Phylogenomics of Nematoda

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Nematode diversity Nematodes are characterized in the wider public and scientific community as being both rare (very few people have ever seen a nematode) and very well understood (the ‘model nematode’ Caenorhabditis elegans is one of the cornerstones of modern biology). However nematologists in particular, and many ecologists, know that nematodes are both numerically abundant and systematically diverse, dominating many ecosystems. The sheer abundance of free-living nematodes and their generally small body size, even as adults, can confound attempts to itemize the presence of species. Whereas 23 000 species have been formally described, estimates of true species-level abundance range from 0.5 million to over 10 million (Lambshead and Boucher 2003; Lambshead 1993; Blaxter 2011). The wide range in these estimates reflects differences in underpinning assumptions as to the efficiency of modern taxonomic methodologies and the likely species–area relationships for meiofaunal taxa. Indeed, many of the currently described taxa are relatively large organisms that are parasites of animals and plants, and the current taxonomic understanding of free-living species, particularly in the tropics and in marine sediments, is likely to be significantly lacking. The small size of individual nematodes (most are less than 1 mm in longest body axis), and the even smaller size of diagnostic morphological characters, has rendered nematode systematics at deeper levels problematic (De Ley and Bert 2002; De Ley and Blaxter 2002; 2004; De Ley et al. 2005). What has been clear from over 150 years of nematode systematics is that morphological character sets have not yielded unequivocal support for any deeper branching patterns within Nematoda. Nematologists have thus been enthusiastic and productive adopters of molecular phylogenetic methods, and molecular data have been employed in analyses from species delimitation to inter-phylum relationships. Nematoda is a phylum within Metazoa, placed in the superphylum Ecdysozoa (arthropods, priapulids and allies) (Aguinaldo et al. 1997). Based on both morphological and molecular data, the sister phylum to Nematoda is Nematomorpha, a species-poor group of parasites of arthropods. Here we discuss briefly the history of molecular analyses of nematode phylogenetics, and explore how multi-locus, genome-sequence-derived datasets are set to resolve many remaining issues. Resolving Nematoda is important for several phylum-specific reasons: defining the origins of parasitism in several different lineages, understanding the assembly of various ecosystems, mapping the patterns of diversification and revealing the evolutionary patterns in developmental and other systems.