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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)

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

We compared mitochondrial genetic data for two spiny lobsters in Hawaii with different geographic ranges and histories of fishing pressure. Panulirus marginatus (Quoy and Gaimard, 1825) is endemic to Hawaii, and experienced a short, intense fishery in the Northwestern Hawaiian Islands (NWHI) and long-term, less intense exploitation in the Main Hawaiian Islands (MHI). Populations show significant overall structure (F ST = 0.0037, P = 0.007; D est_Chao = 0.137), with regional differentiation (F CT = 0.002, P = 0.047) between the MHI and the NWHI. Haplotype diversity did not differ significantly between regions (F2, 8 = 3.740, P = 0.071); however, nucleotide diversity is significantly higher at the primary NWHI fishery banks (0.030) than in the MHI (0.026, Tukey's P = 0.013). In contrast, Panulirus penicillatus (Olivier, 1791), found across the tropical Indo-West Pacific region, was not targeted by the NWHI fishery, but has experienced long-term exploitation in the MHI. Panulirus penicillatus has no significant overall population structure in Hawaii (F ST = 0.0083, P = 0.063; D est_Chao = 0.278), although regional differentiation (F CT = 0.0076, P = 0.0083) between the MHI and the NHWI is significant. Neither haplotype nor nucleotide diversity differed significantly between regions for P. penicillatus While neither species has suffered a loss of genetic diversity from fishing, our results highlight that only by incorporating knowledge of fishing history with genetic connectivity data can we understand the most beneficial management strategy for each species. Neither exemplar species nor specific suites of traits are reliable predictors of the spatial scales of management.

After the gold rush: Population structure of spiny lobsters in Hawaii following a fishery closure and the implications for contemporary spatial management

Isotopic approaches to estimating the contribution of heterotrophic sources to Hawaiian corals

Anthropogenic pressures negatively impact genomic diversity of the vulnerable seagrass Zostera capensis.

The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus, we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range. Phylogenetic analyses reveal that S. hispidus has a Western Atlantic lineage and a widely distributed Indo-Pacific lineage, separated by sequence divergence of 2.1%. Genetic diversity is much higher in the Western Atlantic (h = 0.929; π = 0.004) relative to the Indo-Pacific (h = 0.105; π < 0.001), and coalescent analyses indicate that the Indo-Pacific population expanded more recently (95% HPD (highest posterior density) = 60,000-400,000 yr) than the Western Atlantic population (95% HPD = 300,000-760,000 yr). Divergence of the Western Atlantic and Pacific lineages is estimated at 710,000-1.8 million years ago, which does not readily align with commonly implicated colonization events between the ocean basins. The estimated age of populations contradicts the prevailing dispersal route for tropical marine biodiversity (Indo-Pacific to Atlantic) with the oldest and most diverse population in the Atlantic, and a recent population expansion with a single common haplotype shared throughout the vast Indian and Pacific oceans. In contrast to the circumtropical fishes, this diminutive reef shrimp challenges our understanding of conventional dispersal capabilities of marine species.

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

Robert J. Toonen

Papers

After the gold rush: Population structure of spiny lobsters in Hawaii following a fishery closure and the implications for contemporary spatial management

Isotopic approaches to estimating the contribution of heterotrophic sources to Hawaiian corals

Anthropogenic pressures negatively impact genomic diversity of the vulnerable seagrass Zostera capensis.

The little shrimp that could: phylogeography of the circumtropical Stenopus hispidus (Crustacea: Decapoda), reveals divergent Atlantic and Pacific lineages

Sponging up diversity: Evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community