Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

We redescribe the only previously known species of Myrsidea from bulbuls, M. pycnonoti Eichler. Sixteen new species are described; they and their type hosts are: M. phillipsi ex Pycnonotus goiavier goiavier (Scopoli), M. gieferi ex P. goiavier suluensis Mearns, M. kulpai ex P. flavescens Blyth, M. finlaysoni ex P. finlaysoni Strickland, M. kathleenae ex P. cafer (L.), M. warwicki ex Ixos philippinus (J. R. Forster), M. mcclurei ex Microscelis amaurotis (Temminck), M. zeylanici ex P. zeylanicus (Gmelin), M. plumosi ex P. plumosus Blyth, M. eutiloti ex P. eutilotus (Jardine and Selby), M. adamsae ex P. urostictus (Salvadori), M. ochracei ex Criniger ochraceus F. Moore, M. borbonici ex Hypsipetes borbonicus (J. R. Forster), M. johnsoni ex P. atriceps (Temminck), M. palmai ex C. ochraceus, and M. claytoni ex P. eutilotus. A key is provided for the identification of these 17 species.

A new species

Trabajo presentado en el 39th CIESM Congress, celebrado en Venecia, Italia, del 10 al 14 de mayo de 2010

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Biodiversity of the Mediterranean Sea: estimates, patterns and threats

The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well.

This abstract has been translated to other languages (File S1).

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The Biodiversity of the Mediterranean Sea: Estimates, Patterns, and Threats

http://www.vliz.be/imisdocs/publications/119670.pdf

Reproductive isolation among sympatric cryptic species in marine diatoms.

Diatoms, a major group of photosynthetic microalgae, have a high biotechnological potential that has not been fully exploited because of the paucity of available genetic tools. Here we demonstrate targeted and stable modifications of the genome of the marine diatom Phaeodactylum tricornutum, using both meganucleases and TALE nucleases. When nuclease-encoding constructs are co-transformed with a selectable marker, high frequencies of genome modifications are readily attained with 56 and 27% of the colonies exhibiting targeted mutagenesis or targeted gene insertion, respectively. The generation of an enhanced lipid-producing strain (45-fold increase in triacylglycerol accumulation) through the disruption of the UDP-glucose pyrophosphorylase gene exemplifies the power of genome engineering to harness diatoms for biofuel production. Diatoms are photosynthetic microalgae with underutilized biotechnological potential. Here, the authors carry out targeted gene modifications of lipid metabolism genes in the diatom, Phaeodactylum tricornutum, resulting in a strain that exhibits a 45-fold increase in triacylglycerol accumulation.

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Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology

Pseudo-nitzschia delicatissima (Cleve) Heiden is a very common pennate planktonic diatom found in temperate marine waters, where it is often responsible for blooms. Recently, three distinct internal transcribed spacer types have been recorded during a P. delicatissima bloom in the Gulf of Naples (Mediterranean Sea, Italy), which suggests the existence of cryptic diversity. We carried out mating experiments with clonal strains belonging to the most abundant internal transcribed spacer type. Pseudo-nitzschia delicatissima is heterothallic and produces two functional anisogametes per gametangium. The elongated auxospore possesses a transverse and a longitudinal perizonium. The sexual phase was observed to occur over aw ide size spectrum, spanning 19–80l ma nd corresponding to almost the whole range of cell length observed for P. delicatissima .W e also investigated cell morphology, valve ultrastructure and morphometry of parental, F1-generation strains, and the progeny of crosses between parental and F1 strains. Although ultrastructural features match those described for P. delicatissima, variability in cell shape was recorded in the largest cells of the F1 generation as well as in valves with an abnormal arrangement of poroids. As many other diatoms, P. delicatissima undergoes size reduction over its life cycle, and cells of different size showed differences in growth rates and the amount of size reduction per cell cycle. Cells between 60 and 30l mi n length showed the fastest growth and the slowest rates of size reduction per generation. In culture, P. delicatissima cells can decrease to 8lm in length; however, such small cells ( � 30lm) are not recorded in the sea, and this raises interesting questions about the factors that control their survival in the natural environment.

Life cycle, size reduction patterns, and ultrastructure of the pennate planktonic diatom Pseudo-nitzschia delicatissima (Bacillariophyceae)

There is increasing evidence that cryptic and pseudo-cryptic species are widespread in several diatom taxa. This is the case with the genus Pseudo-nitzschia, which includes chain-forming pennate diatoms that bloom both in coastal and open ocean waters. In the last years, up to 10 new species have been described on the basis of morphological and molecular investigations, and some of them are only distinguishable on the basis of minute ultrastructural features of their siliceous frustule. We here describe the morphology of the vegetative cell and sexual stages of Pseudo-nitzschia mannii sp. nov., and present an ITS2-based phylogeny to illustrate genetic relationships between P. mannii sp. nov. and the closest congeneric species. On the basis of ribosomal and chloroplastidial gene phylogenies, P. mannii is closely related to P. calliantha, from which it can be differentiated by its slightly wider cells and a different arrangement of the poroid sectors. The analysed strains did not produce the ASP-toxin domoic acid.

Morphology, phylogeny, and sexual cycle of Pseudo-nitzschia mannii sp. nov. (Bacillariophyceae): a pseudo-cryptic species within the P. pseudodelicatissima complex

https://hal.archives-ouvertes.fr/hal-02317924/document

Alberto Amato

Papers

Reproductive isolation among sympatric cryptic species in marine diatoms.

Genome engineering empowers the diatom Phaeodactylum tricornutum for biotechnology

Life cycle, size reduction patterns, and ultrastructure of the pennate planktonic diatom Pseudo-nitzschia delicatissima (Bacillariophyceae)

Morphology, phylogeny, and sexual cycle of Pseudo-nitzschia mannii sp. nov. (Bacillariophyceae): a pseudo-cryptic species within the P. pseudodelicatissima complex

The lipid metabolism in thraustochytrids.