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-sequenc03040nas a2200289   4500008004100000245013500041210006900176260007600245300001000321490000600331520198800337653002202325653001302347653001102360653002802371653002202399100002302421700002502444700002402469700002102493700001802514700002602532700001702558700001702575700002102592856013702613       2008                        eng d00aA ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats0 aribosomal DNAbased framework for the detection and quantificatio  a9600 GARSINGTON RD, OXFORD OX4 2DQ, OXON, ENGLANDbBLACKWELL PUBLISHING  a23-340 v83 aIndigenous communities of soil-resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under-exploitation as soil health indicators, and a user-friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress-sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full-length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA-based systematics, Mononchida families (indicated here as M1-M5) are relatively well-supported and, consequently, family-specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (approximate to 1000 bp from the 5'-end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1-D9, PP1-PP3) that shows only distant similarity with 'classical' Dorylaimid systematics. Most subclades were trophically homogeneous, and - in most cases - specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real-time polymerase chain reaction). Our results constitute proof-of-principle for the concept of DNA sequence signatures-based monitoring of stress sensitive nematode families in environmental samples.10aLSU ribosomal DNA10anematode10aRT-PCR10asoil community analysis10aSSU ribosomal DNA1 aHolterman, Martijn1 aRybarczyk, Katarzyna1 avan den Elsen, Sven1 avan Megen, Hanny1 aMooyman, Paul1 aSantiago, Reyes, Pena1 aBongers, Tom1 aBakker, Jaap1 aHelder, Johannes  uhttps://nematoda.myspecies.info/content/ribosomal-dna-based-framework-detection-and-quantification-stress-sensitive-nematode-familie