scholarly journals The molecular phylogenetic status of <i>Elphidium williamsoni</i> (Haynes, 1973) as inferred from partial 18S-rDNA sequences

2001 ◽  
Vol 20 (2) ◽  
pp. 183-183 ◽  
Author(s):  
Martin R. Langer
Keyword(s):  
North Sea ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Small Subunit ◽  
The North ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
The North Sea ◽  
Muddy Sediments

Abstract. Comparative studies on DNA nucleotide sequences have revolutionized our understanding of the phylogenetic relationships of many organisms and have become an important tool in evolutionary, ecological and palaeobiological inquiry. We have analysed partial small-subunit 18S sequences (srDNA) of Elphidium williamsoni (Haynes, 1973), a common intertidal benthic foraminiferid from the North Sea. The molecular phylogenetic analysis of the ribosomal rDNA sequence data indicate that E. williamsoni constitutes a well-defined genetic entity that is closely related to Elphidium aculeatum.Elphidium williamsoni is a prominent and frequently encountered foraminiferid in the North Sea and other tidal flats. It was originally described by Williamson (1858) as Polystomella umbilicata and subsequently renamed by Haynes (1973). Because of its phenotypic similarities with other elphidiids, this species has been frequently confused with, for example E. excavatum or Cribrononion alvarezianum (see Haynes for discussion). The molecular data provided here, and their direct comparison to other benthic foraminifera including one elphidiid, may therefore provide additional insight into the taxonomic status and the validity of this species.Individuals of the foraminiferid Elphidium williamsoni were collected in October 1997 from the intertidal mud flats of the Crildumersiel at the outer Jade Bay near Wilhelmshaven, North Sea (see Langer et al., 1989 for details). The mud flats are characterized by fine-grained, muddy sediments containing high contents of organic material. In the laboratory, specimens were transferred into petri dishes, examined and cleaned under a stereo microscope. Living specimens of E. williamsoni were picked out separately and placed into clean glass dishes containing filtered. . .

A revision of the Leptogium saturninum group in North America

2016 ◽  
Vol 48 (5) ◽  
pp. 387-421 ◽  
Author(s):  
Daphne F. STONE ◽  
James W. HINDS ◽  
Frances L. ANDERSON ◽  
James C. LENDEMER
Keyword(s):  
North American ◽  
Morphological Study ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Lower Surface ◽  
Molecular Data ◽  
The North ◽  
Molecular Phylogenetic ◽  
Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

scholarly journals Use of nuclear genes for phylogeny reconstruction in plants

2004 ◽  
Vol 17 (2) ◽  
pp. 145 ◽  
Author(s):  
Randall L. Small ◽  
Richard C. Cronn ◽  
Jonathan F. Wendel
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Nuclear Genes ◽  
Universal Primers ◽  
Plant Systematics ◽  
Dna Sequence Data ◽  
Rdna Sequences ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Orthologous Loci

Molecular data have had a profound impact on the field of plant systematics, and the application of DNA-sequence data to phylogenetic problems is now routine. The majority of data used in plant molecular phylogenetic studies derives from chloroplast DNA and nuclear rDNA, while the use of low-copy nuclear genes has not been widely adopted. This is due, at least in part, to the greater difficulty of isolating and characterising low-copy nuclear genes relative to chloroplast and rDNA sequences that are readily amplified with universal primers. The higher level of sequence variation characteristic of low-copy nuclear genes, however, often compensates for the experimental effort required to obtain them. In this review, we briefly discuss the strengths and limitations of chloroplast and rDNA sequences, and then focus our attention on the use of low-copy nuclear sequences. Advantages of low-copy nuclear sequences include a higher rate of evolution than for organellar sequences, the potential to accumulate datasets from multiple unlinked loci, and bi-parental inheritance. Challenges intrinsic to the use of low-copy nuclear sequences include distinguishing orthologous loci from divergent paralogous loci in the same gene family, being mindful of the complications arising from concerted evolution or recombination among paralogous sequences, and the presence of intraspecific, intrapopulational and intraindividual polymorphism. Finally, we provide a detailed protocol for the isolation, characterisation and use of low-copy nuclear sequences for phylogenetic studies.

scholarly journals Species identification of echinoderms from the North Sea by combining morphology and molecular data

2016 ◽  
Vol 70 (1) ◽  
Author(s):  
Silke Laakmann ◽  
Karin Boos ◽  
Thomas Knebelsberger ◽  
Michael J. Raupach ◽  
Hermann Neumann
Keyword(s):  
Species Identification ◽  
North Sea ◽  
Molecular Data ◽  
The North ◽  
The North Sea

scholarly journals The application of DNA sequence data for the identification of benthic nematodes from the North Sea

2014 ◽  
Vol 68 (4) ◽  
pp. 549-558 ◽  
Author(s):  
Philipp Vogt ◽  
Maria Miljutina ◽  
Michael J. Raupach
Keyword(s):  
Dna Sequence ◽  
North Sea ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
The North ◽  
The North Sea

scholarly journals Species of the diatom taxa <i>Aulacodiscus</i> and <i>Trinacria</i> with biostratigraphic utility in Palaeogene and Neogene North Sea sediments

2019 ◽  
Vol 38 (1) ◽  
pp. 67-81
Author(s):  
Alexander G. Mitlehner
Keyword(s):  
North Sea ◽  
Taxonomic Status ◽  
Sem Analysis ◽  
Marine Diatom ◽  
Separate Species ◽  
The North ◽  
Northwest Europe ◽  
The North Sea ◽  
A Chain ◽  
Sem Studies

Abstract. Species of Aulacodiscus and Trinacria, two important marine diatom genera with biostratigraphic utility in offshore North Sea exploration and onshore correlation, are identified, described and emended and the North Sea microfaunal zonation scheme is revised accordingly. Occurring mainly as pyritised diatom moulds or steinkerns, detailed scanning electron microscope (SEM) analysis of several specimens, formerly in open nomenclature, has allowed the correct taxonomic identification of pyritised morphologies found to belong to the genus Aulacodiscus, including A. allorgei, A. heterostictus, A. insignis, A. singilewskyanus, A. subexcavatus and A. suspectus. The important marker species Trinacria regina is emended. SEM studies, using specimens preserved in pyrite and original silica, have shed further light on the varying forms and frustule morphology of Trinacria regina so that valves and frustules formerly thought to represent separate species are now found to be grouped within this taxon; SEM studies have shown that many of these variations represent different valves within a chain, whilst others may signify ecophenotypic variants. Emendments are therefore made to clarify the taxonomic status of different variants within T. regina, important in the Palaeocene–Eocene boundary interval onshore and offshore such as the Sele and Balder formations and the Fur Formation diatomite of Jutland, Denmark. Species of taxa formerly in open nomenclature are now assigned to Aulacodiscus insignis, which are important offshore markers in offshore late Oligocene to early Miocene sediments in northwest Europe.

On the Feeding of the Hagfish Myxine Glutinosa in the North Sea

1978 ◽  
Vol 58 (1) ◽  
pp. 81-86 ◽  
Author(s):  
R. G. J. Shelton
Keyword(s):  
North Sea ◽  
Pink Shrimp ◽  
Department Of Agriculture ◽  
Myxine Glutinosa ◽  
The North ◽  
Biological Interest ◽  
The North Sea ◽  
Normal Feeding ◽  
Biological Sampling ◽  
Muddy Sediments

The myxinoid cyclostomes, of which the hagfish Myxine glutinosa L. is one of the best known examples, are of unique biological interest as representatives of a group of jawless vertebrates which probably had their origin in the pteraspidomorph ostracoderms of the Ordovician era (Nybelin, 1973). They have been much studied by comparative anatomists and physiologists but somewhat neglected by ecologists. There is, for instance, very little critical information on their normal feeding biology. Perhaps one reason for this is that, although hagfish may be extremely abundant locally (their principal habitat requirements are stable, soft muddy sediments and a salinity in excess of 31 %, (Gustafson, 1935)), they tend to be missed by most exploratory fishing and biological sampling programmes. This is because benthic sampling techniques are often ill-adapted for the capture of large active organisms capable of swimming and burrowing and because, unless blocked by the catch, the cod-end mesh sizes of the trawls used by most British commercial fishermen would easily permit the escape of even the largest hagfish. However, the research otter trawls used by the Department of Agriculture and Fisheries for Scotland (D.A.F.S.) for surveying the North Sea stocks of the deep water pink shrimp, Pandalus borealis Krøyer, are fitted with cod-end covers of small mesh, and it is found that the catches frequently include small numbers of hagfish, presumably caught while swimming close to the bottom, or possibly when buried in the surface of the sediments. The present study is largely based on the examination of hagfish collected during the D.A.F.S. Pandalus surveys of 1975 and 1976. The remaining material was kindly provided by Dr J. B. Buchanan of the Dove Marine Laboratory at Cullercoats, Northumberland.

Taxonomic status of section Neuropogon in the genus Usnea elucidated by morphological comparisons and ITS rDNA sequences

2004 ◽  
Vol 36 (3-4) ◽  
pp. 217-225 ◽  
Author(s):  
Yoshihito OHMURA ◽  
Hiroshi KANDA
Keyword(s):  
Phylogenetic Analysis ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Taxonomic Position ◽  
Its Sequences ◽  
Rdna Sequences ◽  
Representative Species ◽  
Molecular Phylogenetic ◽  
Black Pigmentation ◽  
Iodine Reaction

The taxonomic position of the Neuropogon group, as inferred from the morphology of representative species of the group and ITS sequences from Usnea antarctica and U. sphacelata, is discussed. Morphological observations revealed that the Neuropogon group does not have annular-pseudocyphellae, which are characteristic of the subgenus Dolichousnea, or a fistulose axis, which is characteristic of the subgenus Eumitria. In addition, the hypothecium of Neuropogon is thin, and the iodine reaction in the axis is negative. These features are consistent with those of the subgenus Usnea. Within the subgenus Usnea, Neuropogon is morphologically distinct from sections Usnea and Ceratinae (i.e. having a sphacelata-type cortex, black pigmentation of the upper thallus and a dark brown apothecial disc). The molecular data suggest that U. antarctica and U. sphacelata are members of the subgenus Usnea and are less closely related to subgenera Dolichousnea and Eumitria. The morphological and molecular phylogenetic analysis suggest that the Neuropogon group is a member of the subgenus Usnea at the level of a section, and the appropriate name for this group is subgenus Usnea section Neuropogon (Nees & Flot.) Mont.

Molecular examination of kalyptorhynch diversity (Platyhelminthes: Rhabdocoela), including descriptions of five meiofaunal species from the north-eastern Pacific Ocean

2014 ◽  
Vol 94 (3) ◽  
pp. 499-514 ◽  
Author(s):  
Rebecca J. Rundell ◽  
Brian S. Leander
Keyword(s):  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Eastern Pacific Ocean ◽  
North West ◽  
The North ◽  
Rdna Sequences ◽  
The Pacific ◽  
North Eastern ◽  
Molecular Phylogenetic ◽  
18S Rdna Sequences

The spaces between sand grains are home to a myriad of microscopic marine eukaryotes, including kalyptorhynch rhabdocoels equipped with an eversible proboscis that enables them to capture microscopic prey living in these environments. The structure of the kalyptorhynch proboscis separates the two major subclades within the group: the Schizorhynchia (bifurcated proboscis) and the Eukalyptorhynchia (unbranched proboscis). A survey of meiofaunal metazoans in the Pacific north-west led to the discovery of three new schizorhynch species (Undicola tofinoensisgen. nov., sp. nov.,Schizorhinos vancouverensisgen. nov., sp. nov. andLinguabana tulaigen. nov., sp. nov.) and two new eukalyptorhynch species (Thinodactylaina tlaoquiahtensisgen. nov., sp. nov. andRostracilla nuuchahnulthensisgen. nov., sp. nov.). This survey also recovered the putative cosmopolitan eukalyptorhynch (Polycystididae)Gyratrix hermaphroditusEhrenberg, 1831. We performed molecular phylogenetic analyses on 18S rDNA sequences from all five novel isolates and from all available kalyptorhynch species in GenBank. The molecular data supported the monophyly of the Eukalyptorhynchia and Schizorhynchia and helped demonstrate the boundaries between different species within the Kalyptorhynchia.

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