Assembling the Tree Of Life: Phylum Nematoda: Integrating Multidisciplinary Expertise and Infrastructure for Resolving Relationships in a Major Branch of the Tree of Life


Assembling the Tree of Life requires phylogenetic resolution of phylum Nematoda, argued to be the most abundant, genetically diverse metazoans on earth, and a key to gaining a wider understanding of controversial invertebrate relationships. Phylogenetic studies of this enormous phylum have been impeded by the difficulty of working with such diverse taxa, most of which are microscopic and known by relatively few experts. Nematode phylogenetics has also been impeded by the fragmentation of taxonomic specialists among different disciplines and by bias toward economically or medically important parasites of plants, vertebrates and invertebrates.

We propose to develop a comprehensive evolutionary framework, bringing together in our Tree of Life research the combined multidisciplinary expertise of over 40 U.S. and international colleagues, representing a huge proportion of the world's leading specialists in nematode systematics. This approach, including a series of ten coordinated research workshops, is designed to add a highly resolved nematode branch to the Tree of Life, build biological infrastructure including a dynamic open database, and integrate the worldwide community of specialists for continuing improvement of nematode phylogenetics beyond the scope of this project.

Our specific aims are twofold. First, we propose to generate 18S sequence data for 1,000 nematode species, selected primarily to maximize systematic diversity. These sequence data will be combined with over 200 currently available 18S sequences to provide the first comprehensive 18S phylogeny for nematodes. In a parallel effort, we will also construct morphological datasets for phylogenetic analyses; completion of this task is expected to extend well beyond the time span of this project. Second, we will use the comprehensive 18S analyses as a basis for selecting 50 nematode species for construction of cDNA libraries. Sequences from these libraries are necessary to independently verify 18S phylogenies and to resolve phylogenetic relationships among the deepest lineages of the phylum. Specifically, these libraries will be used to obtain data from 25 single-copy protein-coding loci from each of 50 nematode species. Orthologous sequences will also be obtained for eight metazoan outgroup taxa, (two from existing genome projects and six for which cDNA libraries will be constructed de novo). These multilocus data will be used to infer phylogenetic relationships (currently unresolved) among the earliest branches within the phylum.

In addition to the production of phylogenetic hypotheses, all recorded morphological and molecular data of each analyzed specimen will be made available through a combined online database, linking nucleotide sequences with multifocal video clips and selected scanning electron microscopy images, thereby facilitating taxonomic identification and phylogenetic interpretation by the worldwide scientific community. This database will also provide a major stimulus to studies of animal phylogenetics and to the molecular systematics of nematodes. Additional products will include the training of several undergraduate students, three graduate students and three postdoctoral associates, as well as the integration of video and traditional vouchers and cryopreserved specimens into major type collections.

The proposed project will not only generate a coordinated series of phylogenetic analyses and publications to address and resolve the evolutionary history of one of the major branches of the Tree of Life, but is also designed to establish lasting foundations for a coherent and sustained worldwide research program on nematode biodiversity and phylogenomics.

Source of support

National Science Foundation


October 1st 2002 - September 30th 2007

Project team



Copyright 2002 Paul De Ley & UC Riverside - All rights reserved - This website is maintained by the De Ley lab