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. 2000 Oct 10;97(21):11359-64.
doi: 10.1073/pnas.97.21.11359.

Changes in Mitochondrial Genetic Codes as Phylogenetic Characters: Two Examples From the Flatworms

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Changes in Mitochondrial Genetic Codes as Phylogenetic Characters: Two Examples From the Flatworms

M J Telford et al. Proc Natl Acad Sci U S A. .
Free PMC article

Abstract

Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate).

Figures

Figure 1
Figure 1
Phylogeny of the Platyhelminthes based on a morphological analysis of Ehlers (2), indicating the major clades and the basal position of the Catenulida and the Acoelomorpha.
Figure 2
Figure 2
Graphs showing SiC values of the 20 amino acids for the two codons AUA (black bars) and AAA (white bars) for 24 flatworms, a mesozoan and a xenoturbellid. The number of codons used to calculate SiC scores are shown in brackets on each graph in the order AUA/AAA.
Figure 3
Figure 3
Mitochondrial genetic codes mapped onto a likely phylogeny of the Metazoa. The trees are rooted by the Fungi as an outgroup. (A) It is most parsimonious (three changes: 1, 2, 3) to assume that both the Echinodermata and Rhabditophora independently evolved AAA = Asn, which must therefore be synapomorphies of the groups. Assuming AAA primitively codes for Asn in the Metazoa requires four changes (1′, 2′, 3′, 4′). AAA is not seen in hemichordate mitochondria. (B) In ignorance of the position of the Acoelomorpha and Catenulida, it is equally parsimonious to presume that, in the Metazoa, AUA primitively coded for Ile [with changes to Met in Chordata (1′), Lophotrochozoa (2′) and Ecdysozoa (3′)] or that AUA changed to coding for Met in a basal metazoan (1) and reverted to Ile in Echinodermata/Hemichordata (2) and Rhabditophora (3). It is hence impossible to polarize the changes based on this knowledge. (C) Positioning the Acoelomorpha and/or Catenulida anywhere on the thickened line forces us to conclude that AUA = Ile in Rhabditophora is a synapomorphy (1, 2, 3 changes) rather than primitive (1′ 2′, 3′, 4′ changes). If Acoela are indeed basal (ref. 8), this also suggests the AUA = Ile in Echinodermata/Hemichordata is a synapomorphy.

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