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)

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Modern Applied Statistics With S

I. the origin of species by means of natural selection

Chloroplast (trnL−F and rbcL) sequences were used to reconstruct the phylogeny of Geraniaceae and Hypseocharitaceae. According to these data Hypseocharitaceae and Geraniaceae are monophyletic. Pelargonium and Monsonia are sisters to the largest clade of Geraniaceae, formed by Geranium, Erodium and California. According to molecular dating and dispersal-vicariance analysis, the split of the stem branches of Geraniaceae probably occurred during the Oligocene, in southern Africa or in southern Africa plus the Mediterranean area. However, their diversification occurred during the Miocene, coinciding with the beginning of major aridification events in their distribution areas. An ancestor of the largest clade of Geraniaceae (Geranium, Erodium, and California) colonised a number of habitats in the northern hemisphere and in South American mountain ranges. In summary, the evolution of the Geraniaceae is marked by the dispersal of ancestors from Southern Africa to cold, temperate and often disturbed habi...

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Phylogeny and Historical Biogeography of Geraniaceae in Relation to Climate Changes and Pollination Ecology

Geographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea: mainland-archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping-stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east-to-west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.

Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations

This study is framed within a biodiversity project in the Galapagos Islands, financed by BBVA Foundation (Spain). We also thank the Charles Darwin Foundation and the Parque Nacional de Galapagos for giving us logistic support while working there.

/pdf/evidence-for-overlooked-mechanisms-of-long-distance-seed-3n7fbekuxo.pdf

Evidence for overlooked mechanisms of long-distance seed dispersal to and between oceanic islands

Historical biogeography and character evolution of Cistaceae (Malvales) based on analysis of plastid rbcL and trnL-trnF sequences

Background 
Adaptive radiation in Mediterranean plants is poorly understood. The white-flowered Cistus lineage consists of 12 species primarily distributed in Mediterranean habitats and is herein subject to analysis.


Methodology/Principal Findings 
We conducted a “total evidence” analysis combining nuclear (ncpGS, ITS) and plastid (trnL-trnF, trnK-matK, trnS-trnG, rbcL) DNA sequences and using MP and BI to test the hypothesis of radiation as suggested by previous phylogenetic results. One of the five well-supported lineages of the Cistus-Halimium complex, the white-flowered Cistus lineage, comprises the higher number of species (12) and is monophyletic. Molecular dating estimates a Mid Pleistocene (1.04±0.25 Ma) diversification of the white-flowered lineage into two groups (C. clusii and C. salviifolius lineages), which display asymmetric characteristics: number of species (2 vs. 10), leaf morphologies (linear vs. linear to ovate), floral characteristics (small, three-sepalled vs. small to large, three- or five-sepalled flowers) and ecological attributes (low-land vs. low-land to mountain environments). A positive phenotype-environment correlation has been detected by historical reconstructions of morphological traits (leaf shape, leaf labdanum content and leaf pubescence). Ecological evidence indicates that modifications of leaf shape and size, coupled with differences in labdanum secretion and pubescence density, appear to be related to success of new species in different Mediterranean habitats.


Conclusions/Significance 
The observation that radiation in the Cistus salviifolius lineage has been accompanied by the emergence of divergent leaf traits (such as shape, pubescence and labdanum secretion) in different environments suggets that radiation in the group has been adaptive. Here we argued that the diverse ecological conditions of Mediterranean habitats played a key role in directing the evolution of alternative leaf strategies in this plant group. Key innovation of morphological characteristics is supported by our dated phylogeny, in which a Mediterranean climate establishment (2.8 Ma) predated the adaptive radiation of the white-flowered Cistus.

/pdf/adaptive-radiation-in-mediterranean-cistus-cistaceae-19zeno5ea4.pdf

Pablo Vargas

Papers

Phylogeny and Historical Biogeography of Geraniaceae in Relation to Climate Changes and Pollination Ecology

Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations

Evidence for overlooked mechanisms of long-distance seed dispersal to and between oceanic islands

Historical biogeography and character evolution of Cistaceae (Malvales) based on analysis of plastid rbcL and trnL-trnF sequences

Adaptive radiation in mediterranean cistus (cistaceae).