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

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

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)

Cooperation is needed for evolution to construct new levels of organization. Genomes, cells, multicellular organisms, social insects, and human society are all based on cooperation. Cooperation means that selfish replicators forgo some of their reproductive potential to help one another. But natural selection implies competition and therefore opposes cooperation unless a specific mechanism is at work. Here I discuss five mechanisms for the evolution of cooperation: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. For each mechanism, a simple rule is derived that specifies whether natural selection can lead to cooperation.

/pdf/five-rules-for-the-evolution-of-cooperation-2bpocasc6i.pdf

Five Rules for the Evolution of Cooperation

The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.

https://science.sciencemag.org/content/sci/307/5717/1915.full.pdf

Host-Bacterial Mutualism in the Human Intestine

Under starvation conditions, the soil bacterium Sinorhizobium meliloti divides into two types of daughter cell: one suited to short-term and the other to long-term starvation.

/pdf/bet-hedging-in-the-underworld-2nfpc01j9s.pdf

Bet hedging in the underworld.

DING proteins constitute a conserved and broadly distributed set of proteins found in bacteria, fungi, plants and animals (including humans) Characterization of DING proteins from animal and plant tissues indicated ligand-binding ability suggesting a role for DING proteins in cell signaling and biomineralization Surprisingly, the genes encoding DING proteins in eukaryotes have not been identified in the eukaryotic genome or EST databases Recent discovery of a DING homologue (named Psp here) in the genome of Pseudomonas fluorescens SBW25 provided a unique opportunity to investigate the physiological roles of DING proteins P fluorescens SBW25 is a model bacterium that can efficiently colonize plant surfaces and enhance plant health In this report we genetically characterize Psp with a focus on conditions under which psp is expressed and the protein exported Psp is closely related to the periplasmic Pi binding component of the ABC-type phosphate transporter system (Pst) psp is flanked by a gene cluster predicted to function as a type II protein secretion system (Hxc) Deletion analysis combined with chromosomally integrated 'lacZ fusions showed that both psp and pstC are induced by Pi limitation and that pstC is required for competitive growth of the bacterium in Pi limited medium hxcR is not regulated by Pi limitation Psp was detected (using anti-DING serum) in the supernatant of wild-type culture but was greatly reduced in the supernatant of an isogenic strain carrying an hxcR mutation (ΔhxcR) A promoter fusion between hxcR and a promoterless copy of a gene ('dapB) essential for growth in the plant environment showed that expression of hxcR is elevated during colonization of sugar beet seedlings A similar analysis of psp showed that it is not induced in the plant environment Psp gene is expressed under conditions of Pi limitation It is an exoprotein secreted mainly via the Hxc type II secretion system, whose expression is elevated on plant surfaces We propose that Psp is involved in extracellular scavenging of phosphates, which are subsequently taken up by the cell-bound Pst transport system

https://link.springer.com/content/pdf/10.1186%2F1471-2180-7-114.pdf

Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25.

BACKGROUND: Studies have reported higher rates of diseases caused by Staphylococcus aureus (S. aureus) amongst Maori and Pacific people, compared with people of other ethnicities. AIM: We aimed to estimate the prevalence of nasal carriage and to explore demographic differences between S. aureus carriers and non-carriers in Auckland, New Zealand. MATERIALS AND METHODS: Nasal swab specimens were obtained from healthy population volunteers, who did not have recent healthcare contact. Each participant completed a short questionnaire. RESULTS: 78/424 (18%; 95%CI, 15-22) S. aureus carriers were identified. Female participants were less likely to be S. aureus carriers than males; but there were no differences in the ages or ethnic groups between S. aureus carriers and non-carriers. Socioeconomic deprivation, recent non-hospital healthcare contact and past history of S. aureus infection were not associated with S. aureus carriage. CONCLUSION: Ethnic variation in the prevalence of S. aureus nasal carriage does not contribute to an increased risk of disease caused by S. aureus.

Nasal carriage of Staphylococcus aureus in healthy Aucklanders.

What makes bacterial pathogens so invincible? The accepted dogma is that they are able to adapt rapidly to the changing environment of their host. In a Perspective, [Rainey and Moxon][1] discuss new evidence ([ Oliver et al .][2]) showing that the opportunistic bacterial pathogen, Pseudomonas aeruginosa , that colonizes the lungs of cystic fibrosis (CF) patients, evolves a very high mutation rate. These mutators enable the bacterial population to adapt rapidly to the changing environment of the CF lung, despite the host's inflammatory response and treatment of CF patients with potent antibiotics.

 [1]: http://www.sciencemag.org/cgi/content/full/288/5469/1186
 [2]: http://www.sciencemag.org/cgi/content/short/288/5469/1251

When Being Hyper Keeps You Fit

https://pure.mpg.de/pubman/item/item_2250297_3/component/file_2251092/Ritchie_et_al_2016.pdf

The turnover of strains in intermittent and persistent nasal carriers of Staphylococcus aureus.

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