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

http://zootis.zoologi.su.se/research/nylin/Wahlberg_et_al.pdf

Towards a better understanding of the higher systematics of Nymphalidae (Lepidoptera: Papilionoidea).

Butterflies in the tribe Melitaeini (Lepidoptera: Nymphalidae) are known to utilize host plants belonging to 16 families, although most host-plant records are from four families. Of the 16 host-plant families, 12 produce secondary plant metabolites called iridoids. Earlier studies have shown that larvae of several melitaeine species use iridoids as feeding stimulants and sequester these compounds for larval defense. I investigate the evolutionary history of host-plant use in the tribe Melitaeini by testing a recent phylogenetic hypothesis of 65 species representing the four major species groups of the tribe. By simple character optimization of host-plant families and presence/absence of iridoids in the host plants, I find that plant chemistry is a more conservative trait than plant taxonomy. The ancestral host plant(s) of the entire tribe most likely contained iridoids and were likely to be in the plant family Plantaginaceae. A major host shift from plants containing iridoids to plants not containing iridoids has happened three times independently. The results show that the evolution of host-plant use in melitaeines has been (and still is) a dynamic process when considering plant taxonomy, but is relatively stable when considering host-plant chemistry.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.0014-3820.2001.tb00786.x

The phylogenetics and biochemistry of host-plant specialization in melitaeine butterflies (lepidoptera: nymphalidae)

The marsh fritillary butterfly Euphydryas aurinia is an endangered species in most of northern Europe. We describe the metapopulation structure of E. aurinia in Finland, where the species has declined drastically in the past decades. We found two types of habitat patches suitable for the species: semi-permanent meadows and transient clearcuts in the forest. Patch area was the most significant variable predicting the occurrence of E. aurinia in a habitat patch. The species tended to be found in young rather than old clearcuts, apparently because the vegetation became too high in the latter. We used the incidence function model to simulate the metapopulation dynamics of E. aurinia in its dynamic landscape and discovered that the continued presence of the semi-permanent meadows is essential for the survival of the species in the study area in southeast Finland.

/pdf/dynamic-populations-in-a-dynamic-landscape-the-1n1li4c3az.pdf

Dynamic populations in a dynamic landscape: the metapopulation structure of the marsh fritillary butterfly

We studied the patterns and rates of migration among habitat patches for five species of checkerspot butterflies (Lepidoptera: Melitaeini) in Finland: Euphydryas aurinia, E. maturna, Melitaea cinxia, M. diamina and M. athalia. We applied the virtual migration (VM) model to mark-release-recapture data collected from multiple populations. The model includes parameters describing migration and survival rates and how they depend on the areas and connectivities of habitat patches. The number of individuals captured varied from 73 to 1,123, depending on species and sex, and the daily recapture probabilities varied between 0.09-0.52. The VM model fitted the data quite well. The results show that the five species are broadly similar in their movement rates and patterns, though, e.g. E. maturna tends to move shorter distances than the other species. There is no indication of any phylogenetic component in the parameter values. The parameter values estimated for each species suggest that a large percentage (80-90%) of migration events were successful in the landscapes that were studied. The area of the habitat patch had a substantial effect on emigration and immigration rates, such that butterflies were more likely to leave small than large patches and large patches were more likely than small patches to receive immigrants.

Metapopulation structure and movements in five species of checkerspot butterflies.

Satyrinae butterflies (Lepidoptera: Nymphalidae) and grasses (Poaceae) are very diverse and distributed worldwide. Most Satyrinae use grasses as host plants, but the temporal scale of this tight association is not known. Here, we present a phylogenetic study of Satyrinae butterflies and related groups, based on 5.1 kilobases from six gene regions and 238 morphological characters for all major lineages in the ‘satyrine clade’. Estimates of divergence times calibrated using a fossil from the Late Oligocene indicate that the species-rich tribe Satyrini diversified to its current 2200 species simultaneously with the expansion and radiation of grasses during the dramatic cooling and drying up of the Earth in the Oligocene. We suggest that the adaptive radiation of grass feeders in Satyrini has been facilitated by the ubiquitousness of grasses since 25 Myr ago, which was triggered by a change in global climate.

/pdf/prehistorical-climate-change-increased-diversification-of-a-21iuaaerlg.pdf

Niklas Wahlberg

Papers

Towards a better understanding of the higher systematics of Nymphalidae (Lepidoptera: Papilionoidea).

The phylogenetics and biochemistry of host-plant specialization in melitaeine butterflies (lepidoptera: nymphalidae)

Dynamic populations in a dynamic landscape: the metapopulation structure of the marsh fritillary butterfly

Metapopulation structure and movements in five species of checkerspot butterflies.

Prehistorical climate change increased diversification of a group of butterflies