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)

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the “Plastisphere”. Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vib...

/pdf/life-in-the-plastisphere-microbial-communities-on-plastic-32nw4vsuum.pdf

Life in the “Plastisphere”: Microbial Communities on Plastic Marine Debris

What determines the number and size of the seeds produced by a plant? How often should it reproduce them? How often should a plant produce them? Why and how are seeds dispersed, and what are the implications for the diversity and composition of vegetation? These are just some of the questions tackled in this wide-ranging review of the role of seeds in the ecology of plants. The authors bring together information on the ecological aspects of seed biology, starting with a consideration of reproductive strategies in seed plants and progressing through the life cycle, covering seed maturation, dispersal, storage in the soil, dormancy, germination, seedling establishment, and regeneration in the field. The text encompasses a wide range of concepts of general relevance to plant ecology, reflecting the central role that the study of seed ecology has played in elucidating many fundamental aspects of plant community function.

The ecology of seeds

Patterns of partial migration of the Dead Sea Sparrow (Passer moabiticus) along the Great Rift Valley in Israel

When a pest-control species becomes a pest: A shift in the foraging habitat of cattle egret (Bubulcus ibis) and the threat to grazed natural ecosystems

Long‐term griffon vulture population dynamics at Gamla Nature Reserve

Direct and indirect valuation of air-quality regulation service as reflected in the preferences towards distinct types of landscape in a biosphere reserve

SUMMARY (1) Fruits of the five common fleshy-fruit plant species in an Israeli Mediterranean scrub were removed by twelve bird species of which seven were transients. (2) Fruits of shrubs Rhamnus palaestinus and Pistacia lentiscus were removed mainly by all-year residents, while fruits of a semi-parasitic dwarf shrub Osyris alba, a vine Rubia tenuifolia and a tree P. palaestina were removed mainly by transients. (3) Rhamnus was visited by most bird species more often than expected from its relative abundance, and the highest density of bird-deposited seeds was found under Rhamnus. Scrub clearings were largely avoided by birds. (4) Fruits of the two shrub species were deposited under conspecific adults more often, but reached a greater diversity of habitat types, than the semi-parasitic shrub and the vine, which depended closely on other plants. (5) Fruits of the semi-parasite and the vine may reach few but high-quality deposition sites, whereas those of bushes and trees reach a wider variety of habitat types. (6) No relation was found between body size, taxonomic affinity or status (resident or transient) of a bird species, and its dispersing efficiency. (7) It is concluded that, as no plant species is more successfully dispersed than another, but a trade-off may exist in dispersal attributes, there is also no 'ideal' disperser bird species.

Ido Izhaki

Papers

Patterns of partial migration of the Dead Sea Sparrow (Passer moabiticus) along the Great Rift Valley in Israel

When a pest-control species becomes a pest: A shift in the foraging habitat of cattle egret (Bubulcus ibis) and the threat to grazed natural ecosystems

Long‐term griffon vulture population dynamics at Gamla Nature Reserve

Direct and indirect valuation of air-quality regulation service as reflected in the preferences towards distinct types of landscape in a biosphere reserve

Seed shadows generated by