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.