Author
J. Donald Lafontaine
Bio: J. Donald Lafontaine is an academic researcher from Agriculture and Agri-Food Canada. The author has contributed to research in topics: Noctuoidea & Erebidae. The author has an hindex of 12, co-authored 34 publications receiving 1743 citations.
Topics: Noctuoidea, Erebidae, Lepidoptera genitalia, Noctuinae, Condicinae
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554 citations
Naturalis1, University of Helsinki2, American Museum of Natural History3, University of Copenhagen4, Institut national de la recherche agronomique5, Centre national de la recherche scientifique6, University of Maryland, College Park7, University of Oulu8, University of Turku9, National Sun Yat-sen University10, National Museum of Natural History11, University of Valencia12, Smithsonian Institution13, Sam Houston State University14, Royal Museum for Central Africa15, California Department of Food and Agriculture16, Walter and Eliza Hall Institute of Medical Research17, Florida Museum of Natural History18, Agriculture and Agri-Food Canada19, National University of San Marcos20, Mississippi State University21, University of New Orleans22, Canadian Food Inspection Agency23
TL;DR: This dissertation aims to provide a history of web exceptionalism from 1989 to 2002, a period chosen in order to explore its roots as well as specific cases up to and including the year in which descriptions of “Web 2.0” began to circulate.
Abstract: van Nieukerken, Erik J.; Kaila, Lauri; Kitching, Ian J.; Kristensen, Niels Peder; Lees, David C.; Minet, Joël; Mitter, Charles; Mutanen, Marko; Regier, Jerome C.; Simonsen, Thomas J.; Wahlberg, Niklas; Yen, Shen-Horn; Zahiri, Reza; Adamski, David; Baixeras, Joaquin; Bartsch, Daniel; Bengtsson, Bengt Å.; Brown, John W.; Bucheli, Sibyl Rae; Davis, Donald R.; de Prins, Jurate; de Prins, Willy; Epstein, Marc E.; Gentili-Poole, Patricia; Gielis, Caes; Hättenschwiler, Peter; Hausmann, Axel; Holloway, Jeremy D.; Kallies, Axel; Karsholt, Ole; Kawahara, Akito Y.; Koster, Sjaak; Kozlov, Mikhail; Lafontaine, J. Donald; Lamas, Gerardo; Landry, JeanFrançois; Lee, Sangmi; Nuss, Matthias; Park, Kyu-Tek; Penz, Carla; Rota, Jadranka; Schintlmeister, Alexander; Schmidt, B. Christian; Sohn, Jae-Cheon; Solis, M. Alma; Tarmann, Gerhard M.; Warren, Andrew D.; Weller, Susan; Yakovlev, Roman V.; Zolotuhin, Vadim V.; Zwick, Andreas
450 citations
TL;DR: A new molecular phylogeny offers hope for a stable family level classification of the Noctuoidea (Lepidoptera) for the first time in more than a century.
Abstract: Zahiri, R., Kitching, I. J., Lafontaine, J. D., Mutanen, M., Kaila, L., Holloway, J. D. & Wahlberg, N. (2010). A new molecular phylogeny offers hope for a stable family level classification of the Noctuoidea (Lepidoptera). —Zoologica Scripta, 40, 158–173.
To examine the higher level phylogeny and evolutionary affinities of the megadiverse superfamily Noctuoidea, an extensive molecular systematic study was undertaken with special emphasis on Noctuidae, the most controversial group in Noctuoidea and arguably the entire Lepidoptera. DNA sequence data for one mitochondrial gene (cytochrome oxidase subunit I) and seven nuclear genes (Elongation Factor-1α, wingless, Ribosomal protein S5, Isocitrate dehydrogenase, Cytosolic malate dehydrogenase, Glyceraldehyde-3-phosphate dehydrogenase and Carbamoylphosphate synthase domain protein) were analysed for 152 taxa of principally type genera/species for family group taxa. Data matrices (6407 bp total) were analysed by parsimony with equal weighting and model-based evolutionary methods (maximum likelihood), which revealed a new high-level phylogenetic hypothesis comprising six major, well-supported lineages that we here interpret as families: Oenosandridae, Notodontidae, Erebidae, Nolidae, Euteliidae and Noctuidae.
243 citations
TL;DR: The first large‐scale molecular phylogenetic analysis of the moth family Erebidae is undertaken, including almost all subfamilies, as well as most tribes and subtribes, revealing a well‐resolved skeleton phylogenetic hypothesis with 18 major lineages.
Abstract: As a step towards understanding the higher-level phylogeny and evolu- tionary affinities of quadrifid noctuoid moths, we have undertaken the first large-scale molecular phylogenetic analysis of the moth family Erebidae, including almost all subfamilies, as well as most tribes and subtribes. DNA sequence data for one mitochondrial gene (COI ) and seven nuclear genes (EF-1α, wingless, RpS5, IDH, MDH, GAPDH and CAD) were analysed for a total of 237 taxa, principally type genera of higher taxa. Data matrices (6407 bp in total) were analysed by parsimony with equal weighting and model-based evolutionary methods (maximum likelihood), which revealed a well-resolved skeleton phylogenetic hypothesis with 18 major lineages, which we treat here as subfamilies of Erebidae. We thus present a new phylogeny for Erebidae consisting of 18 moderate to strongly supported subfami- lies: Scoliopteryginae, Rivulinae, Anobinae, Hypeninae, Lymantriinae, Pangraptinae, Herminiinae, Aganainae, Arctiinae, Calpinae, Hypocalinae, Eulepidotinae, Toxocamp- inae, Tinoliinae, Scolecocampinae, Hypenodinae, Boletobiinae and Erebinae. Where possible, each monophyletic lineage is diagnosed by autapomorphic morphological character states, and within each subfamily, monophyletic tribes and subtribes can be circumscribed, most of which can also be diagnosed by morphological apomorphies. All additional taxa sampled fell within one of the four previously recognized quadrifid families (mostly into Erebidae), which are now found to include two unusual monobasic taxa from New Guinea: Cocytiinae (now in Erebidae: Erebinae) and Eucocytiinae (now in Noctuidae: Pantheinae).
207 citations
TL;DR: A more inclusive definition of the family Noctuidae is proposed that adds the subfamilies Nolinae, Strepsimaninee, Arctiinae, Lymantriinae and Erebinae to theSubfamilies more traditionally included in the NoctUIDae are added.
Abstract: Nous revisons la classification superieure des familles de Noctuoidea possedant une aile anterieure quadrifide (Nolidae, Strepsimanidae, Arctiidae, Lymantriidae, Erebidae et Noctuidae) a la lumiere de classifications recentes et des repartitions actuelles des etats derives des caracteres. D'apres des etudes morphologiques et moleculaires recentes, nous proposons une definition plus comprehensive de la famille des Noctuidae qui ajoute les sous-familles Nolinae, Strepsimaninae, Arctiinae, Lymantriinae et Erebinae a celles qui sont plus traditionnellement incluses dans les Noctuidae. La superfamille des Noctuoidea comprend donc les familles Oenosandridae, Doidae, Notodontidae, Micronoctuidae et Noctuidae. La tribu des Cosmiini, presentement dans la sous-famille des Xyleninae, est reduite au niveau de sous-tribu des Cosmiina et placee dans la tribu des Xylenini. La tribu des Balsini, couramment placee dans la sous-famille des Xyleninae, est elevee au rang de sous-famille des Balsinae. La tribu Phosphilini est transferee de la sous-famille des Psaphidinae a Xyleninae.
142 citations
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: 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.
10,124 citations
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: 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.
4,104 citations
TL;DR: This review concentrates on the entomologically relevant literature published since 1967 onination ecology, and has attempted to cover concepts, related disciplines, and insect taxa by reference to publica tions through which the reader may delve deeper.
Abstract: Pollination ecology has been a fast growing field since the 1960s. A previous review by Baker & Hurd (18) together with books (77, 84, 220, 221 , 244, 264) and various symposia (e.g. 5, 12, 17, 24, 149, 167, 239) have promoted anthecology so that it remains at the heart of evolutionary and ecological research. This review concentrates on the entomologically relevant litera ture published since 1967. Botanical works must be included, as both insects and flowers mutually aSsure reproductive success. We have attempted to cover concepts, related disciplines, and insect taxa by reference to publica tions through which the reader may delve deeper. We apologize to our colleagues for not citing their works more fully. We dedicate this review to the memory of Paul D. Hurd Jr. His en thusiasm for bees and their relations with flowers, and for insects in general, have been an inspiration to us. His contributions would form the hub of a separate review in itself and we have not attempted to cover his works.
833 citations
Smithsonian Tropical Research Institute1, Sewanee: The University of the South2, University of Panama3, Academy of Sciences of the Czech Republic4, University of Western Australia5, University of Évora6, University of York7, University of Helsinki8, University of Erlangen-Nuremberg9, Santa Barbara Museum of Natural History10, University of Victoria11, University of Bristol12, National Autonomous University of Mexico13, Blaise Pascal University14, State University of Santa Cruz15, Royal Belgian Institute of Natural Sciences16, University of Toulouse17, University of Würzburg18, Griffith University19, National Museum of Natural History20, Centre national de la recherche scientifique21, Research Institute for Nature and Forest22, Universidade Federal de Ouro Preto23, Université libre de Bruxelles24, American Museum of Natural History25
TL;DR: This work sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama using a comprehensive range of structured protocols and found that models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well.
Abstract: Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6144 arthropod species from 0.48 hectare and extrapolated total species richness to larger areas on the basis of competing models. The whole 6000-hectare forest reserve most likely sustains 25,000 arthropod species. Notably, just 1 hectare of rainforest yields >60% of the arthropod biodiversity held in the wider landscape. Models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well. This lends credence to global estimates of arthropod biodiversity developed from plant models.
455 citations
Naturalis1, University of Helsinki2, American Museum of Natural History3, University of Copenhagen4, Institut national de la recherche agronomique5, Centre national de la recherche scientifique6, University of Maryland, College Park7, University of Oulu8, University of Turku9, National Sun Yat-sen University10, National Museum of Natural History11, University of Valencia12, Smithsonian Institution13, Sam Houston State University14, Royal Museum for Central Africa15, California Department of Food and Agriculture16, Walter and Eliza Hall Institute of Medical Research17, Florida Museum of Natural History18, Agriculture and Agri-Food Canada19, National University of San Marcos20, Mississippi State University21, University of New Orleans22, Canadian Food Inspection Agency23
TL;DR: This dissertation aims to provide a history of web exceptionalism from 1989 to 2002, a period chosen in order to explore its roots as well as specific cases up to and including the year in which descriptions of “Web 2.0” began to circulate.
Abstract: van Nieukerken, Erik J.; Kaila, Lauri; Kitching, Ian J.; Kristensen, Niels Peder; Lees, David C.; Minet, Joël; Mitter, Charles; Mutanen, Marko; Regier, Jerome C.; Simonsen, Thomas J.; Wahlberg, Niklas; Yen, Shen-Horn; Zahiri, Reza; Adamski, David; Baixeras, Joaquin; Bartsch, Daniel; Bengtsson, Bengt Å.; Brown, John W.; Bucheli, Sibyl Rae; Davis, Donald R.; de Prins, Jurate; de Prins, Willy; Epstein, Marc E.; Gentili-Poole, Patricia; Gielis, Caes; Hättenschwiler, Peter; Hausmann, Axel; Holloway, Jeremy D.; Kallies, Axel; Karsholt, Ole; Kawahara, Akito Y.; Koster, Sjaak; Kozlov, Mikhail; Lafontaine, J. Donald; Lamas, Gerardo; Landry, JeanFrançois; Lee, Sangmi; Nuss, Matthias; Park, Kyu-Tek; Penz, Carla; Rota, Jadranka; Schintlmeister, Alexander; Schmidt, B. Christian; Sohn, Jae-Cheon; Solis, M. Alma; Tarmann, Gerhard M.; Warren, Andrew D.; Weller, Susan; Yakovlev, Roman V.; Zolotuhin, Vadim V.; Zwick, Andreas
450 citations