@article {Bhadury:2010pb,
	title = {Barcoding marine nematodes: an improved set of nematode 18S rRNA primers to overcome eukaryotic co-interference},
	journal = {Hydrobiologia},
	volume = {641},
	year = {2010},
	pages = {245-251},
	publisher = {SPRINGER},
	address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
	abstract = {Nematodes form an important component of many benthic marine ecosystems and DNA barcoding approaches could provide an insight into nematode community composition from different environments globally. We have amplified nematode 18S rRNA sequences using standard nematode18S rRNA primers from environmental DNA extracted from intertidal sediment collected from New Jersey coast, USA to test whether the published marine nematode 18S rRNA sequences from GenBank and EMBL databases can effectively assign unknown nematode sequences into genus or species level. Most of the sequenced clones showed some degree of identities with published marine nematode 18S rRNA sequences. However, relatively very few of the sequences could be assigned even to genus level based on sequence assignment rule. In addition, other eukaryotic 18S rRNA sequences were found to be co-amplified with commonly used nematode 18S rRNA primers. We found that the majority of the current nematode 18S rRNA primers will co-amplify other eukaryotes if environmental DNA is the target template. We therefore designed a new set of nematode 18S rRNA primers and evaluated them using environmental DNA in intertidal sediment from the New Jersey coast. In total, 40 clones were screened and subsequently sequenced and all the sequences showed varying degree of identities with published nematode 18S rRNA sequences from GenBank and EMBL databases, and no obvious eukaryotic co-amplicons were detected with new primers. Only 13 out of 40 clones amplified with the new primer set showed 100\% identity to published Daptonema and Metachromadora 18S rRNA sequences. The current molecular databases for nematodes are dominated by sequences from NW Europe and need to be more extensively populated with new full length 18S rRNA nematode sequences collected from different biogeographic locations. The new primers developed in this study, in combination with an updated nematode 18S rRNA sequence database, would help us to better investigate and understand the diversity and community composition of free-living marine nematodes based on DNA barcoding approaches during biodiversity or biomonitoring surveys on a global-scale.},
	keywords = {18S rRNA primers, DNA barcoding, Eukaryotic co-interference, Marine nematodes},
	doi = {DOI 10.1007/s10750-009-0088-z},
	author = {Bhadury, Punyasloke and Austen, Melanie C.}
}
@article {Meldal:2007qp,
	title = {An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {42},
	year = {2007},
	pages = {622-636},
	publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
	address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
	abstract = {Phylogenetic reconstructions of relations within the phylum Nematoda are inherently difficult but have been advanced with the introduction of large-scale molecular-based techniques. However, the most recent revisions were heavily biased towards terrestrial and parasitic species and greater representation of clades containing marine species (e.g. Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, Enoplida, and Monhysterida) is needed for accurate coverage of known taxonomic diversity. We now add small subunit ribosomal DNA (SSU rDNA) sequences for 100 previously un-sequenced species of nematodes, including 46 marine taxa. SSU rDNA sequences for > 200 taxa have been analysed based on Bayesian inference and LogDet-transformed distances. The resulting phylogenies provide support for (i) the re-classification of the Secernentea as the order Rhabditida that derived from a common ancestor of chromadorean orders Araeolaimida, Chromadorida, Desmodorida, Desmoscolecida, and Monhysterida and (ii) the position of Bunonema close to the Diplogasteroidea in the Rhabditina. Other, previously controversial relationships can now be resolved more clearly: (a) Alaimus, Campydora, and Trischistoma belong in the Enoplida, (b) Isolaimium is placed basally to a big clade containing the Axonolaimidae, Plectidae, and Rhabditida, (c) Xyzzors belongs in the Desmodoridae, (d) Comesomatidae and Cyartonema belongs in the Monhysterida, (e) Globodera belongs in the Hoplolaimidae and (0 Paratylenchus dianeae belongs in the Criconematoidea. However, the SSU gene did not provide significant support for the class Chromadoria or clear evidence for the relationship between the three classes, Enoplia, Dorylaimia, and Chromadoria. Furthermore, across the whole phylum, the phylogenetically informative characters of the SSU gene are not informative in a parsimony analysis, highlighting the short-comings of the parsimony method for large-scale phylogenetic modelling. (c) 2006 Elsevier Inc. All rights reserved.},
	keywords = {Adenophorea, Bayesian inference, Chromadorea, Enoplea, evolution, LogDet transformation, Marine nematodes, Nematoda, parsimony, phylogenetic reconstruction, Rhabditida, Secernentea, SSU rDNA, systematics, taxonomy},
	doi = {DOI 10.1016/j.ympev.2006.08.025},
	author = {Meldal, Birgit H. M. and Debenham, Nicola J. and De Ley, Paul and De Ley, Irma Tandingan and Vanfleteren, Jacques R. and Vierstraete, Andy R. and Bert, Wim and Borgonie, Gaetan and Moens, Tom and Tyler, Paul A. and Austen, Melanie C. and Blaxter, Mark L. and Rogers, Alex D. and Lambshead, P. J. D.}
}
@article {Bhadury:2006ci,
	title = {Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes},
	journal = {Marine Ecology-Progress Series},
	volume = {320},
	year = {2006},
	pages = {1-9},
	publisher = {INTER-RESEARCH},
	address = {NORDBUNTE 23, D-21385 OLDENDORF LUHE, GERMANY},
	abstract = {Free-living nematodes are abundant in all marine habitats, are highly diverse, and can be useful for monitoring anthropogenic impacts on the environment. Despite such attributes, nematodes are effectively ignored by many marine ecologists because of their time-consuming taxonomy. Nematode diagnostics has traditionally relied on detailed comparison of morphological characters which, given their abundance, is difficult and laborious, meaning that the biodiversity of the group is typically underestimated. Molecular methods such as DNA-barcoding offer potentially efficient alternative approaches to studying the biodiversity of marine nematode communities, allowing these organisms to be more effectively exploited in ecological surveys and environmental assessments. In this study, a number of nuclear and mitochondrial genomic regions were evaluated as potential diagnostic loci for marine nematode species identification. Of these, the 18S ribosomal RNA gene amplified most reliably from a range of taxa, and was therefore evaluated as a DNA barcode. In a comparison of molecular and morphological identifications, over 97 \% of specimens sequenced were correctly assigned on the basis of a short stretch of 18S rRNA sequence (approximately 345 bp), making this a potentially useful marker for the rapid molecular assignment of unknown nematode species, and evaluation of nematode species richness during ecological surveys or environmental assessments. This study showed that a single marker approach based on amplification and sequencing may prove invaluable in the rapid identification of nematodes during ecological surveys and, indeed, other taxonomically challenging invertebrate taxa.},
	keywords = {18S rRNA, DNA barcoding, ecological survey, identification, Marine nematodes},
	author = {Bhadury, Punyasloke and Austen, Melanie C. and Bilton, David T. and Lambshead, P. John D. and Rogers, Alex D. and Smerdon, Gary R.}
}
