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

Application of a promoter-trapping strategy to identify plant-inducible genes carried on an indigenous Pseudomonas plasmid, pQBR103, revealed the presence of a putative oligoribonuclease (orn) gene that encodes a highly conserved 3′ to 5′ exoribonuclease specific for small oligoribonucleotides. The deduced amino acid sequence of the plasmid-derived orn (orn
pl) showed three conserved motifs characteristic of Orn from both prokaryotes and eukaryotes. Deletion of orn
pl generated no observable phenotype, but inactivation of the chromosomal copy caused slow growth in Pseudomonas putida KT2440. This defect was fully restored by complementation with orn from Escherichia coli (orn
E.coli). Plasmid-derived orn
pl was capable of partially complementing the P. putida orn mutant, demonstrating functionality of orn
pl. Phylogenetic analysis showed that plasmid-encoded Orn was distinct from Orn encoded by the chromosome of proteobacteria. A survey of orn
pl from related Pseudomonas plasmids showed a sporadic distribution but no sequence diversity. These data suggest that the orn
pl was acquired by pQBR103 in a single gene-transfer event: the donor is unknown, but is unlikely to be a member of the Proteobacteria.

Functional and phylogenetic analysis of a plant-inducible oligoribonuclease (orn) gene from an indigenous Pseudomonas plasmid

The evolutionary transition to multicellularity occurred on numerous occasions, but transitions to complex life forms were rare. Here we present experiments that contrast two ecological frameworks that differ in the way in which nascent multicellular groups, and their constituent cells, compete. Groups of the bacterium Pseudomonas fluorescens were propagated under a regime requiring reproduction via a life cycle with developmental and dispersal phases. By controlling the extent of mixing during the dispersal phase the relative emphasis on the developmental phase versus the dispersal phase was altered. While all groups possessed paradigmatic features of multicellular individuals including bottlenecks and germ lines, the mode of group interaction substantially impacted both the strength and direction of selection operating at group and cell levels. Constraints on meta-population structure may therefore explain the observation that multicellular aggregates rarely complete the transition to individuality.

https://www.biorxiv.org/content/biorxiv/early/2018/09/04/407163.full.pdf

Meta-population structure and the evolutionary transition to multicellularity

Selfish genetic elements, such as insertion sequences and transposons are found in most genomes. Transposons are usually identifiable by their high copy number within genomes. In contrast, REP-associated tyrosine transposases (RAYTs), a recently described class of bacterial transposase, are typically present at just one copy per genome. This suggests that RAYTs no longer copy themselves and thus they no longer function as a typical transposase. Motivated by this possibility we interrogated thousands of fully sequenced bacterial genomes in order to determine patterns of RAYT diversity, their distribution across chromosomes and accessory elements, and rate of duplication. RAYTs encompass exceptional diversity and are divisible into at least five distinct groups. They possess features more similar to housekeeping genes than insertion sequences, are predominantly vertically transmitted and have persisted through evolutionary time to the point where they are now found in 24% of all species for which at least one fully sequenced genome is available. Overall, the genomic distribution of RAYTs suggests that they have been coopted by host genomes to perform a function that benefits the host cell.

/pdf/identification-and-characterization-of-domesticated-4vkwnl1vmq.pdf

Identification and characterization of domesticated bacterial transposases

CbrB is a global sigma(54)-dependent regulator required for nutrient acquisition in Pseudomonas. Located downstream of cbrB on the Pseudomonas fluorescens SBW25 chromosome is pcnB, a putative poly(A) polymerase gene. Presence of a sigma(54) promoter in the intergenic region of cbrB and pcnB led to the hypothesis that CbrB regulates pcnB expression in a sigma(54)-dependent manner. Here we show that transcription of pcnB is CbrB dependent. However, 5'-RACE analysis of the pcnB transcript using primers located in the pcnB coding region shows that transcription starts immediately upstream of the putative ATG site at a sigma(70)-like promoter. Deletion of pcnB caused approximately 80% decrease of ployadenylated 23S rRNA; growth of the pcnB mutant was compromised in a range of laboratory media and on sugar beet seedlings. Further 5'-RACE analysis confirmed the existence of the predicted sigma(54) promoter. Genetic analysis showed that the sigma(54) promoter drives expression of crcZ, a homologue of the recently described small RNA from Pseudomonas aeruginosa, in a CbrB-dependent manner. Taken together, our data show that both pcnB and crcZ are part of the CbrB regulon. Moreover, the data draw further attention to the central regulatory role of CbrB and provides a link between mRNA degradation and cellular catabolism.

https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1462-2920.2010.02228.x

CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens.

Structure Determination of Tolaasin, an Extracellular Lipodepsipeptide Produced by the Mushroom Pathogen Pseudomonas tolaasii Paine.

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