Comparative developmental genetics of the ecdysozoa: tardigrades Mark Blaxter
Tardigrades (water bears) have characters reminiscent of both arthropods (segmentation, limbs) and nematodes (pharynx, eutely). The Ecdysozoa hypothesis links these phyla in a supertaxon of moulting animals, suggesting that the divergent developmental mechanisms of C. elegans and D. melanogaster may derive from an ancestor more recent than their separation from other major lineages. We will perform detailed genomic, developmental biology and developmental genetic analysis (transferring methods from fly and worm fields) in a tardigrade species, Isohypsibius, that we have established in culture. With this data we will compare the evolution of shared and unique features of development in tardigrades, nematodes and arthropods.
The Ecdysozoa hypothesis was first proposed in modern times by Aguinaldo et al. on the basis of small subunit ribosomal RNA gene (SSU rDNA) sequences from a small number of taxa from the “moulting” phyla and other protostome outgroups (Aguinaldo et al. 1997; Halanych et al. 1995). Supertaxa corresponding roughly to the Ecdysozoa were previously proposed by Perrier in 1897 and Seurat in 1920 (discussed in Chitwood & Chitwood 1974) on the basis of morphology alone. More recently, Ecdysozoa has been implicitly or explicitly rejected (Nielsen 1995; Wagele et al. 1999) by a number of authors on morphological grounds. Aguinaldo et al. recovered a robust Ecdysozoa only by rigorously excluding all “long-branch” taxa, and carefully controlling in their models for different base compositions and evolutionary rates. Their choice of taxa has been criticised for lack of inclusiveness and lack of representativeness, but reanalysis of SSU rDNA confirmed the Ecdysozoa (Aleshin et al. 1998) and additional sets of molecular data have been adduced in favour of the superphylum, such as HOX genes (de Rosa et al. 1999), elongation factor 1-alpha (EF1a) genes (Garey & Schmidt-Rhaesa 1998) and whole genome analyses (Mushegian et al. 1998; but see Xie & Ding 2000 for criticism of the genome analyses).
So: Is Ecdysozoa “real”? This question requires an analysis of both molecular and morphological data, including large numbers of taxa representing all relevant phyla (and significant subsections thereof), and using robust and well-founded evolutionary models.
Paterson and Eernisse have recently published a Herculean analysis of all Metazoa, using a dataset of >300 morphological characters and SSU rDNA from >300 taxa, including >90 representatives of all of the “ecdysozoan” phyla (Peterson & Eernisse 2001). They find robust support for Ecdysozoa, using morphology, molecular and combined character sets. Using morphological characters alone, they find 86% bootstrap support for monophyly of Tardigrada, Arthropoda, Nematoda and other ecdysozoan taxa (Onychophora, Nematomorpha, Priapulida, Kinorhyncha and Loricifera) and 64% for monophyly of Gastrotricha plus other Ecdysozoa. Panarthropoda (Onychophora + Tardigrada + Arthropoda) recieves 71% support. Monophyly of Cycloneuralia, the other major lineage within Ecdysozoa, is less well supported (59%). With combined molecular and morphological data, Ecdysozoa is again returned with significant support. Their detailed investigation of the dataset shows that the ecdysozoan monophyly is unlikely to be an artefact brought about through long-branch attraction. In the combined analysis, Tardigrada (six taxa) roots with Nematoda and Nematomorpha rather than with Onychophora and Arthropoda. The position of only two “phyla” are problematic in Paterson and Eernisse’s analyses (Chaetognatha and acoel Platyhelmintha) but this is clearly due to their long branches relative to all other taxa.
We (Aziz Aboobaker, a PhD student, and I) have HOX data from our captive tardigrade, Isohypsibius sp. ED. We also have HOX gene data from a set of nematodes distantly related to C. elegans, and these species’ genomes contain HOX gene complements much more like that of other metazoa. A molecular phylogenetic analysis of these sequences (after the methodology of Cook et al. (Cook et al. 2001)) does recover Ecdysozoa, but this is qualified by the errant evolution of genes from the model nematode Caenorhabditis elegans (which has a much reduced orthologous gene complement and highly divergent sequences). From the nematode most distant from C. elegans, the muscle parasite Trichinella spiralis, we have isolated eight distinct HOX genes, and these correspond to distinct orthology groups of arthropods (see Figure 1 below).
Molecular phylogenetic analysis of these genes supports Ecdysozoa (see for example Figure 2 below, based on analysis of the posterior genes which shows Ecdysozoa recovered with high botstrap. OTU in bold have been sequenced by us).
Thus multiple datasets, morphological and molecular, recover the Ecdysozoa, and place Tardigrada either basal to Panarthropoda or transitional between Panarthropoda and Cycloneuralia (the other non-arthropodan ecdysozoa). The Tardigrada, and therefore our Isohypsibius sp. ED, are well placed to root and illuminate the phylogenetic analysis of ecdysozoan development.
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