02335nas a2200181   4500008004100000022004800041245007100089210006300160260009100223300000900314490000600323520166100329100001901990700001702009700001602026700001802042856009302060       2008                        eng d  a1935-2735 (Electronic); 1935-2727 (Linking)00aOn the extent and origins of genic novelty in the phylum Nematoda.0 aextent and origins of genic novelty in the phylum Nematoda  aInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.  ae2580 v23 aBACKGROUND: The phylum Nematoda is biologically diverse, including parasites of plants and animals as well as free-living taxa. Underpinning this diversity will be commensurate diversity in expressed genes, including gene sets associated specifically with evolution of parasitism. METHODS AND FINDINGS: Here we have analyzed the extensive expressed sequence tag data (available for 37 nematode species, most of which are parasites) and define over 120,000 distinct putative genes from which we have derived robust protein translations. Combined with the complete proteomes of Caenorhabditis elegans and Caenorhabditis briggsae, these proteins have been grouped into 65,000 protein families that in turn contain 40,000 distinct protein domains. We have mapped the occurrence of domains and families across the Nematoda and compared the nematode data to that available for other phyla. Gene loss is common, and in particular we identify nearly 5,000 genes that may have been lost from the lineage leading to the model nematode C. elegans. We find a preponderance of novelty, including 56,000 nematode-restricted protein families and 26,000 nematode-restricted domains. Mapping of the latest time-of-origin of these new families and domains across the nematode phylogeny revealed ongoing evolution of novelty. A number of genes from parasitic species had signatures of horizontal transfer from their host organisms, and parasitic species had a greater proportion of novel, secreted proteins than did free-living ones. CONCLUSIONS: These classes of genes may underpin parasitic phenotypes, and thus may be targets for development of effective control measures.1 aWasmuth, James1 aSchmid, Ralf1 aHedley, Ann1 aBlaxter, Mark  uhttps://nematoda.myspecies.info/content/extent-and-origins-genic-novelty-phylum-nematoda01750nas a2200217   4500008004100000022004300041245006500084210006400149260018000213300001600393490000800409520088700417100001801304700001601322700001701338700001701355700002001372700001701392700001901409856010401428       2005                        eng d  a0962-8436 (Print); 0962-8436 (Linking)00aDefining operational taxonomic units using DNA barcode data.0 aDefining operational taxonomic units using DNA barcode data  aInstitute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh EH9 3JT, UK. mark.baxter@ed.ac.uk  a1935–19430 v3603 aThe scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.1 aBlaxter, Mark1 aMann, Jenna1 aChapman, Tom1 aThomas, Fran1 aWhitton, Claire1 aFloyd, Robin1 aAbebe, Eyualem  uhttps://nematoda.myspecies.info/content/defining-operational-taxonomic-units-using-dna-barcode-data00425nas a2200109   4500008004100000245006600041210006600107300001400173490000700187100001800194856010300212       2000                        eng d00aGenes and genomes of Necator americanus and related hookworms0 aGenes and genomes of Necator americanus and related hookworms  a347–3550 v301 aBlaxter, Mark  uhttps://nematoda.myspecies.info/content/genes-and-genomes-necator-americanus-and-related-hookworms00470nas a2200121   4500008004100000245007500041210006900116300001400185490000700199100001700206700001800223856010700241       2000                        eng d00aThe small subunit ribosomal RNA sequence of Strongyloides stercoralis.0 asmall subunit ribosomal RNA sequence of Strongyloides stercorali  a939–9410 v301 aDorris, Mark1 aBlaxter, Mark  uhttps://nematoda.myspecies.info/content/small-subunit-ribosomal-rna-sequence-strongyloides-stercoralis