of the n-grams are normalized using a dampening factor, which gives more weightage to the n-grams that appear in fewer classes and vice-versa. After the n-grams are normalized, the scoring function identifies discriminative 4- to 8-grams for each class that are frequent enough to be above a selection threshold. By mapping these discriminative n-grams back to the protein sequences, we obtained contiguous n-grams that represent short class-specific motifs in protein sequences. Our method fared well compared to an existing motif finding method known as Wordspy. We have validated our enriched set of class-specific motifs against the functionally important motifs obtained from the NLSdb, Prosite and ELM databases. We demonstrate that this method is very generic; thus can be widely applied to detect class-specific motifs in many protein sequence classification tasks. Conclusion: The proposed scoring function and methodology is able to identify class-specific motifs using discriminative n-grams derived from the protein sequences. The implementation of amino acid substitution scores for similarity detection, and the dampening factor to normalize the unbalanced datasets have significant effect on the performance of the scoring function. Our multipronged validation tests demonstrate that this method can detect class-specific motifs from a wide variety of protein sequence classes with a potential application to detecting proteome-specific motifs of different organisms.

Prediction of whole-genome DNA-DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA-DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA-DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA-DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA-DNA hybridization.

Patentability and Scope of Protection for DNA Sequence

Since the mapping of the human genome and the technical innovations in the field of biotechnology, patent law has gone through great controversies. Protection is required for an investor to make an investment but how broad should the given protection be? Whether the invention is a mi- cro-organism capable of dissolving crude oil, or the gene of a soya plant, the genetic engineering required for their production entails vast amounts of capi- tal. The policy in that respect is tailored by legislative acts and judicial decisions, ensuring a fair balance be- tween the interests of patent right holders and third parties. However, the policy differs from jurisdiction to jurisdiction, thus creating inconsistencies with re- gards to the given protection to the same invention, and as a result this could deter innovation and pro- mote stagnation. The most active actors shaping the patent policy on an international level are the patent offices of the United States of America, Japan and the European Patent Organization. These three patent offices have set up a cooperation programme in order to promote and improve efficiency with regards to their patent policies on a global scale. However, recent judicial de- velopments have shown that the policy in respect to the field of biotechnology differs between the patent regimes of the United States of America and the two- layer system of the European Patent Organisation/ the European Union.

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

Integrating sequence information in microarray data analysis by free energy modeling

Microarray technology is a high-throughput method for genotyping and gene expression profiling. Limited sensitivity and specificity are one of the essential problems for this technology. Most of existing methods of microarray data analysis have an apparent limitation for they merely deal with the numerical part of microarray data and have made little use of gene sequence information. Because it's the gene sequences that precisely define the physical objects being measured by a microarray, it is natural to make the gene sequences an essential part of the data analysis. This dissertation focused on the development of free energy models to integrate sequence information in microarray data analysis. The models were used to characterize the mechanism of hybridization on microarrays and enhance sensitivity and specificity of microarray measurements. ^ Cross-hybridization is a major obstacle factor for the sensitivity and specificity of microarray measurements. In this dissertation, we evaluated the scope of cross-hybridization problem on short-oligo microarrays. The results showed that cross hybridization on arrays is mostly caused by oligo fragments with a run of 10 to 16 nucleotides complementary to the probes. Furthermore, a free-energy based model was proposed to quantify the amount of cross-hybridization signal on each probe. This model treats cross-hybridization as an integral effect of the interactions between a probe and various off-target oligo fragments. Using public spike-in datasets, the model showed high accuracy in predicting the cross-hybridization signals on those probes whose intended targets are absent in the sample. ^ Several prospective models were proposed to improve Positional Dependent Nearest-Neighbor (PDNN) model for better quantification of gene expression and cross-hybridization. ^ The problem addressed in this dissertation is fundamental to the microarray technology. We expect that this study will help us to understand the detailed mechanism that determines sensitivity and specificity on the microarrays. Consequently, this research will have a wide impact on how microarrays are designed and how the data are interpreted. ^

Analyses of a Holocene soil/loess sequence in Southern Siberia

We conducted a high-resolution study of a unique Holocene sequence of wind-blown sediments and buried soils in Southern Siberia, far from marine environment influences. This was accomplished in order to assess the difference between North Atlantic marine and in-land climate variations. Relative wind strength was determined by grain size analyses of different stratigraphic units. Petromagnetic measurements were performed to provide a proxy for the relative extent of pedogenesis. An age model for the sections was built using the radiocarbon dating method. The windy periods are associated with the absence of soil formation and relatively low values of frequency dependence of magnetic susceptibility (FD), which appeared to be a valuable quantitative marker of pedogenic activity. These events correspond to colder intervals which registered reduced solar modulation and sun spot number. Events, where wind strength was lower, are characterized by soil formation with high FD values. Spectral analysis of our results demonstrates periodic changes of 1500, 1000 and 500 years of relatively warm and cold intervals during the Holocene of Siberia. We presume that the 1000 and 500 year climatic cycles are driven by increased solar insolation reaching the Earth surface and amplified by other still controversial mechanisms. The 1500 year cycle associated with the North Atlantic circulation appears only in the Late Holocene. Three time periods - 8400-9300 years BP, 3600-5100 years BP, and the last ~250 years BP - correspond to both the highest sun spot number and the most developed soil horizons in the studied sections

Depths and ages of seismic sequence boundaries in ODP Leg 166 holes

High-resolution, multichannel seismic data collected across the Great Bahama Bank margin and the adjacent Straits of Florida indicate that the deposition of Neogene-Quaternary strata in this transect are controlled by two sedimentation mechanisms: (1) west-dipping layers of the platform margin, which are a product of sea-level-controlled, platform-derived downslope sedimentation; and (2) east- or north-dipping drift deposits in the basinal areas, which are deposited by ocean currents. These two sediment systems are active simultaneously and interfinger at the toe-of-slope. The prograding system consists of sigmoidal clinoforms that advanced the margin some 25 km into the Straits of Florida. The foresets of the clinoforms are approximately 600 m high with variable slope angles that steepen significantly in the Pleistocene section. The seismic facies of the prograding clinoforms on the slope is characterized by dominant, partly chaotic, cut-and-fill geometries caused by submarine canyons that are oriented downslope. In the basin axis, seismic geometries and facies document deposition from and by currents. Most impressive is an 800-m-thick drift deposit at the confluence of the Santaren Channel and the Straits of Florida. This "Santaren Drift" is slightly asymmetric, thinning to the north. The drift displays a highly coherent seismic facies characterized by a continuous succession of reflections, indicating very regular sedimentation. Leg 166 of the Ocean Drilling Program (ODP) drilled a transect of five deep holes between 2 and 30 km from the modern platform margin and retrieved the sediments from both the slope and basin systems. The Neogene slope sediments consist of peri-platform oozes intercalated with turbidites, whereas the basinal drift deposits consist of more homogeneous, fine-grained carbonates that were deposited without major hiatuses by the Florida Current starting at approximately 12.4 Ma. Sea-level fluctuations, which controlled the carbonate production on Great Bahama Bank by repeated exposure of the platform top, controlled lithologic alternations and hiatuses in sedimentation across the transect. Both sedimentary systems are contained in 17 seismic sequences that were identified in the Neogene-Quaternary section. Seismic sequence boundaries were identified based on geometric unconformities beneath the Great Bahama Bank. All the sequence boundaries could be traced across the entire transect into the Straits of Florida. Biostratigraphic age determinations of seismic reflections indicate that the seismic reflections of sequence boundaries have chronostratigraphic significance across both depositional environments.