02574nas a2200289   4500008004100000245010700041210006900148260009100217300001200308490000700320520153900327653002501866653001801891653001401909653002301923653001401946100002101960700002401981700002302005700002002028700001802048700001702066700002602083700001702109700002102126856013702147       2009                        eng d00aA phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences0 aphylogenetic tree of nematodes based on about 1200 fulllength sm  aPLANTIJNSTRAAT 2, P O BOX 9000, 2300 PA LEIDEN, NETHERLANDSbBRILL ACADEMIC PUBLISHERS  a927-S270 v113 aAs a result of the scarcity of informative morphological and anatomical characters, nematode systematics have always been volatile. Differences in the appreciation of these characters have resulted in numerous classifications and this greatly confuses scientific communication. An advantage of the use of molecular data is that it allows for an enormous expansion of the number of characters. Here we present a phylogenetic tree based on 1215 small subunit ribosomal DNA sequences (ca 1700 bp each) covering a wide range of nematode taxa. Of the 19 nematode orders mentioned by De Ley et al. (2006) 15 are represented here. Compared with Holterman et al. (2006) the number of taxa analysed has been tripled. This did not result in major changes in the clade subdivision of the phylum, although a decrease in the number of well supported nodes was observed. Especially at the family level and below we observed a considerable congruence between morphology and ribosomal DNA-based nematode systematics and, in case of discrepancies, morphological or anatomical support could be found for the alternative grouping in most instances. The extensiveness of convergent evolution is one of the most striking phenomena observed in the phylogenetic tree presented here - it is hard to find a morphological, ecological or biological characteristic that has not arisen at least twice during nematode evolution. Convergent evolution appears to be an important additional explanation for the seemingly persistent volatility of nematode systematics.10aconvergent evolution10aDNA barcoding10amolecular10anematode evolution10aphylogeny1 avan Megen, Hanny1 avan den Elsen, Sven1 aHolterman, Martijn1 aKarssen, Gerrit1 aMooyman, Paul1 aBongers, Tom1 aHolovachov, Oleksandr1 aBakker, Jaap1 aHelder, Johannes  uhttps://nematoda.myspecies.info/content/phylogenetic-tree-nematodes-based-about-1200-full-length-small-subunit-ribosomal-dna-sequenc03969nas a2200217   4500008004100000245007600041210006900117260010400186300001200290490000700302520319100309653001703500653001403517653001403531653002103545653002003566653002003586653002103606100001503627856010903642       2006                        eng d00aPhylogeny of Taenia: Species definitions and origins of human parasites0 aPhylogeny of Taenia Species definitions and origins of human par  aELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO, CLARE, 00000, IRELANDbELSEVIER IRELAND LTD  aS23-S300 v553 aPhylogeny is fundamental as it constrains explanations about history and forms our foundation for recognizing and diagnosing species. In the absence of such a framework taxonomists historically relied on intuitive processes, personal judgment and authority, often embracing a typological view of species that disregarded otherwise unequivocal historical and biological criteria. Species of Taenia are among the most characteristic tapeworms infecting carnivores and humans as definitive hosts and indeed Taemidae is unique among the Eucestoda in requiring 2 obligate mammalian hosts for transmission; a high percentage (>80%) of life cycles have been completely elucidated among the approximately 45 species and nominal subspecies of Taenia. Until recently there had been no comprehensive attempts at reconstruction of a phylogeny among these important parasites. Such analyses have allowed us to explore the origins and evolution of those independent species of Taenia that occur in humans (T saginata, T asiatica, and T solium) and to understand the ecological and historical processes serving as determinants of biogeography and host-association. These studies supported the status of T asiatica as a valid species and diagnosed a relationship as the sister-species of T saginata. These conclusions contrasted with a diversity of opinions that would subsume T asiatica as a subspecies. Recognition of a species constitutes a specific and testable hypothesis, is not an arbitrary decision and is most appropriately assessed in the context of phylogenetic or historical data. Considering macrospecies, a process has been outlined by Brooks and McLennan [Brooks DR, McLennan DA. The nature of diversity: an evolutionary voyage of discovery. University of Chicago Press: Chicago; 2002] as follows: (1) Discovery: a systematist describes the species; (2) Phylogenetic reconstruction; (3) Evaluation I: do sister-species show geographical overlap-are they sympatric or allopatric (use phylogeny+geographical distributions)? (4) Evaluation II: are sister-species reproductively isolated based on information from natural history, ecology and reproductive biology? Species may be viewed in the context of microevolutionary and macroevolutionary processes. For instance, microspecies are defined in ecological time and involve populations and contemporary process that are potentially reversible (reticulate). In contrast, macrospecies as exemplified by T saginata and T asiatica are divergent lineages resulting from processes in evolutionary time where an ancestor has undergone a permanent split that is non-reversible (non-reticulate). Applying these criteria in evaluation of T saginata and T asiatica, it becomes clear that in evolutionary time these represent historical lineages with independent spatial and temporal trajectories, having separated from a common ancestor near 0.78 to 1.71 MYBP in Africa, or Eurasia. In ecological time, sympatry, reproductive isolation, and differences in life history evident for T saginata and T asiatica as observed in China, and perhaps other regions of Southeast Asia, further serve to validate these taeniids. Published by Elsevier Ireland Ltd.10abiogeography10aevolution10aphylogeny10aspecies concepts10aTaenia asiatica10aTaenia saginata10aTaenia tapeworms1 aHoberg, EP  uhttps://nematoda.myspecies.info/content/phylogeny-taenia-species-definitions-and-origins-human-parasites01774nas a2200265   4500008004100000245015000041210006900191260009100260300001200351490000700363520079600370653001601166653001501182653001801197653001401215653001601229653001401245653000801259653001301267100003401280700001401314700002401328700001901352856013701371       2009                        eng d00aBernardius lineatus gen. n., sp n. (Enoplida: Enchelidiidae), a remarkable nematode with ornamented cuticle from a Brazilian tropical sandy beach0 aBernardius lineatus gen n sp n Enoplida Enchelidiidae a remarkab  aPLANTIJNSTRAAT 2, P O BOX 9000, 2300 PA LEIDEN, NETHERLANDSbBRILL ACADEMIC PUBLISHERS  a275-2870 v113 aBernardius lineatus gen. n., sp. n. is described from a sandy beach at Tamandare Bay, Brazil. It possesses the main characteristics of the family Enchelidiidae (Nematoda: Enoplida), but is unique by the presence of a body cuticle ornamented with longitudinal ridges formed by small rods, an entirely different character to all other members of the order Enoplida. The new genus is also characterised by a long, subdivided, buccal cavity with two subventral teeth and numerous denticles and the arrangement of the anterior sensilla in two crowns, the anterior crown being papilliform and the posterior crown consisting of six external labial and four cephalic sensilla, setiform. The relationships of the genera within the Enchelidiidae are discussed and an emended family diagnosis provided.10adescription10amorphology10amorphometrics10anew genus10anew species10aphylogeny10aSEM10ataxonomy1 ada Fonseca-Genevois, Veronica1 aSmol, Nic1 aDecraemer, Wilfrida1 aVenekey, Virag  uhttps://nematoda.myspecies.info/content/bernardius-lineatus-gen-n-sp-n-enoplida-enchelidiidae-remarkable-nematode-ornamented-cuticle01723nas a2200265   4500008004100000245015000041210006900191260007600260300001200336490000700348520075700355653001801112653001401130653001401144653001401158653001501172653001701187100002101204700002201225700001501247700001601262700001901278700002301297856013701320       2008                        eng d00aNew data from an enigmatic phylum: evidence from molecular sequence data supports a sister-group relationship between Loricifera and Nematomorpha0 aNew data from an enigmatic phylum evidence from molecular sequen  a9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLANDbBLACKWELL PUBLISHING  a231-2390 v463 aLoricifera is one of the most recently discovered animal phyla. So far, the group has been considered closely related to Kinorhyncha and Priapulida, and assigned to the ecdysozoan clade Cycloneuralia. Using Bayesian inference, we present the first phylogeny that includes 18S rRNA and Histone 3 sequences from two species of Loricifera. Intriguingly, we find support for a sister-group relationship between Loricifera and Nematomorpha. Such relationship has not been suggested previously and the results imply that a revision of our conception of early ecdysozoan evolution is required. Additionally, the data suggest that evolution through progenesis (sexual maturation of larvae) may have played an important role among the ancestral cycloneuralians.10aCycloneuralia10aEcdysozoa10aevolution10aphylogeny10aprogenesis10aScalidophora1 aSorensen, M., V.1 aHebsgaard, M., B.1 aHeiner, I.1 aGlenner, H.1 aWillerslev, E.1 aKristensen, R., M.  uhttps://nematoda.myspecies.info/content/new-data-enigmatic-phylum-evidence-molecular-sequence-data-supports-sister-group-relationshi01562nas a2200205   4500008004100000245008700041210006900128260007400197300001200271490000800283520084700291653001301138653001401151653001301165653001401178100001601192700002201208700000501230856012101235       2002                        eng d00aSystematic relationships of Nematomorpha based on molecular and morphological data0 aSystematic relationships of Nematomorpha based on molecular and   a810 EAST 10TH ST, LAWRENCE, KS 66044-8897 USAbAMER MICROSCOPICAL SOC  a357-3640 v1213 aWe sequenced the 18S rRNA gene from 11 nematomorph species from 9 genera and derived hypotheses concerning the sister group of Nematomorpha and relationships within this taxon. The molecular and morphological data are consistent with the monophyly of Nematomorpha, a sister-group relationship between Nematomorpha and Nematoda, and a sister-group relationship between the marine genus Nectonema and all of the freshwater taxa, Gordiida. Hypotheses of relationships within Gordiida support the traditional taxa Gordiidae, Chordodidae, and Chordodinae but reject Paracbordodinae and Spinochordodidae. The molecular results differ from those of previous morphological studies by suggesting a reduction of the two tail lobes at the posterior end of males in Chordodinae, monophyly of the genus Paragordionus, and paraphyly of the genus Chordodes.10aGordiida10aNectonema10aNematoda10aphylogeny1 aBleidorn, C1 aSchmidt-Rhaesa, A1 a  uhttps://nematoda.myspecies.info/content/systematic-relationships-nematomorpha-based-molecular-and-morphological-data02758nas a2200265   4500008004100000245016000041210006900201260007300270300000900343490000700352520179800359653001602157653002702173653001802200653001402218653002402232100001702256700001902273700001402292700001202306700001902318700001302337700000502350856013702355       2001                        eng d00aPhylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS regions of ribosomal DNA0 aPhylogenetic relationships within the cystforming nematodes Nema  a525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USAbACADEMIC PRESS INC  a1-160 v213 aThe ITS1, ITS2, and 5.8S gene sequences of nuclear ribosomal DNA from 40 taxa of the family Heteroderidae (including the genera Afenestrata, Cactodera, Heterodera, Globodera, Punctodera, Meloidodera, Cryphodera, and Thecavermiculatus) were sequenced and analyzed. The ITS regions displayed high levels of sequence divergence within Heteroderinae and compared to outgroup taxa. Unlike recent findings in root knot nematodes, ITS sequence polymorphism does not appear to complicate phylogenetic analysis of cyst nematodes. Phylogenetic analyses with maximum-parsimony, minimum-evolution, and maximum-likelihood methods were performed with a range of computer alignments, including elision and culled alignments. All multiple alignments and phylogenetic methods yielded similar basic structure for phylogenetic relationships of Heteroderidae. The cyst-forming nematodes are represented by six main clades corresponding to morphological characters and host specialization, with certain clades assuming different positions depending on alignment procedure and/or method of phylogenetic inference. Hypotheses of monophyly of Punctoderinae and Heteroderinae are, respectively, strongly and moderately supported by the ITS data across most alignments. Close relationships were revealed between the Avenae and the Sacchari groups and between the Humuli group and the species H. salixophila within Heteroderinae. The Goettingiana group occupies a basal position within this subfamily. The validity of the genera Afenestrata and Bidera was tested and is discussed based on molecular data. We conclude that ITS sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient speciations within Heteroderidae. (C) 2001 Academic Press.10acoevolution10acyst-forming nematodes10aHeteroderidae10aphylogeny10asequence alignments1 aSubbotin, SA1 aVierstraete, A1 aDe Ley, P1 aRowe, J1 aWaeyenberge, L1 aMoens, M1 a  uhttps://nematoda.myspecies.info/content/phylogenetic-relationships-within-cyst-forming-nematodes-nematoda-heteroderidae-based-analys01805nas a2200217   4500008004100000245006100041210005900102260008600161300001200247490000700259520106200266653002801328653002601356653002201382653003201404653001401436100001301450700001301463700001601476856009501492       2000                        eng d00aA more efficient approximation scheme for tree alignment0 amore efficient approximation scheme for tree alignment  a3600 UNIV CITY SCIENCE CENTER, PHILADELPHIA, PA 19104-2688 USAbSIAM PUBLICATIONS  a283-2990 v303 aWe present a new polynomial time approximation scheme (PTAS) for tree alignment, which is an important variant of multiple sequence alignment. As in the existing PTASs in the literature, the basic approach of our algorithm is to partition the given tree into overlapping components of a constant size and then apply local optimization on each such component. But the new algorithm uses a clever partitioning strategy and achieves a better efficiency for the same performance ratio. For example, to achieve approximation ratios 1.6 and 1.5, the best existing PTAS has to spend time O(kdn(5)) and O(kdn(9)), respectively, where n is the length of each leaf sequence and d, k are the depth and number of leaves of the tree, while the new PTAS only has to spend time O(kdn(4)) and O(kdn(5)). Moreover, the performance of the PTAS is more sensitive to the size of the components, which basically determines the running time, and we obtain an improved approximation ratio for each size. Some experiments of the algorithm on simulated and real data are also given.10aapproximation algorithm10acomputational biology10aevolutionary tree10amultiple sequence alignment10aphylogeny1 aWang, LS1 aJiang, T1 aGusfield, D  uhttps://nematoda.myspecies.info/content/more-efficient-approximation-scheme-tree-alignment00652nas a2200193   4500008004100000245006800041210006700109260003900176653001500215653001600230653001500246653002300261653001400284653001300298653000800311653001300319100002600332856010000358       2006                        eng d00aMorphology and systematics of the order Plectida Malakhov, 19820 aMorphology and systematics of the order Plectida Malakhov 1982  aNetherlandsbWageningen University10acladistics10adevelopment10amorphology10anematode evolution10aphylogeny10aPlectida10aSEM10ataxonomy1 aHolovachov, Oleksandr  uhttps://nematoda.myspecies.info/content/morphology-and-systematics-order-plectida-malakhov-198201365nas a2200205   4500008004100000245002000041210002000061260006300081300001200144490000900156520082300165653001200988653001901000653001201019653002401031653001401055653001401069100001601083856006001099       2007                        eng d00aPhylum Nematoda0 aPhylum Nematoda  aPO BOX 41-383, AUCKLAND, 1030, NEW ZEALANDbMAGNOLIA PRESS  a265-2930 v16683 aThe systematics of nematodes is reviewed, including: an overview of the general biology, ecology, scientific and economic importance of the group; a history of classification; evolutionary affinities and origins of nematodes; and the current diagnosis of the group. Alternative classifications within the Phylum Nematoda are discussed, and a classification to family level incorporating the latest molecular, developmental and morphological research is presented. This classification reflects the current views on evolution within the phylum, as well as significant areas of uncertainty, particularly related to the early evolution of nematodes. It includes 5 classes, 9 subclasses, 23 superorders, 39 orders, 52 suborders, 89 superfamilies and 241 families. There are few changes at the superfamily and family levels.10abiology10aclassification10aecology10aeconomic importance10anematodes10aphylogeny1 aHodda, Mike  uhttps://nematoda.myspecies.info/content/phylum-nematoda