Author
Susan J. Weller
Other affiliations: Purdue University, University of Nebraska–Lincoln, Louisiana State University ...read more
Bio: Susan J. Weller is an academic researcher from American Museum of Natural History. The author has contributed to research in topics: Lepidoptera genitalia & Monophyly. The author has an hindex of 23, co-authored 40 publications receiving 3198 citations. Previous affiliations of Susan J. Weller include Purdue University & University of Nebraska–Lincoln.
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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284 citations
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University of Maryland, College Park1, American Museum of Natural History2, Florida Museum of Natural History3, University of Arizona4, Chungbuk National University5, Smithsonian Institution6, University of Valencia7, United States Department of Agriculture8, University of Minnesota9, Natural History Museum10
TL;DR: This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa and shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others.
Abstract: Background
Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies
Methodology / Principal Findings
483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity
Conclusions / Significance
Support for among-superfamily relationships outside the Apoditrysia is now generally strong Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny
279 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
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TL;DR: It is established that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals and will provide a reliable, cost–effective and accessible solution to the current problem of species identification.
Abstract: Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
9,879 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: This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized.
Abstract: ▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...
2,025 citations
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Commonwealth Scientific and Industrial Research Organisation1, Rutgers University2, Heidelberg Institute for Theoretical Studies3, University of Jena4, University of Bonn5, Naturhistorisches Museum6, University of Vienna7, University of Tsukuba8, Landcare Research9, Johns Hopkins University10, University of Hamburg11, Ehime University12, Florida Museum of Natural History13, Staatliches Museum für Naturkunde Stuttgart14, National Evolutionary Synthesis Center15, Australian National University16, Macquarie University17, American Museum of Natural History18, University of Memphis19, University of Guadalajara20, Bavarian Academy of Sciences and Humanities21, Natural History Museum22, Karlsruhe Institute of Technology23, California Academy of Sciences24, South China Agricultural University25, North Carolina State University26, Hokkaido University27
TL;DR: The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
1,998 citations