There’s an interesting paper in Nature on animal phylogeny. The authors take an EST approach adding multi-gene data for 11 new animal phyla and increasing data for others.

Dunn et al. “Broad phylogenomic sampling improves resolution of the animal tree of life” Nature. Published online 5 March 2008 doi:10.1038/nature06614

Abstract: Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

They show that more data increases support for some nodes and resolves ambiguities at others. More data is always a good thing I guess. Unless that is you are being tortured with systematic biases. I notice that they don’t include either Caenorhabditis species. There have been discussions before that rhabditid sequences may be atypical of most nematodes and lead to long branch artifacts. Most of this involves rDNA sequences which seem to evolve quickly in C.elegans and relatives. The other influence of C. elegans on systematics is the still ongoing debate about the validity of ecdysozoa. Papers to me seem to fall into two broad camps. (1) Those that take a small number of taxa for a lot of genes (whole genomes). These usually reject ecdysozoa. (2) Those that take more taxa, necessarily with fewer loci. These tend to support ecdysozoa. It seems that class 2 can incorporate more than a hundred loci and still support ecdysozoa, suggesting that a lack of signal is not to blame (Philippe et al 2005). This seems to indicate the presence of systematic biases in class 1 datasets and the finger of blame points to C. elegans. It has been suggested that there are fast and slow nematodes and slow are much better to include in phylogenies of animals (Aguinaldo et al 1997).

The authors suggest that for some taxa whose positions are unstable in their tree (Rotifera, Bryozoa, Gnathostomulida) “improved taxon sampling may be the most promising strategy for resolving their positions”. I’ve worked on 2 of these 3 phyla and most people have never even heard of them. Perhaps much more attention needs to be paid to less familiar animal groups. Animals selected for sequencing partly by smallness of genomes (C. elegans, D. melanogaster?) are often not suitable to describe genome structure in all animals (e.g. Raible et al 2005).

Aguinaldo et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature (1997) vol. 387 (6632) pp. 489-93

Philippe et al. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol (2005) vol. 22 (5) pp. 1246-53

Raible et al. Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science (2005) vol. 310 (5752) pp. 1325-6