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 RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Beginning with Emlen (1966) and MacArthur and Pianka (1966) and extending through the last ten years, several authors have sought to predict the foraging behavior of animals by means of mathematical models. These models are very similar,in that they all assume that the fitness of a foraging animal is a function of the efficiency of foraging measured in terms of some "currency" (Schoener, 1971) -usually energy- and that natural selection has resulted in animals that forage so as to maximize this fitness. As a result of these similarities, the models have become known as "optimal foraging models"; and the theory that embodies them, "optimal foraging theory." The situations to which optimal foraging theory has been applied, with the exception of a few recent studies, can be divided into the following four categories: (1) choice by an animal of which food types to eat (i.e., optimal diet); (2) choice of which patch type to feed in (i.e., optimal patch choice); (3) optimal allocation of time to different patches; and (4) optimal patterns and speed of movements. In this review we discuss each of these categories separately, dealing with both the theoretical developments and the data that permit tests of the predictions. The review is selective in the sense that we emphasize studies that either develop testable predictions or that attempt to test predictions in a precise quantitative manner. We also discuss what we see to be some of the future developments in the area of optimal foraging theory and how this theory can be related to other areas of biology. Our general conclusion is that the simple models so far formulated are supported are supported reasonably well by available data and that we are optimistic about the value both now and in the future of optimal foraging theory. We argue, however, that these simple models will requre much modification, espicially to deal with situations that either cannot easily be put into one or another of the above four categories or entail currencies more complicated that just energy.

Citation classic - optimal foraging - a selective review of theory and tests

In this study, we clarify the relationships between the basal lineages in the moth family Noctuidae using DNA sequence data from eight independent gene regions. Data matrices (6.4 kbp) are analysed using parsimony and model-based methods (maximum likelihood and Bayesian inference). Our results support the family Noctuidae as a monophyletic group in which most subfamilies have hindwing vein M2 reduced or absent. Our phylogenetic hypothesis suggests that in the Noctuidae, the plesiomorphic condition is that in which vein M2 arises about one-third of the way up the discocellular vein between the origins of M1 and M3, mainly parallel to M3, and is of thickness similar to vein M3. Most Noctuidae lineages possess an apomorphic (derived) condition in which hindwing vein M2 is markedly reduced or totally absent, so that the cubital vein appears to be three-branched and these lineages are hence referred to as ‘trifine’. However, Noctuidae also include a number of lineages in which vein M2 is unreduced, or only slightly reduced, and these are more problematic for morphological association with the family Noctuidae. Our results also show that the subfamily Acronictinae is not closely related to Pantheinae, but instead shows a closer association with Amphipyrinae. Among the major lineages of Noctuidae, we postulate a general trend, with numerous exceptions, in larval host plants from woody plants in the basal groups towards herb feeding in derived groups. Similarly, the major radiations of monocot-feeding groups within the family Noctuidae are in the higher trifines. The following taxonomic changes are proposed: Thiacidinae, syn. nov., a junior synonym of Pantheinae, and Dyopsinae, stat. nov., are reinstated as a subfamily.

Relationships among the basal lineages of Noctuidae (Lepidoptera, Noctuoidea) based on eight gene regions

How and why the great diversity of phytophagous insects has evolved is not clear but, if the explanation is the diversity of plants as a resource, colonizations of novel plant taxa can be expected to be associated with higher net speciation rates. In the present study, we make use of recent advances in plant and butterfly systematics to trace the evolution of host-plant utilization in the butterfly subfamily Nymphalinae (tribes Nymphalini, Melitaeini, and the probably paraphyletic 'Kallimini'). A clear historical pattern emerges, with an ancestral host-plant theme of 'urticalean rosids' and two major colonizations of novel distantly-related plant clades. The asterid order Lamiales was colonized by an ancestor of 'Kallimini' + Melitaeini and the family Asteraceae in Asterales was later colonized by Melitaeini butterflies. These colonization events appear to have been followed by increases in the rate of net butterfly diversification. Two not mutually exclusive scenarios to explain such patterns have been suggested: (1) adaptive radiation due to release from competition following host-plant shifts or (2) higher rates of net speciation during a relatively long-lasting potentially polyphagous (plastic) state. In support of the 'plasticity scenario', phylogenetic traces of a long-lasting stage with some potential to feed on more than one host-plant clade can still be seen, despite the ancient age of the colonizations. When angiosperm communities changed after the K/T boundary due to extinctions and subsequent diversification, herbivore taxa that could occupy several alternative niches may have had the greatest opportunity to diversify in turn.

Does plasticity drive speciation? Host‐plant shifts and diversification in nymphaline butterflies (Lepidoptera: Nymphalidae) during the tertiary

Evolutionary Patterns of Pheromone Diversity in Lepidoptera

. Mitochondrial DNA variation was studied in the butterfly genus Phyciodes (Lepidoptera: Nymphalidae) by sequencing 1450 bp of the COI gene from 140 individuals of all eleven currently recognized species. The study focused on four species in particular that have been taxonomically difficult for the past century, P. tharos, P. cocyta, P. batesii and P. pulchella. A cladistic analysis of ninety-eight unique haplotypes showed that Phyciodes forms a monophyletic group with P. graphica as the most basal species. Of the three informal species groups described for Phyciodes, only one (the mylitta-group) is unambiguously monophyletic. Within the tharos-group, seven well supported clades were found that correspond to three taxa, P. tharos, P. pulchella and a grade consisting of P. cocyta and P. batesii haplotypes interdigitated with each other. None of the clades is formed exclusively by one species. The patterns of haplotype variation are the result of both retained ancient polymorphism and introgression. Introgression appears to be most common between P. cocyta and P. batesii; however, these two species occur sympatrically and are morphologically and ecologically distinct, suggesting that the level of current introgression does not seem to be enough to threaten their genetic integrity. The results indicate that mitochondrial DNA sequences must be used with great caution in delimiting species, especially when infraspecific samples are few, or introgression seems to be rampant.

Phylogenetic relationships of Phyciodes butterfly species (Lepidoptera: Nymphalidae): complex mtDNA variation and species delimitations

The insect order Trichoptera (caddisflies) forms the second most species-rich monophyletic group of animals in freshwater. So far, several attempts have been made to elucidate its evolutionary history with both morphological and molecular data. However, none have attempted to analyse the time frame for its diversification. The order is divided into three suborders – Annulipalpia, Integripalpia and ‘Spicipalpia’. Historically, the most problematic taxon to place within the order is ‘Spicipalpia’, whose larvae do not build traditional cases or filtering nets like the majority of the caddisflies. They have previously been proposed to be the sister group of all other Trichoptera or more advanced within the order, with equivocal monophyly and with different interordinal placements among various studies. In order to resolve the evolutionary history of the caddisflies as well as timing their diversification, we utilized fragments of three nuclear (carbamoylphosphate synthethase, isocitrate dehydrogenase and RNA polymerase II) and one mitochondrial (cytochrome oxidase I) protein coding genes, with 16 fossil trichopteran taxa used for time calibration. The ‘spicipalpian’ families are recovered as ancestral to all other caddisflies, though paraphyletic. We recover stable relationships among most families and superfamilies, resolving many previously unrecognized phylogenetic affinities amongst extant families. The origin of Trichoptera is estimated to be around 234 Ma, i.e. Middle – Late Triassic.

Niklas Wahlberg

Papers

Relationships among the basal lineages of Noctuidae (Lepidoptera, Noctuoidea) based on eight gene regions

Does plasticity drive speciation? Host‐plant shifts and diversification in nymphaline butterflies (Lepidoptera: Nymphalidae) during the tertiary

Evolutionary Patterns of Pheromone Diversity in Lepidoptera

Phylogenetic relationships of Phyciodes butterfly species (Lepidoptera: Nymphalidae): complex mtDNA variation and species delimitations

The evolutionary history of Trichoptera (Insecta): A case of successful adaptation to life in freshwater