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

Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera, Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis.

This study compiles previously published morphological, colour and behavioural characters and includes new DNA sequence data for eight markers (one mitochondrial and seven nuclear) to re-evaluate phylogenetic relationships and estimate times of divergence for Morpho butterflies using parsimony and Bayesian methods. We note an effect of missing data on phylogenetic inference and calculations of Partitioned Bremer Support. Morphology and DNA trees were moderately congruent, and the combined analyses of all data included elements of both sources. Both morphology and DNA support the monophyly of Morpho and the early separation of the sister pair M. marcus plus M. eugenia, but trees from different data sources are congruent mostly at derived nodes, and differ at several internal nodes. The analyses of combined data indicate that Morpho is composed of four clades each of which include one or more previously proposed subgenera. The subgenera Pessonia and Morpho were not monophyletic, and to address this issue we propose that Pessonia, syn.nov. be subsumed within Morpho. The ancestor of Morpho probably arose during the Oligocene, and most diversification seems to have occurred during the late Miocene. S-DIVA analysis suggests eastern Andean region as the ancestral area for Morpho, and that the South American Atlantic Forest was colonized multiple times.

Diversification of Morpho butterflies (Lepidoptera, Nymphalidae): a re‐evaluation of morphological characters and new insight from DNA sequence data

The life history and ecology of Euphydryas maturna (Nymphalidae: Melitaeini) in Finland

We present results of an eight-gene molecular study of the subfamily Acronictinae and related Noctuidae. Amphipyrinae are recovered as sister to Acronictinae, but with weak support - not surprisingly, the content of the two subfamilies has often been mixed in classifications. Balsinae, previously placed near Acronictinae or within Noctuinae, is recovered within an unresolved polytomy of Cuculliinae, Eustrotiinae, Raphiinae and Dilobinae. Gerbathodes Warren, Moma Hubner and Nacna Fletcher are excluded from Acronictinae. Three genera recently transferred into the subfamily - Cerma Hubner, Chloronycta Schmidt & Anweiler and Comachara Franclemont - are confirmed as acronictines. Lophonycta Sugi (the type genus of Lophonyctinae) is returned to the Acronictinae. Sinocharis Pungeler, formerly considered to be Acontiinae or as the basis of its own subfamily Sinocharinae, is nested within early diverging Acronictinae genera. Both subfamilies are formally synonymized: i.e. Lophonyctinae syn.n. and Sinocharinae syn.n. Nine acronictine genus-level taxa were found to nest within the nominate genus Acronicta Ochsenheimer: Eogena Guenee, Hyboma Hubner, Hylonycta Sugi, Jocheaera Hubner, Oxicesta Hubner, Simyra Ochsenheimer, Subacronicta Kozhanchikov, Triaena Hubner, and Viminia Chapman. Eogena, Oxicesta, and Simyra, currently treated as valid genera, nest within terminal clades of the genus Acronicta and are here subsumed within the genus: Eogena syn.n., Oxicesta syn.n. and Simyra syn.n. Four well-supported species groups within Acronicta are identified: the alni clade, the leporina clade, the nervosa clade and the psi clade. While many previous treatments have stated explicitly that Acronictinae lack abdominal scent brushes, or excluded genera with brushes from the subfamily, we show that well-developed brushes are present in three early diverging acronictine genera: Cerma, Lophonycta, and Sinocharis. We illustrate and describe the brushes of all three genera, and briefly review the taxonomic distribution of the anterior abdominal courtship brushes in Noctuidae, emphasizing the labile evolutionary distribution of these structures. (Less)

Phylogenetic relationships of Acronictinae with discussion of the abdominal courtship brush in Noctuidae (Lepidoptera)

Diverse radiations of insects are often associated with adaptations to host plants, and well-resolved phylogenetic relationships are required to fully understand them. Palearctic Argynnis and related subgenera, together with North American Speyeria butterflies make up a radiation whose species hypotheses are confounded by shared wing colour patterns between sympatric populations of closely related recognized species. Previous studies of this group indicate that Speyeria is a lineage within Argynnis, but sampling in these studies has either involved too few Speyeria species or incomplete sampling of Argynnis species. Thus, no comprehensive phylogenetic analysis exists for all members that answers the question of monophyly of Speyeria, or other subgeneric taxa, and their relationship to Argynnis species. We completed a phylogenetic analysis of all North American Speyeria species and all but one species within Argynnis, using one mitochondrial (cytochrome c oxidase I, COI) and four nuclear genes [elongation factor 1 alpha (EF1α), wingless (WG), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and ribosomal protein S5 (RPS5)]. The results indicate three major lineages within Argynnis s.l.: two Palearctic and one containing both Palearctic and Nearctic species. In summary, the phylogenetic analyses suggest the need for reorganization into three natural groups: Argynnis, Fabriciana and Speyeria. Within each of these genera the phylogenetic hypothesis indicates an evolutionary history marked by rapid diversification and potential extinction, followed by ongoing lineage sorting. The position of North American Speyeria is nested within the Palearctic lineages, which indicates that the radiation began in Asia and was fuelled by existing Viola diversity in North America. Dating analyses of Viola and Speyeria corroborate this hypothesis. The current North American Speyeria species are mixed on the tree, indicating a recent and ongoing radiation. These results provide needed clarity on the evolution of this group, which contains species of conservation concern.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/syen.12236

Niklas Wahlberg

Papers

Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera, Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis.

Diversification of Morpho butterflies (Lepidoptera, Nymphalidae): a re‐evaluation of morphological characters and new insight from DNA sequence data

The life history and ecology of Euphydryas maturna (Nymphalidae: Melitaeini) in Finland

Phylogenetic relationships of Acronictinae with discussion of the abdominal courtship brush in Noctuidae (Lepidoptera)

Interrelationships and diversification of Argynnis Fabricius and Speyeria Scudder butterflies