Discovery and Classification of Ecological Diversity in the Bacterial World: The Role of DNA Sequence Data

AbstractDespite the declining number of traditional taxonomists, our knowledge of Earth's biodiversity continues to grow in the form of DNA sequence data. Freely available through online databases, analyses of sequence datasets are increasingly used as an alternative for the traditional taxonomic process. Species identifications have become “DNA barcoding,” new species discoveries are characterised by genetic divergences, and traditional classification has been supplanted by molecular phylogenetics. These developments are illustrated through a case study investigating the identities of Taygetis butterflies of Costa Rica. Here I review prospects and problems with the molecularization of taxonomy and the key role of publicly available nucleotide sequence databases in efforts to catalogue diversity of life.

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A Show of Character—a further response to Wiley et al.

Zootaxa ◽

10.11646/zootaxa.2946.1.6 ◽

2011 ◽

Vol 2946 (1) ◽

pp. 29 ◽

Cited By ~ 1

Author(s):

ANTHONY C. GILL ◽

RANDALL D. MOOI

Keyword(s):

Dna Sequence ◽

Large Scale ◽

Sequence Data ◽

Molecular Data ◽

Scientific Rigor ◽

Dna Sequence Data ◽

Phylogenetic Hypotheses ◽

Alternative Relationships

Wiley et al. (2011) begin their critique of our paper (Mooi & Gill, 2010) with an assertion: “we need to make itclear that the foundation of their arguments rests not on scientific rigor, but rather on opinions about the re-classification of fishes using molecular data. This bias is the reason that they only targeted researchers who proposed changes in the higher-level taxonomy of fishes using phylogenetic hypotheses based on DNA sequence data (Miya et al. 2007, Smith & Craig 2007, Thacker 2009). In criticizing these studies, they do not suggest any alternative relationships or provide any counter evidence to the proposed relationships.” And on page 8, they apparently read our thoughts (aside from the title, none of the words in quotations was written by us in that context) and concluded: “Mooi & Gill entitled their paper “A crisis in fish systematics” because they long for the days when “real” ichthyologists found “meaningful” characters and “true” relationships.” Finally (p. 9), they contend that “Mooi & Gill’s various studies are usually focused on Johnson & Patterson’s (1993: 555) “disparate twigs of the [percomorph] tree,” whereas the explicit studies they criticize are large-scale and taxon rich datasets that have not otherwise been analyzed in Percomorpha.”

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Listeria monocytogenes: Knowledge Gained Through DNA Sequence-Based Subtyping, Implications, and Future Considerations

Journal of AOAC International ◽

10.1093/jaoac/93.4.1275 ◽

2010 ◽

Vol 93 (4) ◽

pp. 1275-1286 ◽

Cited By ~ 14

Author(s):

Kendra Nightingale

Keyword(s):

Listeria Monocytogenes ◽

Dna Sequence ◽

Foodborne Pathogens ◽

Sequence Data ◽

Human Pathogens ◽

Molecular Subtyping ◽

Genetic Lineages ◽

Dna Sequence Data ◽

Cellular Components

Abstract The purpose of subtyping is to differentiate bacterial isolates beyond the classification of species or subspecies. Subtyping methods can be grouped into two broad categories based on the cellular components targeted: (1) phenotypic subtyping methods that differentiate isolates by the enzymes, proteins, or other metabolites expressed by the cell, and (2) molecular subtyping methods that discriminate isolates based on interrogation of nucleic acid sequences. The two major types of molecular subtyping methods include band-based methods based on fragment pattern data or DNA fingerprints, and methods that generate DNA sequence data. Molecular subtyping methods have shown that Listeria monocytogenes isolates can be classified into four genetic lineages or divisions. Although band-based molecular subtyping methods continue to serve as the gold standard for routine molecular subtyping of most clinically important foodborne pathogens, including L. monocytogenes, the explosion of recently completed and ongoing DNA sequencing projects, and thus available DNA sequence data, have stimulated efforts to develop highly discriminatory and high-throughput DNA sequence-based subtyping methods for L. monocytogenes. L. monocytogenes represents one of the most highly sequenced human pathogens; more than 20 genome sequences are currently available for this organism. This review provides an overview of the concepts behind subtyping and discusses the application of molecular subtyping methods, with an emphasis on DNA sequence-based subtyping methods to characterize L. monocytogenes.

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A revised classification of the Icteridae (Aves) based on DNA sequence data

Zootaxa ◽

10.11646/zootaxa.4093.2.9 ◽

2016 ◽

Vol 4093 (2) ◽

pp. 285 ◽

Cited By ~ 8

Author(s):

J. V. JR. REMSEN ◽

ALEXIS F. L. A. POWELL ◽

RICHARD SCHODDE ◽

F. KEITH BARKER ◽

SCOTT M. LANYON

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Dna Sequence Data

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Freshwater Sordariomycetes

Fungal Diversity ◽

10.1007/s13225-019-00438-1 ◽

2019 ◽

Vol 99 (1) ◽

pp. 451-660 ◽

Cited By ~ 17

Author(s):

Zong-Long Luo ◽

Kevin D. Hyde ◽

Jian-Kui (Jack) Liu ◽

Sajeewa S. N. Maharachchikumbura ◽

Rajesh Jeewon ◽

...

Keyword(s):

Dna Sequence ◽

New Records ◽

Sequence Data ◽

New Order ◽

Stachybotrys Chartarum ◽

Sequence Analyses ◽

Diverse Range ◽

Dna Sequence Data ◽

Comprehensive Classification

Abstract Sordariomycetes is one of the largest classes of Ascomycota that comprises a highly diverse range of fungi mainly characterized by perithecial ascomata and inoperculate unitunicate asci. Freshwater Sordariomycetes play an important role in ecosystems and some of them have the potential to produce bioactive compounds. This study documents and reviews the freshwater Sordariomycetes, which is one of the largest and important groups of fungi in aquatic habitats. Based on evidence from DNA sequence data and morphology, we introduce a new order Distoseptisporales, two new families, viz. Ceratosphaeriaceae and Triadelphiaceae, three new genera, viz. Aquafiliformis, Dematiosporium and Neospadicoides, 47 new species, viz. Acrodictys fluminicola, Aquafiliformis lignicola, Aquapteridospora fusiformis, Arthrinium aquaticum, Ascosacculus fusiformis, Atractospora aquatica, Barbatosphaeria lignicola, Ceratosphaeria aquatica, C. lignicola, Chaetosphaeria aquatica, Ch. catenulata, Ch. guttulata, Ch. submersa, Codinaea yunnanensis, Conioscypha aquatica, C. submersa, Cordana aquatica, C. lignicola, Cosmospora aquatica, Cylindrotrichum submersum, Dematiosporium aquaticum, Dictyochaeta cangshanensis, D. ellipsoidea, D. lignicola, D. submersa, Distoseptispora appendiculata, D. lignicola, D. neorostrata, D. obclavata, Hypoxylon lignicola, Lepteutypa aquatica, Myrmecridium aquaticum, Neospadicoides aquatica, N. lignicola, N. yunnanensis, Ophioceras submersum, Peroneutypa lignicola, Phaeoisaria filiformis, Pseudostanjehughesia lignicola, Rhodoveronaea aquatica, Seiridium aquaticum, Sporidesmiella aquatica, Sporidesmium lageniforme, S. lignicola, Tainosphaeria lunata, T. obclavata, Wongia aquatica, two new combinations, viz. Acrodictys aquatica, Cylindrotrichum aquaticum, and 9 new records, viz. Chaetomium globosum, Chaetosphaeria cubensis, Ch. myriocarpa, Cordana abramovii, Co. terrestris, Cuspidatispora xiphiago, Sporidesmiella hyalosperma, Stachybotrys chartarum,S. chlorohalonata. A comprehensive classification of the freshwater Sordariomycetes is presented based on updated literature. Phylogenetic inferences based on DNA sequence analyses of a combined LSU, SSU, RPB2 and TEF1α dataset comprising species of freshwater Sordariomycetes are provided. Detailed information including their habitats distribution, diversity, holotype, specimens collected and classification are provided.

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Additions to the genus Trapelia (Trapeliaceae: lichenised Ascomycetes)

Australian Systematic Botany ◽

10.1071/sb14037 ◽

2014 ◽

Vol 27 (6) ◽

pp. 395 ◽

Cited By ~ 9

Author(s):

Gintaras Kantvilas ◽

Steven D. Leavitt ◽

John A. Elix ◽

H. Thorsten Lumbsch

Keyword(s):

New Species ◽

Dna Sequence ◽

Western Australia ◽

Sequence Data ◽

Dna Sequence Data ◽

Two New Species

Two new species in the genus Trapelia, namely, T. calvariana Kantvilas & Lumbsch from the Tasmanian highlands and T. thieleana Kantvilas & Lumbsch from south-western Western Australia, are described. Examination of ascus types and analyses of DNA-sequence data confirmed the inclusion of these taxa in Trapelia sensu lato, but raised questions concerning the homogeneity of the genus as currently circumscribed and, in particular, the generic classification of T. lilacea Kantvilas & Elix.

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