Author
Marc E. Epstein
Bio: Marc E. Epstein is an academic researcher from California Department of Food and Agriculture. The author has contributed to research in topics: Species richness & Tortricidae. The author has an hindex of 12, co-authored 26 publications receiving 1710 citations.
Papers
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554 citations
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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
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University of Pennsylvania1, Smithsonian Institution2, Instituto Nacional de Biodiversidad3, North Carolina State University4, California Department of Food and Agriculture5, Missouri Botanical Garden6, University of Guelph7, Natural History Museum8, University of Florida9, American Museum of Natural History10, Carnegie Museum of Natural History11, University of Illinois at Urbana–Champaign12, University of Kentucky13, United States Department of Agriculture14, University of Minnesota15
TL;DR: Adding DNA barcoding to the inventory of the caterpillars, their food plants and parasitoids in northwestern Costa Rica has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution.
Abstract: Inventory of the caterpillars, their food plants and parasitoids began in 1978 for today's Area de Conservacion Guanacaste (ACG), in northwestern Costa Rica This complex mosaic of 120 000 ha of conserved and regenerating dry, cloud and rain forest over 0–2000 m elevation contains at least 10 000 species of non-leaf-mining caterpillars used by more than 5000 species of parasitoids Several hundred thousand specimens of ACG-reared adult Lepidoptera and parasitoids have been intensively and extensively studied morphologically by many taxonomists, including most of the co-authors DNA barcoding — the use of a standardized short mitochondrial DNA sequence to identify specimens and flush out undisclosed species — was added to the taxonomic identification process in 2003 Barcoding has been found to be extremely accurate during the identification of about 100 000 specimens of about 3500 morphologically defined species of adult moths, butterflies, tachinid flies, and parasitoid wasps Less than 1% of the species have such similar barcodes that a molecularly based taxonomic identification is impossible No specimen with a full barcode was misidentified when its barcode was compared with the barcode library Also as expected from early trials, barcoding a series from all morphologically defined species, and correlating the morphological, ecological and barcode traits, has revealed many hundreds of overlooked presumptive species Many but not all of these cryptic species can now be distinguished by subtle morphological and/or ecological traits previously ascribed to ‘variation’ or thought to be insignificant for species-level recognition Adding DNA barcoding to the inventory has substantially improved the quality and depth of the inventory, and greatly multiplied the number of situations requiring further taxonomic work for resolution
334 citations
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University of Maryland Biotechnology Institute1, University of Maryland, College Park2, Chungbuk National University3, University of Minnesota4, University of Alberta5, University of Valencia6, United States Department of Agriculture7, Smithsonian Institution8, California Department of Food and Agriculture9, University of Pennsylvania10, Natural History Museum11, National Sun Yat-sen University12
TL;DR: The results corroborate the broad outlines of the current working phylogenetic hypothesis for Ditrysia, demonstrate that some prominent features of that hypothesis, including the position of the butterflies, need revision, and resolve the majority of family and subfamily relationships within superfamilies as thus far sampled.
Abstract: Background
In the mega-diverse insect order Lepidoptera (butterflies and moths; 165,000 described species), deeper relationships are little understood within the clade Ditrysia, to which 98% of the species belong. To begin addressing this problem, we tested the ability of five protein-coding nuclear genes (6.7 kb total), and character subsets therein, to resolve relationships among 123 species representing 27 (of 33) superfamilies and 55 (of 100) families of Ditrysia under maximum likelihood analysis.
225 citations
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27 Apr 2011
TL;DR: Tortricid larvae damaging grapes in the Napa Valley of California were identified as L. botrana, representing the first records of this species in North America, and could have a significant impact on California agriculture.
Abstract: . The European grape vine moth, Lobesia botrana ([Denis and Schiffermuller]), is one of the most destructive pests of grape in the Palearctic Region. Larvae feed on fruit, causing direct damage and promoting secondary infection by Botrytis cinerea Persoon (botrytis bunch rot or gray mold). On September 30, 2009, tortricid larvae damaging grapes in the Napa Valley of California were identified as L. botrana, representing the first records of this species in North America. The presence of L. botrana could have a significant impact on California agriculture— wine, table, and raisin grapes are grown on more than 800,000 acres throughout the state. We provide descriptions and illustrations to aid in the identification of this newly arrived pest, along with a brief history of its discovery.
55 citations
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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
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TL;DR: It is concluded that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time.
Abstract: Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species. Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth. We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.
1,389 citations
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TL;DR: Insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes, and greater integration of nuclear and mt genomic studies is necessary to further the understanding of insect genomic evolution.
Abstract: The mitochondrial (mt) genome is, to date, the most extensively studied genomic system in insects, outnumbering nuclear genomes tenfold and representing all orders versus very few. Phylogenomic analysis methods have been tested extensively, identifying compositional bias and rate variation, both within and between lineages, as the principal issues confronting accurate analyses. Major studies at both inter- and intraordinal levels have contributed to our understanding of phylogenetic relationships within many groups. Genome rearrangements are an additional data type for defining relationships, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. Hymenoptera and Psocodea have greatly elevated rates of rearrangement offering both opportunities and pitfalls for identifying rearrangement synapomorphies in each group. Finally, insects are model systems for studying aberrant mt genomes, including truncated tRNAs and multichromosomal genomes. Greater integration of nuclear and mt genomic studies is necessary to further our understanding of insect genomic evolution.
910 citations
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TL;DR: With 1 million insect species named, this suggests that 80% remain to be discovered and that a greater focus should be placed on less-studied taxa such as many families of Coleoptera, Diptera, and Hymenoptera and on poorly sampled parts of the world.
Abstract: In the last decade, new methods of estimating global species richness have been developed and existing ones improved through the use of more appropriate statistical tools and new data. Taking the mean of most of these new estimates indicates that globally there are approximately 1.5 million, 5.5 million, and 7 million species of beetles, insects, and terrestrial arthropods, respectively. Previous estimates of 30 million species or more based on the host specificity of insects to plants now seem extremely unlikely. With 1 million insect species named, this suggests that 80% remain to be discovered and that a greater focus should be placed on less-studied taxa such as many families of Coleoptera, Diptera, and Hymenoptera and on poorly sampled parts of the world. DNA tools have revealed many new species in taxonomically intractable groups, but unbiased studies of previously well-researched insect faunas indicate that 1–2% of species may be truly cryptic.
667 citations
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Fujian Agriculture and Forestry University1, University of Cambridge2, University of Adelaide3, Brock University4, Charles Sturt University5, University of British Columbia6, Cornell University7, University of Arizona8, University of Edinburgh9, University of Toronto10, United States Department of Agriculture11, Kansas State University12, University of Copenhagen13
TL;DR: The first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, is reported, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds.
Abstract: How an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants, but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood. We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.
455 citations