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

We review the various proposals of evolutionary and classification schemes for Satyrinae and particularly Euptychiina butterflies, assessing progress and prospects of research for the group. Among the highlights is the proposal to include Morphini, Brassolini and Amathusiini as part of Satyrinae. Although it is clear that this hypothesis requires further investigation, phylogenetic studies recently conducted recover this clade as part of Satyrinae with high support. The phylogenetic analyses for Euptychiina carried out to date recover the monophyly of the group and have identified a variety of genera as non-monophyletic. Further work is necessary to resolve the position of the subtribe and the evolutionary relationships of several genera.

From the Phylogeny of the Satyrinae Butterflies to the Systematics of Euptychiina (Lepidoptera: Nymphalidae): History, Progress and Prospects

The genus Pararge comprises three species: P. aegeria, distributed in Europe and North Africa; P. xiphia, endemic to Madeira; and P. xiphioides ,e ndemic to the Canary Islands. Two subspecies are recognized in P. aegeria, P. a. tircis and P. a. aegeria, distributed in northern and southern Europe, respectively. In the 1970s, P. aegeria appeared on Madeira. However, despite the status of P. aegeria as a model species in ecological studies, the evolutionary history of Pararge remains unknown. We studied the phylogenetic relationships of the three Pararge species, using the mitochondrial gene cytochrome oxidase subunit I and the nuclear gene wingless to infer modes and times of speciation. On the basis of our analyses, Pararge forms a strongly supported monophyletic group, with the DNA haplotypes of the three species also forming well-supported monophyletic groups. We found that P. xiphia diverged first from the common ancestor a maximum of five million years ago, with P. xiphioides and P. aegeria being sister species that diverged a maximum of three million years ago. The two subspecies, P. a. tircis and P. a. aegeria ,w ere not distinguishable on the basis of DNA haplotypes; instead, our data clearly distin- guished between European specimens and those from North Africa. Madeiran P. aegeria has North African haplotypes and thus originated from there rather than from Europe. We raise the name meone Stoll, 1780 from synonymy to subspecies status (Parage aegeria meone stat. rev.) for populations in North Africa and Maderia. We hypothesize that the Mediterranean Sea forms a strong barrier to dispersal for Pararge butterflies, and has done so for approximately the past one million years.

http://www.satyrinae.yolasite.com/resources/Scientific_papers/Speciation%20in%20Pararge%20butterflies.pdf

Speciation in Pararge (Satyrinae: Nymphalidae) butterflies - North Africa is the source of ancestral populations of all Pararge species

We examine the phylogenetic relationships among 29 species of Argynnini based on 141 previously published morphological characters and new data from the mitochondrial gene COI and the two nuclear genes EF-1a and wingless. We investigate the stability and robustness of the resulting phylogenetic hypotheses through various combinations of the 4 functionally separate datasets. Increasing the number of datasets in combined analyses led to increased support for clades, sometimes substantially. We find that the tribe Argynnini is a well-supported, robust, monophyletic clade with the following internal subtribal structure: (Euptoietina (Yrameina (Boloriina Argynnina))). Our analyses support the classification of argynnine species into six robust and stable genera: Euptoieta, Yramea, Boloria, Issoria, Brenthis and Argynnis. We suggest that for moderate amounts of data, a total evidence approach is always best.

http://www.nymphalidae.net/Simonsenetal2006.pdf

Morphology, molecules and fritillaries: approaching a stable phylogeny for Argynnini (Lepidoptera: Nymphalidae)

The immature stages of five Finnish melitaeine butterfly species are described, together with a short discussion of the ecology of each species. The five species are Melitaea cinxia (L.), M diamina (Lang), M. athalia (Rottemburg), Euphydryas maturna (L.) and E. aurinia (Rottemburg). The eggs of the Euphydryas species are distinguished from the eggs of the Melitaea species by their bright yellow colouration when freshly laid which changes to brown after some days. Eggs of the Melitaea species are creamy yellow until hatching. Prediapause larvae are also distinct between these two groups, with Euphydryas species having fine spotting on the body and a very long terminal seta on the spines. These features are absent in the Melitaea species. All larvae diapause as mid-ins tar larvae, usually in the fourth instar. Behaviour of postdiapause larvae varies between species from highly gregarious (M. cinxia and .E. aurinia) through gregarious until diapause (M diamina and E. matuma) to solitary (M. athalia).

/pdf/comparative-descriptions-of-the-immature-stages-and-ecology-45v12zvnzd.pdf

Comparative descriptions of the immature stages and ecology of five Finnish melitaeine butterfly species (Lepidoptera: Nymphalidae)

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both ‘biotic’ interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed-clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno-Ugric, Finnic and Saami languages. Some of the divergences co-occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both ‘biotic’ and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/jeb.12107

Niklas Wahlberg

Papers

From the Phylogeny of the Satyrinae Butterflies to the Systematics of Euptychiina (Lepidoptera: Nymphalidae): History, Progress and Prospects

Speciation in Pararge (Satyrinae: Nymphalidae) butterflies - North Africa is the source of ancestral populations of all Pararge species

Morphology, molecules and fritillaries: approaching a stable phylogeny for Argynnini (Lepidoptera: Nymphalidae)

Comparative descriptions of the immature stages and ecology of five Finnish melitaeine butterfly species (Lepidoptera: Nymphalidae)

Cultural and climatic changes shape the evolutionary history of the Uralic languages