Nematoda is a very diverse animal phylum. Within Nematoda, species display a
multitude of life styles, different reproductive strategies and parasitism has arisen
independently several times. Furthermore, morphological conservation and a high
rate of homoplasy have impeded the resolution of nematode systematics. To address
these issues, single gene (usually the nuclear ribosomal small subunit gene) and
mitochondrial gene phylogenies have been used, but the information contained within
the sequence of these genes is not enough to resolve the topological relationships
between clades that emerged during rapid cladogenesis.
Next generation sequencing data have been shown to produce high quality genomic
and transcriptomic assemblies at low cost, as a result more and more nematode
species are being sequenced. Sequences were gathered or generated for 53 nematode
species from ESTs, gene predictions from full genome assemblies and transcripts
from RNA-Seq experiments. These sequences were screened for orthologous gene
clusters, which were concatenated into a supermatrix with thousands of aminoacid
sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference
methods sheds light into the early splitting clades of the phylogenetic tree
of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic
relationships within the parastitic family Onchocercidae were resolved, unveiling the
evolutionary history of these important taxa. Finally, data produced in this work
will be useful for subsequent evolutionary studies of the phylum Nematoda