Nematode taxonomy - the dr. P.A.A. Loof Literature Collection

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  • Although relatively small and inconspicuous, nematodes are probably one of the most abundant animals on our planet. They are present in enormous numbers in soil and sediments, and play important roles in soil and sediment food webs. Apart from this, nematodes have a reputation as pathogens of humans, animals and plants.

    The phylum Nematoda currently harbours approximately 27,000 documented species, but the relatively conserved morphology of this group of animals make the identification of these vermiform organisms rather difficult. The establishment of a stable phylogeny of the phylum Nematoda has been complicated by the high level of convergent evolution among morphological characters (in other words: numerous morphological characters have arisen multiple times independently).

    These are main underlying reasons that explain why nematode systematics have been unstable for such a long time. The dr. P.A.A. Loof Literature Collection harbours almost all taxonomic papers that have been published from the beginning of the 20th century onwards. Many of these papers have been published in journals that are not yet (and/or will probably not be) digitalized, and this digital portal gives access to this substantial body of (mainly) pre-digital specialized taxonomic literature. The Loof Literature Collection contains 3340 records, out of which eventually 3100 will be offered in full text. When articles cannot be offered in full text due to copyrights, DOIs will be added to the records.

    The information made available over here can be used for taxonomic and systematic nematological studies, and will contribute to the ecological and biological understanding of this highly biodiverse animal group.   

    For questions or information e-mail: Office.nema@wur.nl

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A key and diagnostic compendium to the species of the genus Merlinius Siddiqi, 1970 (Nematoda: Tylenchida), with description of Merlinius khuzdarensis sp. nov. associated with date palm \ Nematology : international journal of fundamental and applied nematological research [Article]
Handoo, Z.A. \ Aly, Khan \ Shamsul, Islam \ 2007
dates - descriptions - head - keys - new species - plant pests - tail - vulva - Merlinius - Phoenix dactylifera - invertebrates - animals - eukaryotes - Phoenix - Arecaceae - Arecales - monocotyledons - angiosperms - Spermatophyta - plants - Pakistan - Commonwealth of Nations - Developing Countries - South Asia - Asia - Balochistan - plant parasitic nematodes - female genitalia - male genitalia - nematoda - taxonomy - Nematodes - Nematodes Research

An identification key to 32 valid species of stunt nematodes (Merlinius spp.) is given. A compendium of the most important diagnostic characters for use in identification of species is included as a practical alternative and supplement to the key. The diagnosis of Merlinius is emended and a list of all valid species of the genus is given. The characters most useful for separating species include body and stylet lengths, shape of head, tail and tail terminus, number of head and tail annules, position of vulva (V), and c' ratio in females. Also useful are length and shape of spicules and gubernacula in males. A new stunt nematode, Merlinius khuzdarensis n. sp., from the rhizosphere of date palm (Phoenix dactylifera L.) from Khuzdar, Balochistan Province, Pakistan, is described and illustrated. This new species resembles M. bavaricus, M. communicus, M. bilqeesae and M. montanus, but differs from these species by the following: body and stylet length, shape of head, tail and tail terminus, number of head and tail annules, and position of phasmids. Because this species is limited in distribution, its economic importance in date palm and other cultivated crops within the region is not known.

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Supplementary characters of Bursaphelenchus lini Braasch, 2004 (Nematoda: Parasitaphelenchidae) and remarks on this nematode \ Zootaxa [Article]
Braasch, H. \ 2006
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Rhaptothyreus typicus Hope & Murphy, 1969 (Nematoda: Rhaptothyreidae): an anatomical study of an unusual deep-sea nematode \ Nematology : international journal of fundamental and applied nematological research [Article]
Miljutin, D.M. \ Tchesunov, A.V. \ Hope, W.D. \ 2006
anatomy - aquatic animals - descriptions - marine environment - marine nematodes - morphometrics - ultrastructure - invertebrates - animals - eukaryotes - marine organisms - nematoda - taxonomy - Nematodes - Nematodes Research

Descriptions are given for the males of Rhaptothyreus typicus, a morphologically unique and incompletely investigated deep-sea nematode, using light microscopy, TEM, and SEM. The cephalic sensilla are arranged in two circles: an anterior circle consisting of six pairs of papilliform sensilla and a posterior circle consisting of four papilliform sensilla. The fovea of the giant, oblong, amphid is covered with cuticle bearing minute perforations. The actual amphidial aperture, revealed only by TEM, is minute and slit-like. The apical oral aperture is reduced to a simple pore and the vestigial pharynx is devoid of an internal lumen and musculature. The mid-gut is a trophosome consisting of a solid mass of irregularly-shaped cells filled with rod-shaped structures that are assumed to be intracellular symbiotic bacteria. There is no evidence of even a vestige of a reproductive system except for the presence of the single spiculum. The phylogenetic relationships of Rhaptothyreus remain unknown.

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Phylogenetic relationships of Steinernema Travassos, 1927 (Nematoda: Cephalobina: Steinernematidae) based on nuclear, mitochondrial and morphological data \ Systematic parasitology [Article]
Nadler, S.A. \ Bolotin, E. \ Stock, S.P. \ 2006
entomopathogens - mitochondrial DNA - natural enemies - pathogens - phylogenetics - Steinernema - Steinernematidae - invertebrates - animals - eukaryotes - DNA - nucleotide sequences - entomophilic nematodes - nematoda - taxonomy

Entomopathogenic nematodes of the genus Steinernema are lethal parasites of insects that are used as biological control agents of several lepidopteran, dipteran and coleopteran pests. Phylogenetic relationships among 25 Steinernema species were estimated using nucleotide sequences from three genes and 22 morphological characters. Parsimony analysis of 28S (LSU) sequences yielded a well-resolved phylogenetic hypothesis with reliable bootstrap support for 13 clades. Parsimony analysis of mitochondrial DNA sequences (12S rDNA and cox 1 genes) yielded phylogenetic trees with a lower consistency index than for LSU sequences, and with fewer reliably supported clades. Combined phylogenetic analysis of the 3-gene dataset by parsimony and Bayesian methods yielded well-resolved and highly similar trees. Bayesian posterior probabilities were high for most clades; bootstrap (parsimony) support was reliable for approximately half of the internal nodes. Parsimony analysis of the morphological dataset yielded a poorly resolved tree, whereas total evidence analysis (molecular plus morphological data) yielded a phylogenetic hypothesis consistent with, but less resolved than trees inferred from combined molecular data. Parsimony mapping of morphological characters on the 3-gene trees showed that most structural features of steinernematids are highly homoplastic. The distribution of nematode foraging strategies on these trees predicts that S. hermaphroditum, S. diaprepesi and S. longicaudum (US isolate) have cruise forager behaviours.

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A new species of Cycliophora from the mouthparts of the American lobster, Homarus americanus (Nephropidae, Decapoda) \ Organisms, diversity & evolution : journal of the Gesellschaft für Biologische Systematik [Article]
Obst, M. \ Funch, P. \ Kristensen, R.M. \ 2006
Homarus americanus
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Description of Pratylenchus dunensis sp. n. (Nematoda: Pratylenchidae), a root-lesion nematode associated with the dune grass Ammophila arenaria (L.) Link \ Nematology : international journal of fundamental and applied nematological research [Article]
Pena, E. de la \ Moens, M. \ Aelst, A. van \ Karssen, G. \ 2006
descriptions - morphology - morphometrics - new species - plant pests - ribosomal DNA - wild relatives - Ammophila arenaria - Elymus farctus - Pratylenchus - Ammophila - Poaceae - Cyperales - monocotyledons - angiosperms - Spermatophyta - plants - eukaryotes - Elymus - invertebrates - animals - Pratylenchidae - nucleotide sequences - plant parasitic nematodes - nematoda - restriction fragment length polymorphism - intergenic DNA - taxonomy - Nematodes - Nematodes Research

A root-lesion nematode, Pratylenchus dunensis sp. n., is described and illustrated from Ammophila arenaria (L.) Link, a grass occurring abundantly in coastal dunes of Atlantic Europe. The new species is characterised by medium sized (454-579 micro m) slender, vermiform, females and males having two lip annuli (sometimes three to four; incomplete incisures only visible with scanning electron microscopy), medium to robust styler (ca 16 micro m) with robust styler knobs slightly set off, long pharyngeal glands (ca 42 micro m), lateral field with four parallel, non-equidistant, lines, the middle ridge being narrower than the outer ones, lateral field with partial areolation and lines converging posterior to the phasmid which is located between the two inner lines of the lateral field in the posterior half of the tail, round spermatheca filled with round sperm, vulva at 78% of total body length and with protruding vulval lips, posterior uterine sac relatively short (ca 19 micro m), cylindrical tail (ca 33 micro m) narrowing in the posterior third with smooth tail tip and with conspicuous hyaline part (ca 2 micro m). Males occur abundantly and present similar characteristics except for smaller dimensions for all morphological characters, but the head region is more truncated in outline than the female, spicule length is ca 15 micro m and testis length is ca 195 micro m. Nucleotide sequences of the rDNA expansion region D2D3 differed from the morphologically similar species P. penetrans and P. brzeskii that also occur in coastal dunes. These differences are supported by PCR-RFLP of the ITS-rDNA. Pratylenchus dunensis sp. n. was also found parasitising roots of Elymus farctus Viv.

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Perplexities concerning the Ecdysozoa: A reply to Pilato et al. \ Zoologischer Anzeiger : zugleich Organ der Deutschen Zoologischen Gesellschaft [Article]
Schmidt-Rhaesa, A. \ 2006
- Zoology
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Two new species of the genus Prionchulus Cobb, 1916 (Nematoda: Mononchina) \ Annales zoologici [Article]
Susulovsky, A. \ Winiszewska, G. \ 2006
habitats - morphology - new species - Prionchulus - Taiwan - Ukraine - Mononchidae - invertebrates - animals - eukaryotes - APEC countries - Developed Countries - South East Asia - Asia - Central Europe - Europe - Formosa (Bacteria) - nematoda - taxonomy - Zoology - Zoology Poland - Animals - Zoology

Prionchulus hygrophilus sp. nov. and P. bogdanowiczi sp. nov., collected from Ukraine and Taiwan, respectively, are described in terms of male and female morphology, type locality, habitat and etymology.

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Female size shows similar trends in all clades of the phylum Nematoda \ Nematology : international journal of fundamental and applied nematological research [Article]
Yeates, G.W. \ Boag, B. \ 2006
biomass - cladistics - habitats - morphology - phylogeny - invertebrates - animals - eukaryotes - zoogeography - nematoda - Nematodes - Nematodes Research

To seek unifying principles underlying adult body size in the phylum Nematoda, the volume of females of 3150 nematode species in 186 genera has been calculated from published length and diameter information; genera are grouped using the rDNA-based clades of De Ley et al. While the mass of females in some of the clades overlap, there are usually distinct differences within any particular clade between those nematodes that exist in living substrates and those that do not, the latter invariably being smaller. In all five clades (but not Chromadorida) the ability for females to achieve relatively great size is normal, but diminutive females are known from most clades and habitats. Bacterial feeding is common in females in non-living substrates and related females in living substrates, which may represent alternate generations, are often larger. If both groups of females are bacterial feeding it would help to understand the conundrum of whether those in living substrates are larger because they utilise better physical conditions or are larger because they are required to produce more propagules. Female body volume has previously been successfully used in zoogeography and further investigations may include not only adult volume but also address the question of stage-to-stage growth for which earlier studies revealed a paucity of data. This survey of the phylum has not been controlled for phylogeny, apart from the use of clades, and detailed studies could be made within clades. In particular, the effect of substrate, controlled through using species with alternate life cycles, should be tractable.

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Nematodes of the order Rhabditida from Andalucia Oriental: Pseudacrobeles elongatus (de Man, 1880) comb. n \ Nematology : international journal of fundamental and applied nematological research [Article]
Abolafia, J. \ Pena-Santiago, R. \ 2005
descriptions - morphology - new combination - synonyms - Cephalobidae - Rhabditidae - Spain - invertebrates - animals - eukaryotes - Developed Countries - European Union Countries - Mediterranean Region - OECD Countries - Southern Europe - Europe - free living nematodes - nematoda - taxonomic revisions - taxonomy - Nematodes - Nematodes Research

Material of the nematode previously known as Heterocephalobus elongatus (and the type of the genus) was collected in four localities from the southern Iberian Peninsula and is described and illustrated. The first SEM study of the species is presented. The species is transferred to the genus Pseudacrobeles on the basis that the lateral field fades out near the phasmid. Within this genus it is classified under the subgenus Pseudacrobeles as the lip region has a triradiate symmetry. The combination Pseudacrobeles (Pseudacrobeles) elongatus (de Man, 1880) comb. n. is proposed. As a result of synonymising the type of Heterocephalobus, the genus itself becomes a junior synonym and is herein placed under the genus Pseudacrobeles, subgenus Pseudacrobeles. The species formerly listed under Heterocephalobus are returned to their original combination and listed as species incertae sedis or species inquirendae.

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A new and a known species of the genus Chrysonema Thorne, 1929 (Nematoda: Dorylaimida) from Costa Rica \ Nematologia Mediterranea [Article]
Ahmad, W. \ Shaheen, A. \ 2005
descriptions - forest pests - lips - morphology - new species - plant pests - tail - vulva - Asteraceae - Dorylaimidae - Ericaceae - Poaceae - Costa Rica - Asterales - dicotyledons - angiosperms - Spermatophyta - plants - eukaryotes - invertebrates - animals - Ericales - Cyperales - monocotyledons - CACM - Central America - America - Developing Countries - Latin America - Threshold Countries - plant parasitic nematodes - female genitalia - nematoda - taxonomy

A new and a known species of the genus Chrysonema are described and illustrated from Costa Rica. Chrysonema inbionis sp. nov. is characterized by having a 1.43- to 1.58-mm long and slender body, continuous lip region with amalgamated lips, slender odontostyle, comparatively anterior vulva, amphidelphic female reproductive system, and elongate ventrally arcuate tail. The habitats of C. inbionis consisted of plants from Gramineae, Ericaceae and Asteraceae. C. attenuatum, a rare species, is re-described based on a single female and a male specimens collected from Costa Rica.

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Defining operational taxonomic units using DNA barcode data \ Philosophical transactions / Royal Society of London. Biological sciences [Article]
full text The Royal Society ; Vol. 352(1997)-
full text Free Access Journals ; (1887)-
full text JSTOR Life Sciences Collection ; Vol. 187(1896)-(2014)
Blaxter, M. \ Mann, J. \ Chapman, T. \ Thomas, F. \ Whitton, C. \ Floyd, R. \ Abebe, E. \ 2005
nematoda - Science - Meteorology Great Britain - Biology - Meteorology - Science
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The unholy trinity: taxonomy, species delimitation and DNA barcoding. (Special issue: DNA barcoding of life.) \ Philosophical transactions / Royal Society of London. Biological sciences [Article]
full text The Royal Society ; Vol. 352(1997)-
full text Free Access Journals ; (1887)-
full text JSTOR Life Sciences Collection ; Vol. 187(1896)-(2014)
DeSalle, R. \ Egan, M.G. \ Siddall, M. \ 2005
databases - DNA - nucleotide sequences - methodology - DNA sequencing - taxonomy - Science - Meteorology Great Britain - Biology - Meteorology - Science

Recent excitement over the development of an initiative to generate DNA sequences for all named species on the planet has in our opinion generated two major areas of contention as to how this 'DNA barcoding' initiative should proceed. It is critical that these two issues are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can be universalized. The first issue concerns how DNA data are to be used in the context of this initiative; this is the DNA barcode reader problem (or barcoder problem). Currently, many of the published studies under this initiative have used tree building methods and more precisely distance approaches to the construction of the trees that are used to place certain DNA sequences into a taxonomic context. The second problem involves the reaction of the taxonomic community to the directives of the 'DNA barcoding' initiative. This issue is extremely important in that the classical taxonomic approach and the DNA approach will need to be reconciled in order for the 'DNA barcoding' initiative to proceed with any kind of community acceptance. In fact, we feel that DNA barcoding is a misnomer. Our preference is for the title of the London meetings - Barcoding Life. In this paper we discuss these two concerns generated around the DNA barcoding initiative and attempt to present a phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of 'DNA barcoding'.

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About teraty (Morphological Anomalies) in Genus Typha L. \ Biologiya Vnutrennikh Vod [Article]
Gagarin, V.G. \ 2005
Typha latifolia
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All living things, online \ Nature : international journal of science [Article]
Gewin, V. \ 2005
- Science
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Morphological and molecular characterization of Longidorus americanum n. sp. (Nematoda: Longidoridae), a needle nematode parasitizing pine in Georgia \ Journal of nematology : official journal of Society of Nematologists [Article]
Handoo, Z.A. \ Carta, L.K. \ Skantar, A.M. \ Ye, W. \ Robbins, R.T. \ Subbotin, S.A. \ Fraedrich, S.W. \ Cram, M.M. \ 2005
descriptions - forest pests - genetic analysis - molecular taxonomy - morphology - new species - phylogenetics - plant pests - ribosomal DNA - seedlings - Longidorus - Pinus taeda - Georgia - Longidoridae - invertebrates - animals - eukaryotes - Pinus - Pinaceae - Pinopsida - gymnosperms - Spermatophyta - plants - South Atlantic States of USA - Southern States of USA - APEC countries - Developed Countries - North America - America - OECD Countries - Southeastern States of USA - plant parasitic nematodes - nematoda - taxonomy - USA

A new needle nematode, Longidorus americanum sp. nov., associated with patches of severely stunted and chlorotic loblolly pine, (Pinus taeda) seedlings in seedbeds in Byromville, Georgia, USA, was described and illustrated. It is characterized by having females with a body length of 5.4-9.0 mm; lip region slightly swollen and anteriorly flattened, giving the anterior end a truncate appearance; long odontostyle (124-165 micro m); vulva at 44-52% of body length; and tail conoid and bluntly rounded. Males are rare but present, and in general, are shorter than females. The new species is morphologically similar to L. biformis, L. paravineacola, L. saginus, and L. tarjani but differs from these species either by the body, odontostyle and total stylet length, or by head and tail shape. Sequence data from the D2-D3 region of the 28S rDNA distinguishes this new species from other Longidorus species. Phylogenetic relationships of L. americanum sp. nov. with other longidorids based on analysis of this DNA fragment are presented. Additional information regarding the distribution of this species within the region is required.

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A molecular phylogenetic approach to Longidoridae (Nematoda: Dorylaimida) \ Nematology : international journal of fundamental and applied nematological research [Article]
He, Y. \ Subbotin, S.A. \ Rubtsova, T.V. \ Lamberti, F. \ Brown, D.J.F. \ Moens, M. \ 2005
genes - molecular taxonomy - phylogenetics - phylogeny - plant pests - Longidoridae - Longidorus - Paralongidorus - Xiphidorus - Xiphinema - Xiphinema americanum - invertebrates - animals - eukaryotes - nucleotide sequences - plant parasitic nematodes - nematoda - ribosomal RNA - taxonomy - Nematodes - Nematodes Research

The Longidoridae are a group of ectoparasitic nematodes including two subfamilies and six genera with hundreds of species. Sequences of the D2 and D3 expansion region of the large subunit (LSU) rRNA nuclear gene were amplified and used to reconstruct the phylogeny of longidorids. Phylogenetic analyses with maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) were performed with one outgroup taxon and 62 longidorid sequences. Confidence of inferred clades was assessed by non-parametric bootstrapping for MP and Bayesian posterior probability for ML. All analyses placed Paralongidorus species as an inner group within the otherwise monophyletic genus Longidorus. The genus Xiphinema, except for X. americanum-group species, was placed as the sister group of Longidorus with strong support from the ML and BI analyses. The Xiphinema americanum-group was strongly supported as an exclusive clade to other genus Xiphinema species. The position of the Xiphidorus clade was not well resolved and the phylogenetic analyses did not support it as a sister group to Longidorus as previously inferred from morphology. Secondary structure models were constructed for the D2/D3 region of LSU rRNA for all studied species. It was found that sequence-based and structural morphometric rRNA phylogenies were incongruent.

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Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences \ Philosophical transactions / Royal Society of London. Biological sciences [Article]
full text The Royal Society ; Vol. 352(1997)-
full text Free Access Journals ; (1887)-
full text JSTOR Life Sciences Collection ; Vol. 187(1896)-(2014)
Markmann, M.andTautz,D. \ 2005
- Science - Meteorology Great Britain - Biology - Meteorology - Science
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Phylogenetic relationships of Nygolaimina and Dorylaimina (Nematoda: Dorylaimida) inferred from small subunit ribosomal DNA sequences \ Nematology : international journal of fundamental and applied nematological research [Article]
Mullin, P.G. \ Harris, T.S. \ Powers, T.O. \ 2005
molecular taxonomy - phylogenetics - phylogeny - plant pests - ribosomal DNA - Dorylaimidae - invertebrates - animals - eukaryotes - nucleotide sequences - plant parasitic nematodes - nematoda - animal parasitic nematodes - taxonomy - Nematodes - Nematodes Research

Phylogenetic reconstructions based on 18S rDNA sequence data indicate that Dorylaimida, comprising the suborders Nygolaimina and Dorylaimina, is a monophyletic lineage, but that there is a deep division within Nygolaimina, giving rise to the possibility that Nygolaimina is paraphyletic. A well-supported clade comprising members of the traditional orders Mermithida and Mononchida (including Bathyodontina) forms the sister taxon to the Dorylaimida. Inferred relationships within this clade indicate that Mermithida shares more recent common ancestry with Mononchina than does Bathyodontina. Vertebrate parasites within Dorylaimia (Dioctophymida and Trichinellida) are reconstructed in a sister-taxon relationship with the Mononchida/Dorylaimida lineage. The enigmatic order Isolaimida (represented by Isolaimium) appears to be ancestral to all other Dorylaimia sampled. Expanded taxon sampling for phylogenetic analyses of the subclass raises new possibilities for the reconstruction of hypothetical character states in the common ancestor of Dorylaimia.

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A new species of Glochinema (Epsilonematidae: Nematoda) from the oxygen minimum zone off Baja California, NE Pacific and phylogenetic relationships at species level within the family \ Cahiers de Biologie Marine [Article]
Neira, C. \ Decraemer, W. \ Backeljau, T. \ 2005
characteristics - illustrations - new species - phylogenetics - sexual dimorphism - Mexico - invertebrates - animals - eukaryotes - APEC countries - Developing Countries - Latin America - America - North America - OECD Countries - Threshold Countries - nematoda - taxonomy

Glochinema spinithorni sp. nov. is described from muddy, bathyal sediments of the oxygen minimum zone (OMZ) of the north eastern Pacific Ocean off Baja California. It is characterized by a rather large body length (over 1 mm), a large number of body rings (242-282), sexual dimorphism in the number and position of pharyngeal thorns near the head region, cuticular ornamentation with numerous hairy spines and two sets of stronger spines ventrally in the anterior body half, mid-sized spiral amphids, and by the number and arrangement of ambulatory setae and long spicules (over 100 micro m). The finding of a second OMZ Glochinema species with similar morphological characteristics supports the presumption that OMZs function as isolated habitats promoting endemism at low taxonomic levels. Results of phylogenetic analyses at the species level restricted to the Glochinematinae and Keratonematinae suggest that both OMZ species form a monophyletic group. An attempt was made to recognize phylogenetic relationships at species level within the family. The phylogenetic analyses were based upon a data matrix of 96 ingroup taxa and 25 characters. The results support the monophyly of the genera Leptepsilonema, Metepsilonema, Perepsilonema and Polkepsilonema (with or without Pternepsilonema).

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